EP4676598A1 - Peptidoglycan hydrolases with bactericidal activity - Google Patents
Peptidoglycan hydrolases with bactericidal activityInfo
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- EP4676598A1 EP4676598A1 EP24709418.8A EP24709418A EP4676598A1 EP 4676598 A1 EP4676598 A1 EP 4676598A1 EP 24709418 A EP24709418 A EP 24709418A EP 4676598 A1 EP4676598 A1 EP 4676598A1
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/04—Antibacterial agents
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
Definitions
- the present invention is generally in the fields of pharmaceuticals, in particular antibacterials, and protein engineering.
- the present invention relates to peptidoglycan hydrolases such as endolysins and nucleic acids, e.g., RNAs, encoding the peptidoglycan hydrolases of the invention, as well as medical uses thereof, for example, for treating diseases caused by and/or associated with a Staphylococcus (e.g., S. aureus) infection.
- a Staphylococcus e.g., S. aureus
- the present invention relates to solidified yeast culture media for screening yeast cells for the secretion of peptidoglycan hydrolases with bactericidal activity and corresponding screening methods.
- Background Staphylococci in particular Staphylococcus aureus strains, are major human pathogens responsible for a vast array of pathologies, both acute and chronic, varying from mild to life threatening, including skin and soft tissue infections, bone-related infections, pneumonia, and sepsis.
- S. aureus is a leading cause of mortality among antibiotic resistant bacterial pathogens, with ⁇ 700.000 deaths per year due to antibiotic resistant S. aureus globally; Antimicrobial Resistance Collaborators (2022), The Lancet, 399. The pathogenesis of S.
- aureus infection involves several critical steps: invasion of host tissues, evasion of the immune system, adhesion to surfaces, and biofilm formation. For example, by persisting in biofilm, bacteria evade neutrophil killing and display decreased susceptibility to antibiotics.
- Peptidoglycan hydrolases (belonging to the class of “enzybiotics”) such as bacteriophage-encoded endolysins, are a promising alternative to antibiotics; Fischetti (2010), International Journal of Medical Microbiology, 300(6); Schmelcher (2012), Future Microbiology, 7; Hojckova (2013), BMC Microbiol. 13.
- Bacteriophages produce these enzymes, in particular endolysins, towards the end of the lytic cycle.
- the enzymes cleave peptidoglycans (PG) in the bacterial cell wall, thus lysing the cells and releasing the progeny phages.
- Peptidoglycan hydrolases in particular endolysins (also abbreviated as “lysins”), have several advantages over antibiotics; especially, their narrow host specificity, which is often limited to a single genus or even a single species (Fischetti (2010), International Journal of Medical Microbiology, 300(6)), and their rather low propensity for generating resistance in their hosts (Schuch (2014), The Journal of Infectious Diseases 209(9)).
- Endolysins Bacteriophages that invade Gram-positive bacteria encode a variety of highly diverse endolysins.
- endolysins typically have a modular structure consisting of one or more enzymatically active domains (EADs) connected by a flexible interdomain linker to at least one cell wall-binding domain (CBD). Both domains may contribute to the specificity for a given genus or species of bacteria; Oliveira (2013), J. Virol. 87.
- bacteriophage derived endolysins containing solely an enzymatically active domain e.g., a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain (but no separate CBD), also exist.
- CHEP histidine-dependent amidohydrolase/peptidase
- Such lysins break down peptidoglycan, in particular, from outside the bacterial cell.
- Another native endolysin, SAL200 administrated intravenously to patients with persistent S.
- aureus bacteremia in a Phase II clinical study, resulted in serious adverse effects including pneumonia and respiratory failure (NCT03089697; Danis-Wlodarczyk (2021), Antibiotics, 10(12)); moreover, a very short half-life and an immune response against the enzyme was believed to limit its usefulness (WHO technical document, January 15, 2022: 2019 antibacterial agents in clinical development: an analysis of the antibacterial clinical development pipeline, https://www.who.int/publications/i/item/9789240000193).
- certain peptidoglycan hydrolases delivered locally have shown some success in S. aureus decolonization, e.g.
- the present invention relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain that has (i) a sequence identity of at least 60% to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1.
- CHAP histidine-dependent amidohydrolase/peptidase
- said CHAP domain is considered herein and in context of the present invention as a variant of the CHAP domain of L0482, i.e., a variant of the sequence from position 72 to position 215 in SEQ ID NO: 1.
- the peptidoglycan hydrolase of the present invention has a killing activity against a Staphylococcus species or strain, preferably Staphylococcus aureus.
- the peptidoglycan hydrolase of the invention has preferably the ability of being secreted from a eukaryotic cell.
- the peptidoglycan hydrolase of the invention is, preferably, stable up to a temperature of at least about 40°C, e.g., at least 37°C.
- the peptidoglycan hydrolase of the present invention is, preferably, an endolysin.
- the peptidoglycan hydrolase of the invention is, preferably, contained in a pharmaceutical composition and/or, preferably, used for the treatment of a disease.
- the disease is, in particular, a bacterial disease, preferably, a disease caused by and/or associated with a Staphylococcus infection, e.g., a S. aureus infection.
- LYSM-CHAP domain architecture selection of the LYSM-CHAP domain architecture as starting point for further protein engineering and directed evolution
- the invention is, partly, based on the surprising finding, as illustrated in the appended Examples, that lysins with a LYSM-CHAP domain architecture such as L0482 (SEQ ID NO: 1) reliably have a good killing activity against Staphylococci, in particular Staphylococcus aureus (S. aureus) including methicillin-resistant Staphylococcus aureus (MRSA) strains such as ATCC43300. Therefore, lysins with a LYSM-CHAP domain architecture such as L0482 provide a particularly good starting point for protein engineering and directed evolution approaches.
- S. aureus Staphylococcus aureus
- MRSA methicillin-resistant Staphylococcus aureus
- LysM-CHAP lysins such as L0482 (SEQ ID NO: 1) can be secreted in active form by eukaryotic cells in order to kill S. aureus; see, e.g., Example 2 and Figure 3.
- a peptidoglycan hydrolase in form of a nucleic acid e.g., an mRNA
- a subject e.g., a human
- a subject e.g., a human
- the advantage of continuous production, i.e., secretion, of the peptidoglycan hydrolase from the cells of the subject at the site of a bacterial infection e.g., a human
- the ability of being efficiently secreted from eukaryotic cells, e.g., human cells is another beneficial property of peptidoglycan hydrolases.
- L0482 (SEQ ID NO: 1) is an optimal starting point for further protein engineering and directed evolution. Accordingly, the invention further relates to a peptidoglycan hydrolase having bactericidal activity which has a sequence identity of at least 60% to the sequence of SEQ ID NO: 1 and which comprises one or more amino acid substitutions as compared to the sequence of SEQ ID NO: 1. This sequence identity is, in particular, calculated over the full length of the sequence of SEQ ID NO: 1 (and not over the full length of the sequence of the peptidoglycan hydrolase of the invention).
- any additional domains, peptides or tags that may be comprised in (or fused to) the peptidoglycan hydrolase of the invention should not be considered when determining the sequence identity of the peptidoglycan hydrolase of the invention to the sequence of SEQ ID NO: 1.
- the peptidoglycan hydrolase of the invention may comprise an amino acid sequence having a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, and, optionally, one or more further domains, peptides or tags, e.g. a signal peptide, a PK tag, a further peptide linker etc., as described herein.
- the peptidoglycan hydrolase of the invention comprises a CHAP domain according to the present invention, i.e., a CHAP domain that has (i) a sequence identity of at least 60% to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1.
- L0482 variants with improved pharmaceutical properties See protein engineering, as illustrated in Example 4, and subsequent directed evolution, as illustrated in Example 5, the inventors surprisingly found L0482 variants which had several improved pharmaceutical properties at the same time. In particular, the inventors found L0482 variants which had an enhanced killing activity against S.
- an enhanced killing activity against a target bacterium such as S. aureus corresponds to a lower minimal inhibitory concentration (MIC).
- the MIC is defined as the minimal concentration at which the optical density at 620 nm (OD620) of a bacterial (e.g. S. aureus) liquid culture comprising 5x10 5 cfu/ml of bacterial (e.g. S. aureus) cells is kept below 0.1 for at least 24h at 37°C.
- the inventive peptidoglycan hydrolases provided herein may be used at a lower concentration for treating a bacterial disease than comparable peptidoglycan hydrolases, which may increase the efficiency and safety of the treatment.
- the hit variants G1 (SEQ ID NO: 3) and H5 (SEQ ID NO: 11) found in context of the present invention have a 4- or 8-fold lower MIC than WT L0482 (SEQ ID NO: 1), respectively, i.e. a MIC of 1 ⁇ g/ml for G1 and a MIC of 0.5 ⁇ g/ml for H5, compared to a MIC of 4 ⁇ g/ml for the WT L0482; see, e.g., Figure 8.
- the lower MICs have been observed with the methicillin-resistant Staphylococcus aureus (MRSA) strain “ATCC43300” further highlighting that the peptidoglycan hydrolases of the invention may be particularly suitable as antibacterials, in particular, for medical uses.
- MRSA methicillin-resistant Staphylococcus aureus
- the enhancement of the killing activity of peptidoglycan hydrolases according to invention was further confirmed with an OD reduction assay showing that, for example, H5 (SEQ ID NO: 11) killed S. aureus cells with faster kinetics than wild-type L0482 (SEQ ID NO: 1); see, e.g., Figure 11.
- an enhanced protein stability e.g., an enhanced thermostability and/or a reduced propensity for aggregation, further improves the pharmaceutical properties of a peptidoglycan hydrolase.
- a sufficient thermostability in particular, the ability of being stable of up to a temperature of at least about 40°C, e.g., at least 37°C, is critical for the use as a pharmaceutical in many mammals including humans (in view of the body temperatures).
- an enhanced thermostability facilitates storage and distribution of a pharmaceutical.
- the inventive peptidoglycan hydrolases provided herein may be particularly suitable as pharmaceuticals.
- a decreased propensity for aggregation enhances the manufacturability of a peptidoglycan hydrolase.
- inventive peptidoglycan hydrolases provided herein may be more efficiently manufactured than comparable peptidoglycan hydrolases.
- a decreased propensity for aggregation further reduces the immunogenicity of a peptidoglycan hydrolase in a mammalian subject, e.g., a human, which, in turn, may further increase the efficiency and/or safety of a treatment.
- Enhanced ability of being secreted from human cells is particularly important for the expression of a peptidoglycan hydrolase from a nucleic acid, e.g., a RNA.
- a nucleic acid e.g., a RNA.
- a suitable nucleic acid construct encoding a peptidoglycan hydrolase of the invention when introduced into cells in a subject (e.g. a human patient), said cells can continuously produce and secrete the peptidoglycan hydrolase protein. This may provide a more efficient treatment of the bacterial infection and, for example, provide a higher efficacy in treating difficult to treat bacterial infections such as bacterial biofilms.
- the peptidoglycan hydrolases of the invention may be particularly suitable for delivery as a nucleic acid, e.g., a RNA.
- the present invention provides more efficient means, e.g., nucleic acids encoding a peptidoglycan hydrolase of the invention, for treating bacterial infections.
- Enhanced solubility An enhanced stability (e.g. a reduced propensity for aggregation) and an enhanced ability of being secreted from human cells may be associated with each other as well as with an enhanced solubility in an aqueous solution such as PBS.
- inventive peptidoglycan hydrolases may have a better solubility in aqueous solutions than comparable peptidoglycan hydrolases. This is highly beneficial, in particular, for the manufacturability and useability of the peptidoglycan hydrolases. Moreover, an enhanced solubility in aqueous solutions may increase the efficiency and/or safety of a peptidoglycan hydrolases in the treatment of a disease.
- a CHAP domain (contained in L0482 and L0482 variants as described herein) may have a dual enzymatic activity, i.e., an amidase activity and a peptidase activity; Frankel (2012), J Biol Chem. 23;287(13). Both, the amidase activity and the peptidase activity, may contribute to the hydrolysis/cleavage of peptidoglycan in the cell wall of bacteria, as described herein. Therefore, a peptidoglycan hydrolase of the present invention comprising a CHAP domain of the invention may have a reduced propensity of generating resistance in target bacteria, e.g., S.
- target bacteria e.g., S.
- the peptidoglycan hydrolases of the invention may be particularly effective for treating bacterial infections for this additional reason.
- Consensus mutations / the variant H3 The inventors unexpectedly found a L0482 variant, i.e., H3 (SEQ ID NO: 9), which (i) had all of the beneficial properties assayed (i.e. an enhanced killing activity against S.
- aureus an enhanced stability and an enhanced ability of being secreted from mammalian cells
- parental L0482 variant L0482ag SEQ ID NO: 2
- H3 (SEQ ID NO: 9) has been obtained by removing two glycosylation sites in L0482 (SEQ ID NO: 1) to yield the aglycosylated variant L0482ag (SEQ ID NO: 2) (see Example 4), followed by two rounds of directed evolution with L0482ag as a starting point; see Example 5.
- H3 (SEQ ID NO: 9) contains in addition to the two aglycosylation mutations of L0482ag, i.e.
- N68K, N73G exclusively the following mutations, i.e., amino acid substitutions: T82S, N85G, R86K, S130N, H136K, D169N, N185Y and N186G, in reference to the wild-type L0482 sequence SEQ ID NO: 1.
- SEQ ID NO: 2 amino acid substitutions identified upon directed evolution of L0482ag
- H136R is considered herein and in context of the present invention as a very good alternative to H136K.
- H3 (SEQ ID NO: 9) reflects the consensus sequence for particularly improved L0482 variants, and the corresponding amino acid substitutions, i.e.
- T82S, N85G, R86K, S130N, H136K/R, D169N, N185Y and N186G, in reference to the wild-type L0482 sequence SEQ ID NO: 1, are considered herein as consensus mutations, in particular, consensus amino acid substitutions.
- the most beneficial amino acid substitutions / the variant H5 Furthermore, it has been surprisingly found in context of the present invention that the L0482 variant H5 (SEQ ID NO: 11), obtained in the same way as H3, had an even more enhanced stability, killing activity against S. aureus, and ability of being secreted from human cells compared to H3 (SEQ ID NO: 9); see, e.g., Example 6.
- H5 SEQ ID NO: 11
- H3 SEQ ID NO: 9
- a single amino acid substitution found in context of the present invention e.g., F155Y
- the amino acid substitutions T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1 are considered herein and in context of the present invention as the most beneficial amino acid substitutions for enhancing the killing activity against a target bacterium, e.g., S.
- L0482 derived peptidoglycan hydrolases L0482 variants
- all of the most beneficial amino acid substitutions occurred in the CHAP domain of L0482, i.e., positions 72 to 215 in SEQ ID NO: 1. It is therefore considered herein and in context of the present invention that the CHAP domain is the most important domain of L0482 derived peptidoglycan hydrolases.
- the present invention further relates, in particular, to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1 and that has (ii) one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 130 in SEQ ID NO: 1 or at a position a
- said CHAP domain further comprises an aglycosylation mutation as described herein, i.e., an amino acid substitution or deletion, preferably an amino acid substitution, at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is, preferably, substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine.
- an amino acid substitution or deletion preferably an amino acid substitution
- L0482 variants e.g., H3 and H5
- L0482 variants wherein several pharmaceutical properties were improved at the same time
- Means and methods for screening peptidoglycan hydrolases for bactericidal activity As illustrated in the appended Examples, the inventors surprisingly found that solidified yeast culture media such as agar plates containing autoclaved (i.e. dead) target bacteria, e.g. dead S.
- aureus cells are particularly suitable for screening yeast cells for the secretion of an active peptidoglycan hydrolase, i.e., for identifying peptidoglycan hydrolases with a good killing activity against target bacteria, e.g., S. aureus.
- the corresponding screening method called “Yeast on dead aureus” (YODA) is based on the inventive concept that only an active (but not an inactive) peptidoglycan hydrolase secreted from a yeast colony cultured on the solidified yeast culture medium of the invention is able to break down the peptidoglycan of the dead bacterial cells in vicinity of the colony.
- YODA-derived methods are extremely simple and efficient methods which allows to easily distinguish yeast cells/colonies expressing peptidoglycan hydrolases with a good killing activity against a target bacterium from yeast cells/colonies expressing inactive peptidoglycan hydrolases. Furthermore, YODA-derived methods are very sensitive since the lysins are constantly secreted from the cells. Thus, small secretion rates may be sufficient to see a halo (when the peptidoglycan hydrolase is active).
- the present invention further relates to a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles.
- the invention relates to a method of screening yeast cells for the secretion of an active peptidoglycan hydrolase (i.e., a peptidoglycan hydrolase with bactericidal activity against a target bacterium, e.g., S.
- an active peptidoglycan hydrolase i.e., a peptidoglycan hydrolase with bactericidal activity against a target bacterium, e.g., S.
- said method comprising the steps of: a) providing a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles; b) culturing yeast cells expressing a peptidoglycan hydrolase on a surface of said solidified medium until at least one yeast colony is detectable, in particular wherein the yeast cells are able to secrete the peptidoglycan hydrolase; c) evaluating whether a halo is apparent around a yeast colony, in particular wherein the halo corresponds to a locally reduced optical density of said solidified medium around said colony, for example, in a radius of about 0.1 to 1 cm from the colony, especially compared to a region of the solidified medium that is free of yeast colonies; d) determining that a yeast colony secretes an active peptidoglycan hydrolase when a halo around the colony is apparent, or determining that a
- the inventive YODA-derived screening method provided herein has been proven very useful for identifying improved peptidoglycan hydrolases with bactericidal activity, e.g., against S. aureus; see, e.g., Examples 4 to 6.
- Aglycosylation mutations enhance bactericidal activity upon expression in eukaryotic cells
- WT L0482 SEQ ID NO: 1
- MIC minimum inhibitory concentration
- L0482 (SEQ ID NO: 1) contains two motifs of N-glycosylation at residues N68 (which is in the linker sequence) and N73 (which is in the CHAP domain). Therefore, the inventors removed the two N- glycosylation motifs in L0482 in a degenerate codon screen by employing the YODA method as described in Example 4 and Figure 5B. The inventors surprisingly found that the most frequent amino acid substitution pairs contained in active L0482 mutants were N68K/N73G (i.e. N68N73 to KG), N68K/N73Y (i.e. N68N73 to KY), and N68A/N73H (i.e. N68N73 to AH).
- the present invention further relates to aglycosylated variants of L0482 (SEQ ID NO: 1) as illustrated by but not limited to the N68K/N73G (i.e., L0482ag; SEQ ID NO: 2) mutant described herein.
- an aglycosylation mutation refers to an amino acid substitution or deletion (preferably to an amino acid substitution) at position 68 or 73 in SEQ ID NO: 1 or at any position corresponding to these positions.
- an aglycosylation mutation refers to an amino acid substitution or deletion (preferably to an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position.
- an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position means that the asparagine (“N”) at position 68 in SEQ ID NO: 1 is substituted with another amino acid, as described herein.
- an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position means that the asparagine (“N”) at position 73 in SEQ ID NO: 1 or the asparagine corresponding to position 73 in SEQ ID NO: 1 is substituted with another amino acid, as described herein.
- the following amino acid substitutions are considered herein and in context of the present invention as particularly effective aglycosylation mutations or aglycosylation amino acid substitutions: N68K, N68A, N68M, N68R, N73G, N73Y, N73H, N73L, N73E, and N73A in SEQ ID NO: 1 or at positions corresponding to these positions.
- an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position e.g. N73G (as contained in L0482ag; SEQ ID NO: 2)
- L0482 variants having at least one aglycosylation mutation e.g., an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position
- L0482ag SEQ ID NO: 2
- L0482 variants having at least one aglycosylation mutation may be introduced into L0482 variants having at least one aglycosylation mutation, in particular in the CHAP domain thereof, to further enhance the pharmaceutical properties of the L0482 variants (e.g. the stability solubility and ability of being secreted from a human cell but also the killing activity against a target bacterium, e.g. S. aureus), as described herein.
- a target bacterium e.g. S. aureus
- an aglycosylation mutation (preferably an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position (more preferably N73G), is, preferably, combined with at least one of the amino acid substitutions described herein in context of the L0482ag variants obtained upon directed evolution, in particular with at least one permissive or beneficial amino acid substitution, preferably with at least one particularly beneficial amino acid substitution, more preferably with at least one of the most beneficial amino acid substitutions, as further described herein, i.e., more preferably with at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in reference to SEQ ID NO: 1.
- the present invention further relates, in particular, to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1 and that has (ii) an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than phenylalanine or lysine such as glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine.
- phenylalanine or lysine such as glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine.
- the present invention relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase has (i) a sequence identity of at least 60% to the sequence of SEQ ID NO: 1 and has (ii) at least one amino acid substitution at positions 68 and 73 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably at least at position 73 in SEQ ID NO: 1 or at a position corresponding to this position.
- the residue at position 68 i.e.
- the “N”) in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than threonine or serine such as lysine, methionine, arginine or alanine, preferably lysine.
- the residue at position 73 (i.e. the “N”) in SEQ ID NO: 1 or at a position corresponding to this position is preferably substituted with another amino acid residue than phenylalanine or lysine such as glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine.
- said peptidoglycan hydrolase comprises a CHAP domain according to the present invention.
- Methods for screening peptidoglycan hydrolases having several improved pharmaceutical properties / directed evolution As already indicated herein above, the inventors evaluated in context of the present invention whether it would be possible to not only improve the bactericidal activity of lysins but also further pharmaceutical properties of the lysins at the same time, (e.g., the solubility, secretion from eukaryotic cells and/or stability). As already indicated above and as further described in the following, the inventors surprisingly found that several pharmaceutical properties (including the bactericidal activity) of L0482 variants, in particular L0482ag, could be further improved.
- the inventors developed a combinatorial screening method based on the inventive YODA-derived method which combines eukaryotic cell display, e.g. yeast display, with YODA; see, e.g., Example 5.
- this inventive combinatorial screening method allows to simultaneously improve, inter alia, the solubility, bactericidal activity and eukaryotic secretion of peptidoglycan hydrolases, e.g., endolysins such as L0482 (SEQ ID NO: 1) or derivatives thereof such as L0482ag (SEQ ID NO: 2).
- endolysins such as L0482 (SEQ ID NO: 1) or derivatives thereof such as L0482ag (SEQ ID NO: 2).
- the display e.g.
- yeast display allows, in particular, to screen for peptidoglycan hydrolase variants which are adapted to the eukaryotic secretory pathway, and, hence, have an improved expression and secretion profile in eukaryotic cells. Moreover, the ability of being efficiently secreted is often associated with a good stability and good solubility of the protein, as described herein. Hence these biophysical and pharmaceutically relevant properties can be also improved by the inventive method.
- the YODA step in particular, allows to screen for secreted peptidoglycan hydrolase variants which have good bactericidal activity, in particular against the desired target bacterium, as described herein.
- the combinatorial screening method of the invention allows to screen for improved peptidoglycan hydrolase variants which are adapted to the eukaryotic secretory pathway and effectively kill a target bacterium, e.g. S. aureus, and which may have further beneficial pharmaceutical properties such as an enhanced stability and an enhanced solubility as described herein and as illustrated in the appended Examples.
- a target bacterium e.g. S. aureus
- the inventive YODA-based method refers to a method of screening yeast cells for the secretion of an active peptidoglycan hydrolase, said method comprising the steps of: a) providing a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles; b) culturing yeast cells expressing a peptidoglycan hydrolase on a surface of said solidified medium until at least one yeast colony is detectable; c) evaluating whether a halo is apparent around a yeast colony; d) determining that a yeast colony secretes an active peptidoglycan hydrolase when a halo around the colony is apparent, or determining that a yeast colony does not secrete an active peptidoglycan hydrolase when no halo around the colony is apparent.
- said YODA-based method can be combined with a eukaryotic cell display method.
- said method of screening yeast cells for the secretion of an active peptidoglycan hydrolase may be performed in step III) of the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell according to the invention, in particular, as described in the following:
- the present invention further relates to a method of identifying an active peptidoglycan hydrolase variant (i.e., a peptidoglycan hydrolase variant with bactericidal activity against a target bacterium, e.g., S.
- aureus that is optimized for secretion by a eukaryotic cell
- said method comprising the steps of: I) preparing a library of eukaryotic cells, preferably yeast cells, expressing peptidoglycan hydrolase variants on the cell surface; II) selecting eukaryotic cells, e.g. yeast cells, based on a high level of peptidoglycan hydrolase on the cell surface relative to other cells in the library; for example, selecting the 10%, 5%, 1% or 0.5% of cells in the library with the highest peptidoglycan level on the cell surface; III) performing the inventive method of screening yeast cells for the secretion of an active peptidoglycan hydrolase provided herein (i.e.
- yeast cells that are able to secrete the peptidoglycan hydrolase variants expressed in the eukaryotic cells selected in step II) are cultured in step b) of said method of screening yeast cells for the secretion of an active peptidoglycan hydrolase; and IV) determining that a yeast colony that has been determined in step d) of said method of screening yeast cells for the secretion of an active peptidoglycan hydrolase to secrete an active peptidoglycan hydrolase produces an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell.
- said method i.e., the combinatorial screening method of the present invention, can be used for directed evolution of peptidoglycan hydrolases, e.g. endolysins, such as L0482 (SEQ ID NO: 1) or derivatives thereof, e.g., L0482ag (SEQ ID NO: 2), as illustrated in the appended Examples.
- endolysins such as L0482 (SEQ ID NO: 1) or derivatives thereof, e.g., L0482ag (SEQ ID NO: 2), as illustrated in the appended Examples.
- step I) of the inventive method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell are performed, wherein in step I) of each subsequent round, a further library of eukaryotic cells is prepared, and wherein the cells in the library express a different set of peptidoglycan variants compared to the library employed in the preceding round(s).
- inventive screening methods contributed to finding the inventive peptidoglycan hydrolases, in particular, L0482 variants, which surprisingly had several improved pharmaceutical properties at the same time.
- L0482 variants especially, aglycosylated L0482 variants derived from L0482ag (SEQ ID NO: 2), have been generated in three rounds of directed evolution; see, e.g., Example 5 to 7.
- L0482 variants had the ability of being secreted by eukaryotic cells, in particular yeast cells, and are deemed to have a killing activity against S. aureus as determined by the YODA method described in Example 3. Based on this large and very informative data set the inventors not only were able to find the most beneficial mutations described herein but many further beneficial, or at least permissive, amino acid substitutions at many positions in SEQ ID NO: 1 (or SEQ ID NO: 2) that were contained in the active and secreted L0482ag variants; see, e.g., Example 7 and Table 3.
- L0482ag variants are beneficial or at least permissive for the desired pharmaceutical properties of L0482 variants.
- essentially all, or at least the vast majority, of these amino acid substitutions alone or in combination confer to the LYSM-CHAP lysins, in particular L0482 variants, a sufficient killing activity against Staphylococcus species or strains, in particular S. aureus, a sufficient ability of being secreted from eukaryotic cells, a sufficient stability and/or a sufficient solubility.
- amino acid substitutions in the CHAP domain of L0482 which may confer, enhance, or, at least, maintain (i) a killing activity against Staphylococcus species or strains, in particular S.
- aureus and (ii) the ability of being secreted from eukaryotic cells, and preferably (iii) a sufficient solubility and/or stability, have been identified to occur, in particular, at positions 72 to 76, 78, 81, 82, 85, 86, 93, 96, 104, 107, 108, 111, 113, 115, 117, 121, 124, 125, 129, 130, 133 to 136, 138, 140 to 142, 144, 145, 148, 149, 152, 153, 155, 157, 159, 169, 173, 175 to 178, 185, 186, 190 to 194, 197, 198, 199, 201, 203, 204, 207, and 212 to 215 in SEQ ID NO: 1, or at positions corresponding to these positions.
- the present invention relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1 and that has (ii) one or more amino acid substitutions at positions 72 to 76, 78, 81, 82, 85, 86, 93, 96, 104, 107, 108, 111, 113, 115, 117, 121, 124, 125, 129, 130, 133 to 136, 138, 140 to 142, 144, 145, 148, 149, 152, 153, 155, 157, 159, 169, 173, 175 to 178, 185, 186, 190 to 194, 197, 198, 199, 201, 203, 204, 207, and 212 to 215 in SEQ ID NO: 1, or at positions corresponding to these positions
- amino acid residue at position 214 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine or threonine, and/or the amino acid residue at position 215 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, valine or serine.
- said CHAP domain has an aglycosylation substitution, i.e., an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position as described herein, and in addition, at least one amino acid substitution at the other positions described herein above, i.e., at positions 72, 74 to 76, 78, 81, 82, 85, 86, 93, 96, 104, 107, 108, 111, 113, 115, 117, 121, 124, 125, 129, 130, 133 to 136, 138, 140 to 142, 144, 145, 148, 149, 152, 153, 155, 157, 159, 169, 173, 175 to 178, 185, 186, 190 to 194, 197, 198, 199, 201, 203, 204, 207, and 212 to 215 in SEQ ID NO: 1, or at positions corresponding to these positions, preferably at
- the present invention further relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and that has (ii) one or more amino acid substitutions at positions 72, 74 to 76, 78, 81, 82, 85, 86, 93, 96, 104, 107, 108, 111, 113, 115, 117, 121, 124, 125, 129, 130, 133 to 136, 140 to 142, 144, 145, 148, 149, 152, 153, 155, 157, 159, 169, 173, 175 to 178, 185, 186, 190 to 192, 194, 197, 198, 199, 201, 203, 204
- said CHAP domain further has an aglycosylation mutation, i.e. an amino acid substitution or deletion, preferably a substitution, at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- an aglycosylation mutation i.e. an amino acid substitution or deletion, preferably a substitution, at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- Particularly beneficial amino acid substitutions / selected hit variants As already indicated herein above, the present inventors found several hit variants of L0482ag (SEQ ID NO: 2) upon each round of directed evolution, i.e., G1 to G4 (SEQ ID NO: 3 to 6) upon round 1, H1 to H10 (SEQ ID NO: 7 to 16) upon round 2 and I1 to I30 (SEQ ID NO: 17 to 46) upon round 3.
- aureus and (ii) the ability of being secreted from eukaryotic cells, and (iii) preferably a sufficient solubility and stability, have been identified to occur, in particular, at positions 73, 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191 to 194, 198, 204, 212 and 215 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein.
- the present invention further relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and that has (ii) one or more amino acid substitutions at positions 73, 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191, 192, 194, 198, 204, 212 and 215 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine or serine, preferably glycine, the amino acid residue at position 75 in SEQ ID NO: 1 or at
- said CHAP domain has an aglycosylation mutation, preferably, an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position as described herein, more preferably N73G, and in addition, at least one particularly beneficial amino acid substitution at the other positions described herein above, i.e., at positions 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191, 192, 194, 198, 204, 212 and 215 in SEQ ID NO: 1, or at positions corresponding to these positions, preferably at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the present invention further relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 2, and that has (ii) one or more amino acid substitutions at positions 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191, 192, 194, 198, 204, 212 and 215 in SEQ ID NO: 1, or at positions corresponding to these positions, as described herein, preferably one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein.
- the most beneficial amino acid substitutions refer to the only amino acid substitutions contained in the hit variant H5 (SEQ ID NO: 11) vis à vis the parental L0482ag variant (SEQ ID NO: 2); see, e.g., Figure 9A.
- H5 is considered herein as the variant obtained by two rounds of directed evolution with the best pharmaceutical properties.
- the most beneficial amino acid substitutions in H5 strongly enhanced the killing activity against S. aureus including S. aureus biofilms, the protein stability and the ability of being secreted from humans cells; see, e.g., Figures 8, 9, 11 and 12.
- the present invention further relates, in particular, to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and that has (ii) one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 130 in SEQ ID NO: 1 or
- said CHAP domain has a plurality of said most beneficial amino acid substitutions (e.g., 2, 3, 4, 5, 6, 7, 8 or 9), preferably at least 6 or 7, more preferably at least 8, most preferably all of said most beneficial amino acid substitutions.
- said CHAP domain has preferably further an aglycosylation mutation, preferably an amino acid substitution, at position 73 in SEQ ID NO: 1 or at a position corresponding to this mutation as described herein, more preferably N73G.
- R86K The most recurrent one of the most beneficial amino acid substitutions: R86K Furthermore, it has been surprisingly found in context of the present invention that the amino acid substitution R86K was contained in all 44 identified hit variants, i.e., G1-G4, H1-H10 and I1-I30, and in 96.08% of all L0482 variants that were secreted from eukaryotic cells and that were determined to have a killing activity against S. aureus, as described herein and as illustrated in the appended Examples; see, e.g., Example 7 and Figure 9. Therefore, R86K in SEQ ID NO: 1 is, herein and in context of the present invention, a particularly preferred amino acid substitution among the most beneficial amino acid substitutions identified.
- the CHAP domain of the present invention has an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine.
- Recurrent pairs of amino acid substitutions among the most beneficial amino acid substitutions It has been further surprisingly found in context of the present invention that certain amino acid substitutions occurred together in pairs in the identified hit variants, i.e., G1-G4, H1-H10 and I1-I30; see, e.g., Example 7 and Figure 9. These mutation pairs are specifically: (i) T82S and N85G, (ii) S130N and H136K/R and (iii) N185Y and N186G.
- Each of said 44 hit variants contained at least one of said mutation pairs.
- these amino acid substitutions i.e., T82S and N85G, S130N and H136K/R, and N185Y and N186G, occur in pairs since among the 252 active L0482 variants secreted from yeast cells found in context of the present invention, variants having only one of these paired mutations (but not the other) were found as well.
- a CHAP domain of the invention having an amino acid substitution at position 82 in SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 85 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- a CHAP domain of the invention having an amino acid substitution at position 85 in SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 82 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- a CHAP domain of the invention having an amino acid substitution at position 130 in SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 136 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- a CHAP domain of the invention having an amino acid substitution at position 136 of SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 130 of SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- a CHAP domain of the invention having an amino acid substitution at position 185 in SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 186 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- a CHAP domain of the invention having an amino acid substitution at position 186 of SEQ ID NO: 1 or at a position corresponding to this position as described herein has preferably, in addition, an amino acid substitution at position 185 of SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the hit variant H3 (SEQ ID NO: 9) reflects the consensus sequence for particularly improved L0482 variants.
- H3 contains exclusively, the following amino acid substitutions, also referred to herein as “consensus mutations”: T82S, N85G, R86K, S130N, H136K/R (esp. H136K), D169N, N185Y and N186G in reference to SEQ ID NO: 1.
- the inventors found five consensus mutation units for particularly improved L0482 variants based on the 44 L0482ag hit variants and the consensus sequence reflected by H3 (SEQ ID NO: 9) found in context of the present invention.
- the CHAP domain of the present invention has at least one amino acid substitution or substitution pair (i.e.
- At least one consensus mutation unit selected from the group consisting of the following (i) to (v): (i) an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine; (ii) an amino acid substitution at positions 82 and 85 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, and the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine; (iii) an amino acid substitution at positions 130 and 136 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, and the amino acid residue at position 136 in SEQ ID NO: 1 or at a
- said CHAP domain has at least two, preferably at least three, more preferably at least four, most preferably all of said consensus mutation units.
- said CHAP domain has further an aglycosylation mutation as described herein, preferably an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein, more preferably the substitution N73G.
- said CHAP domain has preferably the amino acid substitution F155Y.
- the CHAP domain of the present invention has a sequence identity of at least 94% (in particular, at least 93.9%), at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to the sequence from position 72 to position 215 in SEQ ID NO: 9 (H3).
- said CHAP domain has a) (i) at least one of the consensus mutations or consensus mutation units described herein and (ii) at least one aglycosylation mutation, preferably an amino acid substitution at position 73 as described herein, and/or b) at least two of the consensus mutations, e.g., at least one amino acid substitution pair, as described herein.
- the CHAP domain of the present invention has at most 8, at most 7, at most 6, at most 5, at most 4, at most 3, at most 2, at most 1 or no amino acid substitutions in the sequence from position 72 to position 215 in SEQ ID NO: 9 (H3) or in the sequence from a position corresponding to position 72 in SEQ ID NO: 9 to a position corresponding to position 215 in SEQ ID NO: 9. Furthermore, said CHAP domain has preferably the amino acid substitution F155Y.
- the peptidoglycan hydrolase of the present invention has a sequence identity of at least 95% (in particular at least 95.4%), at least 96%, at least 97%, at least 98% or at least 99% to the sequence of SEQ ID NO: 9 (H3).
- the peptidoglycan hydrolase of the present invention has at most 9, at most 8, at most 7, at most 6, at most 5, at most 4, at most 3, at most 2, at most 1 or no amino acid substitutions in SEQ ID NO: 9.
- said peptidoglycan hydrolase comprises a CHAP domain according to the present invention.
- a single amino acid substitution improving several pharmaceutical properties at once F155Y
- the best performing L0482 variant found and characterized in context of the present invention, i.e. H5 (SEQ ID NO: 11), surprisingly contained exclusively one additional amino acid substitution vis à vis H3 (SEQ ID NO: 9), i.e., F155Y.
- said amino acid substitution improved several pharmaceutical properties compared to H3 (SEQ ID NO: 9) at the same time, i.e. the killing activity against S. aureus, the protein stability and the ability of being secreted from human cells; see, e.g, Figure 8.
- F155Y in SEQ ID NO: 1 is considered herein and in context of the present invention as a further particularly preferred amino acid substitution among the most beneficial amino acid substitutions identified. Accordingly, in particularly preferred embodiments, the CHAP domain of the present invention has an amino acid substitution at position 155 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with tyrosine.
- said CHAP domain further has at least one consensus mutation, as described herein, (i.e., T82S, N85G, R86K, S130N, H136K/R (preferably H136K), D169N, N185Y and/or N186G), or, more preferably, at least one consensus mutation unit, as described herein, i.e., (i) R86K (particularly preferred), (ii) T82S and N85G, (iii) S130N and H136K/R (preferably H136K), (iv) D169N, and/or (v) N185Y and N186G; and/or an aglycosylation substitution as described herein, i.e., an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein, preferably N73G.
- at least one consensus mutation as described herein, (i.e., T82S, N85G, R86K, S130N, H136K/R (preferably H136
- the CHAP domain of the present invention has a sequence identity of at least 93% (in particular, at least 93.2%), at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to the sequence from position 72 to position 215 in SEQ ID NO: 11 (H5).
- said CHAP domain has a) (i) at least one of the most beneficial amino acid substitutions and/or at least one consensus mutation unit, as described herein and (ii) at least one aglycosylation mutation, preferably an amino acid substitution at position 73, as described herein, and/or b) at least two of the most beneficial amino acid substitutions, e.g., at least one amino acid substitution pair, as described herein.
- the CHAP domain of the present invention has at most 9, at most 8, at most 7, at most 6, at most 5, at most 4, at most 3, at most 2, at most 1 or no amino acid substitutions in the sequence from position 72 to position 215 in SEQ ID NO: 11 (H5) or in the sequence from a position corresponding to position 72 in SEQ ID NO: 11 to a position corresponding to position 215 in SEQ ID NO: 11.
- the peptidoglycan hydrolase of the present invention has a sequence identity of at least 95% (in particular at least 95.0%), at least 96%, at least 97%, at least 98% or at least 99% to the sequence of SEQ ID NO: 11 (H5).
- the peptidoglycan hydrolase of the present invention has at most 10, at most 9, at most 8, at most 7, at most 6, at most 5, at most 4, at most 3, at most 2, at most 1 or no amino acid substitutions in SEQ ID NO: 11.
- said peptidoglycan hydrolase comprises a CHAP domain according to the present invention.
- the peptidoglycan hydrolase of the present invention is, in particular, a single polypeptide, i.e., a single amino acid chain.
- a nucleic acid e.g., an mRNA
- administration of a peptidoglycan hydrolase of the invention in form of a nucleic acid (e.g., an mRNA) encoding said peptidoglycan hydrolase to a subject e.g., a human
- a subject e.g., a human
- introducing the nucleic acid into cells in a subject has certain advantages.
- a nucleic acid (e.g., an mRNA) encoding a peptidoglycan hydrolase of the invention is introduced and expressed in cells in a subject, e.g., in a patient that has a bacterial, e.g.
- the cells can continuously produce and secrete the peptidoglycan hydrolase protein. This may provide a more efficient treatment of the bacterial infection and, for example, provide a higher efficacy in treating difficult to treat bacterial infections such as bacterial biofilms, e.g., Staphylococcus biofilms.
- the nucleic acid may be introduced into cells at a particular location, e.g. the site of a bacterial infection, and/or specific cell types which may further improve the efficiency and/or safety of the treatment.
- nucleic acids, in particular RNAs have further certain practical advantages over proteins with respect to their manufacturing, safety profile and/or adaptability.
- the present invention further relates to a nucleic acid encoding the peptidoglycan hydrolase of the invention, preferably comprising a CHAP domain that has at least one of the most beneficial mutations (i.e.
- the nucleic acid of the invention is a RNA, preferably a mRNA.
- the RNA e.g., the mRNA
- the RNA comprises at least one modified nucleoside such as pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ) or 5-methyl-uridine (m5U), preferably N1-methyl- pseudouridine (m1 ⁇ ), in place of at least one uridine, preferably in place of multiple, more preferably all uridines.
- modified nucleoside such as pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ) or 5-methyl-uridine (m5U), preferably N1-methyl- pseudouridine (m1 ⁇ ), in place of at least one uridine, preferably in place of multiple, more preferably all uridines.
- peptidoglycan hydrolase refers to a polypeptide (i.e., a single amino acid chain) which is capable of hydrolyzing peptidoglycan (also called “murein”) of at least one bacterial species or strain, preferably at least one Staphylococcus species or strain, more preferably Staphylococcus aureus.
- a peptidoglycan hydrolase of the invention may comprise naturally occurring amino acids and/or non- naturally occurring amino acids as well as modifications such as, but not limited to, glycosylation (in particular O- glycosylation and/or N-glycosylation), acetylation, phosphorylation, amidation, palmitoylation, myristoylation, isoprenylation, lipidation, alkylation, or a protective group.
- glycosylation in particular O- glycosylation and/or N-glycosylation
- acetylation acetylation
- phosphorylation amidation
- palmitoylation myristoylation
- isoprenylation amidation
- palmitoylation myristoylation
- isoprenylation amidation
- lipidation lipidation
- alkylation or a protective group
- the peptidoglycan hydrolase of the invention is comprised of at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at
- peptidoglycan hydrolase encompasses, for example, endolysins, lysozymes, tail-spike depolymerases, Virion- associated peptidoglycan hydrolases (VAPGH), bacteriocins and autolysins.
- VAPGH Virion- associated peptidoglycan hydrolases
- peptidoglycan hydrolase refers to an endolysin.
- endolysin and lysin are used interchangeably herein and in context of the present invention.
- Isolated peptidoglycan hydrolases The peptidoglycan hydrolase of the present invention may be an isolated peptidoglycan hydrolase, e.g., an isolated endolysin.
- isolated means removed (e.g., purified) from the natural state.
- a nucleic acid, peptide or polypeptide naturally present in a living animal is not “isolated”, but the same nucleic acid, peptide or polypeptide partially or completely separated from the coexisting materials of its natural state is “isolated”.
- An isolated nucleic acid, peptide or polypeptide can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
- an isolated peptidoglycan hydrolase refers to a peptidoglycan hydrolase which is isolated (e.g.
- peptidoglycan hydrolase or an “endolysin”, is, preferably, a modified, i.e., an engineered, “peptidoglycan hydrolase” or “endolysin”, respectively.
- a “modified” i.e., an “engineered”, synthetic”, “recombinant”, or “artificial” peptidoglycan hydrolase or endolysin does not occur in nature and thus may be also considered herein and in context of the present invention as a “non-natural” (i.e., “non-native”) peptidoglycan hydrolase or endolysin, respectively.
- the peptidoglycan hydrolase of the invention is an engineered peptidoglycan hydrolase.
- the peptidoglycan hydrolase of the invention is a non-natural peptidoglycan hydrolase.
- the peptidoglycan hydrolases may also include natural (i.e. native) peptidoglycan hydrolases, in particular, natural endolysins, for example, in context of pharmaceutical compositions, medical uses, fusion proteins of a peptidoglycan hydrolase and another (poly)peptide (e.g. a PK tag), RNA constructs, and/or modified nucleic acids, e.g. RNAs containing a modified nucleoside such as N1-methyl- pseudouridine (m1 ⁇ ) in place of at least one uridine, as described herein.
- natural endolysins for example, in context of pharmaceutical compositions, medical uses, fusion proteins of a peptidoglycan hydrolase and another (poly)peptide (e.g. a PK tag), RNA constructs, and/or modified nucleic acids, e.g. RNAs containing a modified nucleoside such as N1-methyl- pseudouridine (m1 ⁇ ) in place of at
- endolysin refers, in particular, to natural peptidoglycan hydrolases encoded by bacteriophages (or bacterial viruses), or engineered peptidoglycan hydrolases, in particular modified endolysins, derived from such natural peptidoglycan hydrolases (e.g., from L0482; SEQ ID NO: 1). Natural endolysins act, in particular, by hydrolyzing the host cell wall and subsequently allow the release of bacteriophage progenies.
- the peptidoglycan hydrolases, e.g., the endolysins, of the present invention are also capable of hydrolyzing peptidoglycan in the cell wall of a bacterial species or strain (e.g., S. aureus) and, thus, have a killing activity against said bacterial species or strain (e.g., S. aureus), as described herein.
- a bacterial species or strain e.g., S. aureus
- cell wall refers to all components that form the outer cell enclosure of bacteria (containing, in particular, peptidoglycan), as commonly understood in the art.
- Natural endolysins usually have a molecular weight ranging from about 15 to about 60 kDa, which is also a preferred range for the peptidoglycan hydrolases (e.g. modified endolysins) of the present invention.
- the peptidoglycan hydrolases of the invention may also have a different, e.g., higher, molecular weight, for example when they further comprise additional domains or tags such as a PK tag, as described herein.
- natural endolysins typically have a modular configuration.
- an endolysin refers, in particular, to a modular endolysin, i.e., a polypeptide (i.e., a single amino acid chain) comprising one or more enzymatically active domains (EADs) and, preferably, additionally one or more cell wall-binding domains (CBDs).
- EADs enzymatically active domains
- CBDs cell wall-binding domains
- the endolysin only comprises one module, namely an EAD, e.g. a CHAP domain of the invention, but not a separate cell wall-binding domain.
- the peptidoglycan hydrolase of the invention comprises at least one EAD, in particular the CHAP domain of the invention, and additionally at least one CBD.
- the various domains in a modular endolysin e.g., an EAD and a CBD, may be separated by linker regions, in particular, by short and flexible linkers, as described herein.
- An EAD may be N-terminally or C-terminally of a CBD.
- a single cell wall-binding domain i.e. the LYSM domain
- EAD i.e. the CHAP domain.
- L0482 i.e., wild-type L0482; also called “lytN”
- L0482 has the following sequence, wherein the LYSM domain (positions 1 to 51) is underlined, the linker (positions 52 to 71) is in italics, and the CHAP domain (positions 72 to 215) is in bold: REAPKTQIYTVKKGDTLSAIALKYKTTVSNIQNTNNIANPNLIFIGQKLKVPMTPLVEPKPKTVSSNNKSNSNSSTLNYLKTLEN RGWDFDGSYGWQCFDLVNVYWNHLYGHGLKGYGAKDIPYANNFNSEAKIYHNTPTFKAEPGDLVVFSGRFGG GYGHTAIVLNGDYDGKLMKFQSLDQNWNNGGWRKAEVAHKVVHNYENDMIFIRPFKKA (SEQ ID NO: 1)
- positions which may be substituted with the most beneficial amino acid residues contained in the best performing characterized variant, i.e., H5 (SEQ ID NO: 11), as described herein, i.e., positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1, are shown in white on black background.
- the CHAP domain of L0482 (SEQ ID NO: 1) is further shown in SEQ ID NO: 301; the LYSM domain of of L0482 (SEQ ID NO: 1) is further shown in SEQ ID NO: 302; and the linker region of L0482 (SEQ ID NO: 1) is further shown in SEQ ID NO: 303.
- a natural peptidoglycan hydrolase in particular the endolysin L0482 (SEQ ID NO: 1), is usually modified by at least one amino acid substitution, as described herein. Furthermore, one or more deletions, insertions and/or additions of amino acid residues may also occur.
- a modified L0482 protein is also considered herein as an L0482 variant.
- the peptidoglycan hydrolase according to the present invention in particular a modified L0482 variant, may lack the LYSM domain or the CHAP domain of L0482, as well as the linker region, as described herein.
- the peptidoglycan hydrolase according to the present invention comprises (I) a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, as described herein; and/or (II) a LYSM domain that has (i) a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1 and (ii) one or more amino acid substitutions as compared to the sequence from position 1 to position 51 in SEQ ID NO: 1, as described herein.
- EAD enzymatically active domains of modular endolysins
- CBD Cell wall-binding domains
- the cell wall binding domain is a peptidoglycan binding domain which binds, in particular, to the peptidoglycan structure of a target bacterium.
- the different domains of an endolysin can be connected by a peptide linker, also called “domain linker”.
- an EAD e.g. a CHAP domain
- an EAD such as a CHAP domain may have (in addition to the peptidoglycan hydrolase activity) some intrinsic cell wall-binding activity and, therefore, have bactericidal activity by itself.
- some peptidoglycan hydrolases such as lysozyme.
- binding of a substrate in the cell wall of a target bacterium to or close to the catalytic pocket of an EAD may be sufficient to initiate docking and subsequent lysis of the bacterium. Therefore, a CHAP domain of the invention may be also considered herein and in context of the present invention as a peptidoglycan hydrolase which may have a bactericidal activity by itself.
- a peptidoglycan hydrolase according to the present invention comprises at least one enzymatically active domain (EAD) which is also called “catalytic domain” herein.
- said at least one enzymatically active domain comprises at least a CHAP domain of the invention, as described herein, i.e., a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1.
- Enzymatic peptidoglycan cleavage mechanisms As used herein, the term “peptidoglycan hydrolase” is, in general, not restricted to a specific enzymatic cleavage mechanism.
- an enzymatically active domain of a peptidoglycan hydrolase may function as a glycosidase, as an amidase (i.e. an amidohydrolase) and/or as a peptidase.
- a peptidoglycan hydrolase comprising one or more EADs as described herein and in context of the present invention, e.g., an endolysin, may function as a glycosidase, an amidase and/or a peptidase.
- glycosidases such as acetylmuramidases, lytic transglycosylases or glucosaminidases generally cleave the backbone of glycan.
- glycosidases may cleave the ⁇ -1,4 glycosidic bonds linking alternating polymeric structures of N-acetylmuramic acids (MurNAc) and N-acetylglucosamines (GlcNAc) in a peptidoglycan layer.
- Amidases i.e.
- amidohydrolases generally cleave the side- chain peptide, in particular they may catalyze the cleavage of amide bonds between the MurNAc and the first amino acid in the peptide stem moiety, i.e., L-alanine.
- Peptidases in particular, endopeptidases and carboxypeptidases
- Peptidases generally cleave within the peptide side-chain, in particular they may cleave bonds between two amino acids of the stem peptide of peptidoglycan, whereby bond cleavage can either occur within interpeptide bridge or stem peptide– interpeptide bridge.
- CHAP domain refers to a cysteine, histidine-dependent amidohydrolase/peptidase domain which is an enzymatically active domain (EAD) of a peptidoglycan hydrolase (in particular of a L0482 variant), as described herein.
- EAD enzymatically active domain
- a CHAP domain may be further considered herein and in context of the present invention as a peptidoglycan hydrolase.
- the CHAP domain of L0482 (SEQ ID NO: 1) may function as an amidase and as a peptidase in order to hydrolyse peptidoglycan.
- the CHAP domain has an N-acetylmuramyl L-Ala amidase activity and a D-Ala-Gly endopeptidase activity; Frankel (2012), J Biol Chem.23;287(13).
- the CHAP domain of the invention may also function, in particular, as an amidase and/or as a peptidase, preferably as an amidase and as a peptidase.
- the peptidoglycan hydrolase of the present invention functions, preferably, as an amidase (i.e. it has, preferably, an amidase activity) and/or as a peptidase (i.e.
- the peptidoglycan hydrolase of the present invention may have an N- acetylmuramyl L-Ala amidase activity and/or a D-Ala-Gly endopeptidase activity. More preferably the peptidoglycan hydrolase of the present invention functions as an amidase and as a peptidase, in particular, wherein it may have an N-acetylmuramyl L-Ala amidase activity and a D-Ala-Gly endopeptidase activity.
- a CHAP domain which functions as an amidase and/or as a peptidase in order to hydrolyse peptidoglycan may be also considered herein and in context of the present invention as a peptidoglycan hydrolase with amidase and/or peptidase activity, respectively.
- the CHAP domain of the invention may be a peptidoglycan hydrolase with amidase (e.g. N-acetylmuramyl L-Ala amidase activity) and/or peptidase activity (e.g. D-Ala-Gly endopeptidase activity).
- a peptidoglycan hydrolase of the present invention comprising the CHAP domain of the invention has, preferably, an amidase and/or peptidase activity, as described herein.
- hydrolyzing peptidoglycan in the cell wall of a bacterium may refer also to breaking down and/or cleaving said peptidoglycan.
- Bactericidal activity Hydrolyzing, in particular breaking down and/or cleaving, peptidoglycan in the cell wall of a bacterium, usually kills the bacterium. Therefore, the peptidoglycan hydrolase of the present invention has, in particular, a bactericidal activity.
- bactericidal activity refers to the ability of a peptidoglycan hydrolase to kill at least one bacterium, i.e., at least one bacterial species or strain, in particular at least one target bacterium (i.e., a bacterial species or strain to be killed).
- a peptidoglycan hydrolase of the invention has the ability to kill at least one gram-positive bacterium, more preferably a Staphylococcus species or strain, most preferably at least Staphylococcus aureus, preferably, including methicillin-resistant Staphylococcus aureus (MRSA) strains.
- MRSA methicillin-resistant Staphylococcus aureus
- a peptidoglycan hydrolase which has the ability to kill a certain bacterium, e.g., S. aureus is also referred to herein as a peptidoglycan hydrolase which has a “killing activity” against said bacterium, e.g., S. aureus.
- the killing activity of a peptidoglycan hydrolase against a certain bacterium, e.g., S. aureus is preferably measured by determining the minimum concentration at which the peptidoglycan hydrolase growth-inhibits a liquid culture of said bacterium, e.g., S. aureus.
- the “minimal inhibitory concentration” is, in particular, defined as the minimum concentration which keeps the optical density at 620 nm (OD620) of a liquid culture comprising 5x10 5 cfu/ml of a target bacterium (e.g., S. aureus) below 0.1 for at least 24h at 37°C incubation.
- a target bacterium e.g., S. aureus
- the culture medium of said liquid culture is cation adjusted Müller-Hinton broth (caMHB) medium supplemented with 25% horse serum, in particular, when the target bacterium is a Staphylococcus species or strain such as S. aureus.
- the S. aureus cells in the liquid culture correspond, preferably, to 5x10 5 cfu/ml of ATCC43300 which is a methicillin-resistant Staphylococcus aureus (MRSA) strain.
- MRSA methicillin-resistant Staphylococcus aureus
- cfu is the abbreviation of “colony forming units”, and refers to the estimated number of viable bacterial cells as commonly understood in the art.
- a detailed assay for measuring the killing activity against a target bacterium, e.g., a Staphylococcus species or strain such as S. aureus is provided in Example 6: First, a peptidoglycan hydrolase (e.g., a L0482 variant of the present invention) is produced in E.
- the peptidoglycan hydrolase e.g., the L0482 variant of the present invention
- the bactericidal activity of the peptidoglycan hydrolase (e.g., the L0482 variant of the present invention) against a target bacterium is determined as described in Example 6 under the heading “Determination of bactericidal activity of L0482 variants”.
- Example 6 Detailed assays for measuring the killing activity of a peptidoglycan hydrolase against a biofilm or free-floating aggregate of a target bacterium, e.g., a biofilm or free-floating aggregate of Staphylococcus species or strain such as S. aureus, are provided in Example 6 under the heading “Determination of anti-biofilm activity of L0482 variants” which may be preferably employed.
- One of these assays makes use of a peg biofilm in plasma (PBA) and is particularly well suitable for determining the killing activity of a peptidoglycan hydrolase against a classical biofilm that is attached to a surface.
- PBA peg biofilm in plasma
- the other assay makes use of a free-floating aggregate in synovial fluid (FBA) and is particularly well suitable for determining the killing activity of a peptidoglycan hydrolase against a free-floating (biofilm-like) aggregate.
- FBA synovial fluid
- activity refers, in particular, to the bactericidal activity of the peptidoglycan hydrolase, as described herein.
- bactericidal activity of a peptidoglycan hydrolase against a certain bacterial species or strain e.g. S.
- aureus as described herein is tightly correlated to its capability of hydrolyzing (and breaking down and/or cleaving) peptidoglycan in the cell wall of said bacterial species or strain, it is not necessary to further measure or determine the ability of the peptidoglycan hydrolase according to the present invention to hydrolyze, break down and/or cleave peptidoglycan by an enzymatic assay; it is sufficient to determine the bactericidal activity of the peptidoglycan hydrolase, i.e., its killing activity against the bacterial species or strain, e.g. S. aureus, as described herein.
- a peptidoglycan hydrolase e.g.
- an endolysin according to the present invention is considered to implicitly have the ability to hydrolase peptidoglycan in a target bacterium when it is able to kill said target bacterium, as described herein.
- a peptidoglycan hydrolase functions indeed as a “peptidoglycan hydrolase”
- additional assays For example, the reduction of purified peptidoglycan at OD620 nm in the present of a peptidoglycan hydrolase of the invention may be easily measured.
- purified peptidoglycan may be incubated with a peptidoglycan hydrolase of the invention followed by analysis and identification of cleavage products by mass spectrometry.
- the YODA-derived method of screening yeast cells for the secretion of an active peptidoglycan hydrolase according to the invention may be employed.
- the “activity” of a peptidoglycan hydrolase i.e., its killing activity against a certain bacterium, is determined by measuring its ability to break down peptidoglycan contained in dead bacterial cells of said bacterium and/or fragments thereof or corresponding peptidoglycan particles (in particular via hydrolysis of the peptidoglycan).
- Gram-positive and gram-negative bacteria In gram-positive bacteria, the cytoplasmic membrane is surrounded by a peptidoglycan layer.
- Peptidoglycan or murein is a polymer composed of sugar and amino acid.
- the sugar component is composed of N-acetylglucosamine residues and a N-acetylmuramic acid residues that are ⁇ -(1,4) linked.
- a peptide chain consisting of 3 to 5 amino acids is bound to N-acetylmuramic acid.
- Peptide chains can be cross-linked to peptide chains of other chains to form a 3D mesh-like layer.
- the peptide chain can contain D- and L-amino acid residues, and its composition can vary depending on the type of bacteria.
- gram-negative bacteria In contrast to gram-positive bacteria, gram-negative bacteria have an outer membrane with a characteristic asymmetric bilayer.
- the outer membrane bilayer consists of an inner monolayer containing phospholipids (primarily phosphatidylethanolamine) and an outer monolayer composed primarily of lipopolysaccharide (LPS).
- LPS lipopolysaccharide
- This outer membrane overlays a peptidoglycan layer which is normally much thinner than in gram-positive bacteria.
- the peptidoglycan hydrolase of the invention has, in particular, a killing activity against at least one gram-positive bacterium, preferably a Staphylococcus species or strain, more preferably at least Staphylococcus aureus, as described herein.
- a polypeptide e.g., a peptidoglycan hydrolase of the invention
- a part thereof e.g., a CHAP domain of the invention
- a certain polypeptide e.g. L0482
- a part thereof e.g. the CHAP domain of L0482
- a peptidoglycan hydrolase of the invention comprising a CHAP domain of the invention, i.e., a CHAP domain derived from the CHAP domain of L0482, is also considered herein and in context of the present invention as an L0482 variant.
- the terms “variant” and “mutant” may be used interchangeably.
- a variant e.g. the CHAP domain of the invention
- a reference sequence usually, refers to the sequence of the (poly)peptide or part thereof from which the variant is derived (e.g. the CHAP domain of L0482).
- a variant itself is employed as a reference sequence (e.g. H5; SEQ ID NO: 11) for describing another variant.
- a variant i.e. a polypeptide (e.g., a peptidoglycan hydrolase of the invention) or a part thereof (e.g., a CHAP domain of the invention) which is derived from a certain polypeptide (e.g. L0482) or a part thereof (e.g.
- the CHAP domain of L0482 that is used as a reference sequence, has at least one mutation, i.e., at least one amino acid substitution, deletion, insertion and/or addition, preferably at least one amino acid substitution, relative to the reference sequence (e.g. at least one mutation in SEQ ID NO: 1, or in the sequence from position 72 to position 215 in SEQ ID NO: 1, respectively).
- sequence identity refers to the extent to which two (nucleotide or amino acid) sequences have the same residues at the same positions in an alignment. Typically, the “sequence identity” is expressed as a percentage.
- one of the two sequences may be considered as a reference sequence to which the other sequence has a sequence identity of at least n %.
- a certain (poly)peptide e.g., a peptidoglycan hydrolase of the invention
- a part thereof e.g., a CHAP domain of the invention
- n being an integer between 60 and 99, in particular 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99.
- said reference sequence refers to a (poly)peptide (e.g. SEQ ID NO: 1) or a part thereof (e.g. the sequence from position 72 to position 215 in SEQ ID NO: 1) from which said (poly)peptide or part thereof is derived, respectively.
- a certain polypeptide or part thereof has a higher minimal sequence identity to a corresponding reference sequence than “at least 60%”, i.e., a sequence identity of at least n %, with n being an integer between 61 and 99.
- n is an integer between 80 and 99.
- n may also refer to a decimal number with one decimal place between 89.5 and 99.9, in particular, 89.5, 89.6, 89.7, 89.9, 90.0, 90.1, 90.2 etc. or 99.9.
- the minimal sequence identity is indicated by an integer, i.e., at least n % with n being an integer (e.g.
- n may also refer to a decimal number with one decimal place that can be rounded by conventional rounding rules to said integer.
- a sequence identity of at least 95% may also refer to a sequence identity of at least 94.5%, at least 94.6%, at least 94.7%, at least 94.8%, at least 94.9%, at least 95.0%, at least 95.1%, at least 95.2%, at least 95.3% or at least 95.4%.
- sequence identity may also refer to a sequence identity of at least 94.5%, at least 94.6%, at least 94.7%, at least 94.8%, at least 94.9%, at least 95.0%, at least 95.1%, at least 95.2%, at least 95.3% or at least 95.4%.
- certain minimal sequence identities are indicated herein in specific contexts and thus are considered as preferred minimal sequence identities in these contexts.
- sequence identity of at least n %, with n being an integer between 60 and 99, or n % with n being a decimal number with one decimal place between 89.5 and 99.9, are considered herein as well in context of any (poly)peptide or part thereof described herein.
- (poly)peptide can refer to a polypeptide or a peptide, as commonly understood in the art.
- the degree of sequence identity can be determined according to methods well known in the art using, preferably, suitable computer algorithms such as BLAST and/or CLUSTAL Omega. In particular, BLAST may be used in combination with CLUSTAL Omega.
- BLAST binds to a reference sequence.
- the coverage is a filter that selects sequences with the same architecture as the reference sequence, e.g., LYSM-CHAP endolysins.
- endolysin sequences were isolated from the NCBI nucleotide database using BLAST, wherein the sequences were first sorted with a cutoff of 80% sequence coverage and then with a cutoff of 60% identity to L0482 (SEQ ID NO: 1) or a certain variant thereof.
- CLUSTAL Omega was then employed to align the sequences.
- Clustal Omega analysis method e.g. in combination with BLAST
- Clustal Omega e.g. in combination with BLAST
- Clustal Omega e.g. in combination with BLAST
- Clustal Omega e.g. in combination with BLAST
- BLAST BLAST
- default settings may be used.
- Clustal Omega (Madeira F, Park YM, Lee J, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research. 2019 Jul;47(W1):W636-W641. DOI: 10.1093/nar/gkz268. PMID: 30976793; PMCID: PMC6602479) is used for the comparison of amino acid sequences in context of the present invention.
- Program clustalo; Version : 1.2.4; Input Parameters: Output guide tree: true; Output distance matrix: false; Dealign input sequences: false; mBed-like clustering guide tree: true; mBed-like clustering iteration: true; Number of iterations: 0; Maximum guide tree iterations: -1; Maximum HMM iterations: -1; Output alignment format: clustal_num; Output order: aligned; Sequence Type: protein.
- the degree of sequence identity is calculated over the complete length of the reference sequence.
- Amino acid residues located at a position corresponding to a position in a reference sequence can be easily identified by the skilled person by methods known in the art.
- such amino acid residues can be identified by aligning the sequence in question with the reference sequence, e.g., the sequence shown in SEQ ID NO:1, and by identifying the positions which correspond to the indicated positions in the reference sequence, e.g. in SEQ ID NO:1.
- the alignment can be done with means and methods known to the skilled person, e.g. by using a known computer algorithm such as the Lipman-Pearson method (Science 227 (1985), 1435) or the CLUSTAL algorithm.
- Clustal Omega is used for the comparison of amino acid sequences in context of the present invention, and hence for determining positions corresponding to positions in a reference sequence.
- SEQ ID NO: 1 WT L0482
- R arginine
- SEQ ID NO: 9 The L0482 hit variant H3 (SEQ ID NO: 9), for example, does not show any deletions, insertions or additions compared to the sequence of SEQ ID NO: 1 but has a lysine (“K”) at position 86.
- H3 (SEQ ID NO: 9) has an amino acid substitution at position 86 in reference to SEQ ID NO: 1, wherein the residue at said position (i.e., the arginine) is substituted with lysine.
- H3 has the R86K mutation in reference to SEQ ID NO: 1, as described herein.
- H1 the L0482 hit variant “H1” (SEQ ID NO: 7)
- five amino acid residues are deleted at the N-terminus.
- H1 only has a length of 210 amino acid residues.
- H1 SEQ ID NO: 7
- H1 has a lysine (“K”) at a position corresponding to position 86 in SEQ ID NO: 1, similarly as H3; see, e.g., Figure 9A.
- H1 (SEQ ID NO: 7) is considered herein and in context to the present invention to have an amino acid substitution at a position corresponding to position 86 in SEQ ID NO: 1, wherein the residue at said position (i.e., the arginine) is substituted with lysine.
- H1 has the same R86K mutation in reference to SEQ ID NO: 1 as other hit variants such as H3.
- a similar logic also applies to any other mutations, e.g., amino acid substitutions, described herein and in context of the present invention.
- an “amino acid substitution” or short “substitution” at a certain position in a reference amino acid sequence or at a position corresponding to a certain position in a reference sequence means that the amino acid residue at said position is substituted with another amino acid residue, as described herein.
- amino acid substitution or “substituted with another amino acid residue” mean that the respective amino acid residue at the indicated position can be substituted with any other possible amino acid residue, e.g. a naturally occurring amino acid or a non-naturally occurring amino acid (Brustad and Arnold, Curr. Opin. Chem.
- a naturally occurring amino acid i.e., an amino acid residue selected from the group consisting of alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine.
- “deleted” or “deletion” means that the amino acid at the indicated position is deleted.
- inserted or “insertion” means that at the respective position at least one amino acid residue, e.g., one or two, preferably one residue, is inserted after the indicated position.
- added or “addition” means that at least one amino acid residue is added at the N-terminus and/or the C-terminus of the reference sequence.
- a standard tool preferably Clustal Omega, is used for determining the sequence identity of a nucleic acid sequence to a corresponding reference nucleic acid sequence in context of the present invention, preferably by using default settings.
- the present invention relates, in some aspects, to a peptidoglycan hydrolase comprising a CHAP domain according to the present invention.
- said peptidoglycan hydrolase has bactericidal activity, preferably a killing activity against a gram-positive bacterium, more preferably against Staphylococcus species or strain, most preferably against Staphylococcus aureus, preferably including methicillin-resistant Staphylococcus aureus strains, as described herein.
- the peptidoglycan hydrolase of the invention may have a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, as described herein.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, as described herein.
- the CHAP domain of the invention may have one or more amino acid deletions, insertions or additions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1.
- the CHAP domain according to the invention functions as a peptidoglycan hydrolase and, preferably, has bactericidal activity, as described herein.
- the sequence from position 72 to position 215 in SEQ ID NO: 1 is also shown in SEQ ID NO: 301.
- the CHAP domain according to the invention has, in other words, a sequence identity of at least 60% to the sequence of SEQ ID NO: 301 and one or more amino acid substitutions as compared to the sequence of SEQ ID NO: 301.
- the comparison to a reference sequence comprises, in particular, performing a sequence alignment.
- positions in the CHAP domain of the invention corresponding to positions in SEQ ID NO: 1 can be readily identified.
- the CHAP domain of the invention has one or more amino acid substitutions in the sequence from position 72 to position 215 in SEQ ID NO: 1.
- the CHAP domain of the invention may have one or more amino acid substitutions in the sequence from a position corresponding to position 72 in SEQ ID NO: 1 to a position corresponding to position 215 in SEQ ID NO: 1, i.e., in the sequence which corresponds to the sequence from position 72 to position 215 in SEQ ID NO: 1 in a sequence alignment (and which may have deletions, insertions and/or additions relative to the sequence from position 72 to position 215 in SEQ ID NO: 1).
- positions corresponding to positions 72 and 215 are present in the CHAP domain of the invention because other positions between these positions are sufficient to perform a sequence alignment.
- the peptidoglycan hydrolase of the invention consists of the CHAP domain of the invention, in particular, a sequence that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1.
- said CHAP domain (and hence said peptidoglycan hydrolase) has bactericidal activity, preferably a killing activity against a Staphylococcus species or strain, more preferably against Staphylococcus aureus, as described herein.
- the invention relates to the CHAP domain of the invention, i.e.
- CHAP domain which has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and which has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, as described herein.
- the CHAP domain of the invention may be advantageously employed in a peptidoglycan hydrolase of the invention (e.g. in combination with a cell wall binding domain) or considered itself as a peptidoglycan hydrolase of the invention.
- the peptidoglycan hydrolase of the invention i.e., a peptidoglycan hydrolase comprising or consisting of the CHAP domain of the invention
- any additional domains, peptides or tags that may be comprised in (or fused to) the peptidoglycan hydrolase of the invention e.g., a signal peptide or a PK tag, should not be considered when determining the sequence identity of the peptidoglycan hydrolase of the invention to the sequence of SEQ ID NO: 1.
- the peptidoglycan hydrolase of the invention may comprise (I) an amino acid sequence having a sequence identity of at least 60% to the sequence of SEQ ID NO: 1 (comprising the CHAP domain of the invention, and optionally the LYSM domain and/or peptide linker of the invention), and, optionally, (II) one or more further domains, peptides or tags, e.g. a signal peptide, a PK tag, a further peptide linker etc., as described herein.
- said CHAP domain has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1, and has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, as described herein.
- Aglycosylation mutations As described herein and as illustrated in the appended Examples, the removal of glycosylation sites in L0482 (i.e. at positions 68 and 73 in SEQ ID NO: 1) resulting in so-called “aglycosylated” L0482 variants strongly enhanced the bactericidal activity upon expression in eukaryotic cells; see, e.g., Example 4.
- Position 68 in SEQ ID NO: 1 is in the linker sequence of L0482, whereas position 73 in SEQ ID NO: 1 is in the CHAP domain of L0482.
- the CHAP domain is considered herein and in context of the invention as particularly important for the function of the peptidoglycan hydrolases of the invention, especially more important than the linker.
- an aglycosylation mutation at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is more preferred in context of the present invention than an aglycosylation mutation at position 68 in SEQ ID NO: 1 or at a position corresponding to this position.
- the inventive CHAP domain of the invention has a mutation, in particular, an amino acid substitution or a deletion, at position 73 in SEQ ID NO: 1 or at a position corresponding to this position as described herein, e.g., as specified in the subsequent embodiments.
- the arginine (“N”) at position 73 in SEQ ID NO: 1 or the arginine at a position corresponding to position 73 in SEQ ID NO: 1 may be deleted or, preferably, substituted with another amino acid residue, as described herein.
- said position 73 may be considered herein and in context of the present invention as a glycosylation position which is, preferably, aglycosylated. Therefore, the inventive CHAP domain of the invention has preferably an aglycosylation mutation, preferably an amino acid substitution, at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein. Thus, in some preferred embodiments, the inventive CHAP domain of the invention has an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, in particular, an aglycosylation substitution as described herein.
- the peptidoglycan hydrolase of the invention does not have a sequence as shown in any one of SEQ ID NO: 276 to 278.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position may be, for example, substituted with another amino acid residue than methionine, phenylalanine or lysine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than methionine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than phenylalanine or lysine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, for example, glycine, tyrosine, leucine, glutamic acid, alanine, or histidine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than phenylalanine, lysine or serine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention may have a sequence as shown in positions 72 to 215 in SEQ ID NO: 2.
- the peptidoglycan hydrolase of the invention further comprises a deletion or an amino acid substitution (preferably an amino acid substitution) at position 68 in SEQ ID NO: 1 or at a position corresponding to this position.
- the arginine at position 68 in SEQ ID NO: 1 or at a position corresponding to this position may be deleted or, preferably, substituted with another amino acid residue, as described herein.
- a mutation at position 68 in SEQ ID NO: 1 or at a position corresponding to this position may be considered herein and in context of the present invention as an aglycosylation mutation, in particular in context of a peptidoglycan hydrolase having a sequence identity of at least 60% to the sequence of SEQ ID NO: 1.
- the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted, for example, with another amino acid residue than threonine, serine or lysine, e.g., another amino acid residue than threonine or serine.
- the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than threonine, serine or lysine, e.g. another amino acid residue than threonine or serine, and/or the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than phenylalanine, lysine or serine, e.g., another amino acid residue than phenylalanine or lysine.
- the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, methionine, arginine or alanine, preferably lysine.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position may be substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine.
- the peptidoglycan hydrolase in particular in context of the inventive peptidoglycan hydrolase that has a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, the peptidoglycan hydrolase has a pair of amino acid substitutions at positions 68 and 73 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein a) the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, and the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, serine, tyrosine or leucine, b) the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with methionine, and the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with leucine, c) the residue at position 68 in SEQ ID NO: 1 or at
- the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, and the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- a peptidoglycan hydrolase of the invention having at least one aglycosylation mutation, in particular in the CHAP domain, e.g.
- an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position such as K73G, for example as show in SEQ ID NO: 2) is, inter alia, a particularly good starting point for further protein engineering and/or directed evolution.
- the peptidoglycan hydrolase of the invention may have instead or in addition (preferably in addition) to the mutations at positions 68 and/or 73 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, for example in the embodiments just above, at least one amino acid substitution described herein in context of beneficial/permissive, particularly beneficial or most beneficial amino acid substitutions found in L0482 variants obtained by the directed evolution (see, e.g., Examples 5-7) or found in context of deimmunization analyses or experiments (see, e.g., Example 10).
- beneficial/permissive, particularly beneficial, most beneficial amino acid or deimmunizing amino acid substitutions are described herein, for example, in the following.
- Beneficial and permissive amino acid substitutions found by the aglycosylation screen, directed evolution or the in silico deimmunization screen As described herein and as illustrated in the appended Examples, the inventors found 252 L0482 variants that were active and secreted from eukaryotic cells. These variants contained various amino acid substitutions which are considered herein as beneficial or at least permissive with respect to the pharmaceutical properties of the peptidoglycan hydrolases of the invention; see, e.g., Example 7 and Table 3. In particular, said amino acid substitutions may be beneficial (or at least permissive) for the bactericidal activity (e.g. against S. aureus) and the ability of being secreted from eukaryotic cells (e.g.
- L0482 variants human cells
- the deimmunizing amino acid substitutions identified in silico may be considered as beneficial for the safety and/or efficacy of the L0482 variants in context of medical uses and at least permissive for other pharmaceutical properties such as the bactericidal activity; see, e.g., Example 10 and Table 5.
- the inventors found amino acid substitutions at position 73 in SEQ ID NO: 1, i.e. aglycosylation substitutions in the CHAP domain of L0482, which enhance the bactericidal activity upon expression in eukaryotic cells; see, e.g., Example 4.
- a permissive amino acid substitution does not worsen the pharmaceutical properties of an L0482 variant to extent that it no longer can be used as a pharmaceutical.
- a L0482 variant must have a bactericidal activity as described herein.
- the L0482 variant should, ideally, have a sufficient stability as described herein when being used as a pharmaceutical.
- the L0482 variant should, ideally, further have the ability of being secreted from a mammalian cell.
- a permissive amino acid substitution renders a L0482 variant suitable for a pharmaceutical use by itself or improves the pharmaceutical properties of a L0482 variant.
- permissive amino acid substitutions may be rather employed in combination with at least one particularly beneficial amino acid substitution, or, preferably, with at least one of the most beneficial amino acid substitutions, as described herein.
- a “beneficial” amino acid substitution may improve or contribute to the improvement of at least one pharmaceutical property of a L0482 variant, e.g., the bactericidal activity, the ability of being secreted from mammalian cells, the stability and/or the reduction of the immunogenicity.
- beneficial amino acid substitution may be employed alone, they are, preferably, employed in combination with at least one particularly beneficial amino acid substitution, or, more preferably, with at least one of the most beneficial amino acid substitutions, as described herein.
- the CHAP domain of the invention has one or more amino acid substitutions at positions 72 to 83, 85, 86, 93, 96, 99, 102 to 104, 107, 108, 111, 113 to 115, 117, 121 to 125, 129 to 131, 133 to 145, 148, 149, 152, 153, 155, 157, 159, 166, 169, 170, 173 to 178, 185, 186, 190 to 194, 196 to 199, 201, 203 to 207, and 212 to 215 in SEQ ID NO: 1, or at positions corresponding to these positions.
- the amino acid residue at position 72 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with phenylalanine, aspartic acid, histidine or threonine
- the amino acid residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine, serine, aspartic acid or threonine
- the amino acid residue at position 74 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine or proline
- the amino acid residue at position 75 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with phenylalanine, proline, aspartic acid or glutamine
- the amino acid residue at position 76 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, aspartic acid or asparagine
- amino acid residue at position 214 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine or threonine, and/or the amino acid residue at position 215 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, valine or serine.
- amino acid substitutions just listed herein above correspond to the amino acid residues shown in Example 7 in Table 3 in the column “beneficial/permissive residues” which are not surrounded by parentheses, i.e. not marked by “( )”, as well as the amino acid residues shown in Example 10 in Table 5 in the column “deimm”.
- the positions (short: “pos”) in Tables 3 and 5 corresponds to the positions in SEQ ID NO: 1.
- an amino acid residue listed at a certain position in these Tables means that the amino acid at said position or at a position corresponding to said position in SEQ ID NO: 1 is substituted with an amino acid residue indicated at said position in the column “beneficial/permissive residues” in Table 3 and/or in the column “deimm” in Table 5.
- “ER(H)” in the column “beneficial/permissive residues” in Table 3 means that the amino acid residue (i.e.
- the lysine; “K”) at position 176 in SEQ ID NO: 1 or at a position corresponding to position 176 SEQ ID NO: 1 is substituted with glutamic acid (“E”) or arginine (“R”) in the L0482ag variants that were secreted from yeast cells and found to be active by YODA, as described herein and as illustrated in the appended Examples.
- said mutations, i.e. amino acid substitutions are considered herein and in context of the present invention as “beneficial” or at least “permissive” for the desired pharmaceutical properties of peptidoglycan hydrolases, in particular, a sufficient killing activity (e.g., against S.
- amino acid residues shown within parentheses in the column “beneficial/permissive residues” in Table 3 may be also at least permissive for said pharmaceutical properties.
- Table 3 shows positions in SEQ ID NO: 1 where beneficial or permissive amino acid substitutions have been found. These are the positions for which the column “beneficial/permissive residues” in Table 3 shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses. These positions are also called “permissive positions” herein.
- positions 72 to 215 in Table 3 for which the column “beneficial/permissive residues” shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses are considered as “permissive positions” in the CHAP domain herein.
- an amino acid residue in SEQ ID NO: 1 corresponding to a beneficial or permissive position may be substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said position, i.e. a residue shown without parentheses or in parentheses in said column in Table 3, preferably with a residue that is shown without parentheses in said column in Table 3.
- the CHAP domain of the present invention has at least one amino acid substitution at the permissive positions in the CHAP domain or at positions corresponding to said permissive positions in the CHAP domain.
- at least one amino acid residue at said permissive positions in the CHAP domain or at positions corresponding to said permissive positions in the CHAP domain is substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said positions, more preferably with a residue that is shown without parentheses in said column in Table 3.
- the peptidoglycan hydrolase of the present invention has at least one amino acid substitution at the permissive positions or at positions corresponding to said permissive positions.
- at least one amino acid residue at said permissive positions or at positions corresponding to said permissive positions is substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said positions, more preferably with a residue that is shown without parentheses in said column in Table 3.
- the CHAP domain of the invention has one or more amino acid substitutions at positions 72 to 76, 78, 81, 82, 85, 86, 93, 96, 104, 107, 108, 111, 113, 115, 117, 121, 124, 125, 129, 130, 133 to 136, 138, 140 to 142, 144, 145, 148, 149, 152, 153, 155, 157, 159, 169, 173, 175 to 178, 185, 186, 190 to 194, 197, 198, 199, 201, 203, 204, 207, and 212 to 215 in SEQ ID NO: 1, or at positions corresponding to these positions.
- the amino acid residue at position 72 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with phenylalanine
- the amino acid residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine or serine
- the amino acid residue at position 74 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine or proline
- the amino acid residue at position 75 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with phenylalanine or proline
- the amino acid residue at position 76 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue at position 78 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine or tyrosine
- the amino acid residue at position 81 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with
- amino acid residue at position 214 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine or threonine, and/or the amino acid residue at position 215 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, valine or serine.
- amino acid substitutions described just herein above refer to all the substitutions found in the sequenced L0482 variants that were secreted from yeast cells and determined to be active by the YODA method as described herein and as illustrated in the appended Examples; see, e.g., Example 7 and Table 3, in particular the “beneficial/permissive residues” shown without parentheses in Table 3.
- the inventors determined hit variants among all these L0482 variants, which are particularly well adapted for the production in eukaryotic cells and which may have particularly beneficial pharmaceutical properties, as described herein; see, e.g., Examples 5-7, Table 4 and Figures 8 and 9.
- the amino acid substitutions found in these hit variants i.e. G1-G4, H1-H10 and I1-I30, are considered herein and in context of the present invention as “particularly beneficial mutations” or “particularly beneficial amino acid substitutions” which may be particularly beneficial for maintaining or enhancing the desired pharmaceutical properties of peptidoglycan hydrolases, in particular, the bactericidal activity (e.g., against S.
- aureus the stability and/or the ability of being secreted from eukaryotic cells, e.g. human cells.
- eukaryotic cells e.g. human cells.
- particularly beneficial amino acid substitutions are preferred over amino acid substitutions that are described as “beneficial” or “permissive” herein.
- the CHAP domain of the invention has one or more amino acid substitutions at positions 73, 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191, 192, 194, 198, 204, 212 and 215 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the amino acid residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine or serine
- the amino acid residue at position 75 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with phenylalanine
- the amino acid residue at position 78 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue at position 81 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid
- the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the CHAP domain of the invention has an aglycosylation mutation at position 73 or at a position corresponding to this positions, as described herein, and additionally one or more amino acid substitutions at positions 75, 78, 81, 82, 85, 86, 104, 107, 115, 124, 125, 130, 133, 135, 136, 140, 141, 155, 169, 173, 175, 178, 185, 186, 191 to 194, 198, 204, 212 and 215 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, for example, as just described herein above.
- G1 as an exemplary first-round hit variant comprising particularly beneficial amino acid substitutions is a hit variant obtained in the first round of the directed evolution, which showed an increased thermostability, an enhanced bactericidal activity and an enhanced secretion from eukaryotic cells as compared to the starting for the directed evolution (L0482ag); see Figure 8.
- G1 (SEQ ID NO: 3) contains the following amino acid substitutions in the CHAP domain as compared to L0482ag (SEQ ID NO: 2): T82S, N85G, R86K, D169N, K173N, M175Q and A192Q.
- the CHAP domain of the invention has one or more amino acid substitutions at positions 82, 85, 86, 169, 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position (i.e. threonine) is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position (i.e. asparagine) is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position (i.e.
- arginine is substituted with lysine
- the amino acid residue at position 169 in SEQ ID NO: 1 or at a position corresponding to this position i.e. aspartic acid
- the amino acid residue at position 173 in SEQ ID NO: 1 or at a position corresponding to this position i.e. lysin
- the amino acid residue at position 175 in SEQ ID NO: 1 or at a position corresponding to this position i.e. methionine
- glutamine and/or the amino acid residue at position 192 in SEQ ID NO: 1 or at a position corresponding to this position (i.e. alanine) is substituted with glutamine.
- the CHAP domain may have a sequence identity of at least 95% to the sequence from position 72 to position 215 in SEQ ID NO: 3.
- the CHAP domain has (a) an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; (b) an amino acid substitution pair at positions 82 and 85 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, and the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine; and/or (c) an amino acid substitution at position 169 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid at position 169 in SEQ ID NO: 1 or
- said CHAP domain may comprise one or more amino acid substitutions at positions 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 173 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 175 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine, and/or the amino acid residue at position 192 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine.
- the CHAP domain further has an aglycosylation mutation at position 73 or at a position corresponding to this position, as described herein, preferably wherein the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, more preferably with glycine.
- the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 80% to the sequence from position 72 to position 215 in SEQ ID NO: 1; (ii) an amino acid substitution or a deletion at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and (iii) one or more amino acid substitutions at positions 82, 85, 86, 169, 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 169 in SEQ ID NO: 1
- the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 91% to the sequence from position 72 to position 215 in SEQ ID NO: 1; (ii) an amino acid substitution or a deletion at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and (iii) one or more amino acid substitutions at positions 82, 85, 86, 169, 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 169 in SEQ ID NO: 1
- the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 80% to the sequence from position 72 to position 215 in SEQ ID NO: 1; (ii) an amino acid substitution or a deletion at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and (iii) at least two amino acid substitutions at positions 82, 85, 86, 169, 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 169 in SEQ ID NO: 1
- the peptidoglycan hydrolase comprises a CHAP domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; (ii) an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine; and (iii) one or more amino acid substitutions at positions 82, 85, 86, 169, 173, 175 and 192 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue at position 86 in SEQ ID NO: 1 or at a
- the inventors found a set of most beneficial mutations, in particular a set of 9 most beneficial amino acid substitutions, i.e., T82S, N85G, R86K, S130N, H136K/R (preferably H136K), F155Y, D169N, N185Y and N186G in reference to SEQ ID NO: 1.
- the variant H5 SEQ ID NO: 11 which has been found to have overall the best pharmaceutical properties among the L0482 variants obtained by two rounds of directed evolution, contains exclusively these 9 most beneficial amino acid substitutions; see, e.g., Figures 8 and 9.
- H5 (SEQ ID NO: 11) has a strongly enhanced ability of being secreted from human cells, a strongly enhanced killing activity against S. aureus, and an improved (thermo)stability as compared to the parental L0482ag (SEQ ID NO: 2) and also as compared to WT L0482 (SEQ ID NO: 1); see, e.g., Examples 4-6 and 12 and Figures 8, 10 and 6.
- H5 (SEQ ID NO: 11) showed a 8-fold lower MIC than WT L0482 (SEQ ID NO: 1), i.e. WT L0482 had a MIC of 4 ⁇ g/ml, whereas H5 had a MIC of 0.5 ⁇ g/ml.
- H5 (SEQ ID NO: 11) showed the strongest killing activity against S. aureus (together with H7; SEQ ID NO: 13), the best stability (in particular a melting temperature of 47°C), and a good secretion from human cells; see Figure 8.
- H5 also showed an enhanced ability of being secreted from human cells, an enhanced killing activity against S. aureus, and an improved (thermo)stability as compared to G1 (SEQ ID NO: 3) which is an improved L0482 variant obtained in the first round of the directed evolution; see Figure 8.
- G1 had a MIC of 1 ⁇ g/ml
- H5 had a MIC of 0.5 ⁇ g/ml.
- H5 (SEQ ID NO: 11) further showed enhanced (i.e. faster) killing kinetics against S. aureus in an OD reduction assay than WT L0482 (SEQ ID NO: 1); see Example 6 and Figure 11.
- H5 (SEQ ID NO: 11) effectively killed S. aureus biofilms and showed an even greater anti-biofilm activity than G1 (SEQ ID NO: 3); see Example 6 and Figure 12. This is in line with the particularly low MIC observed for H5, which is lower than the MIC of G1.
- the most beneficial amino acid substitutions i.e the “H5” mutations
- aureus including S. aureus biofilms
- the stability and/or the ability of being secreted from eukaryotic cells e.g. human cells.
- the most beneficial amino acid substitutions are preferred over amino acid substitutions described as “particularly beneficial” and even more preferred over amino acid substitutions described as “beneficial” or “permissive”.
- the L0482 variant H3 (SEQ ID NO: 9) obtained by the directed evolution contained 8 out of the 9 most beneficial amino acid substitutions and exclusively these 8 mutations.
- H3 reflects the consensus sequence.
- the 8 consensus mutations refer to T82S, N85G, R86K, S130N, H136K/R, D169N, N185Y and N186G, in reference to the sequence of SEQ ID NO: 1.
- H3 (SEQ ID NO: 9) has improved pharmaceutical properties, e.g., an improved ability of being secreted from eukaryotic cells compared to WT L0482 and L0482ag as well as a good killing activity against S. aureus; see, e.g., Figures 8 and 10.
- This further demonstrates the advantageous effects of the consensus mutations with respect to the pharmaceutical properties of L0482 variants, as described herein.
- the CHAP domain of the present invention has one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has, in some particularly preferred embodiments, at least one consensus mutation, i.e. at least one amino acid substitution selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, D169N, N185Y and N186G in SEQ ID NO: 1.
- said CHAP domain i.e.
- a CHAP domain comprising at least one of the consensus mutations described herein further comprises (i) an aglycosylation mutation at position 73 or at a position corresponding to this position, as described herein, for example, wherein the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine or serine, more preferably glycine; and/or (ii) an amino acid substitution at position 155 or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the amino acid substitution H136R occurred in many of the hit variants (i.e. G1-G4, H1-H10 and I1 to I30) instead of H136K and thus is a very good alternative to H136K.
- the L0482 variant H3 has the following sequence, wherein the LYSM domain (positions 1 to 51) is underlined, the linker (positions 52 to 71) is in italics, and the CHAP domain (positions 72 to 215) is in bold: REAPKTQIYTVKKGDTLSAIALKYKTTVSNIQNTNNIANPNLIFIGQKLKVPMTPLVEPKPKTVSSNKKSNSGSSTLNYLKSLEG KGWDFDGSYGWQCFDLVNVYWNHLYGHGLKGYGAKDIPYANNFNNEAKIYKNTPTFKAEPGDLVVFSGRFGG GYGHTAIVLNGNYDGKLMKFQSLDQNWYGGGWRKAEVAHKVVHNYENDMIFIRPFKK
- the L0482 variant H5 has the following sequence, wherein the LYSM domain (positions 1 to 51) is underlined, the linker (positions 52 to 71) is in italics, and the CHAP domain (positions 72 to 215) is in bold: GYGHTAIVLNGNYDGKLMKFQSLDQNWYGGGWRKAEVAHKVVHNYENDMIFIRPFKKA (SEQ ID NO: 11).
- SEQ ID NO: 9 and SEQ ID NO 11, respectively the two glycosylation positions, i.e., positions 68 and 73, wherein aglycosylation amino acid residues have been introduced in H3 and H5 (i.e.
- amino acid residues in SEQ ID NO: 9 shown in white on black background refer to the consensus mutations
- amino acid residues in SEQ ID NO: 11 shown in white on black background refer to the most beneficial amino acid substitutions, as described herein and in context of the present invention.
- H3 SEQ ID NO: 9 contains all of the most beneficial amino acid substitutions except F155Y. Also see Figure 9A for the alignments. Notably, all of the most beneficial amino acid substitutions, i.e.
- any of these most beneficial mutations or any combination thereof is, preferably, combined with an aglycosylation mutation at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein, e.g., with the amino acid substitution N73G in SEQ ID NO: 1.
- an aglycosylation mutation at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein, e.g., with the amino acid substitution N73G in SEQ ID NO: 1.
- any of these most beneficial mutations or any combination thereof is further combined with at least one aglycosylation mutation at positions 68 and 73 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, e.g., with the amino acid substitutions N68K and/or N73G in SEQ ID NO: 1.
- the peptidoglycan hydrolase or CHAP domain of the invention contains all of the 9 most beneficial mutations described herein at once.
- the L0482 variant H1 (SEQ ID NO: 7) did not show any mutations at positions corresponding to positions 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 and, nevertheless, had enhanced pharmaceutical properties compared to the parental L0482ag lysin (SEQ ID NO: 2), in particular, an enhanced killing activity against S. aureus, an enhanced stability (e.g. thermostability/melting temperature), and an enhanced ability of being secreted from human cells.
- the L0482 variant H9 did not show any mutations at positions corresponding to positions 82, 85, 155, 185 and 185 in SEQ ID NO: 1, and also showed enhanced pharmaceutical properties compared to the parental L0482ag lysin (SEQ ID NO: 2); see, e.g., Figures 8 and 9.
- the amino acid substitution R86K is the only one among the most beneficial substitutions which H1 (SEQ ID NO: 7) and H9 (SEQ ID NO: 15) have in common.
- the CHAP domain of the present invention has one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the amino acid residue i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has, in some particularly preferred embodiments, at least one amino acid substitution selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1.
- said CHAP domain i.e.
- a CHAP domain comprising at least one of the most beneficial amino acid substitutions described herein further comprises an aglycosylation mutation at position 73 or at a position corresponding to this position, as described herein, for example, wherein the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, preferably glycine or serine, more preferably glycine.
- Amino acid substitution pairs and consensus mutation units As further described herein above, the inventors further surprisingly found that certain amino acid substitutions, in particular some of the consensus mutations (i.e.
- T82S, N85G, R86K, S130N, H136K/R (esp. H136K), D169N, N185Y and N186G in reference to SEQ ID NO: 1) occurred very often as substitution pairs in the active and secreted L0482 variants obtained by the directed evolution, in particular in the hits variants, i.e., G1 to G4, H1 to H10 and I1 to I30.
- the consensus mutations (which are particularly preferred amino acid substitutions in context of the invention) may be further grouped as consensus mutation units herein and in context of the present invention.
- these consensus mutation units consist of 1 or 2 amino acid substitutions and refer to: (i) R86K (which is particularly preferred), (ii) T82S and N85G, (iii) S130N and H136K/R (preferably H136K), (iv) D169N, and (v) N185Y and N186G.
- the CHAP domain of the invention has at least one pair of amino acid substitutions a) at positions 82 and 85 in SEQ ID NO: 1 or at positions corresponding to these positions, b) at positions 130 and 136 in SEQ ID NO: 1 or at positions corresponding to these positions, and/or c) at positions 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the amino acid residue at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, and the amino acid residue at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine;
- the amino acid residue at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, and the amino acid residue at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine; and/or in c), preferably, the amino acid residue at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine, and the amino acid residue at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention has, in some preferred embodiments, at least one substitution pair selected from the group consisting of: a) T82S and N85G, b) S130N and H136K/R (preferably H136K), and c) N185Y and N186G.
- said CHAP domain i.e. a CHAP domain having at least one substitution pair
- said CHAP domain further has, preferably, an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- said CHAP domain i.e.
- a CHAP domain having at least one substitution pair, and preferably an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position further has, preferably, an amino acid substitution at position 155 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- said CHAP domain has, preferably, an aglycosylation mutation at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the CHAP domain of the present invention has at least one consensus mutation unit, i.e., at least one amino acid substitution or substitution pair selected from the group consisting of the following (i) to (v): (i) an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the arginine) at said position is substituted with lysine (i.e. R86K); (ii) an amino acid substitution at positions 82 and 85 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine (i.e. H136K/R), preferably lysine (H136K);
- H136K/R lysine
- H136K an amino acid substitution at position 169 (i.e. the aspartic acid) in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with asparagine (i.e. D169N); and
- the CHAP domain of the invention has at least 2, preferably at least 3, more preferably at least 4 of the amino acid substitutions or substitution pairs (i) to (v) (i.e. consensus mutation units), as just described herein above.
- the CHAP domain of the invention has (i) an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the arginine) at said position is substituted with lysine; and has at least one, preferably at least two, more preferably at least three of the following amino acid substitutions or substitution pairs (ii) to (v) (i.e. consensus mutation units): (ii) an amino acid substitution at positions 82 and 85 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine;
- a consensus mutation or any combination thereof i.e. at least one substitution selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, D169N, N185Y and N186G, in SEQ ID NO: 1 or a consensus mutation unit or any combination thereof (i.e.
- At least one consensus mutation unit selected from the group consisting of: (i) R86K, (ii) T82S and N85G, (iii) S130N and H136K/R, (iv) D169N, (v) N185Y and N186G) is, preferably, combined with an amino acid substitution at position 155 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the amino acid residue at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine (i.e. F155Y), as described herein.
- a consensus mutation or consensus mutation unit or any combination thereof (which may be further combined with F155Y as just described) is, preferably, combined with at least one aglycosylation mutation (preferably at least one aglycosylation substitution) as described herein, preferably an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position.
- the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, tyrosine, leucine, glutamic acid, alanine, histidine or serine, more preferably, with glycine, as described herein.
- the CHAP domain of the invention has the amino acid substitution R86K, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K, T82S and N85G, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K, S130N and H136K/R, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K and D169N, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K and N185Y and N186, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, S130N and H136K/R, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, and D169N, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, and N185Y and N186G, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, D169N, N185Y and N186G, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, S130N, H136K/R, N185Y and N186G, as described herein. In some preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, S130N, H136K/R, and D169N, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, N185Y and N186G, as described herein. In some particularly preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, S130N, H136K/R and D169N, as described herein. In some particularly preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, S130N, H136K/R, N185Y and N186, as described herein.
- the CHAP domain of the invention has the amino acid substitutions R86K, S130N, H136K/R, D169N, N185Y and N186G, as described herein. In some particularly preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, D169N, N185Y and N186G, as described herein. In some of the most preferred embodiments, the CHAP domain of the invention has the amino acid substitutions R86K, T82S, N85G, S130N, H136K/R, D169N, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions T82S and N85G, as described herein.
- the CHAP domain of the invention has the amino acid substitutions T82S, N85G, S130N and H136K/R, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions T82S, N85G and D169N, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions T82S, N85G, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions T82S, N85G, S130N, H136K/R and D169N, as described herein.
- the CHAP domain of the invention has the amino acid substitutions T82S, N85G, S130N, H136K/R, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions T82S, N85G, S130N, H136K/R, D169N, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions S130N and H136K/R, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions S130N, H136K/R and D169N, as described herein.
- the CHAP domain of the invention has the amino acid substitutions S130N, H136K/R, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions S130N, H136K/R, D169N, N185Y and N186G, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitution D169N, as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions D169N, N185Y and N186G as described herein. In some embodiments, the CHAP domain of the invention has the amino acid substitutions N185Y and N186G, as described herein.
- substitution H136K is preferred over the substitution H136R.
- Particularly important individual amino acid substitutions: R86K and F155Y As already mentioned above and as illustrated in the appended Examples, all hit variants, i.e. G1-G4, H1-H10 and I1-I30, had the amino acid substitution R86K in reference to SEQ ID NO: 1. Thus, this amino acid substitution is considered herein and in context of the present invention as a particularly important substitution among the most beneficial amino acid substitutions, as described herein.
- the CHAP domain of the present invention has an amino acid substitution at position 86 in SEQ ID NO: 1 or at a position corresponding to this position.
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position may be substituted with another amino acid residue than serine.
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or methionine.
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine.
- said CHAP domain has, preferably, an aglycosylation mutation at position 73 in SEQ ID NO 1 or at a position corresponding to this position, as described herein.
- the amino acid substitution F155Y further improved several pharmaceutical properties (e.g. the killing activity against S. aureus, the stability and the ability of being secreted from human cells) in H5 (SEQ ID NO: 11) compared to H3 (SEQ ID NO: 9) containing only the consensus mutations.
- the CHAP domain of the invention has an amino acid substitution at position 155 in SEQ ID NO: 1 or at a position corresponding to this position.
- the amino acid residue i.e. the phenylalanine
- the CHAP domain has, preferably, an aglycosylation mutation at position 73 in SEQ ID NO 1 or at a position corresponding to this position, as described herein.
- the CHAP domain of the invention has (i) a sequence identity of at least 91% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 84% to the sequence of SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has (i) a sequence identity of at least 78% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) at least two amino acid substitutions at positions 82, 85, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 73% to the sequence in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) at least two amino acid substitutions at positions 82, 85, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has (i) a sequence identity of at least 78% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine, and/or the amino acid residue (i.e.
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 73% to the sequence in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine, and/or the amino acid residue (i.e.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; and has (iii) at least six amino acid substitutions at positions 82, 85, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, the amino acid residue (i.e.
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; has (iii) an amino acid substitution at position 82 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine; and has (iv) an amino acid substitution at position 85 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- said CHAP domain has the R86K substitution and a substitution pair consisting of T82S and N85G in reference to SEQ ID NO: 1.
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 60% to the sequence of SEQ ID NO: 1; has (ii) an amino acid substitution at position 86 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e.
- the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine; has (iii) an amino acid substitution at position 82 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine; and has (iv) an amino acid substitution at position 85 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- said peptidoglycan hydrolase has the R86K substitution and the substitution pair consisting of T82S and N85G in reference to SEQ ID NO: 1.
- the CHAP domain of the invention has (i) a sequence identity of at least 83% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution or a deletion (preferably, an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and has (iii) one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine, and/or the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 73% to the sequence of SEQ ID NO: 1; has (ii) an amino acid substitution or a deletion (preferably, an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and has (iii) one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; and (ii) an amino acid substitution at position 73 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e.
- said CHAP domain further has (iii) one or more amino acid substitutions at positions 82, 85, 86, 130, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue (i.e.
- the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution or a deletion (preferably, an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and has (iii) an amino acid substitution at position 82 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the threonine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution or a deletion (preferably, an amino acid substitution) at position 73 in SEQ ID NO: 1 or at a position corresponding to this position; and has (iii) an amino acid substitution at position 130 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 73 or a deletion (preferably, an amino acid substitution) in SEQ ID NO: 1 or at a position corresponding to this position; and has (iii) an amino acid substitution at position 185 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 130 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine; and has (iii) one or more amino acid substitutions at positions 82, 85, 86, 136, 155, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention has (i) a sequence identity of at least 78% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 155 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine; and has (iii) at least two amino acid substitutions at positions 82, 85, 86, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 73% to the sequence of SEQ ID NO: 1; has (ii) an amino acid substitution at position 155 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine; and has (iii) at least two amino acid substitutions at positions 82, 85, 86, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention has (i) a sequence identity of at least 78% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 155 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the peptidoglycan hydrolase of the invention has (i) a sequence identity of at least 73% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 155 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine; and has (iii) one or more amino acid substitutions at positions 82, 85, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the CHAP domain of the invention has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; has (ii) an amino acid substitution at position 155 in SEQ ID NO: 1, or at a position corresponding to this position, wherein the amino acid residue (i.e. the phenylalanine) at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine; and has (iii) at least six amino acid substitutions at positions 82, 85, 86, 130, 136, 169, 185 and 186 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue (i.e.
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the amino acid residue (i.e. the arginine) at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- the amino acid residue (i.e. the serine) at position 130 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the amino acid residue (i.e. the asparagine) at position 82 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine
- the amino acid residue (i.e. the asparagine) at position 85 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine
- the histidine) at position 136 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine or arginine, preferably lysine
- the amino acid residue (i.e. the aspartic acid) at position 169 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine
- the amino acid residue (i.e. the asparagine) at position 185 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine
- the amino acid residue (i.e. the asparagine) at position 186 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine.
- the peptidoglycan hydrolase of the invention does not have a sequence as shown in any one of SEQ ID NO: 279 to 293.
- the CHAP domain of the present invention has a sequence identity of at least 90%, preferably at least 95%, more preferably at least 97% or at least 98%, e.g.
- the CHAP domain of a hit variant refers to the sequence from a position in the sequence of said hit variant (e.g. SEQ ID NO: 7) which corresponds to position 72 in SEQ ID NO: 1 to a position in the sequence of said hit variant (e.g. SEQ ID NO: 7) which corresponds to position 215 in SEQ ID NO: 1.
- said CHAP domain has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to the sequence from position 72 to position 215 in SEQ ID NO: 1 as a reference sequence, as described herein.
- the peptidoglycan hydrolase of the present invention has a sequence identity of at least 90%, preferably at least 95%, more preferably at least 97%, e.g. at least 96.8%, to a hit variant as described herein, i.e., to any one of SEQ ID NO: 3 to 46.
- said peptidoglycan hydrolase has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to SEQ ID NO: 1 as a reference sequence, as described herein.
- the CHAP domain of the invention has a sequence identity of at least 93.2% or at least 94% to the sequence from position 72 to position 215 in SEQ ID NO: 11.
- said CHAP domain has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to the sequence from position 72 to position 215 in SEQ ID NO: 1 as a reference sequence, as described herein.
- the peptidoglycan hydrolase of the invention has a sequence identity of at least 95.0% or at least 96% to the sequence of SEQ ID NO: 11.
- said peptidoglycan hydrolase has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to SEQ ID NO: 1 as a reference sequence, as described herein.
- the CHAP domain of the invention has a sequence identity of at least 93.9% or at least 94% to the sequence from position 72 to position 215 in SEQ ID NO: 9.
- said CHAP domain has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to the sequence from position 72 to position 215 in SEQ ID NO: 1 as a reference sequence, as described herein.
- the peptidoglycan hydrolase of the invention has a sequence identity of at least 95.4% or at least 96% to the sequence of SEQ ID NO: 9.
- said peptidoglycan hydrolase has at least one of the amino acid substitutions selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1, i.e. with respect to SEQ ID NO: 1 as a reference sequence, as described herein.
- conserved positions and conserved segment In some embodiments, a segment of the inventive CHAP domain has a sequency identity of at least 80%, preferably at least 90%, to the sequence from position 87 to position 128 in SEQ ID NO: 1.
- said segment is contained in the inventive CHAP domain at positions corresponding to positions 87 to 128 in SEQ ID NO: 1, i.e., it is a corresponding segment.
- said segment may be considered herein and in context of the present invention as a particularly conserved CHAP segment.
- the CHAP domain of the invention has at most six, five, four, three or two, more preferably at most one, most preferably no amino acid substitutions or deletions at positions 80, 87, 88, 98, 99, 103, 106, 110, 114, 122, 126, 128, 137, 182, 202, and 208 of SEQ ID NO: 1 or at positions corresponding to these positions.
- said positions may be considered herein and in context of the present invention as conserved positions within the CHAP domain.
- the CHAP domain of the invention has, preferably, one or more amino acid substitutions at other positions than at the conserved positions described herein.
- the CHAP domain may also comprise one or more mutations, e.g. amino acid substitutions, at the conserved positions.
- the in-silico de-immunizing screen illustrated in Example 10 revealed possible amino acid substitutions at many different positions including “conserved positions”.
- this de-immunizing screen has been designed such that advantageous pharmaceutical properties, in particular the bactericidal activity, stability and ability of being secreted from eukaryotic cells, are maintained upon the de-immunization.
- mutations such as the de-immunization mutations found in context of the invention may be also introduced at positions which are considered as “conserved” herein.
- a conserved CHAP segment has in context of the present invention, preferably, less mutations than other segments of the CHAP domain of the invention.
- a corresponding segment of the CHAP domain of the invention has, preferably, a higher sequency identity (e.g. about 90%) to the sequence from position 87 to position 128 in SEQ ID NO: 1, as compared to the sequence identity of the CHAP domain of the invention to the sequence from position 72 to position 215 in SEQ ID NO: 1 (which may be in this example, e.g., about 60% to 80%).
- the present invention further relates to a peptidoglycan hydrolase having bactericidal activity, wherein the peptidoglycan hydrolase comprises a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain that has (i) a sequence identity of at least 60% to the sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, and wherein (a) a corresponding segment of said CHAP domain has a sequency identity of at least 80%, preferably at least 90%, to the sequence from position 87 to position 128 in SEQ ID NO: 1, and/or (b) said CHAP domain has at most six, five, four, three or two, preferably at most one, more preferably no amino acid substitutions or deletions at positions 80, 87, 88, 98, 99, 103, 106, 110, 114, 122, 126
- said CHAP domain comprises at least one aglycosylation mutation at position 73 in SEQ ID NO: 1 or at a position corresponding to this position as described herein, preferably the substitution N73G, and/or at least one amino acid substitution described herein in context of the L0482ag variants obtained upon directed evolution, preferably at least one of the most beneficial mutations, as described herein, i.e., at least amino acid substitution selected from the group consisting of: T82S, N85G, R86K, S130N, H136K/R, F155Y, D169N, N185Y and N186G in SEQ ID NO: 1.
- the peptidoglycan hydrolase of the invention comprises, in addition to the CHAP domain of the invention, at least one cell wall binding domain.
- endolysins often have at least one cell wall-binding domain (CBD) which recognize and bind to certain epitopes in the cell wall of the host bacterium for proper fixation of the catalytic effect of an enzymatically active domain (EAD).
- CBDs are enzymatically inactive by themselves.
- a domain which has catalytic activity and is able to recognize and bind to certain epitopes in the cell wall of a bacterium is rather considered herein as a an enzymatically active domain (EAD).
- the cell wall binding domain is a peptidoglycan binding domain which binds, in particular, to the peptidoglycan structure of a target bacterium.
- Suitable cell wall binding domains to be used in context of the present invention include, inter alia: a LYSM domain, a SH3 domain and a choline binding domain.
- the LYSM domain is derived from an endolysin comprising a LYSM domain and a CHAP domain, wherein the LYSM domain is, preferably, N-terminally of the CHAP domain.
- the LYSM domain of the invention is, preferably, derived from an endolysin having a LYSM-CHAP architecture, as described herein, e.g. L0482 (SEQ ID NO: 1) or L0499 (SEQ ID NO: 47).
- the peptidoglycan of the invention comprises, in addition, to the CHAP domain of the invention, a LYSM domain, as described herein.
- the cell wall binding domain e.g.
- the LYSM domain is N-terminally of the CHAP domain.
- the LYSM domain according to the invention is defined by the sequence from position 1 to position 51 in SEQ ID NO: 1 or it has a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1.
- the LYSM domain according to the invention is, preferably, defined by the sequence of SEQ ID NO: 302 or has a sequence identity of at least 60% to the sequence of SEQ ID NO: 302.
- the LYSM domain is defined by the sequence from position 1 to position 47 in SEQ ID NO: 47 or it has a sequence identity of at least 60% to the sequence from position X to position Y in SEQ ID NO: 47.
- the SH3 domain is defined by the sequence of SEQ ID NO: 376 or has a sequence identity of at least 60% to the sequence of SEQ ID NO: 376. In some embodiments, the SH3 domain is defined by the sequence of SEQ ID NO: 377 or has a sequence identity of at least 60% to the sequence of SEQ ID NO: 377.
- the cell wall binding domain of the invention e.g. the LYSM domain of the invention, has, preferably, the ability to bind to the cell wall of a Staphylococcus species or strain, more preferably to Staphylococcus aureus, as described herein.
- the inventors found deimmunizing substitutions in the LYSM domain of L0482 variants which may decrease the immunogenicity of the LYSM domain of the invention and peptidoglycan hydrolases containing the LYSM domain of the invention; see, e.g., Table 5, column “deimm”.
- the LYSM domain of the invention (which preferably has a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1) may have one or more amino acid substitutions at positions 1 to 6, 8, 10 to 13, 16 to 20, 22 to 30, 32 to 45 and 47 to 51 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably, wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan, glutamine or asparagine, the amino acid residue at position 2 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine, the amino acid residue at position 3 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 4 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid, the amino acid residue at position 5 in SEQ ID NO: 1 or at a position corresponding to this position
- the amino acid residue at position 45 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with alanine, aspartic acid, glutamic acid, lysine, proline, glutamine or threonine
- the amino acid residue at position 47 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with leucine
- the amino acid residue at position 48 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with aspartic acid, glutamic acid, asparagine, glutamine, isoleucine or arginine
- the amino acid residue at position 49 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with isoleucine, methionine or asparagine
- the amino acid residue at position 50 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with aspartic acid, histidine, asparagine, threonine or isoleucine, and/or
- amino acid substitutions may be considered as beneficial or, at least, permissive for the desired pharmaceutical properties of the peptidoglycan hydrolases of the invention, as described herein, e.g., as described in context of beneficial or permissive amino acid substitutions in the CHAP domain.
- the LYSM domain of the invention (which preferably has a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1) may have one or more amino acid substitutions at positions 1, 8, 10, 12, 13, 17, 19, 22 to 25, 28 to 30, 32 to 45 and 48 to 51 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably, wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan or glutamine, the amino acid residue at position 8 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 10 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with valine, the amino acid residue at position 12 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with aspartic acid, glycine, glutamine or serine, the amino acid residue at position 13 in SEQ ID NO: 1 or at a position a
- amino acid substitutions may be considered as beneficial or, at least, permissive for the desired pharmaceutical properties of the peptidoglycan hydrolases of the invention, as described herein.
- Table 3 shows positions in SEQ ID NO: 1 where beneficial or permissive amino acid substitutions have been found. These are the positions for which the column “beneficial/permissive residues” in Table 3 shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses. These positions are also called “permissive positions” herein.
- positions 1 to 51 in Table 3 for which the column “beneficial/permissive residues” shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses are considered as “permissive positions” in the LYSM domain herein.
- an amino acid residue in SEQ ID NO: 1 corresponding to a beneficial or permissive position may be substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said position, i.e. a residue shown without parentheses or in parentheses in said column in Table 3, preferably with a residue that is shown without parentheses in said column in Table 3.
- the LYSM domain has at least one amino acid substitution at the permissive positions in the LSYM domain or at positions corresponding to said permissive positions in the LYSM domain.
- at least one amino acid residue at said permissive positions in the LSYM domain or at positions corresponding to said permissive positions in the LYSM domain is substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said positions, more preferably with a residue that is shown without parentheses in said column in Table 3.
- Particularly beneficial amino acid substitutions in the LYSM domain Furthermore, as described herein, the inventors found hits variants, i.e. G1 to G4, H1 to H10 and I1 to I30, which contained certain amino acid substitutions in the LYSM domain; see, e.g., Table 4. These amino acid substitutions are thus considered in context of the invention as particularly beneficial mutations, i.e., amino acid substitutions, in the LYSM domain. As described herein, e.g., in context of the CHAP domain of the invention, “particularly beneficial amino acid substitutions” may be particularly beneficial for maintaining or enhancing the desired pharmaceutical properties of peptidoglycan hydrolases, in particular, the bactericidal activity (e.g., against S.
- the LYSM domain of the invention (which preferably has a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1), has, preferably, one or more amino acid substitutions at positions 1, 8, 10, 13, 23 to 25, 30, 33, 37, and 39 to 41 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably, wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan, the amino acid residue at position 8 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 10 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with valine, the amino acid residue at position 13 in SEQ ID NO: 1 or
- the cell wall binding domain of the invention e.g. the LYSM domain of the invention
- a peptidoglycan hydrolase comprising a CHAP domain and/or a LYSM domain as described herein has, preferably, a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, as described herein.
- the peptidoglycan hydrolase comprises a peptide linker between the CHAP domain and the cell wall binding domain.
- the peptide linker is not limited to any specific linkers and any linkers used in the art for connecting different domains or parts of proteins such as fusion proteins may be used herein and in context of the present invention.
- peptide linker refers to a peptide or polypeptide sequence which connects two or more domains (e.g., the CHAP domain or the invention and a cell wall binding domain, and/or the CHAP of the invention and an extended pharmacokinetic (PK) peptide) in a linear amino acid sequence of a polypeptide chain.
- the linker is a flexible linker.
- Exemplary linkers include glycine-serine-polypeptide linkers, glycine-proline- polypeptide linkers, and proline-alanine polypeptide linkers.
- linker with a furin cleavage site (which may be also used in context of the present invention) is shown in SEQ ID NO: 370.
- the linker is a glycine-serine linker, i.e., a peptide that predominantly, essentially or exclusively consists of glycine and serine residues.
- a glycine-serine linker may comprise, for example, one or multiple copies (e.g.2 to 5 copies) of the sequence shown in SEQ ID NO: 297 (i.e. GGGGS).
- said copies are directly adjacent to each other, for example, as shown in SEQ ID NO: 298 or 299 (i.e.
- the peptide linker is a L0482-derived linker, i.e. a linker which has a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1.
- Beneficial and permissive amino acid substitutions in the L0482 linker found by aglycosylation screen, directed evolution, or in silico deimmunization screen As described herein and as illustrated in the appended Examples, the inventors found a variety of amino acid substitutions which were contained in the linker sequence of L0482 variants obtained by directed evolution; see, e.g., Table 3, the column “beneficial/permissive residues”.
- the L0482 variants containing these amino acid substitutions were all well secreted from eukaryotic cells and determined to be active by the YODA method. Furthermore, as also described herein and as illustrated in the appended Examples, the inventors found deimmunizing substitutions in the linker sequence of L0482 variants which may decrease the immunogenicity of the linker sequence and peptidoglycan hydrolases containing such a linker; see, e.g., Table 5, column “deimm”. Furthermore, the inventors found amino acid substitutions at position 68 in SEQ ID NO: 1, i.e.
- the L0482-derived linker (which may have a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1), may have one or more amino acid substitutions at positions 52 to 56, 58, 60 to 66, and 68, to 71 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably wherein the amino acid residue at position 52 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, alanine, glycine, lysine, glutamine or serine, the amino acid residue at position 54 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with
- amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine, aspartic acid or serine
- amino acid residue at position 56 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine or isoleucine
- amino acid residue at position 58 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine
- amino acid residue at position 60 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid or isoleucine
- amino acid residue at position 61 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with leucine or glutamine
- amino acid residue at position 62 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid or asparagine
- amino acid substitutions may be considered as beneficial or, at least, permissive for the desired pharmaceutical properties of the peptidoglycan hydrolases of the invention, as described herein, e.g., as described in context of beneficial or permissive amino acid substitutions in the CHAP domain.
- the peptide linker (which may have a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1) may have one or more amino acid substitutions at positions 52 to 56, 58, 63, 65, 68, 69 and 71 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably wherein the amino acid residue at position 52 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, alanine, glycine, lysine, glutamine or serine, the amino acid residue at position 54 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with aspartic acid, glutamic acid, histidine or asparagine, the amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine or aspart
- amino acid substitutions may be considered as beneficial or, at least, permissive for the desired pharmaceutical properties of the peptidoglycan hydrolases of the invention, as described herein.
- Table 3 shows positions in SEQ ID NO: 1 where beneficial or permissive amino acid substitutions have been found. These are the positions for which the column “beneficial/permissive residues” in Table 3 shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses. These positions are also called “permissive positions” herein.
- positions 52 to 71 in Table 3 for which the column “beneficial/permissive residues” shows at least one amino acid residue, regardless of whether said residue is shown without parentheses or in parentheses are considered as “permissive positions” in the linker of L0482 herein.
- an amino acid residue in SEQ ID NO: 1 corresponding to a beneficial or permissive position may be substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said position, i.e. a residue shown without parentheses or in parentheses in said column in Table 3, preferably with a residue that is shown without parentheses in said column in Table 3.
- the L0482-derived peptide linker has at least one amino acid substitution at the permissive positions in the linker region of L0482 or at positions corresponding to said permissive positions in the linker region of L0482.
- at least one amino acid residue at said permissive positions the linker region of L0482 or at positions corresponding to said permissive positions in the linker region of L0482 is substituted with an amino acid residue shown in the column “beneficial/permissive residues” in Table 3 for said positions, more preferably with a residue that is shown without parentheses in said column in Table 3.
- amino acid substitutions in the L0482 linker Furthermore, as described herein, the inventors found hits variants, i.e. G1 to G4, H1 to H10 and I1 to I30, which contained certain amino acid substitutions in the linker region of L0482 variants; see, e.g., Table 4. These amino acid substitutions are thus considered in context of the invention as particularly beneficial mutations, i.e., amino acid substitutions, in the L0482-derived peptide linker.
- “particularly beneficial amino acid substitutions” may be particularly beneficial for maintaining or enhancing the desired pharmaceutical properties of peptidoglycan hydrolases, in particular, the bactericidal activity (e.g., against S. aureus), the stability and/or the ability of being secreted from eukaryotic cells, e.g. human cells. This is also true for the particularly beneficial amino acid substitutions in the linker of L0482.
- the peptide linker has a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1, and has one or more amino acid substitutions at positions 53, 55, 56, 58, 63, 65 and 68 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably wherein the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, the amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine, the amino acid residue at position 56 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 58 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 63 in SEQ ID NO: 1 or at a position
- said peptide linker has an aglycosylation mutation, e.g., a deletion (preferably and amino acid substitution) at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the L0482-derived peptide linker has an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine, methionine, arginine or alanine, preferably lysine.
- said peptide linker has (in addition to said aglycosylation mutation), preferably, at least one amino acid substitution at positions 53, 55, 56, 58, 63 and 65 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, e.g., as just described above.
- a peptidoglycan hydrolase comprising a CHAP domain, a LYSM domain and/or an L0482-derived peptide linker, as described herein, has, preferably, a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, as described herein.
- the present invention relates, in some aspects, to a LYSM domain that has (i) a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions at positions 1, 8, 10, 13, 23 to 25, 30, 33, 37, and 39 to 41 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan, the amino acid residue at position 8 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 10 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with
- said LYSM domain has the ability to bind to the cell wall of a Staphylococcus species or strain, more preferably to Staphylococcus aureus, as described herein.
- said LYSM domain is particularly advantageous for use in a peptidoglycan hydrolase having bactericidal activity, as described herein and in context of the present invention.
- the present invention further relates, e.g.
- a peptidoglycan hydrolase having bactericidal activity wherein the peptidoglycan hydrolase comprises (a) an enzymatically active domain and (b) a LYSM domain that has (i) a sequence identity of at least 60% to the sequence from position 1 to position 51 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions at positions 1, 8, 10, 13, 23 to 25, 30, 33, 37, and 39 to 41 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan, the amino acid residue at position 8 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 10 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with valine, the amino acid residue at position 13 in SEQ ID NO: 1
- said LYSM domain has the ability to bind to the cell wall of a Staphylococcus species or strain, more preferably to Staphylococcus aureus, as described herein.
- said enzymatically active domain is, preferably, a CHAP domain, more preferably a CHAP domain of the invention as described herein.
- said peptidoglycan hydrolase may have a peptide linker, preferably an L0482-derived peptide linker as described herein.
- said peptidoglycan hydrolase (comprising an enzymatic domain and a LYSM domain of the invention) has, preferably, a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, as described herein.
- L0482-derived peptide linker of the invention and peptidoglycan hydrolases comprising an L0482- derived peptide linker of the invention As described herein and as illustrated in the appended Examples, the inventors found particularly beneficial amino acid substitutions in the L0482-derived peptide linker of L0482.
- the present invention relates, in some aspects, to a peptide linker that has (i) a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1, and that has (ii) one or more amino acid substitutions at positions 53, 55, 56, 58, 63, 65 and 68 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, the amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine, the amino acid residue at position 56 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 58 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 63 in SEQ ID NO: 1 or at a position corresponding to this positions
- said peptide linker has an aglycosylation mutation, e.g., a deletion (preferably and amino acid substitution) at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the L0482-derived peptide linker has an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine, methionine, arginine or alanine, preferably lysine.
- said peptide linker has (in addition to said aglycosylation mutation), preferably, at least one amino acid substitution at positions 53, 55, 56, 58, 63 and 65 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, e.g., as just described above.
- said L0482-derived peptide linker is particularly advantageous for use in a peptidoglycan hydrolase having bactericidal activity, as described herein and in context of the present invention.
- the present invention further relates, e.g.
- a peptidoglycan hydrolase having bactericidal activity wherein the peptidoglycan hydrolase comprises (a) an enzymatically active domain, (b) a cell wall binding domain and (c) a linker that has (i) a sequence identity of at least 60% to the sequence from position 52 to position 71 in SEQ ID NO: 1, and that has (ii) one or more amino acid substitutions at positions 53, 55, 56, 58, 63, 65 and 68 in SEQ ID NO: 1 or at positions corresponding to these positions, wherein the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, the amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine, the amino acid residue at position 56 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine,
- said peptide linker has an aglycosylation mutation, e.g., a deletion (preferably and amino acid substitution) at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein. More preferably, the L0482-derived peptide linker has an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine, methionine, arginine or alanine, preferably lysine.
- aglycosylation mutation e.g., a deletion (preferably and amino acid substitution) at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, as described herein.
- the L0482-derived peptide linker has an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, wherein the amino acid residue at said position is substituted with lysine, methion
- said peptide linker has (in addition to said aglycosylation mutation), preferably, at least one amino acid substitution at positions 53, 55, 56, 58, 63 and 65 in SEQ ID NO: 1 or at positions corresponding to these positions, as described herein, e.g., as just described above.
- said enzymatically active domain is, preferably, a CHAP domain, more preferably a CHAP domain of the invention as described herein.
- said cell wall binding domain is, preferably, a LYSM domain, more preferably a LYSM domain of the invention as described herein.
- said peptidoglycan hydrolase (comprising an enzymatic domain, a LYSM domain of the invention and a L0482 derived peptide linker of the invention) has, preferably, a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, as described herein.
- Pharmaceutical properties of the peptidoglycan hydrolase of the invention Bactericidal activity, in particular against Staphylococci
- the peptidoglycan hydrolase of the invention (or the CHAP domain of the invention) has, preferably, a killing activity against at least one gram-positive bacterium, more preferably against at least one Staphylococcus species or strain, most preferably against S.
- the peptidoglycan hydrolase of the invention may have a killing activity, inter alia, against Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis), Staphylococcus warneri (S. warneri), Staphylococcus capitis (S. capitis), and/or Staphylococcus simulans (S. simulans).
- the peptidoglycan hydrolase of the invention has, in particular, the ability to lyse the cell wall of a Staphylococcus species or strain, preferably Staphylococcus aureus, as described herein. More specifically, the peptidoglycan hydrolase of the invention may have the ability to break down, cleave and/or hydrolyze peptidoglycan in the cell wall of a Staphylococcus species or strain, preferably Staphylococcus aureus, as described herein. In some embodiments, the peptidoglycan hydrolase of the invention may have a killing against a Streptococcus species or strain, for example, in addition to a killing activity against a Staphylococcus species or strain.
- the peptidoglycan hydrolase of the invention has a killing activity against S. aureus, as described herein.
- WT L0482 has a killing activity against methicillin-resistant Staphylococcus aureus (MRSA) strains, e.g., ATCC43300, A57, B94, A1; see Figure 2.
- MRSA methicillin-resistant Staphylococcus aureus
- ATCC43300 has been employed in context of the present invention to assess the killing activity of L0482 variants against S. aureus.
- the peptidoglycan hydrolase of the invention may further have a killing activity against at least one Staphylococcus aureus strain that is resistant to at least one antibiotic, e.g., methicillin, vancomycin, daptomycin and/or linezolid.
- antibiotic e.g., methicillin, vancomycin, daptomycin and/or linezolid.
- the peptidoglycan hydrolase of the invention may have a killing activity against at least one methicillin-resistant Staphylococcus aureus (MRSA) strain, at least one vancomycin-intermediate Staphylococcus aureus (VISA) strain, at least one vancomycin-resistant Staphylococcus aureus (VRSA) strain, at least one daptomycin-resistant Staphylococcus aureus (DRSA) strain and/or at least one linezolid-resistant Staphylococcus aureus (LRSA) strain.
- MRSA methicillin-resistant Staphylococcus aureus
- VRSA vancomycin-resistant Staphylococcus aureus
- DRSA daptomycin-resistant Staphylococcus aureus
- LRSA linezolid-resistant Staphylococcus aureus
- the peptidoglycan hydrolase of the invention has a killing activity against at least one methicillin-resistant Staphylococcus aureus strain.
- the peptidoglycan hydrolase of the invention may have a killing activity against at least one coagulate- negative Staphylococcus species or strain, e.g. S. epidermidis.
- the peptidoglycan hydrolase of the invention (or the CHAP domain of the invention) may, preferably, have a killing activity against a biofilm and/or a (biofilm-like) free-floating aggregate, in particular, a biofilm/free- floating aggregate of at least one gram-positive bacterium, more preferably against a biofilm/free-floating aggregate of at least one Staphylococcus species or strain, most preferably against a biofilm/free-floating aggregate of S. aureus.
- Said biofilm/free-floating aggregate of S. aureus may comprise or consist of at least one Staphylococcus aureus strain that is resistant to at least one antibiotic, e.g., methicillin and/or vancomycin, as described herein.
- the peptidoglycan hydrolase of the invention (or the CHAP domain of the invention) may have a killing activity against a biofilm of such a gram-positive bacterium which is attached to a surface and/or against a free-floating aggregate of such a gram-positive bacterium; see also the section “Pharmaceutical compositions and medical uses of the peptidoglycan hydrolase of the invention”, infra, Example 6 and Figure 12.
- bactericidal activity refers, preferably, to a killing activity against at least one Staphylococcus species or strain, more preferably, to a killing activity against Staphylococcus aureus, as described herein.
- the killing activity of a peptidoglycan hydrolase against a certain bacterium e.g., S.
- aureus is, preferably, measured by determining the minimum concentration at which the peptidoglycan hydrolase growth-inhibits a liquid culture of said bacterium, e.g., S. aureus. Said minimum concentration is also referred to herein as “minimal inhibitory concentration” (MIC).
- MIC minimum inhibitory concentration
- the “minimal inhibitory concentration” (MIC) is, in particular, defined as the minimum concentration which keeps the optical density at 620 nm (OD620) of a liquid culture comprising 5x10 5 cfu/ml of a target bacterium (e.g., S. aureus) below 0.1 for at least 24h at 37°C incubation.
- the culture medium of said liquid culture is cation adjusted Müller-Hinton broth (caMHB) medium supplemented with 25% horse serum, in particular, when the target bacterium is a Staphylococcus species or strain such as S. aureus.
- the S. aureus cells in the liquid culture correspond, preferably, to 5x10 5 cfu/ml of ATCC43300.
- a detailed assay for measuring the killing activity against a target bacterium e.g., a Staphylococcus species or strain such as S.
- Example 6 First, a peptidoglycan hydrolase (e.g., a L0482 variant of the present invention) is produced in E. coli, as described in Example 6 under the heading “Production of L0482 variants in E. coli”. Then, the peptidoglycan hydrolase (e.g., the L0482 variant of the present invention) is purified from E. coli, as described under the heading “Purification of L0482 variants from E. coli” in Example 6. Finally, the bactericidal activity of the peptidoglycan hydrolase (e.g., the L0482 variant of the present invention) against a target bacterium (e.g. S.
- a target bacterium e.g. S.
- the peptidoglycan hydrolase of the invention is able to growth-inhibit a Staphylococcus aureus liquid culture at a concentration of about 40 ⁇ g/ml or less, about 20 ⁇ g/ml or less or about 10 ⁇ g/ml or less, preferably at a concentration of about 4 ⁇ g/ml or less, more preferably at a concentration of about 2 ⁇ g/ml, about 1 ⁇ g/ml or less, or about 0.5 ⁇ g/ml or less.
- growth-inhibiting a Staphylococcus aureus liquid culture is, in particular, defined as keeping the optical density at 620 nm (OD620) of a Staphylococcus aureus liquid culture comprising 5x10 5 cfu/ml of Staphylococcus aureus, preferably ATCC43300, below 0.1 for at least 24h at 37°C, preferably wherein the culture medium of said liquid culture is cation adjusted Müller-Hinton broth (caMHB) medium supplemented with 25% horse serum, as described herein, and as illustrated in the appended Examples.
- OD620 optical density at 620 nm
- a Staphylococcus aureus liquid culture comprising 5x10 5 cfu/ml of Staphylococcus aureus, preferably ATCC43300, below 0.1 for at least 24h at 37°C, preferably wherein the culture medium of said liquid culture is cation adjusted Müller-Hinton broth (caMHB) medium supplemented with 25% horse serum, as
- Said “growth-inhibition” of a bacterial liquid culture may also refer, herein and in context of the present invention, as sterilizing said bacterial liquid culture.
- the peptidoglycan hydrolase of the invention has, preferably, the ability of being secreted from a eukaryotic cell, in particular, when expressed in said cell.
- Said cell may be, for example, a yeast cell or a mammalian cell.
- a peptidoglycan hydrolase of the invention which has the ability of being secreted from a eukaryotic cell preferably, further comprises a signal peptide, as described herein.
- a peptidoglycan hydrolase of the invention which has the ability of being secreted from a eukaryotic cell and/or which comprises a signal peptide is, preferably, provided in form of a nucleic acid (preferably an RNA), i.e., as a nucleic acid encoding the peptidoglycan hydrolase of the invention, as described herein.
- a mammalian cell as used herein and in context of the present invention (e.g.
- a mammalian cell in context of the ability of being secreted from a eukaryotic or mammalian cell), may be a cell from any mammalian species including (but not limited to) humans, livestock such as cows, pets such as dogs, sports animals such as horses, endangered animals or zoo animals such as tigers, or laboratory animals such as mice.
- a mammalian cell may be, inter alia, a human, a cow (e.g. cattle), a horse, a pig, a sheep, a goat, a camel, a yak, a monkey, a dog, a cat, a hamster, a tiger, a polar bear, a mouse, a rat etc.
- said cell is a human cell, as described herein.
- the eukaryotic cell, in particular the mammalian cell is not particularly limited to a certain cell type.
- the eukaryotic cell, in particular the mammalian cell may refer to an in vivo cell, an in vitro cell (e.g. a cell line) or an ex vivo cell (e.g. a primary cell).
- the ability of being secreted from a mammalian cell is not to be understood in such a way that the peptidoglycan hydrolase needs to have the ability of being secreted from each and every cell type of the corresponding mammalian species.
- the peptidoglycan hydrolase has the ability of being secreted from a relevant cell type of the corresponding species, e.g. a model cell type such as HEK293 cells, and/or a cell type which is associated with a bacterial infection to be treated.
- a relevant cell type of the corresponding species e.g. a model cell type such as HEK293 cells, and/or a cell type which is associated with a bacterial infection to be treated.
- the ability of a peptidoglycan hydrolase of being secreted by a human cell is, preferably, measured by determining the amount of the peptidoglycan hydrolase in the supernatant of HEK293 cells (preferably EXPI293 cells) expressing the peptidoglycan hydrolase.
- thermostability a peptidoglycan hydrolase of the invention
- the peptidoglycan hydrolase of the invention is, preferably, stable up to a temperature of about 40°C, e.g., 37°C, 38°C, 39°C, 40°C, 41°C or 42°C, preferably about 42°C, more preferably about 44°C or about 47°C. This stability also refers to a sufficient or good thermostability.
- thermostability is determined by a thermofluor assay, as described herein.
- thermostability of a peptidoglycan hydrolase is measured by determining the melting temperature, i.e., the inflecting point of the melting curve, in a thermofluor assay.
- said temperature refers, in particular, to the melting temperature of said peptidoglycan hydrolase, preferably as determined by a thermofluor assay, as described herein.
- a SYPRO orange dye and a quantitative PCR device are employed in said thermofluor assay.
- Example 6 A detailed assay for measuring the stability, in particular, the thermostability, of a peptidoglycan hydrolase (e.g., a L0482 variant of the present invention) is provided in Example 6: First, a peptidoglycan hydrolase (e.g., a L0482 variant of the present invention) is produced in E. coli, as described in Example 6 under the heading “Production of L0482 variants in E. coli”. Then, the peptidoglycan hydrolase (e.g., the L0482 variant of the present invention) is purified from E. coli, as described under the heading “Purification of L0482 variants from E. coli” in Example 6.
- a peptidoglycan hydrolase e.g., a L0482 variant of the present invention
- thermostability of the peptidoglycan hydrolase is determined as described in Example 6 under the heading “Determination of protein stability of L0482 variants by the Thermofluor assay”. Solubility Furthermore, the peptidoglycan hydrolase of the invention is, preferably, soluble in an aqueous solution such as PBS.
- a peptidoglycan hydrolase can be produced as described, e.g., in Example 6 herein: First, a peptidoglycan hydrolase (e.g., a L0482 variant of the present invention) is produced in E. coli, as described in Example 6 under the heading “Production of L0482 variants in E. coli”.
- the peptidoglycan hydrolase (e.g., the L0482 variant of the present invention) is purified from E. coli, as described under the heading “Purification of L0482 variants from E. coli” in Example 6.
- the solubility of the (purified) peptidoglycan hydrolase can then be measured by methods known in the art.
- the solubility of a peptidoglycan hydrolase can be measured by determining the opalescence in an aqueous solution such as PBS at increasing concentrations, or by a PEG precipitation method.
- the solubility of a peptidoglycan hydrolase is measured by the PEG precipitation method described in Li (2013), Protein Sci.
- the peptidoglycan hydrolase of the invention further has, preferably, a low tendency for aggregation, in particular in an aqueous solution such as PBS.
- a peptidoglycan hydrolase can be produced as described herein, e.g., in Example 6. The tendency for aggregation can then be measured by methods known in the art, e.g., by dynamic light scattering or by size exclusion chromatography.
- the peptidoglycan hydrolase of the invention has, compared to the peptidoglycan hydrolase of SEQ ID NO: 1, (i) a similar or enhanced bactericidal activity, preferably a similar or enhanced killing activity against Staphylococcus aureus, as described herein, (ii) a similar or enhanced ability of being secreted by a eukaryotic cell, preferably in a yeast cell or a human cell, e.g., a HEK293 cell, as described herein, (iii) a similar or enhanced solubility in an aqueous solution such as PBS, as described herein, (iv) a similar or enhanced stability, preferably an enhanced thermostability, as described herein and/or (v) a similar or reduced tendency to form aggregates in an aqueous solution such as PBS, as described herein.
- a similar or enhanced bactericidal activity preferably a similar or enhanced killing activity against Staphylococcus aureus
- the peptidoglycan hydrolase of the invention has, compared to the peptidoglycan hydrolase of SEQ ID NO: 1: a similar or enhanced killing activity against Staphylococcus aureus, as described herein; a similar or enhanced ability of being secreted by a human cell, as described herein; and/or a similar or enhanced stability (preferably an enhanced thermostability), as described herein.
- the peptidoglycan hydrolase of the invention has, compared to the peptidoglycan hydrolase of SEQ ID NO: 1: an enhanced killing activity against Staphylococcus aureus, as described herein; an enhanced ability of being secreted by a human cell, as described herein; and/or an enhanced thermostability, as described herein.
- an enhanced killing activity against Staphylococcus aureus as described herein
- an enhanced ability of being secreted by a human cell as described herein
- thermostability as described herein.
- the peptidoglycan hydrolase of the invention is compared with the peptidoglycan hydrolase of SEQ ID NO: 1 for a specific feature (e.g., the killing activity against S.
- any specific functional domains or peptides within the peptidoglycan hydrolase of the invention which have been purposefully fused to the peptidoglycan hydrolase and which have a negligible sequence identity to L0482 (SEQ ID NO: 1), e.g. below 30%, for example a signal peptide or a PK tag as described herein, should be added the same way to the peptidoglycan hydrolase of SEQ ID NO: 1 for such comparative measurements.
- a peptidoglycan hydrolase of the present invention comprising a CHAP domain of the invention may have a reduced propensity of generating resistance in target bacteria, e.g., S. aureus, compared to other peptidoglycan hydrolases not having a CHAP domain such as lysostaphin.
- Extended pharmacokinetic peptides The peptidoglycan hydrolase of the invention may further comprise an extended pharmacokinetic (PK) peptide.
- PK extended pharmacokinetic
- an extended pharmacokinetic (PK) peptide is also called an “PK tag” or a half-life extension module.
- a PK tag may increase the half-life of a peptidoglycan hydrolase (e.g., in the blood) of a host, in particular a mammal (preferably a human).
- a PK tag may further improve the pharmaceutical properties of the peptidoglycan hydrolase of the invention.
- addition of a PK peptide may further enhance the anti-bacterial efficiency in vivo.
- Suitable PK tags are well known in the art and any of these may be used in context of the present invention.
- the extended pharmacokinetic (PK) peptide is selected from the group consisting of: a human FC domain (e.g.
- the PK peptide comprises or consists of the sequence of SEQ ID NO: 294 or it has a sequence identity of at least 90% to the sequence of SEQ ID NO: 294.
- the PK peptide comprises or consists of the sequence of SEQ ID NO: 295 or it has a sequence identity of at least 90% to the sequence of SEQ ID NO: 295.
- the PK peptide comprises of consists of the sequence of SEQ ID NO: 296 or it has a sequence identity of at least 90% to the sequence of SEQ ID NO: 296.
- the PK peptide may be positioned at the C- or N-terminus of the CHAP domain of the invention, the cell wall binding domain (e.g. a LYSM domain), or the peptidoglycan hydrolase of the invention.
- the PK peptide may be, preferably, positioned at the C- or N-terminus of the peptidoglycan hydrolase of the invention.
- the PK peptide is, preferably, positioned C- terminally of the signal peptide (in particular, C-terminally of the signal peptide and N-terminally of all other of the peptidoglycan hydrolase of the invention).
- the PK peptide is, more preferably, C-terminally of any signal peptide and N-terminally of all CBDs and EADs contained in the peptidoglycan hydrolase of the invention (e.g. N- terminally of the LYSM domain and the CHAP domain according to the invention), preferably N-terminally of all other parts of the peptidoglycan hydrolase of the invention (i.e. all other parts than the signal peptide).
- the peptidoglycan hydrolase of the invention preferably, comprises between the PK peptide and the CHAP domain or the cell wall binding domain a peptide linker, for example, a glycine-serine linker, as described herein.
- a peptidoglycan hydrolase of the invention comprising a PK peptide may be also considered as a fusion protein herein, in particular, wherein one part of the fusion protein refers to the EADs (e.g. the CHAP domain of the invention), and (if present) the CBDs (e.g. a LYSM domain) and any peptide linkers in between, and another part of the fusion protein refers to the PK peptide.
- Re-glycosylation of peptidoglycan hydrolases of the invention As illustrated in Example 8, re-glycosylation of lysin variants, e.g., a L0482 variant comprising at least one aglycosylation mutation, as described herein, may further enhance stability and/or solubility of the protein.
- the peptidoglycan hydrolase of the invention e.g. a peptidoglycan hydrolase of the invention having one or more aglycosylation mutations as described herein, may further comprise at least one glycosylation motif which is not present in the peptidoglycan hydrolase of SEQ ID NO: 1.
- a glycosylation motif consists of the amino acids X 1 , X 2 , and X 3 , wherein X 1 is asparagine, X 2 is any amino acid except proline, and X 3 is serine or threonine.
- X 1 is asparagine
- X 2 is any amino acid except proline
- X 3 is serine or threonine.
- the inventors developed approaches to deimmunize peptidoglycan hydrolases of the invention; see, e.g., Example 10.
- the terms “deimmunization” or “deimmunizing” refer to the removal of T cell epitopes, B-cell epitopes and/or aggregation hot spots in proteins such as the peptidoglycan hydrolases of the invention.
- the deimmunization refers to the removal of T cell epitopes in a peptidoglycan hydrolases of the invention.
- the peptidoglycan hydrolase of the invention is, preferably, deimmunized, as described herein.
- the peptidoglycan hydrolase of the invention may have less T cell epitopes than the peptidoglycan hydrolase of SEQ ID NO: 1.
- the terms “immunogenic” or “immunogenicity” refer to the ability of a foreign substance, e.g. a peptidoglycan hydrolase of the invention, to induce an immune response in a mammal such as a human.
- immune response refers to a an adaptive and/or innate immune response, as commonly understood in the art.
- an immune response may include a cellular and/or a humoral immune response.
- the immune response comprises, preferably, an adaptive immune response, in particular, involving T cells such as CD8+ and/or CD4+ T cells. More preferably, the immune response, in this context, is mediated, at least partly, by CD4+ T cells.
- CD4+ T cells refer, in particular, to T helper cells.
- CD8+ T cells may be cytotoxic T cells.
- the immune response may be mediated by antibodies.
- the peptidoglycan hydrolase of the invention e.g., a deimmunized peptidoglycan hydrolase of the invention, is less immunogenic than the peptidoglycan hydrolase of SEQ ID NO: 1.
- T cell epitopes in the peptidoglycan hydrolase of the invention are removed which, preferably, reduces the propensity for generating a T cell mediated immune response in a subject, more preferably a CD4+ T cell mediated immune response, as described herein.
- said T cell mediated immune response may be accompanied by a humoral immune response and, thus, further be mediated by antibodies.
- Avoiding or reducing an immune response in a subject to which the peptidoglycan hydrolase of the invention is administered decreases the risk for elimination and/or degradation of the peptidoglycan hydrolase in the subject and thus enhance the efficacy. Furthermore, avoiding or reducing an immune response in a subject to which the peptidoglycan hydrolase of the invention is administered (in form of a protein and/or a nucleic acid such as an RNA) decreases the risk of adverse side effects associated with an immune response such as fever, pain, fatigue, rash, nausea, auto-immune responses, anaphylaxis etc.
- deimmunization may further enhance the safety and/or efficacy of a peptidoglycan hydrolases of the invention for medical uses, in particular, for use as a pharmaceutical in large and/or diverse patient populations.
- the immunogenicity of peptidoglycan hydrolases may be determined by method known in the art.
- the immunogenicity is determined by a T cell activation assay with peripheral blood mononuclear cells (PBMCs), more preferably an INF ⁇ ELISPOT assay, which is well-known in the art.
- PBMCs peripheral blood mononuclear cells
- the immunogenicity may be determined by performing an ELISA on blood samples from healthy donors for preexisting B-cell epitopes.
- a specific feature e.g., the immunogenicity
- the exact same assay is employed for the measurements for the peptidoglycan hydrolases that are compared to each other, and only the peptidoglycan hydrolase itself (and/or, where applicable, the corresponding coding sequence) is changed.
- Example 10 the inventors found deimmunizing amino acid substitutions in L0482 variants which may remove T cell epitopes from the peptidoglycan hydrolase of the invention, e.g. from the H5 variant (SEQ ID NO: 11); see, e.g., Table 5.
- the CHAP domain of the invention may have one or more amino acid substitutions at positions 72, 73, 75 to 77, 79 to 83, 86, 99, 102 to 104, 107, 108, 114, 115, 117, 122 to 124, 130, 131, 133 to 137, 139 to 141, 143, 144, 166, 169, 170, 173 to 176, 178, 185, 190 to 192, 194, 196, 197, 199, 201, 203 to 207, 212 and 213 in SEQ ID NO: 1, or at positions corresponding to these positions, preferably wherein one or more amino acid residues at said positions are substituted with any of the substitute amino acid residues shown for the corresponding positions in the following Table I.
- the peptidoglycan hydrolase of the invention in particular a peptidoglycan hydrolase which has a sequence identity of at least 60% to the sequence of SEQ ID NO: 1, may have one or more amino acid substitutions at positions 1, 12, 13, 17, 19, 22 to 25, 28 to 30, 32 to 34, 36 to 45, 48 to 55, 65, 68, 69, 71 to 73, 75 to 77, 79 to 83, 86, 99, 102 to 104, 107, 108, 114, 115, 117, 122 to 124, 130, 131, 133 to 137, 139 to 141, 143, 144, 166, 169, 170, 173 to 176, 178, 185, 190 to 192, 194, 196, 197, 199, 201,
- the LYSM domain of the invention may have one or more amino acid substitutions at positions 1, 12, 13, 17, 19, 22 to 25, 28 to 30, 32 to 34, 36 to 45, 48 to 51 in SEQ ID NO: 1, or at positions corresponding to these positions, preferably wherein one or more amino acid residues at said positions are substituted with any of the substitute amino acid residues shown for the corresponding positions in the above Table I.
- the L0482-derived peptide linker of the invention may have one or more amino acid substitutions at positions 52 to 55, 65, 68, 69, and 71 in SEQ ID NO: 1, or at positions corresponding to these positions, preferably wherein one or more amino acid residues at said positions are substituted with any of the substitute amino acid residues shown for the corresponding positions in the above Table I.
- the CHAP domain of the invention and/or the peptidoglycan hydrolase of the invention comprises any of the deimmunizing mutations (e.g. as just described above) in addition to any particularly beneficial mutations or any most beneficial mutations as described herein as well as any aglycosylation mutations as described herein.
- the particularly beneficial mutations, the most beneficial mutations as well as any aglycosylation mutations, as described herein, are, preferably not overwritten by the deimmunizing mutations.
- the deimmunizing mutations are, preferably, employed at positions, where no particularly beneficial mutation, most beneficial mutations or aglycosylation mutation, as described herein, is employed.
- the CHAP domain of the invention and the peptidoglycan hydrolase of the invention have at positions 82, 85, 86, 130, 136, 155, 169, 185 and/or 186 in SEQ ID NO: 1 or at positions corresponding to these positions, preferably, at least one of the most beneficial amino acid substitutions, and at position 73 or at a position corresponding to this position, preferably, an aglycosylation substitution, as described herein.
- the CHAP domain of the invention and the peptidoglycan hydrolase of the invention have, preferably, deimmunizing mutations at other positions than at positions 73, 82, 85, 86, 130, 136, 155, 169, 185 and/or 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the peptidoglycan hydrolase of the invention and the L0482-derived peptide linker of the invention have at position 68 or at a position corresponding to this position, preferably, an aglycosylation substitution, as described herein.
- the peptidoglycan hydrolase of the invention has, in certain embodiments, deimmunizing mutations, preferably, at other positions than at positions 68, 73, 82, 85, 86, 130, 136, 155, 169, 185 and/or 186 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the L0482-derived peptide linker of the invention has, preferably, deimmunizing mutations, preferably, at another position than at position 68 or at a position corresponding to this position.
- Nucleic acids encoding the peptidoglycan hydrolase of the invention Administration of a peptidoglycan hydrolase of the invention in form of a nucleic acid (e.g., an mRNA) encoding said peptidoglycan hydrolase to a subject (e.g., a human) has certain advantages.
- a subject e.g., a human
- cells in a subject to which a nucleic acid of the invention has been introduced may continuously produce and secrete the peptidoglycan hydrolase protein of the invention. This may provide a more efficient treatment of the bacterial infection and, for example, provide a higher efficacy in treating difficult to treat bacterial infections such as bacterial biofilms, e.g., Staphylococcus biofilms.
- the nucleic acid may be introduced into cells at a particular location which may further improve the efficiency and/or safety of the treatment.
- nucleic acids in particular RNAs, have further certain practical advantages over proteins with respect to their manufacturing, safety profile and/or adaptability.
- the present invention relates, in some aspects, to a nucleic acid (e.g. an RNA or RNA construct) encoding the peptidoglycan hydrolase of the invention, as described herein.
- said peptidoglycan hydrolase comprises the CHAP domain of the invention, as described herein.
- said peptidoglycan hydrolase preferably, comprises a signal peptide, as described herein.
- said peptidoglycan hydrolase has, preferably, the ability of being secreted from a eukaryotic cell, preferably a human cell, as described herein. More preferably, said peptidoglycan hydrolase has an enhanced ability of being secreted from a eukaryotic cell (preferably a human cell) compared to the peptidoglycan hydrolase of SEQ ID NO: 1, as described herein. Furthermore, as described herein and as illustrated in the appended Examples, the peptidoglycan hydrolases of the invention may be particularly well adapted for the production in and secretion from eukaryotic cells.
- the peptidoglycan hydrolases of the invention may be particularly suitable for administration to a subject (in particular a mammal such as a human) in form of a nucleic acid; see, e.g., Figures 8 and 10.
- a peptidoglycan hydrolase “in form of a nucleic acid” refers to a nucleic acid encoding the peptidoglycan hydrolase of the invention.
- a peptidoglycan hydrolase which is administered in form of a nucleic acid refers to the administration of a nucleic acid encoding the peptidoglycan hydrolase of the invention from which the peptidoglycan hydrolase protein can be expressed.
- nucleic acid comprises deoxyribonucleic acid (DNA), ribonucleic acid (RNA), combinations thereof, and modified forms thereof.
- the term comprises genomic DNA, cDNA, mRNA, recombinantly produced and chemically synthesized molecules.
- a nucleic acid is DNA.
- a nucleic acid is RNA.
- a nucleic acid is a mixture of DNA and RNA.
- a nucleic acid may be present as a single-stranded or double-stranded and linear or covalently circularly closed molecule.
- the nucleic acid of the invention can be isolated.
- isolated nucleic acid means, according to the present disclosure, that the nucleic acid (i) was amplified in vitro, for example via polymerase chain reaction (PCR) for DNA or in vitro transcription (using, e.g., an RNA polymerase) for RNA, (ii) was produced recombinantly by cloning, (iii) was purified, for example, by cleavage and separation by gel electrophoresis, or (iv) was synthesized, for example, by chemical synthesis.
- PCR polymerase chain reaction
- RNA polymerase RNA polymerase
- purified for example, by cleavage and separation by gel electrophoresis
- iv was synthesized, for example, by chemical synthesis.
- N in context of nucleic acids
- nucleoside is a nucleobase linked to a sugar (e.g., ribose or deoxyribose)
- a nucleotide is composed of a nucleoside and one or more phosphate groups.
- the five standard nucleosides which usually make up naturally occurring nucleic acids are uridine, adenosine, thymidine, cytidine and guanosine.
- the five nucleosides are commonly abbreviated to their one letter codes U, A, T, C and G, respectively.
- uridine in RNA may be also denoted by the letter “T”, e.g., in the enclosed sequence listing pursuant to WIPO St.26.
- thymidine may be written as "dT" ("d” represents “deoxy”) as it contains a 2'-deoxyribofuranose moiety rather than the ribofuranose ring found in uridine.
- d represents "deoxy”
- uridine is found in RNA and not DNA.
- the remaining three nucleosides may be found in both RNA and DNA. In RNA, they would be represented as A, C and G, whereas in DNA they may be represented as dA, dC and dG.
- the nucleic acid e.g.
- the RNA) of the invention is, preferably, an engineered nucleic acid, preferably an engineered RNA.
- the nucleic acid (e.g. the RNA) of the invention is, preferably, a non-natural nucleic acid, preferably a non-natural RNA.
- a nucleic acid (e.g. the RNA) may be considered as “engineered”, “modified” or “non-natural”, when it comprises a sequence that does not occur in nature, e.g. when it encodes a non-natural peptidoglycan hydrolase of the invention.
- the RNA of the invention may be codon-optimized for protein expression in cells of a certain mammalian species, preferably a human, as described herein.
- the peptidoglycan hydrolase of the invention may further comprise a signal peptide.
- a nucleic acid (e.g. an RNA) of the invention encodes, preferably, a peptidoglycan hydrolase of the invention that comprises a signal peptide as described herein.
- the peptidoglycan hydrolase protein may be initially expressed from the nucleic acid in a eukaryotic cell in an immature form containing the signal peptide. The signal peptide may then be cleaved off during maturation of the protein, in particular, during secretion or export of the peptidoglycan hydrolase from the cell.
- the peptidoglycan hydrolase of the invention may comprise a signal peptide, in particular, when the peptidoglycan hydrolase is contained in a cell, as described herein.
- the terms “signal peptide” and “signal sequence” are used interchangeably herein and in context of the present invention.
- a signal peptide targets a polypeptide with which it is associated, i.e., in which it is contained (e.g. the peptidoglycan hydrolase of the invention) to a secretory pathway in a cell.
- a signal peptide may target a polypeptide with which it is associated, i.e., in which it is contained (e.g.
- a signal peptide contained in a polypeptide promotes the secretion of said polypeptide from a cell.
- said cell is, preferably, a eukaryotic cell, more preferably a mammalian cell, most preferably a human cell. Suitable signal peptides are well known in the art and any of these may be used in context of the present invention.
- Suitable signal peptides include, inter alia, an N-terminal mouse IgKappa signal peptide (e.g. as shown in SEQ ID NO: 300), a HSV-1 envelope glycoprotein D signal peptide (e.g. as shown in SEQ ID NO: 321, 323,325, 380 or UniProtKB GD_HHV1K), HSV-2 envelope glycoprotein D signal peptide (e.g. as shown in SEQ ID NO: 327 or 329), a Plasmodium falciparum Csp signal peptide (e.g. as shown in SEQ ID NO: 331), an Ebola spike glycoprotein GP signal peptide (e.g.
- SEQ ID NO: 333 a SARS-CoV-2- spike signal peptide (e.g. as shown in SEQ ID NO: 335), a human Ig heavy chain signal peptide (e.g. as shown in SEQ ID NO: 337, 344, 346, 348, 350, 352, 354, 356 or 358), a human insulin signal peptide (SEQ ID NO: 378), a human Ig kappa chain signal peptide (e.g. as shown in SEQ ID NO: 338, 360 or 362), a Japanese encephalitis PRM signal peptide (e.g.
- RNA sequences encoding signal peptides are shown in SEQ ID NO: 320, 322, 324, 326, 328, 330, 332, 334, 336, 343, 345, 347, 349, 351, 353, 355, 357, 359 or 361.
- the signal peptide may be, for example, from a pathogen such as a bacterium or virus (e.g. a Herpes simplex virus, a Japanese encephalitis virus or an Ebola virus), as described herein.
- the signal peptide may be from another organism than a human, e.g., from a mouse, as described herein.
- the signaling peptide contained in the peptidoglycan hydrolase of the invention is not human.
- the signal peptide is located at the N-terminus of the peptidoglycan hydrolase, in particular N-terminal of the cell-wall binding domain (e.g.
- the signal peptide is cleaved off during secretion or export from the cell.
- the signal peptide is able to direct the peptidoglycan hydrolase of the invention to a secretory pathway in a mammalian cell, preferably a co-translational translocation pathway.
- the signal peptide contained in the peptidoglycan hydrolase of the invention comprises or consists of the sequence of SEQ ID NO: 378, SEQ ID NO: 300, SEQ ID NO: 321, SEQ ID NO: 323, SEQ ID NO: 325, SEQ ID NO: 327, SEQ ID NO: 331, SEQ ID NO: 335, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, SEQ ID NO: 344, SEQ ID NO: 346, SEQ ID NO: 348, SEQ ID NO: 350, SEQ ID NO: 352, SEQ ID NO: 354, SEQ ID NO: 356, SEQ ID NO: 358, SEQ ID NO: 360 or SEQ ID NO: 362.
- the signal peptide contained in the peptidoglycan hydrolase of the invention comprises the sequence of SEQ ID NO: 378.
- a peptidoglycan hydrolase of the invention comprising a signal peptide may be also considered as a fusion protein herein, in particular, wherein one part of the fusion protein refers to the EADs (e.g. the CHAP domain of the invention), and (if present) the CBDs (e.g. a LYSM domain) and any peptide linkers in between, and another part of the fusion protein refers to the signal peptide.
- the peptidoglycan hydrolase is, preferably, adapted for secretion, as described herein.
- the peptidoglycan hydrolase of the invention has, preferably, the ability of being secreted from a eukaryotic cell and may be particularly well adapted to a eukaryotic (preferably human) secretory pathway. More preferably, e.g., in context of the nucleic acid or the RNA of the invention, the peptidoglycan hydrolase of the invention has an enhanced ability of being secreted from a human cell compared to the WT L0482 endolysin (SEQ ID NO: 1).
- DNA relates to a nucleic acid molecule which is entirely or at least substantially composed of deoxyribonucleotide residues. In preferred embodiments, the DNA contains all or a majority of deoxyribonucleotide residues.
- deoxyribonucleotide refers to a nucleotide which lacks a hydroxyl group at the 2'- position of a ⁇ -D-ribofuranosyl group.
- DNA encompasses without limitation, double stranded DNA, single stranded DNA, isolated DNA such as partially purified DNA, essentially pure DNA, synthetic DNA, recombinantly produced DNA, as well as modified DNA that differs from naturally occurring DNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations may refer to addition of non-nucleotide material to internal DNA nucleotides or to the end(s) of DNA. It is also contemplated herein that nucleotides in DNA may be non- standard nucleotides, such as chemically synthesized nucleotides or ribonucleotides. For the present disclosure, these altered DNAs are considered analogs of naturally-occurring DNA.
- a molecule contains "a majority of deoxyribonucleotide residues" if the content of deoxyribonucleotide residues in the molecule is more than 50% (such as at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%), based on the total number of nucleotide residues in the molecule.
- the total number of nucleotide residues in a molecule is the sum of all nucleotide residues (irrespective of whether the nucleotide residues are standard (i.e., naturally occurring) nucleotide residues or analogs thereof).
- DNA may be recombinant DNA and may be obtained by cloning of a nucleic acid, in particular cDNA.
- the cDNA may be obtained by reverse transcription of RNA.
- the nucleic acid of the invention is a DNA, as described herein.
- the DNA of the invention is comprised in a plasmid, for example, an expression vector.
- the expression vector is suitable for expressing the polypeptide hydrolase of the invention in a cell, or, at least, the vector is suitable for transcribing an mRNA encoding the polypeptide hydrolase of the invention in a cell.
- said cell is a eukaryotic cell, more preferably a human cell, as described herein.
- RNA relates to a nucleic acid molecule which includes ribonucleotide residues. In preferred embodiments, the RNA contains all or a majority of ribonucleotide residues.
- ribonucleotide refers to a nucleotide with a hydroxyl group at the 2'-position of a ⁇ -D-ribofuranosyl group.
- RNA encompasses without limitation, double stranded RNA, single stranded RNA, isolated RNA such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinantly produced RNA, as well as modified RNA that differs from naturally occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations may refer to addition of non-nucleotide material to internal RNA nucleotides or to the end(s) of RNA. It is also contemplated herein that nucleotides in RNA may be non-standard nucleotides, such as chemically synthesized nucleotides or deoxynucleotides.
- altered/modified nucleotides can be referred to as analogs of naturally occurring nucleotides, and the corresponding RNAs containing such altered/modified nucleotides (i.e., altered/modified RNAs) can be referred to as analogs of naturally occurring RNAs.
- a molecule contains "a majority of ribonucleotide residues" if the content of ribonucleotide residues in the molecule is more than 50% (such as at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%), based on the total number of nucleotide residues in the molecule.
- the total number of nucleotide residues in a molecule is the sum of all nucleotide residues (irrespective of whether the nucleotide residues are standard (i.e., naturally occurring) nucleotide residues or analogs thereof).
- RNA includes mRNA, tRNA, ribosomal RNA (rRNA), small nuclear RNA (snRNA), self-amplifying RNA (saRNA), trans-amplifying RNA (taRNA), single-stranded RNA (ssRNA), dsRNA, inhibitory RNA (such as antisense ssRNA, small interfering RNA (siRNA), or microRNA (miRNA)), activating RNA (such as small activating RNA) and immunostimulatory RNA (isRNA).
- RNA refers to mRNA.
- ITT immunostimulatory RNA
- RNA polymerase preferably T7, T3 or SP6 polymerase
- the term '"RNA includes "mRNA”.
- mRNA means "messenger-RNA” and includes a "transcript” which may be generated by using a DNA template.
- mRNA encodes a peptide or polypeptide, e.g., a peptidoglycan hydrolase of the invention.
- RNA is single-stranded but may contain self-complementary sequences that allow parts of the mRNA to fold and pair with itself to form double helices.
- dsRNA means double-stranded RNA and is RNA with two partially or completely complementary strands.
- mRNA generally contains a 5' untranslated region (5'-UTR), a peptide/polypeptide coding region (e.g. a sequence encoding a peptidoglycan hydrolase of the invention) and a 3' untranslated region (3'- UTR).
- RNA is in vitro transcribed RNA (IVT-RNA) and may be obtained by in vitro transcription of an appropriate DNA template.
- the promoter for controlling transcription can be any promoter for any RNA polymerase.
- RNA polymerases are the T7, T3, and SP6 RNA polymerases.
- the in vitro transcription is controlled by a T7 or SP6 promoter.
- a DNA template for in vitro transcription may be obtained by cloning of a nucleic acid, in particular cDNA, and introducing it into an appropriate vector for in vitro transcription.
- the cDNA may be obtained by reverse transcription of RNA.
- the RNA is "replicon RNA" or simply a "replicon", in particular "self- replicating RNA” or "self-amplifying RNA".
- the replicon or self-replicating RNA is derived from or comprises elements derived from an ssRNA virus, in particular a positive-stranded ssRNA virus such as an alphavirus.
- Alphaviruses are typical representatives of positive-stranded RNA viruses.
- Alphaviruses replicate in the cytoplasm of infected cells (for review of the alphaviral life cycle see Jose et al., Future Microbiol., 2009, vol.4, pp. 837–856).
- the total genome length of many alphaviruses typically ranges between 11,000 and 12,000 nucleotides, and the genomic RNA typically has a 5’-cap, and a 3’ poly(A) tail.
- the genome of alphaviruses encodes non- structural proteins (involved in transcription, modification and replication of viral RNA and in protein modification) and structural proteins (forming the virus particle). There are typically two open reading frames (ORFs) in the genome.
- ORFs open reading frames
- the four non-structural proteins (nsP1–nsP4) are typically encoded together by a first ORF beginning near the 5′ terminus of the genome, while alphavirus structural proteins are encoded together by a second ORF which is found downstream of the first ORF and extends near the 3’ terminus of the genome.
- the first ORF is larger than the second ORF, the ratio being roughly 2:1.
- RNA RNA molecule that resembles eukaryotic messenger RNA
- mRNA messenger RNA
- (+) stranded genomic RNA directly acts like a messenger RNA for the translation of the open reading frame encoding the non-structural poly-protein (nsP1234).
- Alphavirus-derived vectors have been proposed for delivery of foreign genetic information into target cells or target organisms.
- Alphavirus-based trans-replication (trans-amplification) systems rely on alphavirus nucleotide sequence elements on two separate nucleic acid molecules: one nucleic acid molecule encodes a viral replicase, and the other nucleic acid molecule is capable of being replicated by said replicase in trans (hence the designation trans-replication system).
- Trans-replication requires the presence of both these nucleic acid molecules in a given host cell.
- the nucleic acid molecule capable of being replicated by the replicase in trans must comprise certain alphaviral sequence elements to allow recognition and RNA synthesis by the alphaviral replicase.
- the RNA (in particular, mRNA) described herein contains one or more modifications, e.g., in order to increase its stability and/or increase translation efficiency and/or decrease immunogenicity and/or decrease cytotoxicity.
- the RNA in particular, mRNA
- it may be modified within the coding region, i.e., the sequence encoding the expressed peptide or polypeptide, preferably without altering the sequence of the expressed peptide or polypeptide.
- Such modifications are described, for example, in WO 2007/036366 and PCT/EP2019/056502, and include the following: a 5'-cap structure; an extension or truncation of the naturally occurring poly(A) tail; an alteration of the 5'- and/or 3'- untranslated regions (UTR) such as introduction of a UTR which is not related to the coding region of said RNA; the replacement of one or more naturally occurring nucleotides with synthetic nucleotides; and codon optimization (e.g., to alter, preferably increase, the GC content of the RNA).
- UTR 5'-cap structure
- an extension or truncation of the naturally occurring poly(A) tail an alteration of the 5'- and/or 3'- untranslated regions (UTR) such as introduction of a UTR which is not related to the coding region of said RNA
- UTR 5'- and/or 3'- untranslated regions
- codon optimization e.g., to alter, preferably increase,
- a combination of the above described modifications i.e., incorporation of a 5'-cap structure, incorporation of a poly-A sequence, unmasking of a poly-A sequence, alteration of the 5'- and/or 3'-UTR (such as incorporation of one or more 3'-UTRs), replacing one or more naturally occurring nucleotides with synthetic nucleotides (e.g., 5-methylcytidine for cytidine and/or pseudouridine ( ⁇ ) or N(1)-methylpseudouridine (m1 ⁇ ) or 5-methyluridine (m5U) for uridine), and codon optimization, has a synergistic influence on the stability of RNA (preferably mRNA) and increase in translation efficiency.
- RNA preferably mRNA
- the RNA (in particular, mRNA) described in the present disclosure contains a combination of at least two, at least three, at least four or all five of the above-mentioned modifications, i.e., (i) incorporation of a 5'-cap structure, (ii) incorporation of a poly-A sequence, unmasking of a poly-A sequence; (iii) alteration of the 5'- and/or 3'-UTR (such as incorporation of one or more 3'-UTRs); (iv) replacing one or more naturally occurring nucleotides with synthetic nucleotides (e.g., 5-methylcytidine for cytidine and/or pseudouridine ( ⁇ ) or N(1)- methylpseudouridine (m1 ⁇ ) or 5-methyluridine (m5U) for uridine), and (v) codon optimization.
- synthetic nucleotides e.g., 5-methylcytidine for cytidine and/or pseudouridine ( ⁇ ) or N(1)
- the nucleic acid of the invention is an RNA, as described herein.
- the RNA or RNA construct of the invention is, preferably, suitable for translating the peptidoglycan hydrolase of the invention encoded by said RNA or RNA construct in a suitable cell, preferably a eukaryotic cell, more preferably a human cell.
- the RNA is an mRNA as described herein.
- the RNA is a replicon RNA as described herein.
- the mRNA according to the present invention is a nucleoside-modified RNA, as described herein.
- the mRNA of the invention comprises (i) a modified nucleoside selected from pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ), and 5-methyl- uridine (m5U), preferably N1-methyl-pseudouridine (m1 ⁇ ), in place of uridine, preferably in place of each uridine; (ii) a cap05’ cap, for example, m 2 7,2'O G(5’)ppSp(5')G; or a cap15’ cap, for example, m2 7,3’-O Gppp(m1 2’-O )ApG (iii) a 5’ UTR and/or a 3’ UTR, and/or (iv) a poly-A sequence comprising preferably at least 100 nucleotides; as described herein.
- a modified nucleoside selected from pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ), and 5-methyl- uridine (
- RNA construct comprising in 5' to 3' order: (i) a 5' UTR, preferably, comprising or consisting of a modified human alpha-globin 5'-UTR; (ii) a sequence encoding a peptidoglycan hydrolase of the invention; (iii) a 3' UTR, preferably, comprising or consisting of a first sequence from the amino terminal enhancer of split (AES) messenger RNA and a second sequence from the mitochondrial encoded 12S ribosomal RNA; and (iv) a poly-A sequence, comprising preferably at least about 100 nucleotides.
- a 5' UTR preferably, comprising or consisting of a modified human alpha-globin 5'-UTR
- a sequence encoding a peptidoglycan hydrolase of the invention preferably, comprising or consisting of a first sequence from the amino terminal enhancer of split (AES) messenger RNA and a second sequence from the mitochondrial encoded 12S ribo
- the 5' UTR of the RNA construct comprises or consists of a sequence according to SEQ ID NO: 371; the 3' UTR of the RNA construct comprises or consists of a sequence according to SEQ ID NO: 374; and/or the polyA tail sequence of the RNA construct is a split polyA tail sequence which, preferably, comprises or consists of a sequence according to SEQ ID NO: 375.
- the RNA construct comprises between the 3’UTR and the poly-A sequence a sequence according to SEQ ID NO: 379 which may have a further beneficial effect on the expression level of the encoded peptidoglycan hydrolase.
- the RNA construct further comprises a 5' cap.
- the RNA construct is an mRNA, and preferably the mRNA contains a modified nucleoside selected from pseudouridine ( ⁇ ), N1-methyl- pseudouridine (m1 ⁇ ), and 5-methyl-uridine (m5U) in place of uridine, preferably in place of each uridine, as described herein.
- said modified nucleoside is N1-methyl-pseudouridine (m1 ⁇ ).
- the RNA construct of the invention is an embodiment of the RNA of the invention. It is to be understood that all features, aspects and embodiments described in the context of the RNA of the invention are equally applicable to the RNA construct of the invention.
- the RNA of the invention is formulated as a particle comprising said RNA, preferably as a lipid nanoparticle (LNP) or lipoplex (LPX).
- LNP lipid nanoparticle
- LPX lipoplex
- the poly-A sequence i.e. poly-A tail
- the 5’ UTR the 5’ UTR
- the 3’ UTR modified nucleosides and particles such as LNP and LPX
- 5'-Cap the RNA (in particular, mRNA) of the invention comprises a 5'-cap structure.
- the RNA does not have uncapped 5'-triphosphates.
- the RNA in particular, mRNA may comprise a conventional 5'-cap and/or a 5'-cap analog.
- conventional 5'-cap refers to a cap structure found on the 5'-end of an RNA molecule and generally comprises a guanosine 5'-triphosphate (Gppp) which is connected via its triphosphate moiety to the 5'-end of the next nucleotide of the RNA (i.e., the guanosine is connected via a 5' to 5' triphosphate linkage to the rest of the RNA).
- Gppp guanosine 5'-triphosphate
- the guanosine may be methylated at position N7 (resulting in the cap structure m7Gppp).
- 5'-cap analog includes a 5'-cap which is based on a conventional 5'-cap but which has been modified at either the 2'- or 3'-position of the m7guanosine structure in order to avoid an integration of the 5'-cap analog in the reverse orientation (such 5'-cap analogs are also called anti-reverse cap analogs (ARCAs)).
- ARCAs anti-reverse cap analogs
- Particularly preferred 5'-cap analogs are those having one or more substitutions at the bridging and non-bridging oxygen in the phosphate bridge, such as phosphorothioate modified 5'-cap analogs at the ⁇ -phosphate (such as m27,2'OG(5')ppSp(5')G (referred to as beta-S-ARCA or ⁇ -S-ARCA)), as described in PCT/EP2019/056502.
- phosphorothioate modified 5'-cap analogs at the ⁇ -phosphate such as m27,2'OG(5')ppSp(5')G (referred to as beta-S-ARCA or ⁇ -S-ARCA)
- RNA in particular, mRNA
- a 5'-cap structure as described herein may be achieved by in vitro transcription of a DNA template in presence of a corresponding 5'-cap compound, wherein said 5'-cap structure is co- transcriptionally incorporated into the generated RNA (in particular, mRNA) strand, or the RNA (in particular, mRNA) may be generated, for example, by in vitro transcription, and the 5'-cap structure may be attached to the RNA post-transcriptionally using capping enzymes, for example, capping enzymes of vaccinia virus.
- the RNA in particular, mRNA
- the RNA comprises a cap0, cap1, or cap2, preferably cap1.
- cap0 means the structure “m7GpppN", wherein N is any nucleoside bearing an OH moiety at position 2'.
- cap1 means the structure “m7GpppNm”, wherein Nm is any nucleoside bearing an OCH3 moiety at position 2'.
- cap2 means the structure "m7GpppNmNm", wherein each Nm is independently any nucleoside bearing an OCH3 moiety at position 2'.
- the RNA comprises a 5'-cap structure selected from the group consisting of m27,2'OG(5’)ppSp(5')G (in particular its D1 diastereomer), m27,3'OG(5')ppp(5')G, and m27,3'- OGppp(m12'-O)ApG.
- RNA comprises m27,2'OG(5’)ppSp(5')G (in particular its D1 diastereomer) as 5'-cap structure.
- the RNA comprises m27,3'-OGppp(m12'-O)ApG as 5'-cap structure.
- the 5'-cap analog beta-S-ARCA ( ⁇ -S-ARCA) has the following structure:
- the "D1 diastereomer of beta-S-ARCA” or "beta-S-ARCA(D1)” is the diastereomer of beta-S-ARCA which elutes first on an HPLC column compared to the D2 diastereomer of beta-S-ARCA (beta-S-ARCA(D2)) and thus exhibits a shorter retention time.
- the HPLC preferably is an analytical HPLC.
- a Supelcosil LC-18-T RP column preferably of the format: 5 ⁇ m, 4.6 x 250 mm is used for separation, whereby a flow rate of 1.3 ml/min can be applied.
- UV-detection (VWD) can be performed at 260 nm and fluorescence detection (FLD) can be performed with excitation at 280 nm and detection at 337 nm.
- the 5'-cap analog m27,3'-OGppp(m12'-O)ApG which is a building block of a cap1 has the following structure:
- An exemplary cap0 mRNA comprising ⁇ -S-ARCA and mRNA has the following structure:
- An exemplary cap1 mRNA comprising m27,3'-OGppp(m12'-O)ApG and mRNA has the following structure:
- Poly-A tail
- the RNA (in particular, mRNA) of the invention comprises a poly-A sequence, in particular at the 3’ end of the RNA.
- poly-A tail or "poly-A sequence” refers to an uninterrupted or interrupted sequence of adenylate residues which is typically located at the 3'-end of an RNA (in particular, mRNA) molecule.
- Poly-A tails or poly-A sequences are known to those of skill in the art and may follow the 3’-UTR in the RNAs (in particular, mRNAs) described herein.
- An uninterrupted poly-A tail is characterized by consecutive adenylate residues. In nature, an uninterrupted poly-A tail is typical.
- RNAs in particular, mRNAs
- RNAs can have a poly-A tail attached to the free 3'-end of the RNA by a template-independent RNA polymerase after transcription or a poly-A tail encoded by DNA and transcribed by a template-dependent RNA polymerase. It has been demonstrated that a poly-A tail of about 120 A nucleotides has a beneficial influence on the levels of RNA in transfected eukaryotic cells, as well as on the levels of protein that is translated from an open reading frame that is present upstream (5’) of the poly-A tail (Holtkamp et al., 2006, Blood, vol.108, pp.4009-4017).
- the poly-A tail may be of any length.
- a poly-A tail comprises, essentially consists of, or consists of at least 20, at least 30, at least 40, at least 80, or at least 100 and up to 500, up to 400, up to 300, up to 200, or up to 150 A nucleotides, and, in particular, about 120 A nucleotides.
- nucleotides in the poly-A tail typically at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% by number of nucleotides in the poly-A tail are A nucleotides, but permits that remaining nucleotides are nucleotides other than A nucleotides, such as U nucleotides (uridylate), G nucleotides (guanylate), or C nucleotides (cytidylate).
- consists of means that all nucleotides in the poly-A tail, i.e., 100% by number of nucleotides in the poly-A tail, are A nucleotides.
- a nucleotide or “A” refers to adenylate.
- a poly-A tail is attached during RNA transcription, e.g., during preparation of in vitro transcribed RNA, based on a DNA template comprising repeated dT nucleotides (deoxythymidylate) in the strand complementary to the coding strand.
- the DNA sequence encoding a poly-A tail (coding strand) is referred to as poly(A) cassette.
- the poly(A) cassette present in the coding strand of DNA essentially consists of dA nucleotides, but is interrupted by a random sequence of the four nucleotides (dA, dC, dG, and dT). Such random sequence may be 5 to 50, 10 to 30, or 10 to 20 nucleotides in length.
- a cassette is disclosed in WO 2016/005324 A1, hereby incorporated by reference. Any poly(A) cassette disclosed in WO 2016/005324 A1 may be used in the present disclosure.
- a poly(A) cassette that essentially consists of dA nucleotides, but is interrupted by a random sequence having an equal distribution of the four nucleotides (dA, dC, dG, dT) and having a length of e.g., 5 to 50 nucleotides shows, on DNA level, constant propagation of plasmid DNA in E. coli and is still associated, on RNA level, with the beneficial properties with respect to supporting RNA stability and translational efficiency is encompassed.
- the poly-A tail contained in an RNA (in particular, mRNA) molecule described herein essentially consists of A nucleotides, but is interrupted by a random sequence of the four nucleotides (A, C, G, U). Such random sequence may be 5 to 50, 10 to 30, or 10 to 20 nucleotides in length.
- the poly(A) tail comprises 30 adenine nucleotides followed by 70 adenine nucleotides, wherein the 30 adenine nucleotides and 70 adenine nucleotides are separated by a linker sequence of 10 nucleotides.
- a poly-A tail may comprise at least 20, at least 30, at least 40, at least 80, or at least 100 and up to 500, up to 400, up to 300, up to 200, or up to 150 nucleotides.
- the poly-A tail may essentially consist of at least 20, at least 30, at least 40, at least 80, or at least 100 and up to 500, up to 400, up to 300, up to 200, or up to 150 nucleotides.
- the poly-A tail may consist of at least 20, at least 30, at least 40, at least 80, or at least 100 and up to 500, up to 400, up to 300, up to 200, or up to 150 nucleotides. In some embodiments, the poly-A tail comprises the poly-A tail shown in SEQ ID NO: 375. In some embodiments, the poly-A tail comprises at least 100 nucleotides. In some embodiments, the poly-A tail comprises about 150 nucleotides. In some embodiments, the poly-A tail comprises about 120 nucleotides.
- RNA comprises a poly-A tail comprising the nucleotide sequence of SEQ ID NO: 375, or a nucleotide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, or 80% identity to the nucleotide sequence of SEQ ID NO: 375.
- Untranslated regions UTR
- the RNA (in particular, mRNA) of the invention comprises a 5'-UTR and/or a 3'-UTR.
- untranslated region relates to a region in a DNA molecule which is transcribed but is not translated into an amino acid sequence, or to the corresponding region in an RNA molecule, such as an mRNA molecule.
- An untranslated region (UTR) can be present 5' (upstream) of an open reading frame (5'-UTR) and/or 3' (downstream) of an open reading frame (3'-UTR).
- a 5'-UTR if present, is located at the 5'-end, upstream of the start codon of a protein-encoding region.
- a 5'-UTR is downstream of the 5'-cap (if present), e.g., directly adjacent to the 5'-cap.
- a 3'-UTR if present, is located at the 3'-end, downstream of the termination codon of a protein-encoding region, but the term "3'-UTR" does generally not include the poly-A sequence.
- the 3'-UTR is upstream of the poly-A sequence (if present), e.g., directly adjacent to the poly-A sequence.
- Incorporation of a 3'-UTR into the 3'-non translated region of an RNA (preferably mRNA) molecule can result in an enhancement in translation efficiency.
- a synergistic effect may be achieved by incorporating two or more of such 3'-UTRs (which are preferably arranged in a head-to-tail orientation; cf., e.g., Holtkamp et al., Blood 108, 4009-4017 (2006)).
- the 3'-UTRs may be autologous or heterologous to the RNA (e.g., mRNA) into which they are introduced.
- a 5’-UTR is or comprises a modified human alpha-globin 5’-UTR.
- a particularly preferred 5’- UTR comprises the nucleotide sequence of SEQ ID NO: 371.
- a 3’-UTR comprises a first sequence from the amino terminal enhancer of split (AES) messenger RNA (SEQ ID NO: 372) and a second sequence from the mitochondrial encoded 12S ribosomal RNA (SEQ ID NO: 373).
- a particularly preferred 3’-UTR comprises the nucleotide sequence of SEQ ID NO: 374.
- a 3’-UTR comprises a first sequence comprising, or consisting of, the nucleotide sequence of SEQ ID NO: 372, or a nucleotide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, or 80% identity to the nucleotide sequence of SEQ ID NO: 372, and a second sequence comprising, or consisting of, the nucleotide sequence of SEQ ID NO: 373, or a nucleotide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, or 80% identity to the nucleotide sequence of SEQ ID NO: 373.
- the RNA comprises a 5’-UTR comprising the nucleotide sequence of SEQ ID NO: 371, or a nucleotide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, or 80% identity to the nucleotide sequence of SEQ ID NO: 371.
- the RNA comprises a 3’-UTR comprising the nucleotide sequence of SEQ ID NO: 374, or a nucleotide sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 85%, or 80% identity to the nucleotide sequence of SEQ ID NO: 374.
- RNA (in particular, mRNA) of the invention may have modified ribonucleotides in order to increase its stability and/or decrease immunogenicity and/or decrease cytotoxicity.
- uridine in the RNA (in particular, mRNA) of the invention is replaced (partially or completely, preferably completely) by a modified nucleoside.
- the modified nucleoside is a modified uridine.
- the modified uridine replacing uridine is selected from the group consisting of pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ), 5-methyl-uridine (m5U), and combinations thereof.
- the modified nucleoside replacing (partially or completely, preferably completely) uridine in the RNA may be any one or more of 3-methyl-uridine (m3U), 5-methoxy-uridine (mo5U), 5-aza-uridine, 6-aza- uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-uridine (ho5U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridineor 5-bromo-uridine), uridine 5- oxyacetic acid (cmo5U), uridine 5-oxyacetic acid methyl ester (mcmo5U), 5-carboxymethyl-uridine (cm5U), 1- carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm5
- RNA preferably mRNA which is modified by pseudouridine (replacing partially or completely, preferably completely, uridine) is referred to herein as " ⁇ -modified", whereas the term “m1 ⁇ -modified” means that the RNA (preferably mRNA) contains N(1)-methylpseudouridine (replacing partially or completely, preferably completely, uridine). Furthermore, the term “m5U-modified” means that the RNA (preferably mRNA) contains 5-methyluridine (replacing partially or completely, preferably completely, uridine).
- RNA preferably mRNA
- the RNA (preferably mRNA) of the invention contains N(1)-methylpseudouridine replacing completely uridine, in particular in context of RNA used in pharmaceutical compositions and/or for medical uses.
- Codon optimization and GC enrichment The codons of the RNA (in particular, mRNA) of the invention may further be optimized, e.g., to increase the GC content of the RNA and/or to replace codons which are rare in the cell (or subject) in which the peptide or polypeptide of interest is to be expressed by codons which are synonymous frequent codons in said cell (or subject).
- the amino acid sequence encoded by the RNA (in particular, mRNA) described in the present disclosure is encoded by a coding sequence which is codon-optimized and/or the G/C content of which is increased compared to wild type coding sequence.
- This also includes embodiments, wherein one or more sequence regions of the coding sequence are codon-optimized and/or increased in the G/C content compared to the corresponding sequence regions of the wild type coding sequence.
- the codon- optimization and/or the increase in the G/C content does not change the sequence of the encoded amino acid sequence.
- the term "codon-optimized” refers, in particular, to the alteration of codons in the coding region of a nucleic acid molecule to reflect the typical codon usage of a host organism without altering the amino acid sequence encoded by the nucleic acid molecule.
- the guanosine/cytosine (G/C) content of the coding region of the RNA (in particular, mRNA) described herein is increased compared to the G/C content of the corresponding coding sequence of the wild type RNA, wherein the amino acid sequence encoded by the RNA is not modified compared to the amino acid sequence encoded by the wild type RNA.
- This modification of the RNA sequence is based on the fact that the sequence of any RNA region to be translated is important for efficient translation of that RNA. Sequences having an increased G (guanosine)/C (cytosine) content are more stable than sequences having an increased A (adenosine)/U (uracil) content.
- codons which contain A and/or U nucleotides can be modified by substituting these codons by other codons, which code for the same amino acids but contain no A and/or U or contain a lower content of A and/or U nucleotides.
- the G/C content of the coding region of the RNA (in particular, mRNA) described herein is increased by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 55%, or even more compared to the G/C content of the coding region of the wild type RNA.
- Non-immunogenic RNA In some embodiments, the RNA (in particular, mRNA) of the present invention is non-immunogenic.
- non-immunogenic RNA refers to RNA that does not induce a response by the immune system upon administration, e.g., to a mammal such as a human, or induces a weaker response than would have been induced by the same RNA that differs only in that it has not been subjected to the modifications and treatments that render the non-immunogenic RNA non-immunogenic, i.e., than would have been induced by standard RNA (stdRNA).
- stdRNA standard RNA
- non-immunogenic RNA is rendered non- immunogenic by incorporating modified nucleosides suppressing RNA-mediated activation of innate immune receptors into the RNA and/or limiting the amount of double-stranded RNA (dsRNA), e.g., by limiting the formation of double-stranded RNA (dsRNA), e.g., during in vitro transcription, and/or by removing double-stranded RNA (dsRNA), e.g., following in vitro transcription.
- dsRNA double-stranded RNA
- non-immunogenic RNA is rendered non- immunogenic by incorporating modified nucleosides suppressing RNA-mediated activation of innate immune receptors into the RNA and/or by removing double-stranded RNA (dsRNA), e.g., following in vitro transcription.
- dsRNA double-stranded RNA
- any modified nucleoside may be used as long as it lowers or suppresses immunogenicity of the RNA.
- Particularly preferred are modified nucleosides that suppress RNA-mediated activation of innate immune receptors.
- the modified nucleosides comprise a replacement of one or more uridines with a nucleoside comprising a modified nucleobase.
- the modified nucleobase is a modified uracil.
- the nucleoside comprising a modified nucleobase is selected from the group consisting of 3-methyl- uridine (m3U), 5-methoxy-uridine (mo5U), 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-uridine (ho5U), 5-aminoallyl-uridine, 5- halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), uridine 5-oxyacetic acid (cmo5U), uridine 5-oxyacetic acid (cmo5U), uridine 5-
- the nucleoside comprising a modified nucleobase is pseudouridine ( ⁇ ), N1-methyl- pseudouridine (m1 ⁇ ) or 5-methyl-uridine (m5U), in particular N1-methyl-pseudouridine.
- the replacement of one or more uridines with a nucleoside comprising a modified nucleobase comprises a replacement of at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 10%, at least 25%, at least 50%, at least 75%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% of the uridines.
- dsRNA double-stranded RNA
- IVT in vitro transcription
- dsRNA double-stranded RNA
- formation of dsRNA can be limited during synthesis of mRNA by in vitro transcription (IVT), for example, by limiting the amount of uridine triphosphate (UTP) during synthesis.
- UTP may be added once or several times during synthesis of mRNA.
- dsRNA can be removed from RNA such as IVT RNA, for example, by ion-pair reversed phase HPLC using a non-porous or porous C-18 polystyrene-divinylbenzene (PS-DVB) matrix.
- PS-DVB polystyrene-divinylbenzene
- an enzymatic based method using E. coli RNaseIII that specifically hydrolyzes dsRNA but not ssRNA, thereby eliminating dsRNA contaminants from IVT RNA preparations can be used.
- dsRNA can be separated from ssRNA by using a cellulose material.
- an RNA preparation is contacted with a cellulose material and the ssRNA is separated from the cellulose material under conditions which allow binding of dsRNA to the cellulose material and do not allow binding of ssRNA to the cellulose material.
- Suitable methods for providing ssRNA are disclosed, for example, in WO 2017/182524.
- "remove” or “removal” refers to the characteristic of a population of first substances, such as non-immunogenic RNA, being separated from the proximity of a population of second substances, such as dsRNA, wherein the population of first substances is not necessarily devoid of the second substance, and the population of second substances is not necessarily devoid of the first substance.
- a population of first substances characterized by the removal of a population of second substances has a measurably lower content of second substances as compared to the non-separated mixture of first and second substances.
- the amount of double-stranded RNA (dsRNA) is limited, e.g., dsRNA (especially dsmRNA) is removed from non-immunogenic RNA , such that less than 10%, less than 5%, less than 4%, less than 3%, less than 2%, less than 1%, less than 0.5%, less than 0.3%, less than 0.1%, less than 0.05%, less than 0.03%, less than 0.01%, less than 0.005%, less than 0.004%, less than 0.003%, less than 0.002%, less than 0.001%, or less than 0.0005% of the RNA in the non-immunogenic RNA composition is dsRNA.
- the non- immunogenic RNA is free or essentially free of dsRNA.
- the non- immunogenic RNA (especially mRNA) composition comprises a purified preparation of single-stranded nucleoside modified RNA.
- the non-immunogenic RNA (especially mRNA) composition comprises single- stranded nucleoside modified RNA (especially mRNA) and is substantially free of double stranded RNA (dsRNA).
- the non-immunogenic RNA (especially mRNA) composition comprises at least 90%, at least 91%, at least 92%, at least 93 %, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.9%, at least 99.99%, at least 99.991%, at least 99.992%, , at least 99.993%,, at least 99.994%, , at least 99.995%, at least 99.996%, at least 99.997%, or at least 99.998% single stranded nucleoside modified RNA, relative to all other nucleic acid molecules (DNA, dsRNA, etc.).
- RNA may be spotted onto a membrane, e.g., nylon blotting membrane. The membrane may be blocked, e.g., in TBS-T buffer (20 mM TRIS pH 7.4, 137 mM NaCl, 0.1% (v/v) TWEEN-20) containing 5% (w/v) skim milk powder.
- TBS-T buffer (20 mM TRIS pH 7.4, 137 mM NaCl, 0.1% (v/v) TWEEN-20) containing 5% (w/v) skim milk powder.
- the membrane may be incubated with dsRNA-specific antibody, e.g., dsRNA-specific mouse mAb (English & Scientific Consulting, Szirák, Hungary). After washing, e.g., with TBS-T, the membrane may be incubated with a secondary antibody, e.g., HRP-conjugated donkey anti-mouse IgG (Jackson ImmunoResearch, Cat #715-035-150), and the signal provided by the secondary antibody may be detected.
- dsRNA-specific antibody e.g., dsRNA-specific mouse mAb (English & Scientific Consulting, Szirák, Hungary). After washing, e.g., with TBS-T, the membrane may be incubated with a secondary antibody, e.g., HRP-conjugated donkey anti-mouse IgG (Jackson ImmunoResearch, Cat #715-035-150), and the signal provided by the secondary antibody may be detected.
- translation is enhanced by a factor of 2-fold relative to its unmodified counterpart. In some embodiments, translation is enhanced by a 3-fold factor. In some embodiments, translation is enhanced by a 4-fold factor. In some embodiments, translation is enhanced by a 5- fold factor. In some embodiments, translation is enhanced by a 6-fold factor. In some embodiments, translation is enhanced by a 7-fold factor. In some embodiments, translation is enhanced by an 8-fold factor. In some embodiments, translation is enhanced by a 9-fold factor. In some embodiments, translation is enhanced by a 10- fold factor. In some embodiments, translation is enhanced by a 15-fold factor. In some embodiments, translation is enhanced by a 20-fold factor.
- translation is enhanced by a 50-fold factor. In some embodiments, translation is enhanced by a 100-fold factor. In some embodiments, translation is enhanced by a 200-fold factor. In some embodiments, translation is enhanced by a 500-fold factor. In some embodiments, translation is enhanced by a 1000-fold factor. In some embodiments, translation is enhanced by a 2000-fold factor. In some embodiments, the factor is 10-1000-fold. In some embodiments, the factor is 10-100-fold. In some embodiments, the factor is 10-200-fold. In some embodiments, the factor is 10-300-fold. In some embodiments, the factor is 10-500-fold. In some embodiments, the factor is 20-1000-fold. In some embodiments, the factor is 30-1000-fold.
- the factor is 50-1000-fold. In some embodiments, the factor is 100-1000- fold. In some embodiments, the factor is 200-1000-fold. In some embodiments, translation is enhanced by any other significant amount or range of amounts.
- the non-immunogenic RNA (especially mRNA) exhibits significantly less innate immunogenicity than standard RNA with the same sequence. In some embodiments, the non-immunogenic RNA (especially mRNA) exhibits an innate immune response that is 2-fold less than its unmodified counterpart. In some embodiments, innate immunogenicity is reduced by a 3-fold factor. In some embodiments, innate immunogenicity is reduced by a 4-fold factor.
- innate immunogenicity is reduced by a 5-fold factor. In some embodiments, innate immunogenicity is reduced by a 6-fold factor. In some embodiments, innate immunogenicity is reduced by a 7-fold factor. In some embodiments, innate immunogenicity is reduced by an 8-fold factor. In some embodiments, innate immunogenicity is reduced by a 9-fold factor. In some embodiments, innate immunogenicity is reduced by a 10-fold factor. In some embodiments, innate immunogenicity is reduced by a 15-fold factor. In some embodiments, innate immunogenicity is reduced by a 20-fold factor. In some embodiments, innate immunogenicity is reduced by a 50-fold factor.
- innate immunogenicity is reduced by a 100- fold factor. In some embodiments, innate immunogenicity is reduced by a 200-fold factor. In some embodiments, innate immunogenicity is reduced by a 500-fold factor. In some embodiments, innate immunogenicity is reduced by a 1000-fold factor. In some embodiments, innate immunogenicity is reduced by a 2000-fold factor.
- the term "exhibits significantly less innate immunogenicity" refers to a detectable decrease in innate immunogenicity. In some embodiments, the term refers to a decrease such that an effective amount of the non- immunogenic RNA (especially mRNA) can be administered without triggering a detectable innate immune response.
- the term refers to a decrease such that the non-immunogenic RNA (especially mRNA) can be repeatedly administered without eliciting an innate immune response sufficient to detectably reduce production of the protein encoded by the non-immunogenic RNA.
- the decrease is such that the non- immunogenic RNA (especially mRNA) can be repeatedly administered without eliciting an innate immune response sufficient to eliminate detectable production of the protein encoded by the non-immunogenic RNA.
- immunogenicity refers to the ability of a foreign substance, e.g. an RNA encoding a peptidoglycan hydrolase of the invention, to induce an immune response in a mammal such as a human.
- RNA delivery The RNA of the invention may be delivered for therapeutic applications described herein using any appropriate methods known in the art, including, e.g., delivery as naked RNA, or delivery mediated by delivery vehicles.
- RNA in particular, mRNA
- at least a portion of the RNA is delivered to a target cell, target tissue or target organ.
- at least a portion of the RNA is delivered to the cytosol of a target cell.
- the RNA is translated by a target cell to produce the encoded peptide or polypeptide.
- the target cell is a cell in the liver.
- the target cell is a muscle cell.
- at least a portion of the RNA is delivered to cells of the subject for translation of the encoded peptide or polypeptide. Delivery vehicles To overcome the barriers to safe and effective RNA delivery, RNA may be administered with one or more delivery vehicles that protect the RNA from degradation, maximize delivery to on-target cells and minimize exposure to off- target cells.
- RNA delivery vehicles may complex or encapsulate RNA and include a range of materials, including polymers and lipids.
- such RNA delivery vehicles may form particles with RNA.
- RNA, in particular mRNA, described herein may be present in particles comprising (i) the RNA, and (ii) at least one cationic or cationically ionizable compound such as a polymer or lipid complexing the RNA. Electrostatic interactions between positively charged molecules such as polymers and lipids and negatively charged RNA are involved in particle formation. This results in complexation and spontaneous formation of RNA particles.
- RNA containing particles have been described previously to be suitable for delivery of RNA in particulate form (cf., e.g., Kaczmarek, J. C. et al., 2017, Genome Medicine 9, 60).
- nanoparticle encapsulation of RNA physically protects RNA from degradation and, depending on the specific chemistry, can aid in cellular uptake and endosomal escape.
- the term "particle” relates to a structured entity formed by molecules or molecule complexes, in particular particle forming compounds.
- the term "particle” relates to a micro- or nano-sized structure, such as a micro- or nano-sized compact structure.
- RNA particles described herein include lipid nanoparticle (LNP)-based and lipoplex (LPX)-based formulations.
- a lipoplex (LPX) described herein is obtainable from mixing two aqueous phases, namely a phase comprising RNA and a phase comprising a dispersion of lipids.
- the lipid phase comprises liposomes.
- liposomes are self-closed unilamellar or multilamellar vesicular particles wherein the lamellae comprise lipid bilayers and the encapsulated lumen comprises an aqueous phase.
- liposomes comprise unilamellar or multilamellar phospholipid bilayers enclosing an aqueous core (also referred to herein as an aqueous lumen). They may be prepared from materials possessing polar head (hydrophilic) groups and nonpolar tail (hydrophobic) groups.
- cationic lipids employed in formulating liposomes designed for the delivery of RNA are amphiphilic in nature and consist of a positively charged (cationic) amine head group linked to a hydrocarbon chain or cholesterol derivative via glycerol.
- lipoplexes are multilamellar liposome-based formulations that form upon electrostatic interaction of cationic liposomes with RNAs.
- formed lipoplexes possess distinct internal arrangements of molecules that arise due to the transformation from liposomal structure into compact RNA– lipoplexes.
- an LPX particle comprises an amphiphilic lipid, in particular cationic or cationically ionizable amphiphilic lipid, and RNA (especially mRNA) as described herein.
- electrostatic interactions between positively charged liposomes made from one or more amphiphilic lipids, in particular cationic or cationically ionizable amphiphilic lipids
- negatively charged RNA especially mRNA results in complexation and spontaneous formation of RNA lipoplex particles.
- Positively charged liposomes may be generally synthesized using a cationic or cationically ionizable amphiphilic lipid, such as DOTMA and/or DODMA, and optionally additional lipids, such as DOPE or DSPC.
- a lipid nanoparticle is typically obtainable from direct mixing of RNA in an aqueous phase with lipids in a phase comprising an organic solvent, such as ethanol.
- lipids or lipid mixtures can be used for particle formation, which do not form lamellar (bilayer) phases in water.
- LNPs comprise or consist of a cationic/cationically ionizable lipid and helper lipids such as phospholipids, cholesterol, and/or polymer-conjugated lipids (e.g., polyethylene glycol (PEG) lipids).
- helper lipids such as phospholipids, cholesterol, and/or polymer-conjugated lipids (e.g., polyethylene glycol (PEG) lipids).
- PEG polyethylene glycol
- the particles (e.g., LNPs and LPXs) described herein have an average diameter that in some embodiments ranges from about 50 nm to about 1000 nm, from about 50 nm to about 800 nm, from about 50 nm to about 700 nm, from about 50 nm to about 600 nm, from about 50 nm to about 500 nm, from about 50 nm to about 450 nm, from about 50 nm to about 400 nm, from about 50 nm to about 350 nm, from about 50 nm to about 300 nm, from about 50 nm to about 250 nm, from about 50 nm to about 200 nm, from about 100 nm to about 1000 nm, from about 100 nm to about 800 nm, from about 100 nm to about 700 nm, from about 100 nm to about 600 nm, from about 100 nm to about 500 nm, from about 100 nm to about 450
- the particles (e.g., LNPs and LPXs) described herein have an average diameter that in some embodiments ranges from about 40 nm to about 200 nm, such as from about 50 nm to about 180 nm, from about 60 nm to about 160 nm, from about 80 nm to about 150 nm or from about 80 nm to about 120 nm.
- RNA particles (especially mRNA particles) described herein may exhibit a polydispersity index (PDI) less than about 0.5, less than about 0.4, less than about 0.3, less than about 0.2, less than about 0.1, or less than about 0.05.
- PDI polydispersity index
- the RNA particles can exhibit a polydispersity index in a range of about 0.01 to about 0.4 or about 0.1 to about 0.3.
- the N/P ratio gives the ratio of the nitrogen groups in the lipid to the number of phosphate groups in the RNA. It is correlated to the charge ratio, as the nitrogen atoms (depending on the pH) are usually positively charged and the phosphate groups are negatively charged.
- the N/P ratio where a charge equilibrium exists, depends on the pH. Lipid formulations may be formed at N/P ratios larger than four up to twelve, because positively charged nanoparticles can be favorable for transfection. In that case, RNA is considered to be completely bound to nanoparticles.
- RNA particles comprise more than one type of RNA molecules, where the molecular parameters of the RNA molecules may be similar or different from each other, like with respect to molar mass or fundamental structural elements such as molecular architecture, capping, coding regions or other features,
- each RNA species is separately formulated as an individual particulate formulation.
- each individual particulate formulation will comprise one RNA species.
- the individual particulate formulations may be present as separate entities, e.g. in separate containers. Such formulations are obtainable by providing each RNA species separately (typically each in the form of an RNA-containing solution) together with a particle-forming agent, thereby allowing the formation of particles.
- Respective particles will contain exclusively the specific RNA species that is being provided when the particles are formed (individual particulate formulations).
- a composition such as a pharmaceutical composition comprises more than one individual particle formulation.
- Respective pharmaceutical compositions are referred to as mixed particulate formulations.
- Mixed particulate formulations according to the present disclosure are obtainable by forming, separately, individual particulate formulations, followed by a step of mixing of the individual particulate formulations. By the step of mixing, a formulation comprising a mixed population of RNA-containing particles is obtainable. Individual particulate populations may be together in one container, comprising a mixed population of individual particulate formulations. Alternatively, it is possible that all RNA species of the pharmaceutical composition are formulated together as a combined particulate formulation.
- Such formulations are obtainable by providing a combined formulation (typically combined solution) of all RNA species together with a particle-forming agent, thereby allowing the formation of particles.
- a combined particulate formulation will typically comprise particles which comprise more than one RNA species.
- different RNA species are typically present together in a single particle.
- Polymers Given their high degree of chemical flexibility, polymers are commonly used materials for nanoparticle-based delivery. Typically, cationic polymers are used to electrostatically condense the negatively charged RNA into nanoparticles.
- a "polymer,” as used herein, is given its ordinary meaning, i.e., a molecular structure comprising one or more repeat units (monomers), connected by covalent bonds.
- the repeat units can all be identical, or in some cases, there can be more than one type of repeat unit present within the polymer.
- the following disclosure with respect to “polymers” is, in particular, relevant in context of RNA and/or delivery vehicles, as described herein.
- the polymer is biologically derived, i.e., a biopolymer such as a protein.
- additional moieties can also be present in the polymer, for example targeting moieties.
- the polymer is said to be a "copolymer.” It is to be understood that the polymer being employed herein can be a copolymer.
- the repeat units forming the copolymer can be arranged in any fashion. For example, the repeat units can be arranged in a random order, in an alternating order, or as a "block" copolymer, i.e., comprising one or more regions each comprising a first repeat unit (e.g., a first block), and one or more regions each comprising a second repeat unit (e.g., a second block), etc.
- Block copolymers can have two (a diblock copolymer), three (a triblock copolymer), or more numbers of distinct blocks.
- the polymer is biocompatible. Biocompatible polymers are polymers that typically do not result in significant cell death at moderate concentrations. In certain embodiments, the biocompatible polymer is biodegradable, i.e., the polymer is able to degrade, chemically and/or biologically, within a physiological environment, such as within the body. In certain embodiments, polymer may be protamine or polyalkyleneimine.
- protamine refers to any of various strongly basic proteins of relatively low molecular weight that are rich in arginine and are found associated especially with DNA in place of somatic histones in the sperm cells of various animals (as fish).
- protamine refers to proteins found in fish sperm that are strongly basic, are soluble in water, are not coagulated by heat, and yield chiefly arginine upon hydrolysis. In purified form, they are used in a long-acting formulation of insulin and to neutralize the anticoagulant effects of heparin.
- the term "protamine” as used herein is meant to comprise any protamine amino acid sequence obtained or derived from natural or biological sources including fragments thereof and multimeric forms of said amino acid sequence or fragment thereof as well as (synthesized) polypeptides which are artificial and specifically designed for specific purposes and cannot be isolated from native or biological sources.
- the polyalkyleneimine comprises polyethylenimine and/or polypropylenimine, preferably polyethyleneimine.
- a preferred polyalkyleneimine is polyethyleneimine (PEI).
- the average molecular weight of PEI is preferably 0.75 ⁇ 102 to 107 Da, preferably 1000 to 105 Da, more preferably 10000 to 40000 Da, more preferably 15000 to 30000 Da, even more preferably 20000 to 25000 Da.
- Preferred according to the disclosure is linear polyalkyleneimine such as linear polyethyleneimine (PEI).
- Cationic polymers (including polycationic polymers) contemplated for use herein include any cationic polymers which are able to electrostatically bind nucleic acid.
- cationic polymers contemplated for use herein include any cationic polymers with which nucleic acid can be associated, e.g.
- lipids and “lipid-like material” is, in particular, relevant in context of RNA and/or delivery vehicles, as described herein.
- Lipids are usually insoluble or poorly soluble in water, but soluble in many organic solvents. In an aqueous environment, the amphiphilic nature allows the molecules to self-assemble into organized structures and different phases. One of those phases consists of lipid bilayers, as they are present in vesicles, multilamellar/unilamellar liposomes, or membranes in an aqueous environment.
- Hydrophobicity can be conferred by the inclusion of apolar groups that include, but are not limited to, long-chain saturated and unsaturated aliphatic hydrocarbon groups and such groups substituted by one or more aromatic, cycloaliphatic, or heterocyclic group(s).
- the hydrophilic groups may comprise polar and/or charged groups and include carbohydrates, phosphate, carboxylic, sulfate, amino, sulfhydryl, nitro, hydroxyl, and other like groups.
- hydrophobic refers to any molecule, moiety or group which is substantially immiscible or insoluble in aqueous solution.
- hydrophobic group includes hydrocarbons having at least 6 carbon atoms.
- the monovalent radical of a hydrocarbon is referred to as hydrocarbyl herein.
- the hydrophobic group can have functional groups (e.g., ether, ester, halide, etc.) and atoms other than carbon and hydrogen as long as the group satisfies the condition of being substantially immiscible or insoluble in aqueous solution.
- the term "lipid-like material", “lipid-like compound” or “lipid-like molecule relates to substances, in particular amphiphilic substances, that structurally and/or functionally relate to lipids but may not be considered as lipids in a strict sense.
- the term includes compounds that are able to form amphiphilic layers as they are present in vesicles, multilamellar/unilamellar liposomes, or membranes in an aqueous environment and includes surfactants, or synthesized compounds with both hydrophilic and hydrophobic moieties.
- the term includes molecules, which comprise hydrophilic and hydrophobic moieties with different structural organization, which may or may not be similar to that of lipids.
- lipid-like compounds capable of spontaneous integration into cell membranes include functional lipid constructs such as synthetic function-spacer- lipid constructs (FSL), synthetic function-spacer-sterol constructs (FSS) as well as artificial amphipathic molecules.
- Lipids comprising two long alkyl chains and a polar head group are generally cylindrical. The area occupied by the two alkyl chains is similar to the area occupied by the polar head group. Such lipids have low solubility as monomers and tend to aggregate into planar bilayers that are water insoluble.
- Traditional surfactant monomers comprising only one linear alkyl chain and a hydrophilic head group are generally cone shaped. The hydrophilic head group tends to occupy more molecular space than the linear alkyl chain. In some embodiments, surfactants tend to aggregate into spherical or elliptoid micelles that are water soluble.
- lipids also have the same general structure as surfactants - a polar hydrophilic head group and a nonpolar hydrophobic tail - lipids differ from surfactants in the shape of the monomers, in the type of aggregates formed in solution, and in the concentration range required for aggregation.
- the term "lipid” is to be construed to cover both lipids and lipid-like materials unless otherwise indicated herein or clearly contradicted by context.
- Cationic/Cationically ionizable lipids In some embodiments, the RNA compositions and formulations and RNA particles described herein comprise at least one cationic or cationically ionizable lipid as particle forming agent.
- Cationic or cationically ionizable lipids contemplated for use herein include any cationic or cationically ionizable lipids (including lipid-like materials) which are able to electrostatically bind nucleic acid.
- cationic or cationically ionizable lipids contemplated for use herein can be associated with nucleic acid, e.g. by forming complexes with the nucleic acid or forming vesicles in which the nucleic acid is enclosed or encapsulated.
- a "cationic lipid” refers to a lipid or lipid-like material having a net positive charge.
- Cationic lipids bind negatively charged nucleic acid by electrostatic interaction.
- cationic lipids possess a lipophilic moiety, such as a sterol, an acyl chain, a diacyl or more acyl chains, and the head group of the lipid typically carries the positive charge.
- a cationic lipid has a net positive charge only at certain pH, in particular acidic pH, while it has preferably no net positive charge, preferably has no charge, i.e., it is neutral, at a different, preferably higher pH such as physiological pH. This ionizable behavior is thought to enhance efficacy through helping with endosomal escape and reducing toxicity as compared with particles that remain cationic at physiological pH.
- a “cationically ionizable lipid” refers to a lipid or lipid-like material which has a net positive charge or is neutral, i.e., which is not permanently cationic. Thus, depending on the pH of the composition in which the cationically ionizable lipid is solved, the cationically ionizable lipid is either positively charged or neutral. For purposes of the present disclosure, cationically ionizable lipids are covered by the term “cationic lipid” unless contradicted by the circumstances.
- the cationic or cationically ionizable lipid comprises a head group which includes at least one nitrogen atom (N) which is positive charged or capable of being protonated, e.g., under physiological conditions.
- N nitrogen atom
- cationic or cationically ionizable lipids include, but are not limited to N,N-dimethyl-2,3- dioleyloxypropylamine (DODMA), 1,2-dioleoyl-3-trimethylammonium propane (DOTAP); 1,2-di-O-octadecenyl-3- trimethylammonium propane (DOTMA), 3-(N—(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol (DC-Chol), dimethyldioctadecylammonium (DDAB); 1,2-dioleoyl-3-dimethylammonium-propane (DODAP); 1,2-diacyloxy-3- dimethylam
- the cationic or cationically ionizable lipid is DOTMA. In some embodiments, the cationic or cationically ionizable lipid is DODMA.
- DOTMA is a cationic lipid with a quaternary amine headgroup.
- the structure of DOTMA may be represented as follows: DODMA is an ionizable cationic lipid with a tertiary amine headgroup.
- the cationic or cationically ionizable lipid may comprise from about 10 mol % to about 95 mol %, from about 20 mol % to about 95 mol %, from about 20 mol % to about 90 mol %, from about 30 mol % to about 90 mol %, from about 40 mol % to about 90 mol %, or from about 40 mol % to about 80 mol % of the total lipid present in the particle.
- RNA compositions and formulations and RNA particles described herein may also comprise lipids (including lipid-like materials) other than cationic or cationically ionizable lipids (also collectively referred to herein as cationic lipids), i.e., non-cationic lipids (including non-cationic or non-cationically ionizable lipids or lipid-like materials).
- cationic lipids also collectively referred to herein as cationic lipids
- non-cationic lipids including non-cationic or non-cationically ionizable lipids or lipid-like materials.
- RNA particles by addition of other hydrophobic moieties, such as cholesterol and lipids, in addition to a cationic or cationically ionizable lipid may enhance particle stability and efficacy of RNA delivery.
- One or more additional lipids may or may not affect the overall charge of the RNA particles.
- the or more additional lipids are a non-cationic lipid or lipid-like material.
- the non-cationic lipid may comprise, e.g., one or more anionic lipids and/or neutral lipids.
- an "anionic lipid" refers to any lipid that is negatively charged at a selected pH.
- a neutral lipid refers to any of a number of lipid species that exist either in an uncharged or neutral zwitterionic form at a selected pH.
- the RNA compositions and formulations and RNA particles described herein comprise a cationic or cationically ionizable lipid and one or more additional lipids.
- the amount of the cationic or cationically ionizable lipid compared to the amount of the one or more additional lipids may affect important RNA particle characteristics, such as charge, particle size, stability, tissue selectivity, and bioactivity of the RNA.
- the molar ratio of the cationic or cationically ionizable lipid to the one or more additional lipids is from about 10:0 to about 1:9, about 4:1 to about 1:2, about 4:1 to about 1:1, about 3:1 to about 1:1, or about 3:1 to about 2:1.
- the one or more additional lipids comprised in the RNA compositions and formulations and RNA particles described herein comprise one or more of the following: neutral lipids, steroids, and combinations thereof.
- the one or more additional lipids comprise a neutral lipid which is a phospholipid.
- the phospholipid is selected from the group consisting of phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, phosphatidic acids, phosphatidylserines and sphingomyelins.
- Specific phospholipids that can be used include, but are not limited to, phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, phosphatidic acids, phosphatidylserines or sphingomyelin.
- Such phospholipids include in particular diacylphosphatidylcholines, such as distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dimyristoylphosphatidylcholine (DMPC), dipentadecanoylphosphatidylcholine, dilauroylphosphatidylcholine, dipalmitoylphosphatidylcholine (DPPC), diarachidoylphosphatidylcholine (DAPC), dibehenoylphosphatidylcholine (DBPC), ditricosanoylphosphatidylcholine (DTPC), dilignoceroylphatidylcholine (DLPC), palmitoyloleoyl-phosphatidylcholine (POPC), 1,2-di-O-octadecenyl-sn-glycero-3-phosphocholine (18:0 Diether PC), 1-oleoyl-2
- the neutral lipid is selected from the group consisting of DSPC, DOPC, DMPC, DPPC, POPC, DOPE, DOPG, DPPG, POPE, DPPE, DMPE, DSPE, and SM. In some embodiments, the neutral lipid is selected from the group consisting of DSPC, DPPC, DMPC, DOPC, POPC, DOPE and SM. In some embodiments, the neutral lipid is DSPC. In some embodiments, the neutral lipid is DOPE. In some embodiments, the additional lipid comprises one of the following: (1) a phospholipid, (2) cholesterol or a derivative thereof; or (3) a mixture of a phospholipid and cholesterol or a derivative thereof.
- RNA compositions and formulations and RNA particles described herein comprise (1) a cationic or cationically ionizable lipid, and a phospholipid such as DSPC or DOPE or (2) a cationic or cationically ionizable lipid and a phospholipid such as DSPC or DOPE and cholesterol.
- the RNA particles (especially the particles comprising mRNA) described herein comprise (1) DOTMA and DOPE, (2) DOTMA, DOPE and cholesterol, (3) DODMA and DOPE or (4) DODMA, DOPE and cholesterol.
- DSPC is a neutral phospholipid.
- the structure of DSPC may be represented as follows: DOPE is a neutral phospholipid.
- the structure of DOPE may be represented as follows:
- the structure of cholesterol may be represented as follows:
- the additional lipid e.g., one or more phospholipids and/or cholesterol
- the additional lipid may comprise from about 0 mol % to about 90 mol %, from about 0 mol % to about 80 mol %, from about 2 mol % to about 80 mol %, from about 5 mol % to about 80 mol %, from about 5 mol % to about 60 mol %, from about 5 mol % to about 50 mol %, from about 7.5 mol % to about 50 mol %, or from about 10 mol % to about 40 mol % of the total lipid present in the particle.
- the additional lipid (e.g., one or more phospholipids and/or cholesterol) comprises about 10 mol %, about 15 mol %, or about 20 mol % of the total lipid present in the particle.
- Polymer-conjugated lipids RNA compositions and formulations and RNA particles described herein may comprise at least one polymer-conjugated lipid.
- a polymer-conjugated lipid is typically a molecule comprising a lipid portion and a polymer portion conjugated thereto.
- a polymer-conjugated lipid is a PEG-conjugated lipid, also referred to herein as pegylated lipid or PEG-lipid.
- pegylated lipid refers to a molecule comprising both a lipid portion and a polyethylene glycol portion. Pegylated lipids are known in the art.
- a polymer-conjugated lipid is a polysarcosine-conjugated lipid, also referred to herein as sarcosinylated lipid or pSar-lipid.
- sarcosinylated lipid refers to a molecule comprising both a lipid portion and a polysarcosine portion.
- a polymer-conjugated lipid is designed to sterically stabilize a lipid particle by forming a protective hydrophilic layer that shields the hydrophobic lipid layer.
- a polymer-conjugated lipid can reduce its association with serum proteins and/or the resulting uptake by the reticuloendothelial system when such lipid particles are administered in vivo.
- Polyethyleneglycol (PEG)-conjugated lipids In some embodiments, RNA compositions/formulations and RNA particles described herein comprise a PEG- conjugated lipid.
- the PEG-conjugated lipid is a lipid having the structure of the following general formula: or a pharmaceutically acceptable salt, tautomer or stereoisomer thereof, wherein: each of R12 and R13 is each independently a straight or branched, alkyl or alkenyl chain containing from 10 to 30 carbon atoms, wherein the alkyl/alkenyl chain is optionally interrupted by one or more ester bonds; and w has a mean value ranging from 30 to 60. In some embodiments of this formula, each of R12 and R13 is independently a straight alkyl chain containing from 10 to 18 carbon atoms, preferably from 12 to 16 carbon atoms.
- R12 and R13 are identical. In some embodiments, each of R12 and R13 is a straight alkyl chain containing 12 carbon atoms. In some embodiments, each of R12 and R13 is a straight alkyl chain containing 14 carbon atoms. In some embodiments, each of R12 and R13 is a straight alkyl chain containing 16 carbon atoms. In some embodiments of this formula, R12 and R13 are different. In some embodiments, one of R12 and R13 is a straight alkyl chain containing 12 carbon atoms and the other of R12 and R13 is a straight alkyl chain containing 14 carbon atoms.
- w has a mean value ranging from 40 to 50, such as a mean value of 45. In some embodiments of this formula, w is within a range such that the PEG portion of the pegylated lipid has an average molecular weight of from about 400 to about 6000 g/mol, such as from about 1000 to about 5000 g/mol, from about 1500 to about 4000 g/mol, or from about 2000 to about 3000 g/mol. In some embodiments, each of R12 and R13 is a straight alkyl chain containing 14 carbon atoms and w has a mean value of 45.
- PEG-conjugated lipids include, but are not limited to pegylated diacylglycerol (PEG-DAG) such as 1-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG), a pegylated phosphatidylethanoloamine (PEG-PE), a PEG succinate diacylglycerol (PEG-S-DAG) such as 4-O-(2' ,3 '- di(tetradecanoyloxy)propyl-1-O-(w-methoxy(polyethoxy)ethyl)butanedioate (PEG-S-DMG), a pegylated ceramide (PEG-cer), or a PEG dialkoxypropylcarbamate such as w-methoxy(polyethoxy)ethyl-N-(2,3- di(tetradecanoxy)
- PEG-DAG
- the PEG-conjugated lipid is or comprises 2-[(polyethylene glycol)-2000]- N,N-ditetradecylacetamide.
- the pegylated lipid has the following structure:
- the PEG-conjugated lipid (pegylated lipid) is DMG-PEG 2000, e.g., having the following structure:
- the PEG-conjugated lipid (pegylated lipid) has the following structure: wherein n has a mean value ranging from 30 to 60, such as about 50.
- the PEG-conjugated lipid is PEG2000-C-DMA which preferably refers to 3-N-[( ⁇ -methoxy poly(ethylene glycol)2000)carbamoyl]-1,2-dimyristyloxy-propylamine (MPEG-(2 kDa)-C-DMA) or methoxy-polyethylene glycol- 2,3-bis(tetradecyloxy)propylcarbamate (2000).
- RNA compositions/formulations described herein may comprise one or more PEG- conjugated lipids or pegylated lipids as described in WO 2017/075531 and WO 2018/081480, the entire contents of each of which are incorporated herein by reference for the purposes described herein.
- the pegylated lipid comprises from about 1 mol % to about 10 mol %, preferably from about 1 mol % to about 5 mol %, more preferably from about 1 mol % to about 2.5 mol % of the total lipid present in the RNA compositions/formulations and RNA particles described herein.
- LNPs Lipid nanoparticles
- the RNA of the invention is present in the form of lipid nanoparticles (LNPs).
- LNPs typically comprise four components: cationically ionizable lipid, neutral lipids such as phospholipids, a steroid such as cholesterol, and a polymer-conjugated lipid such as PEG-lipid.
- LNPs may be prepared by mixing lipids dissolved in ethanol with RNA in an aqueous buffer.
- the LNP comprises from 35 to 65 mol percent, 40 to 60 mol percent, 40 to 55 mol percent, from 45 to 55 mol percent, or from 45 to 50 mol percent of the cationically ionizable lipid.
- the neutral lipid is present in a concentration ranging from 5 to 15 mol percent, from 7 to 13 mol percent, or from 9 to 11 mol percent.
- the steroid is present in a concentration ranging from 30 to 50 mol percent, from 30 to 45 mol percent, from 35 to 45 mol percent or from 35 to 43 mol percent.
- the LNP comprises from 1 to 10 mol percent, from 1 to 5 mol percent, or from 1 to 2.5 mol percent of the polymer-conjugated lipid.
- the LNP comprises from 45 to 55 mol percent of a cationically ionizable lipid; from 5 to 15 mol percent of a neutral lipid; from 30 to 45 mol percent of a steroid; from 1 to 5 mol percent of a polymer- conjugated lipid; and the RNA, encapsulated within or associated with the lipid nanoparticle.
- the mol percent is determined based on total mol of lipid present in the lipid nanoparticle. In some embodiments, the mol percent is determined based on total mol of cationically ionizable lipid, neutral lipid, steroid and polymer-conjugated lipid present in the lipid nanoparticle.
- the neutral lipid is selected from the group consisting of DSPC, DPPC, DMPC, DOPC, POPC, DOPE, DOPG, DPPG, POPE, DPPE, DMPE, DSPE, and SM. In some embodiments, the neutral lipid is selected from the group consisting of DSPC, DPPC, DMPC, DOPC, POPC, DOPE and SM. In some embodiments, the neutral lipid is DSPC. In some embodiments, the steroid is cholesterol. In some embodiments, the polymer conjugated lipid is a pegylated lipid, e.g., a pegylated lipid as described above.
- the cationically ionizable lipid component of the LNPs is selected from the group consisting of 3D-P-DMA, ALC-0366 and ALC-0315.
- RNA described herein is formulated in an LNP composition comprising 3D-P-DMA, a neutral lipid, a steroid, and a pegylated lipid.
- RNA described herein is formulated in an LNP composition comprising ALC-0366, a neutral lipid, a steroid, and a pegylated lipid.
- RNA described herein is formulated in an LNP composition comprising ALC-0315, a neutral lipid, a steroid, and a pegylated lipid.
- the neutral lipid is DSPC.
- the steroid is cholesterol.
- the pegylated lipid is DMG-PEG 2000, PEG2000-C-DMA, or ALC-0159.
- RNA described herein is formulated in an LNP composition comprising 3D-P-DMA, DSPC, cholesterol, and PEG2000-C-DMA.
- RNA described herein is formulated in an LNP composition comprising ALC-0366, DSPC, cholesterol, and ALC-0159. In some embodiments, RNA described herein is formulated in an LNP composition comprising ALC-0315, DSPC, cholesterol, and ALC-0159.
- 3D-P-DMA (6Z,16Z)-12-((Z)-dec-4-en-1-yl)docosa-6,16-dien-11-yl 5-(dimethylamino)pentanoate
- ALC-0366 ((3-hydroxypropyl)azanediyl)bis(nonane-9,1-diyl) bis(2-butyloctanoate)
- ALC-0315 ((4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis(2-hexyldecanoate) 6-[N-6-(2- hexyldecanoyloxy)hexyl-N-(4-hydroxybutyl)amino]hexyl 2-hexyldecanoate
- PEG2000-C-DMA 3-N-[( ⁇ -Methoxy poly(ethylene glycol)2000) carbamoyl]-1,2-dimyristyl
- ALC-0159 2-[(polyethylene glycol)-2000]-N,N-ditetradecylacetamide / 2-[2-( ⁇ -methoxy (polyethyleneglycol2000) ethoxy]-N,N-ditetradecylacetamide
- DSPC 1,2-Distearoyl-sn-glycero-3-phosphocholine
- the N/P value is preferably at least about 4. In some embodiments, the N/P value ranges from 4 to 20, 4 to 12, 4 to 10, 4 to 8, or 5 to 7. In some embodiments, the N/P value is about 6.
- dose refers to a "dose amount" which relates to the amount of RNA administered per administration, i.e., per dosing.
- administration of RNA of the present disclosure may be performed by single administration or boosted by multiple administrations.
- an amount the RNA described herein from 0.1 ⁇ g to 300 ⁇ g, 0.5 ⁇ g to 200 ⁇ g, or 1 ⁇ g to 100 ⁇ g, such as about 1 ⁇ g, about 3 ⁇ g, about 10 ⁇ g, about 30 ⁇ g, about 50 ⁇ g, or about 100 ⁇ g may be administered per dose.
- a regimen described herein includes at least one dose.
- a regimen includes a first dose and at least one subsequent dose. In some embodiments, a regimen includes a first dose and two subsequent doses. In some embodiments, the first dose is the same amount as at least one subsequent dose. In some embodiments, the first dose is the same amount as all subsequent doses. In some embodiments, the first dose is a different amount as at least one subsequent dose. In some embodiments, the first dose is a different amount than all subsequent doses. In some embodiments, a regimen comprises two doses. In some embodiments, a regimen consists of two doses. In some embodiments, a regimen comprises three doses. In some embodiments, a regimen consists of three doses. In one embodiment, the disclosure envisions administration of a single dose.
- the disclosure envisions administration of at least two consecutive doses.
- Routes of administration of pharmaceutical compositions comprising an RNA of the invention may be administered intravenously, intraarterially, subcutaneously, intradermally, dermally, intranodally, intramuscularly, intratumorally, or peritumorally.
- the pharmaceutical compositions described herein may be administered intramuscularly.
- the pharmaceutical composition comprising an RNA of the invention is formulated for local administration or systemic administration. Systemic administration may include enteral administration, which involves absorption through the gastrointestinal tract, or parenteral administration.
- parenteral administration refers to the administration in any manner other than through the gastrointestinal tract, such as by intravenous injection.
- the pharmaceutical compositions are formulated for systemic administration.
- the systemic administration is by intravenous administration.
- the pharmaceutical compositions are formulated for intrmuscular administration.
- viral vectors Furthermore, the nucleic acid, plasmid or RNA construct of the invention may be contained in a viral vector. Suitable viral vectors that may be employed in context of the present invention include, inter alia, an adeno-associated virus (AAV) vector, a lentiviral vector, an Adenoviral vector, a Herpes-Simplex Virus vector, and a VSV vector.
- AAV adeno-associated virus
- the invention relates, in some embodiments, to a viral vector comprising the nucleic acid of the invention, as described herein.
- Host cells Furthermore, the nucleic acid of the invention, the RNA construct of the invention, the plasmid of the invention and/or the viral vector of the invention may be contained in a cell, in particular a host cell, e.g. a bacterial cell or a eukaryotic cell.
- a host cell e.g. a bacterial cell or a eukaryotic cell.
- the invention relates, in some embodiments, to a cell comprising the nucleic acid of the invention, as described herein.
- Said cell may be a bacterial cell or a eukaryotic cell.
- said cell is a yeast cell such as Pichia pastoris cell, or a mammalian cell, more preferably a human cell.
- Pichia pastoris also refers to Komagataella phaffii.
- Pharmaceutical compositions and medical uses of the peptidoglycan hydrolase of the invention Preferably herein and in context of the present invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention, the RNA construct of the invention, the plasmid of the invention, the viral vector of the invention and/or the cell (e.g. host cell) of the invention is contained in a pharmaceutical composition.
- the present invention further relates, in some aspects, to a pharmaceutical composition comprising the peptidoglycan hydrolase of the invention.
- the present invention relates, in some aspects, to a pharmaceutical composition comprising the nucleic acid of the invention.
- said nucleic acid encodes a peptidoglycan hydrolase of the invention, as described herein.
- said nucleic acid is an RNA of the invention or a RNA construct of the invention, as described herein.
- the pharmaceutical composition comprising a RNA of the invention or a RNA construct of the invention further details and embodiments are described herein above in context of the RNA.
- the pharmaceutical composition of the invention comprises, at least, one pharmaceutically acceptable excipient.
- the term "pharmaceutical composition” relates to a composition comprising a therapeutically effective agent (e.g the peptidoglycan hydrolase of the invention or the nucleic acid of the invention), preferably together with pharmaceutically acceptable excipients such as carriers, diluents or stabilizing agents.
- a therapeutically effective agent e.g the peptidoglycan hydrolase of the invention or the nucleic acid of the invention
- pharmaceutically acceptable excipients such as carriers, diluents or stabilizing agents.
- Said pharmaceutical composition is useful for treating, preventing, or reducing the severity of a disease by administration of said pharmaceutical composition to a subject.
- compositions of the present disclosure may be in a storable form (e.g., in a frozen or lyophilized/freeze-dried form) or in a "ready-to-use form" (i.e., in a form which can be immediately administered to a subject, e.g., without any processing such as diluting).
- a storable form of a pharmaceutical composition prior to administration of a storable form of a pharmaceutical composition, this storable form has to be processed or transferred into a ready-to-use or administrable form.
- a frozen pharmaceutical composition has to be thawed, or a freeze-dried pharmaceutical composition has to be reconstituted, e.g.
- compositions according to the present disclosure are generally applied in a "pharmaceutically effective amount" and in "a pharmaceutically acceptable preparation".
- pharmaceutically acceptable refers to the non-toxicity of a material which does not interact with the action of the active component of the pharmaceutical composition.
- pharmaceutically effective amount refers to the amount which achieves a desired reaction or a desired effect alone or together with further doses. In some embodiments relating to the treatment of a particular disease, the desired reaction may relate to inhibition of the course of the disease.
- the desired reaction in a treatment of a disease may also be delay of the onset or a prevention of the onset of said disease or said condition.
- An effective amount of the pharmaceutical compositions described herein will depend on the condition to be treated, the severeness of the disease, the individual parameters of the patient, including age, physiological condition, size and weight, the duration of treatment, the type of an accompanying therapy (if present), the specific route of administration and similar factors. Accordingly, the doses administered of the pharmaceutical compositions described herein may depend on various of such parameters.
- RNA RNA-containing RNA
- suitable doses are further described herein above in context of the RNA.
- the pharmaceutical compositions of the present disclosure may contain buffers, preservatives, and optionally other therapeutic agents.
- the pharmaceutical compositions of the present disclosure comprise one or more pharmaceutically acceptable excipients such as carriers or diluents.
- Suitable preservatives for use in the pharmaceutical compositions of the present disclosure include, without limitation, benzalkonium chloride, chlorobutanol, paraben and thimerosal.
- excipient refers to a substance which may be present in a pharmaceutical composition of the present disclosure but is not an active ingredient.
- excipients include without limitation, carriers, binders, diluents, lubricants, thickeners, surface active agents, preservatives, stabilizers, emulsifiers, buffers, flavoring agents, or colorants.
- diluent relates a diluting and/or thinning agent.
- the term “diluent” includes any one or more of fluid, liquid or solid suspension and/or mixing media. Examples of suitable diluents include ethanol, glycerol and water.
- carrier refers to a component which may be natural, synthetic, organic, inorganic in which the active component is combined in order to facilitate, enhance or enable administration of the pharmaceutical composition.
- a carrier as used herein may be one or more compatible solid or liquid fillers, diluents or encapsulating substances, which are suitable for administration to subject.
- Suitable carrier include, without limitation, sterile water, Ringer, Ringer lactate, sterile sodium chloride solution, isotonic saline, polyalkylene glycols, hydrogenated naphthalenes and, in particular, biocompatible lactide polymers, lactide/glycolide copolymers or polyoxyethylene/polyoxy- propylene copolymers.
- the pharmaceutical composition of the present disclosure includes isotonic saline.
- Pharmaceutically acceptable excipients for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R Gennaro edit. 1985).
- Pharmaceutical excipients, e.g., carriers or diluents can be selected with regard to the intended route of administration and standard pharmaceutical practice.
- the pharmaceutical compositions described herein may be administered intravenously, intraarterially, subcutaneously, intradermally, dermally, intranodally, or intramuscularly.
- the pharmaceutical composition is formulated for local administration or systemic administration.
- Systemic administration may include enteral administration, which involves absorption through the gastrointestinal tract, or parenteral administration.
- parenteral administration refers to the administration in any manner other than through the gastrointestinal tract, such as by intravenous injection.
- the pharmaceutical compositions are formulated for systemic administration.
- the systemic administration is by intravenous administration.
- the pharmaceutical compositions are formulated for respiratory/pulmonary administration route and/or administered by respiratory/pulmonary administration route, e.g., by inhalation.
- the peptidoglycan hydrolase or nucleic acid (e.g. RNA) described herein may be locally/regionally or systemically delivered to lungs and/or the respiratory tract.
- the lungs may also be used as a portal of entry to the body, enabling delivery of the RNA via the airways into the bloodstream.
- inhaled formulations may be used for systemic delivery.
- the pharmaceutical composition may be formulated, for example, inter alia, as a solution, a suspension, an ointment, a pill such as a tablet or a capsule, a powder, a gel, a foam, a spray, an aerosol, or a suppository.
- the pharmaceutical composition of the invention is, in particular, used for treating a disease, i.e., a disease in a subject, as described herein.
- treatment further refers to clinical intervention in an attempt to alter the natural course of the individual being treated.
- Desirable effects of treatment include, but are not limited to, prophylaxis, preventing occurrence or recurrence of disease or symptoms associated with disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, improved prognosis and cure.
- the subject e.g. a subject to be treated, a subject having a disease or a subject suspected of having a disease, preferably, a mammal, more preferably a human.
- a mammal as used herein and in context of the present invention or grammatical versions thereof such as “mammalian” (e.g. mammalian cells), may refer, to any mammalian species including (but not limited to) humans, livestock such as cows, pets such as dogs, sports animals such as horses, endangered animals or zoo animals such as tigers, or laboratory animals such as mice.
- a mammal may be, inter alia, a human, a cow (e.g.
- the peptidoglycan hydrolase of the invention has, preferably, the ability of being efficiently secreted from a cell of the mammal that is treated.
- the pharmaceutical composition of the invention is used for treating a disease caused by and/or associated with a Staphylococcus infection and/or a subject that has or is suspected of having a Staphylococcus infection.
- the pharmaceutical composition of the invention is used for treating a disease caused by and/or associated with a Staphylococcus aureus infection and/or a subject that has or is suspected of having a Staphylococcus aureus infection.
- the peptidoglycan hydrolase of the invention is, preferably, used for treating a disease caused by and/or associated with a Staphylococcus (preferably, S. aureus) infection and/or a subject that has or is suspected of having a Staphylococcus (preferably, S. aureus) infection.
- RNA or RNA construct of the invention is, preferably, used for treating a disease caused by and/or associated with a Staphylococcus (preferably, S.
- a Staphylococcus aureus infection may be an infection of a skin, soft tissue, bone, lung, sinus and/or urinary tract.
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention may be used for treating a bacterial disease, i.e., a disease that is associated with and/or caused by a bacterial infection, preferably an infection with a Staphylococcus species or strain such as Staphylococcus aureus (S.
- the bacterial infection may be an infection with a coagulate-negative Staphylococcus species or strain such as S. epidermidis.
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention may be used for treating a disease selected from the group consisting of: pneumonia, meningitis, osteomyelitis, endocarditis, toxic shock syndrome, bacteremia, sepsis, a respiratory infection such as sinusitis, pimples, impetigo, boils, cellulitis, folliculitis, carbuncles, scalded skin syndrome, abscesses, food poisoning, necrotizing fasciitis, pyomyositis, mediastinitis, infected dermatitis, wound infection, diabetic foot ulcer, septic arthritis, osteoarticular infections, prosthetic infection such as infection of a prosthetic joint or a cardiac device, and urinary tract infections.
- a disease selected from the group consisting of: pneumonia, meningitis, osteomyelitis, endocarditis, toxic shock syndrome, bacteremia, sepsis, a respiratory infection such as sinus
- said disease is caused by and/or associated with an infection with a Staphylococcus species or strain (preferably S. aureus), as described herein.
- a Staphylococcus species or strain preferably S. aureus
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention is used for treating pneumonia, bacteremia, endocarditis, and/or a prosthetic infection.
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention is particularly useful for treating a bacterial biofilm or free-floating (biofilm-like) aggregate of bacteria; see, e.g., Example 6 and Figure 12.
- a biofilm is defined as an aggregate or aggregate of microorganisms (in particular bacteria) attached to a surface. Adherent bacteria are often surrounded and protected by extracellular polymeric substances produced by Gram- negative and Gram-positive bacteria. Bacteria are more resistant to antibacterials (in particular antibiotics) through biofilms.
- a free-floating aggregate is defined as aggregate of microorganisms (in particular bacteria) that forms (or formed) in suspension, for example, in a synovial fluid during joint infections (e.g., prosthetic joint infections).
- free-floating aggregates are sometimes also denoted as biofilms.
- the properties of free-floating aggregates are similar to an attached biofilm, as they are more resistant to antibiotics and may secrete different virulence factors.
- free-floating aggregates are considered as “biofilm-like” and the same applies to free-floating aggregates as described herein in context of biofilms mutatis mutandis.
- peptidoglycan hydrolases of the invention such as H5 (SEQ ID NO: 11) or G1 (SEQ ID NO: 3) may effectively kill biofilms or free-floating aggregates of S. aureus.
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention (in particular the RNA or RNA construct of the invention) may be used for treating a bacterial disease that is associated with or suspected of forming a biofilm and/or a free-floating aggregate.
- the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, the nucleic acid of the invention is used for treating a disease caused by and/or associated with a Staphylococcus (preferably, S. aureus) infection and/or a subject that has or is suspected of having a Staphylococcus (preferably, S. aureus) infection, wherein said Staphylococcus (preferably Staphylococcus aureus), is present in form of a biofilm and/or a free-floating aggregate or is suspected of forming a biofilm and/or a free-floating aggregate.
- a Staphylococcus preferably, S. aureus
- the biofilm may be present at a site of a Staphylococcus infection, for example, at an endocardium in an endocarditis.
- the free-floating aggregate may be present in a synovial fluid in a joint infection, e.g., a prosthetic joint infection.
- the present invention relates, in some aspects, to a method of treating a disease (e.g. a disease caused by and/or associated with a Staphylococcus infection), as described herein, wherein said method comprises administering an effective amount of the pharmaceutical composition of the invention, the peptidoglycan hydrolase of the invention, or the nucleic acid of the invention (in particular the RNA or RNA construct of the invention) to a subject in need.
- the peptidoglycan hydrolase of the invention may be used for sterilizing a device, preferably a medical device such as a catheter, a pacemaker or a prosthetic joint, in vitro or in vivo.
- the peptidoglycan hydrolase may be used to kill or eliminate one or more Staphylococcus species or strains, e.g., S. aureus, on and/or in such a device. Further reference in this respect is made to Choi (2021), Front Microbiol. 12.
- Solidified yeast culture media As described herein and as illustrated in the appended Examples, the inventors found solidified yeast culture media dead target bacteria, e.g. dead S. aureus cells, which can be advantageously used for screening yeast cells for the secretion of an active peptidoglycan hydrolase, i.e., for identifying peptidoglycan hydrolases with a good killing activity against target bacteria, e.g., S. aureus.
- the present invention relates further, in some aspects, to a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles.
- said substrate particles comprise or essentially consist of dead bacterial cells, as described herein.
- said substrate particles have a size which renders the medium turbid, at least when they are used at a suitable concentration as described herein.
- the solidified yeast culture medium of the invention is, preferably, turbid.
- the solidified yeast culture medium of the invention contains dead bacterial cells at an optical density at 620 nm (OD620) of about 1 to 10, preferably about 2 to 4.
- the solidified yeast culture medium of the invention is particularly useful for screening yeast cells for the secretion of an active peptidoglycan hydrolase, and thus is, preferably, used in such a method.
- said culture medium comprises agar, preferably at a concentration of about 0.5% to about 5%, more preferably at a concentration of about 1% to about 2%, e.g., at a concentration of about 1.5%, in particular wherein the % is % weight by volume (w/v).
- the opacity of the solidified medium is reduced at a location where the substrate particles are lysed or broke down (e.g. because of the secretion of an active peptidoglycan hydrolase from a yeast colony cultured on said solidified yeast culture medium).
- the yeast may be, for example, Pichia pastoris or Saccharomyces (e.g., Saccharomyces cerevisiae).
- Saccharomyces e.g., Saccharomyces cerevisiae
- the yeast is Pichia pastoris.
- the dead bacterial cells are, preferably, dead gram-positive bacterial cells and/or the peptidoglycan in the peptidoglycan particles is, preferably, from gram-positive bacteria.
- the dead bacterial cells are, preferably, autoclaved bacterial cells.
- the dead bacterial cells are, preferably, dead Staphylococcus cells and/or the peptidoglycan in the peptidoglycan particles is from a Staphylococcus species or strain. More preferably, the dead bacterial cells are dead Staphylococcus aureus cells and/or the peptidoglycan in the peptidoglycan particles is from Staphylococcus aureus.
- the substrate particles comprise or essentially consist of autoclaved Staphylococcus aureus cells.
- the solidified yeast culture medium of the invention may be used for (or be a part of) a yeast culture, as described herein.
- the solidified yeast culture medium of the invention comprises at least one surface for culturing yeast cells on said surface.
- the invention relates to a yeast culture comprising (i) the solidified yeast culture medium of the invention, and (ii) yeast cells (e.g., at least one yeast colony), on the solidified yeast culture medium, i.e., on a surface of said solidified medium.
- a yeast cell or yeast colony that is cultured on the solidified yeast culture medium of the invention or that intended for this purpose, preferably, expresses and/or secretes a peptidoglycan hydrolase, as described herein.
- said peptidoglycan hydrolase is an endolysin, as described herein.
- said peptidoglycan hydrolase e.g. said endolysin
- the peptidoglycan hydrolase may be considered as active when it is able to lyse and/or break down the substrate particles (in particular the peptidoglycan therein) in the solidified yeast culture medium, as described herein. As described herein, and as illustrated in the appended Examples, lysing and/or breaking down the substrate particles renders the solidified yeast culture medium locally translucent or, at least, less opaque.
- Method of screening yeast cells for the secretion of an active peptidoglycan hydrolase i.e., YODA-derived methods.
- yeast on dead aureus (YODA)-derived methods are extremely simple and efficient methods which allows to easily distinguish yeast cells/colonies expressing peptidoglycan hydrolases with a good killing activity against a target bacterium from yeast cells/colonies expressing inactive peptidoglycan hydrolases. Furthermore, YODA-derived methods are very sensitive since the lysins are constantly secreted from the cells.
- the present invention relates, in some aspects, to a YODA-derived method, i.e., a method of screening yeast cells for the secretion of an active peptidoglycan hydrolase, as described herein, said method comprising the steps of: a) providing a solidified yeast culture medium of the invention, i.e., a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles, as described herein; b) culturing yeast cells expressing a peptidoglycan hydrolase on a surface of said solidified medium until at least one yeast colony is detectable, in particular wherein the yeast cells are able to secrete the peptidoglycan hydrolase; c) evaluating whether a halo is apparent around a yeast colony; d) determining that a yeast colony secretes an active peptidoglycan hydrolase when
- a halo corresponds to a locally reduced optical density of the solidified medium around a colony, for example, in a radius of about 0.1 to 1 cm from the colony, especially compared to a region of the solidified medium that is free of yeast colonies.
- an active peptidoglycan hydrolase may be considered to have a killing activity against a live bacterium comprising a peptidoglycan in its cell wall which corresponds to the peptidoglycan comprised in the substrate particles in the solidified yeast culture medium of the invention.
- a peptidoglycan hydrolase secreted from a yeast colony which is able to lyse and/or break down dead Staphylococcus aureus in the solidified yeast culture medium may be considered as an active peptidoglycan hydrolase that has killing activity against live Staphylococcus aureus, as described herein.
- Methods for screening peptidoglycan hydrolases having several improved pharmaceutical properties and directed evolution As described herein and as illustrated in the appended Examples, the inventors found a combinatorial screening method which is based on the YODA-derived method of invention and which allows to simultaneously improve, inter alia, the solubility, bactericidal activity and eukaryotic secretion of peptidoglycan hydrolases, e.g., endolysins such as L0482.
- said method allows to screen for peptidoglycan hydrolase variants which are adapted to the eukaryotic secretory pathway, and, hence, have an improved expression and secretion profile in eukaryotic cells.
- the combinatorial screening method may be advantageously used for directed evolution of peptidoglycan hydrolases, e.g., endolysins, as described herein.
- the invention further relates to a combinatorial screening method, i.e., a method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, said method comprising the steps of: I) preparing a library of eukaryotic cells expressing peptidoglycan hydrolase variants on the cell surface; II) selecting eukaryotic cells based on a high level of peptidoglycan hydrolase on the cell surface relative to other cells in the library; for example, selecting the 10% of cells in the library with the highest peptidoglycan level on the cell surface; III) performing the method of screening yeast cells for the secretion of an active peptidoglycan hydrolase of the invention, wherein yeast cells that are able to secrete the peptidogly
- the eukaryotic cells are, preferably, yeast cells.
- other eukaryotic cells e.g. mammalian cells such as human cells, may be also used.
- the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell comprises, preferably, between said steps II) and III) the steps of: II’) isolating DNA encoding at least one peptidoglycan hydrolase variant from the eukaryotic cells, e.g. the yeast cells, selected in step II); and II’’) introducing the isolated DNA into yeast cells, e.g., by means of transformation.
- step I) of the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell comprises, preferably, comprises (i) fragmenting and reassembling DNA encoding different peptidoglycan hydrolases, preferably endolysins, e.g. endolysin homologues (e.g.
- the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell comprises, preferably, before said step II) a step I’) of attaching a detectable label to the peptidoglycan hydrolase variants on the cell surface.
- said detectable label is a fluorescent dye or a magnetic particle, preferably a fluorescent dye.
- the detectable label is preferably attached by means of immunostaining.
- a labeled antibody preferably a fluorescently labeled antibody
- the peptidoglycan hydrolase variant may comprise a tag to which the antibody binds specifically. Suitable tags, antibodies and labels are well known in the art and any of these may be employed in context of the present invention.
- step II) of the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell preferably, comprises, sorting (i.e.
- FACS fluorescent activated cell sorting
- MACS magnetic activated cell sorting
- the combinatorial screening method of the invention i.e., the inventive method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell
- the inventive method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell can be used for directed evolution, e.g., when it is repeatedly employed.
- at least two (e.g. 2, 3, 4 or 5) rounds of steps I) to IV) of said combinatorial screening method are performed.
- step I) of each subsequent round a further library of eukaryotic cells is prepared, wherein the cells in the library express a different set of peptidoglycan variants compared to the library employed in the preceding round(s).
- step I) of a subsequent round comprises, preferably, (i) fragmenting and reassembling DNA encoding different peptidoglycan hydrolases (in particular “DNA shuffling”), wherein at least one, preferably at least 50%, of said peptidoglycan hydrolases has been identified in a preceding round as an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, thereby generating a further DNA library of peptidoglycan hydrolase variants, and (ii) introducing said further DNA library into eukaryotic cells (e.g.
- yeast cells thereby generating a further library of eukaryotic cells (e.g. yeast cells) expressing a different set of peptidoglycan hydrolase variants compared to the library employed in the preceding round(s).
- eukaryotic cells e.g. yeast cells
- Performing at least two rounds of steps I) to IV) of the method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, as just described, further refers to “directed evolution”, as described herein, and as illustrated in the appended Examples.
- inventive method of screening yeast cells for the secretion of an active peptidoglycan hydrolase may further comprise a step of obtaining from a yeast colony an active peptidoglycan hydrolase or a nucleic acid encoding an active peptidoglycan hydrolase, as described herein.
- the inventive method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell may further comprise a step of obtaining from a yeast colony an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell or a nucleic acid encoding an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, as described herein.
- the present invention further relates, in some aspects, to a peptidoglycan hydrolase or peptidoglycan hydrolase variant that is obtained or obtainable by a method of the invention.
- the present invention further relates, in some aspects, to a nucleic acid encoding a peptidoglycan hydrolase or peptidoglycan hydrolase variant of the invention, wherein said nucleic acid and/or said peptidoglycan hydrolase or peptidoglycan hydrolase variant is obtained or obtainable by a method of the invention.
- any peptidoglycan hydrolase of the invention may be obtainable by a method of the invention, as described herein.
- any nucleic acid of the invention may be obtainable by a method of the invention, as described herein. Items according to the invention The present invention further relates to the following items: 1.
- a peptidoglycan hydrolase having bactericidal activity wherein the peptidoglycan hydrolase comprises a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain that has (i) a sequence identity of at least 60% to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1; and that has (ii) one or more amino acid substitutions as compared to the amino acid sequence from position 72 to position 215 in SEQ ID NO: 1.
- CHAP histidine-dependent amidohydrolase/peptidase
- a corresponding segment of said CHAP domain has a sequency identity of at least 80%, preferably at least 90%, to the sequence from position 87 to position 128 in SEQ ID NO: 1, and/or (ii) said CHAP domain has at most six, five, four, three or two, preferably at most one, more preferably no amino acid substitutions or deletions at positions 80, 87, 88, 98, 99, 103, 106, 110, 114, 122, 126, 128, 137, 182, 202, and 208 of SEQ ID NO: 1 or at positions corresponding to these positions. 4.
- the peptidoglycan hydrolase of item 4 wherein the residue at position 73 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than phenylalanine or lysine; and, preferably, wherein said peptidoglycan hydrolase does not have a sequence as shown in any one of SEQ ID NO: 276 to 278.
- the peptidoglycan hydrolase of item 9 wherein the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than threonine or serine.
- the peptidoglycan hydrolase of item 9 or 10 wherein the residue at position 68 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, methionine, arginine or alanine.
- amino acid residue at position 214 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine or threonine, and/or the amino acid residue at position 215 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, valine or serine.
- amino acid residue at position 214 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamine or threonine, and/or the amino acid residue at position 215 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glycine, valine or serine.
- the peptidoglycan hydrolase of item 25 wherein the amino acid residue at position 86 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with another amino acid residue than serine.
- the peptidoglycan hydrolase of item 32 wherein the amino acid residue at position 155 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tyrosine.
- the peptidoglycan hydrolase of any one of items 1 to 35 which has a sequence identity of at least 96% to the sequence of SEQ ID NO: 11.
- the peptidoglycan hydrolase of item 35 or 36, wherein said CHAP domain has one or more amino acid substitutions or substitution pairs as compared to the sequence from position 72 to position 215 in SEQ ID NO: 1, as defined in any one of items 22, 24, 29, 31 and 34.
- the peptidoglycan hydrolase of any one of items 1 to 37 which is an endolysin.
- the peptidoglycan hydrolase of any one of items 1 to 38 further comprising a cell wall binding domain, preferably a LYSM domain or a SH3 domain, more preferably a LYSM domain.
- the peptidoglycan hydrolase of item 39 wherein the cell wall binding domain is derived from an endolysin, preferably an endolysin comprising a LYSM domain or a SH3 domain, more preferably an endolysin comprising a LYSM domain and a CHAP domain, wherein the LYSM domain is, preferably, N-terminally of the CHAP domain.
- the peptidoglycan hydrolase of item 44 wherein the amino acid residue at position 1 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with tryptophan, the amino acid residue at position 8 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with asparagine, the amino acid residue at position 10 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with valine, the amino acid residue at position 13 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid, the amino acid residue at position 23 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with arginine, the amino acid residue at position 24 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with cysteine, the amino acid residue at position 25 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with glutamic acid, the amino acid residue at position 30 in SEQ ID NO
- the peptidoglycan hydrolase of any one of items 39 to 46 further comprising a peptide linker between said CHAP domain and said cell wall binding domain.
- the peptidoglycan hydrolase of item 48, wherein the glycine-serine linker comprises one or multiple, e.g., 2 to 5, copies of the sequence as shown in SEQ ID NO: 297, and wherein said copies are, preferably, directly adjacent to each other.
- the peptidoglycan hydrolase of item 47 wherein the peptide linker is derived from an endolysin.
- the peptidoglycan hydrolase of item 50 wherein the peptide linker is derived from an endolysin that has a killing activity against a Staphylococcus species or strain, preferably Staphylococcus aureus.
- the peptidoglycan hydrolase of item 52 wherein the peptide linker has one or more amino acid substitutions at positions 53, 55, 56, 58, 63, 65 and 68 in SEQ ID NO: 1 or at positions corresponding to these positions.
- the peptidoglycan hydrolase of item 53 wherein the amino acid residue at position 53 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, the amino acid residue at position 55 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with histidine, the amino acid residue at position 56 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with serine, the amino acid residue at position 58 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with lysine, the amino acid residue at position 63 in SEQ ID NO: 1 or at a position corresponding to this position is substituted with threonine, the amino acid residue at position 65 in SEQ
- the peptidoglycan hydrolase of any one of items 52 to 54 wherein the peptide linker has an amino acid substitution at position 68 in SEQ ID NO: 1 or at a position corresponding to this position, and wherein the amino acid residue at said position is substituted with lysine, methionine, arginine or alanine, preferably lysine.
- the peptidoglycan hydrolase of any one of items 1 to 55 wherein said bactericidal activity is a killing activity against a Staphylococcus species or strain.
- the peptidoglycan hydrolase of any one of items 1 to 57 wherein the peptidoglycan hydrolase is able to growth-inhibit a Staphylococcus aureus liquid culture at a concentration of about 40 ⁇ g/ml or less, about 20 ⁇ g/ml or less or about 10 ⁇ g/ml or less, preferably at a concentration of about 4 ⁇ g/ml or less, more preferably at a concentration of about 2 ⁇ g/ml or less.
- Staphylococcus aureus is a methicillin-resistant Staphylococcus aureus (MRSA) strain, a vancomycin- intermediate Staphylococcus aureus (VISA) strain, a vancomycin-resistant Staphylococcus aureus (VRSA) strain, a daptomycin-resistant Staphylococcus aureus (DRSA) strain or a linezolid-resistant Staphylococcus aureus (LRSA) strain.
- MRSA methicillin-resistant Staphylococcus aureus
- VISA vancomycin- intermediate Staphylococcus aureus
- VRSA vancomycin-resistant Staphylococcus aureus
- DRSA daptomycin-resistant Staphylococcus aureus
- LRSA linezolid-resistant Staphylococcus aureus
- the peptidoglycan hydrolase of any one of items 1 to 59 which has the ability to lyse the cell wall of a Staphylococcus species or strain, preferably Staphylococcus aureus; in particular wherein said protein has the ability to break down or cleave peptidoglycan in the cell wall of Staphylococcus aureus.
- the peptidoglycan hydrolase of any one of items 1 to 60 which has the ability of being secreted from a eukaryotic cell when expressed in said cell, for example a yeast cell or a mammalian cell, preferably a human cell.
- the peptidoglycan hydrolase of any one of items 1 to 61 which is stable up to a temperature of about 40°C, e.g.37°C, 38°C, 39°C, 40°C, 41°C or 42°C, preferably about 42°C, more preferably about 44°C or about 47°C, as determined by a thermofluor assay.
- the peptidoglycan hydrolase of any one of items 1 to 62 which has, compared to the peptidoglycan hydrolase of SEQ ID NO: 1, (i) a similar or enhanced bactericidal activity, preferably a similar or enhanced killing activity against Staphylococcus aureus, (ii) a similar or enhanced ability of being secreted by a eukaryotic cell, preferably in a yeast cell or a human cell, e.g., a HEK293 cell, (iii) a similar or enhanced solubility in an aqueous solution such as PBS, (iv) a similar or enhanced stability, preferably an enhanced thermostability, and/or (v) a similar or reduced tendency to form aggregates in an aqueous solution such as PBS.
- a similar or enhanced bactericidal activity preferably a similar or enhanced killing activity against Staphylococcus aureus
- the peptidoglycan hydrolase of any one of items 1 to 63 which has, compared to the peptidoglycan hydrolase of SEQ ID NO: 1 an enhanced killing activity against Staphylococcus aureus, an enhanced ability of being secreted by a human cell, and/or an enhanced thermostability.
- the peptidoglycan hydrolase of any one of items 63 to 65 wherein the ability of a peptidoglycan hydrolase of being secreted by a human cell is measured by determining the amount of the peptidoglycan hydrolase in the supernatant of HEK293 cells expressing the peptidoglycan hydrolase.
- the peptidoglycan hydrolase of any one of items 1 to 67 further comprising a signal peptide, preferably a signal peptide that is able to direct the peptidoglycan hydrolase to a secretory pathway in a mammalian cell, preferably a co-translational translocation pathway; preferably, wherein said signal peptide is cleaved off during secretion or export from the cell; and, preferably, wherein said signal peptide is at the N- terminus.
- PK pharmacokinetic
- a C-terminal peptide of human chorionic gonadotropin e.g. as shown in SEQ ID NO: 295
- human lysozyme e.g. as shown in SEQ ID NO: 296
- said PK peptide is positioned at the C- or N-terminus of said CHAP domain, said cell wall binding domain, or said peptidoglycan hydrolase, and preferably C-terminally of any signal peptide; and, preferably, wherein the peptidoglycan hydrolase comprises between said PK peptide and said CHAP domain or said cell wall binding domain a peptide linker such as a glycine-serine linker, preferably a glycine-serine linker as defined in item 49.
- a peptide linker such as a glycine-serine linker, preferably a glycine-serine linker as defined in item 49.
- id nucleic acid is a RNA.
- id RNA is a mRNA.
- id mRNA is nucleoside-modified.
- id mRNA comprises (i) a modified nucleoside selected from pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ), and 5- methyl-uridine (m5U), preferably N1-methyl-pseudouridine (m1 ⁇ ), in place of uridine, preferably in place of each uridine; (ii) a cap05’ cap, for example, m 2 7,2'O G(5’)ppSp(5')G; or a cap15’ cap, for example, m2 7,3’-O Gppp(m1 2’-O )ApG (iii) a 5’ UTR and/or a 3’ UTR, and/or (iv) a poly-A sequence comprising, preferably, at least 100 nucleotides.
- a cap05’ cap for example, m 2 7,2'O G(5’)ppSp(5')G
- a cap15’ cap for example, m2 7,
- nucleic acid of any one of items 75 to 79 which is an engineered nucleic acid, preferably an engineered RNA.
- the nucleic acid of any one of items 75 to 80 which is an isolated nucleic acid, preferably an isolated RNA.
- nucleic acid of any one of items 75 to 81 which is codon-optimized for protein expression in cells of a certain mammalian species, preferably a human.
- RNA construct comprising in 5' to 3' order: (i) a 5' UTR that, preferably, comprises or consists of a modified human alpha-globin 5'-UTR; (ii) a sequence encoding a peptidoglycan hydrolase of any one of items 1 to 74; (iii) a 3' UTR that, preferably, comprises or consists of a first sequence from the amino terminal enhancer of split (AES) messenger RNA and a second sequence from the mitochondrial encoded 12S ribosomal RNA; and (iv) a poly-A sequence, comprising preferably at least about 100 nucleotides.
- AES amino terminal enhancer of split
- the RNA construct of item 83 wherein the 5' UTR comprises or consists of a sequence according to SEQ ID NO: 371.
- the RNA construct of item 86, wherein the split polyA tail sequence comprises or consists of a sequence according to SEQ ID NO: 375.
- RNA construct of any one of items 83 to 88 wherein the RNA is mRNA and wherein, optionally, the mRNA comprises modified nucleosides selected from pseudouridine ( ⁇ ), N1-methyl-pseudouridine (m1 ⁇ ), and 5-methyl-uridine (m5U), preferably N1-methyl-pseudouridine (m1 ⁇ ), in place of uridine, preferably in place of each uridine.
- LNP lipid nanoparticle
- LPX lipoplex
- nucleic acid of any one of items 75 and 80 to 82 wherein said nucleic acid is a DNA.
- a plasmid comprising the nucleic acid of item 91.
- a viral vector comprising the nucleic acid of any one of items 75 to 82, 90 and 91, the RNA construct of any one of items 83 to 90 or the plasmid of item 92.
- a cell comprising the nucleic acid of any one of items 75 to 82, 90 and 91, the RNA construct of any one of items 83 to 90, the plasmid of item 92 or the viral vector of item 93.
- the cell of item 94 wherein said cell is a bacterial cell or a eukaryotic cell.
- the cell of item 94 or 95 wherein said cell is a yeast cell such as Pichia pastoris or a mammalian cell, preferably a human cell.
- a pharmaceutical composition comprising the peptidoglycan hydrolase of any one of items 1 to 74, the nucleic acid of any one of items 75 to 82, 90 and 91, the RNA construct of any one of items 83 to 90, the plasmid of item 92, the viral vector of item 93 and/or the cell of any one of items 94 to 96; and, preferably, a pharmaceutically acceptable excipient.
- a pharmaceutical composition comprising the peptidoglycan hydrolase of any one of items 1 to 74.
- a pharmaceutical composition comprising the RNA of any one of items 76 to 82 and 90 or the RNA construct of any one of items 83 to 90.
- the peptidoglycan hydrolase of any one of items 1 to 74 for use in treating a disease caused by and/or associated with a Staphylococcus aureus infection and/or a subject that has or is suspected of having a Staphylococcus aureus infection.
- RNA of any one of items 76 to 82 and 90 or the RNA construct of any one of items 83 to 90 for use in treating a disease caused by and/or associated with a Staphylococcus aureus infection and/or a subject that has or is suspected of having a Staphylococcus aureus infection The pharmaceutical composition for use according to item 100, the peptidoglycan hydrolase for use according to item 101, or the RNA or RNA construct for use according to item 102, wherein said Staphylococcus aureus infection is an infection of a skin, soft tissue, bone, lung, sinus and/or urinary tract.
- a respiratory infection such as sinusitis, pimples, impetigo, boils, cellulitis, folliculitis
- Staphylococcus preferably Staphylococcus aureus
- a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles.
- the solidified yeast culture medium of item 106 containing dead bacterial cells at an optical density at 620 nm (OD620) of about 1 to 10, preferably about 2 to 4.
- a yeast culture comprising (i) the solidified yeast culture medium of item 106 or 107, and (ii) yeast cells, e.g., at least one yeast colony, on the solidified yeast culture medium.
- a method of screening yeast cells for the secretion of an active peptidoglycan hydrolase comprising the steps of: a) providing a solidified yeast culture medium comprising substrate particles intermixed with said medium, wherein said substrate particles comprise dead bacterial cells and/or fragments thereof, and/or peptidoglycan particles, preferably as defined in item 107; b) culturing yeast cells expressing a peptidoglycan hydrolase on a surface of said solidified medium until at least one yeast colony is detectable, in particular wherein the yeast cells are able to secrete the peptidoglycan hydrolase; c) evaluating whether a halo is apparent around a yeast colony, in particular wherein the halo corresponds to a locally reduced optical density of said solidified medium around said colony, for example, in a radius of about 0.1 to 1 cm from the colony, especially compared to a region of the solidified medium that is free of yeast colonies; d) determining that a yeast colony secretes an
- a method of identifying an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell comprising the steps of: I) preparing a library of eukaryotic cells, preferably yeast cells, expressing peptidoglycan hydrolase variants on the cell surface; II) selecting eukaryotic cells, e.g.
- yeast cells based on a high level of peptidoglycan hydrolase on the cell surface relative to other cells in the library; for example, selecting the 10% of cells in the library with the highest peptidoglycan level on the cell surface; III) performing the method of screening yeast cells for the secretion of an active peptidoglycan hydrolase as defined in item 110, wherein yeast cells that are able to secrete the peptidoglycan hydrolase variants expressed in the eukaryotic cells, e.g.
- the yeast cells, selected in step II) are cultured in step b) of said method; and IV) determining that a yeast colony that has been determined in said step d) to secrete an active peptidoglycan hydrolase produces an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell.
- the method of item 111 further comprising between said steps II) and III) the steps of: II’) isolating DNA encoding at least one peptidoglycan hydrolase variant from the eukaryotic cells, e.g.
- step II comprises (i) fragmenting and reassembling DNA encoding different peptidoglycan hydrolases, preferably endolysins, e.g. endolysin homologues, thereby generating a DNA library of peptidoglycan hydrolase variants, and (ii) introducing said DNA library into eukaryotic cells, e.g.
- a detectable label to the peptidoglycan hydrolase variants on the cell surface, preferably a fluorescent dye, e.g., by means of immunostaining.
- cells with a high level of peptidoglycan hydrolase on the cell surface relative to other cells in the library are sorted from these other cells, e.g., by means of fluorescent activated cell sorting or magnetic activated cell sorting.
- step I) of each subsequent round a further library of eukaryotic cells is prepared, wherein the cells in the library express a different set of peptidoglycan variants compared to the library employed in the preceding round(s).
- step I) of a subsequent round comprises (i) fragmenting and reassembling DNA encoding different peptidoglycan hydrolases, wherein at least one, preferably at least 50%, of said peptidoglycan hydrolases has been identified in a preceding round as an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, thereby generating a further DNA library of peptidoglycan hydrolase variants, and (ii) introducing said further DNA library into eukaryotic cells or yeast cells, thereby generating a further library of eukaryotic cells or yeast cells expressing a different set of peptidoglycan hydrolase variants compared to the library employed in the preceding round(s).
- any one of items 110 to 127 further comprising a step of obtaining from a yeast colony an active peptidoglycan hydrolase or an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell, or a nucleic acid encoding an active peptidoglycan hydrolase or an active peptidoglycan hydrolase variant that is optimized for secretion by a eukaryotic cell.
- the invention is also characterized by the following figures, figure legends and the following non-limiting examples. Brief description of the Figures Figure 1: Lysin domain architectures screened 36 lysins of 13 different domain architectures were screened for killing activity against S. aureus.
- Figure 2 Minimal inhibitory concentrations of L0482 against a panel of Staphylococcus strains 5x10 5 bacteria were incubated with varying concentrations of lysins. MICs are shown in ⁇ g/ml.
- the MICs were determined as the minimal concentrations where regrowth was inhibited by the lysins.
- L0466 i.e. exebacase
- MRSA methicillin-resistant Staphylococcus aureus” strain
- MSSA methicillin- sensitive Staphylococcus aureus” strain
- Bactericidal activity of LysM-CHAP expressed and secreted in P.pastoris Supernatants of P.pastoris cultures expressing different L0482 or L0499 constructs were mixed with lysin buffer at the indicated dilutions and incubated with S.aureus cells. Bacterial growth was monitored by measuring the culture OD over the course of 24 hours.
- YODA allows to overcome issues of expression, solubility and toxicity of lysins in E. coli. Turnaround time: 3-4 days.
- YODA may be modified to contain other dead bacteria for assaying lysin activity against these bacteria (YODB), in particular, Gram-positives such as C. difficile.
- YODA allowed the detection of enzymatic activity of a broad spectrum of lysin families, including some which are not active when expressed in E. coli. Figure 5.
- L0482 contains two consensus sites which are N-glycosylated in the secretory pathway. Glycosylation at these sites strongly reduces the enzymatic activity of L0482 when measured in a growth inhibition assay.
- YODA was used to identify active variants with mutated N-glycosylation motifs.
- C) YODA selected active aglycosylated variants YODA hits were confirmed to be aglycosylated by SDS-PAGE after purification from P.pastoris supernatants.
- mutant L0482-18 with mutations N68K, N73G SEQ ID NO: 2
- mutant L0482-18 with mutations N68K, N73G retained an enzymatic activity in the same range as the wild type L0482 protein (SEQ ID NO: 1) in a growth inhibition assay (8 vs 4 ⁇ g/ml MIC, respectively).
- DNA shuffling generates a highly diverse library of lysin sequences.
- B) The lysin library is cloned as a fusion to the SAG1 cell wall anchor domain and transformed into P.pastoris. ⁇ 10 6 variants are screened for high expression levels by FACS and the top expressing cells are isolated.
- Figure 8. Improvement of L0482ag after two rounds of directed evolution A) Frequencies of selected lysin variants in round 1,2 and 3 of directed evolution.96 (Round 1) or 182 (Round 2 and Round 3) YODA-active P.pastoris clones from the second FACS sort were sequenced after colony PCR. Each lysin sequence was counted and the most frequently observed variants were selected as hits.
- the optical density (OD) at 620 nm of the mixture was measured at 37°C.
- the minimal inhibitory concentration (MIC) was determined as the concentration at which the OD at 620 nm of the culture remained below 0.1 during a 24h time period.
- L0482ag SEQ ID NO: 1
- the hit variants i.e G1-G4 and H1-H10*; SEQ ID NO: 3-16
- displayed 2-16 fold decreased MICs (between 4-0.5 ⁇ g/ml).
- the data point for H3 is missing for technical reasons. It is expected that the MIC of H3 is in the same range as for H1-H10.
- Hits G1-4 (round 1), H1- 10 (round 2) and I1-30 (round 3) are aligned to L0482ag (SEQ ID NO: 2). Amino acid substitutions relative to L0482ag are indicated. These amino acid substitutions are considered as “particularly beneficial amino acid substitutions”, as described herein. Furthermore, the “K” at position 68 and the “G” at position 73 (as also contained in L0482ag) are also considered as “particularly beneficial amino acid substitutions” vis à vis WT L0482 (SEQ ID NO: 1) herein and, furthermore, as preferred “aglycosylation substitutions”.
- the mutation units shown consist of the 5 consensus mutation units as reflected in “H3” and the additional substitution F155Y as in “H5”). The presence of each mutation unit in each hit is indicated with an “X”.
- Figure 10. Expression of ribolysin variants in human cells 5 mg of mRNA were transfected in HEK293T/17 cells and ribolysin variant expression (i.e., expression of a lysin variant from an mRNA construct) was analyzed by Western Blot. A) Protein levels of different ribolysin variants in supernatants (SN) and cell lysates (L). Cell lysates were 22-fold more concentrated than supernatants. B) Quantification of ribolysin protein levels in supernatants. Figure 11.
- L0482 variant H5 showed enhanced killing kinetics against S. aureus as compared to the WT L0482 lysin Data from an OD reduction assay are shown.
- Figure 12. L0482 variants show bactericidal activity against S. aureus biofilms and free-floating aggregates
- Statistical analysis was performed using One-way ANOVA (Dunnett ⁇ s multiple comparisons test), p ⁇ 0.0001; LOD: limit of detection, 500cfu/ml; cfu: colony-forming units.
- Example 1 Selection of the LysM-CHAP architecture as represented by L0482
- a set of 36 endolysins with 13 different domain architectures ( Figure 1) was compiled from literature and BLAST searches, expressed in E. coli, purified and tested in functional assays, such as growth inhibition assays. Briefly, purified lysins were incubated with 5x10 5 staphylococcal (i.e.
- Staphylococcus aureus cells in 96 well plates and outgrowth of the culture was monitored for 24 hours by regularly measuring OD620nm.
- Five endolysins, belonging to three different architectures (CHAP-Ami2-SH3, LysM-CHAP and PepM23-SH3, i.e., “lysostaphin”) were found to be able to inhibit S. aureus outgrowth in said growth inhibition assays. (Figure 1).
- L0482 SEQ ID NO: 1
- L0499 SEQ ID NO: 47
- L0482, L0499 and 11 homologues of this domain architecture were included in the 65 sequences that were tested in the second screening round (the first 36 were also included as a control for the screening procedure).
- L0466 SEQ ID NO: 304
- exebacase which has been used in clinical trials
- Fowler 2020
- J Clin Invest 130(7)
- L0482 is relatively small (25kDa) which is advantageous, inter alia, for engineering.
- the active LysM-CHAP lysins were then expressed in yeast cells, in particular, P.pastoris (see Example 2).
- Example 2 Bactericidal activity of LysM-CHAP lysins secreted from P.pastoris cells
- P.pastoris is a well-established eukaryotic expression system for the high level production of recombinant proteins.
- Proteins in P.pastoris are typically translated, folded and processed by a similar set of factors as in higher eukaryotes, such as human cells.
- expression of proteins containing N-terminal signal sequences results in their targeting to the secretory pathway and secretion into the extracellular space.
- the steps occurring during this process are highly conserved between eukaryotes and involve the translocation of the protein across the membrane of the endoplasmic reticulum (ER), its glycosylation and its trafficking to the plasma membrane.
- ER endoplasmic reticulum
- lysins are able to pass through the secretory pathway in an active state in those cells. Since the majority of lysins are derived from phages and have evolved to be synthesized in a bacterial cytoplasm, it has been unclear if different lysins can be expressed and secreted in a eukaryotic cell. Therefore, the inventors checked whether LysM-CHAP lysins can be trafficked through the eukaryotic secretory pathway and at the same time maintain their bactericidal activity (e.g. against S.aureus). For this purpose, the inventors employed P.pastoris as an expression system.
- amino acid sequences (excluding the start methionine) of wild type (WT) L0482 and L0499 were modified by adding the N-terminal pre- and pro sequences of S. cerevisiae alpha mating factor, followed by a Kex2/Ste13 signal peptidase site, a hexa- histidine tag and a 3C protease cleavage site (see SEQ ID NO: 48 and 50, respectively).
- the signal sequences target the lysin constructs to the secretory pathway and are cleaved off at the signal peptidase sites after translocation into the ER.
- the hexa-histidine tag and 3C sites were further introduced to facilitate lysin purification by affinity capture and removal of the hexa-histidine tag after proteolytic cleavage, respectively.
- the constructs were codon optimized for expression in P.pastoris (see SEQ ID NO: 49 and 51, respectively) and ordered from Genescript in plasmids conferring antibiotic resistance and control of lysin expression by an AOX1 methanol- inducible promoter. Plasmids were linearized by restriction and transformed into a wild type (mut+) P.pastoris strain, followed by selection of transformants on YPD plates containing 100 ⁇ g/ml Zeocin.
- Example 3 Yeast on dead aureus (YODA) screening method
- YODA Yeast on dead aureus screening method
- the inventors sought to establish a robust, easy-to-use and high-throughput screening method for determining the secretion and activity of lysins (e.g. against S. aureus) expressed in eukaryotic cells, e.g. in yeast cells such as P.pastoris.
- a yeast on dead aureus (YODA) screening method has been developed ( Figure 4A): First, a stationary phase suspension culture of S.aureus was sterilized by autoclaving, which destroys most cellular components with exception of the peptidoglycan layer, causing the autoclaved suspensions to retain its turbidity. The resulting dead S. aureus cell (i.e. peptidoglycan) suspension was washed with water by centrifugation and resuspension and then integrated at an optical density at 620nm of 4.0 into yeast plates supplemented with 50mM NaPO4, pH 6.0, yeast nitrogen base, 0.00004% biotin, 1% methanol, and 1.5% agar.
- YODA yeast on dead aureus
- P.pastoris cells expressing (and potentially) secreting lysins from derivatives of the pPIC9K or the pPICZ vectors are plated on the agar (containing the dead S.aureus) and grown into colonies.
- Secreted lysins cleave the surrounding peptidoglycan in the agar, causing the vicinity of the colony to become translucent.
- colonies secreting active lysins can be easily identified by visual inspection for the presence of a halo.
- the size of the halo depends on the secretion level while its opacity depends on the enzymatic activity of the expressed lysin.
- yeast e.g. P.pastoris
- YODA allowed for the detection of enzymatic activity of a diverse set of lysins with different architectures ( Figure 4B).
- P.pastoris strains expressing various lysins with different architectures were plated on YODA plates at a density of 150 colonies per plate and incubated at room temperature for 3-4 days.
- Enzymatic activity could be detected in the form of halos around lysin-secreting P.pastoris colonies for different lysin constructs.
- the principle of the YODA method described above is not limited to P.pastoris as a host or S. aureus as a target.
- lysins may be also expressed in other yeast model organisms, such as S. cerevisae, as well as in other secreting bacteria, such as B. subtilis.
- bacteria including both gram-positive and gram-negative bacteria, such as Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacteriaceae, Porphyromonas gingivalis, Helicobacter pylori, Chlamydia trachomatis, Enterobacteriaceae, E.
- coli Klebsiella pneumoniae, Salmonella, Shigella, Borellia, Campylobacter jejuni, Neisseria gonorrhoeae, Chlamydia trachomatis, Vibrio cholerae, and Fusobacterium nucleatum, Staphylococci, Streptococci, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, Cutibacterium acnes, Mycobacterium tuberculosis, Gardnerella, Enterococcus faecalis, Enterococcus faecium, Lactobacillus iners, Bacillus subtilis and Bacillus anthracis, may be autoclaved and integrated into the agar depending on the target bacterium of the lysins to be screened.
- the above-describe method is not limited to screening or evaluating lysins against S.aureus but it may be easily modified for screening or evaluating lysins against other bacteria (e.g. other Gram-positives such as, inter alia, Clostridioides difficile).
- other bacteria e.g. other Gram-positives such as, inter alia, Clostridioides difficile.
- analogous methods to the “YODA” employing other bacteria for screening of lysins against these other bacteria are contemplated herein as well and encompassed by the term “YODA”.
- the term “YODA” is not only employed in sensu strictu or necessarily limited to S. “aureus” but may also concern other bacteria.
- YODA may be replaced herein by the term “Yeast on dead bacteria” (“YODB”) where suitable.
- secreting bacteria such as B. subtilis may be used instead of yeast, further generalizing the method to “Microorganism on dead bacteria”, i.e. “MODB”.
- YODA or YODB may be replaced herein by the term “Microorganism on dead bacteria” (“MODB”) where suitable.
- MODB Microorganism on dead bacteria
- the term “YODA” usually refers to “Yeast on dead aureus” in a strict sense, i.e., wherein yeast cells are used and dead S.
- aureus and/or peptidoglycan thereof is comprised in the agar plates.
- a method has been described for screening for active lysin variants secreted from P.pastoris colonies using a double agar layer (DAL) assay.
- DAL double agar layer
- transformed P.pastoris cells are first grown to colonies on agar plates, followed by overlaying the colonies with a molten low percentage top agar solution containing live S.aureus cells (Zhao (2014). Appl Environ Microbiol 80(9)).
- live (and not dead) S. aureus cells are employed.
- the S. aureus cells live (and not dead)
- aureus cells are only contained in a distinct agar layer (and not in the entire agar plate, or in a homogenous manner). Further differences are apparent when comparing the above-mentioned YODA method to the DAL method described in (Zhao (2014). Appl Environ Microbiol 80(9)). Due to these differences, the YODA (or “YODB”) method of the present invention has several advantages over the DAL method, for example: 1. Throughput and plate homogeneity are strongly increased because agar plates can be generated in batch and stored at 4°C for up to 1 month. This also provides an easier handling and is more practical. 2.
- DAL method can detect strong enzymatic activities, such as those observed for lysostaphin, initially weaker lysins either show only faint or no halos at all. In contrast, these weaker lysins show clear halos in the YODA method. Initial bactericidal activity can therefore be detected early in the lysin development process. The reason is likely that in the DAL, live bacteria need to be killed to generate a halo. In other words, in DAL, the yeast growth and lysin secretion rate need to compete with the growth rate of S.aureus to generate well detectable halos.
- the YODA/YODB method of the present invention provides a higher throughput and is more practical, more efficient, less error-prone, more sensitive, more robust, and/or more flexible compared to screening methods in the prior art such as the DAL method. Therefore, the YODA/YODB method of the present invention allows to evaluate the secretion and/or activity (in particular the activity) of lysin variants in a large-scale and/or high-throughput manner.
- lysin variants with improved properties e.g., with a greater activity (against a target bacterium such as, inter alia, S.aureus), improved solubility and/or improved secretion from eukaryotic cells, e.g., human cells.
- YODA/YODB method can be readily combined with yeast display methods (e.g. as described herein) which further improves the screening and identification of lysin variants with desired properties, e.g., a higher activity, better expression in and/or secretion from eukaryotic cells, and/or better solubility in aqueous solutions.
- Example 4 Generation of aglycosylated L0482 variants Native secretory proteins are typically N-and O-glycosylated during their maturation in the secretory pathway. While secretory proteins are evolutionary adapted to these modifications, transgenes may be glycosylated at sites essential for folding and activity, which could potentially lead to the secretion of a less active or even inactive protein. Therefore, the inventors sought to determine whether glycosylation of lysins in eukaryotic cells (e.g.
- L0482 SEQ ID NO: 1 which they found to be produced and secreted in an active form in both, P. pastoris and E. coli (see Examples 1 and 2).
- L0482 contains two motifs of N-glycosylation at residues N68 and N73. Secretory expression of L0482 in P.pastoris results in quantitative N-glycosylation, as determined by SDS-PAGE and PNGase F treatment. It was found that these modifications, i.e.
- yeast minimal growth medium 50mM NaPO4, pH6.0, 0.00004% biotin, 1.34% yeast nitrogen base, 2% dextrose.
- Transformants were then plated on YODA agar, i.e., agar comprising dead S.aureus (see Example 3). Colonies with halos emerged 3 days after plating and were picked for sequence identification by PCR followed by Sanger Sequencing.
- N68K / N73G also referred to in the present Examples herein as “L0482ag” or “aglycosylated L0482”
- Example 5 Directed evolution of lysins
- L0482 SEQ ID NO: 1
- L0482 SEQ ID NO: 1
- Low solubility is expected to strongly reduce the potency of a lysin (such as, for example, a lysin expressed from an mRNA or plasmid in patient cells) when used to treat human infections.
- a tendency to aggregate may further elicit undesired immune responses, resulting in reduced potency upon repeated administration (Ratanji (2014). J Immunotoxicol 11(2)).
- lysins may result in low expression and secretion levels of lysins when expressed as transgenes (e.g. from an mRNA or a plasmid) in mammalian cells (e.g. in a patient).
- transgenes e.g. from an mRNA or a plasmid
- the inventors developed a directed evolution approach which allows to simultaneously improve the solubility, activity and eukaryotic secretion of lysins.
- L0482ag SEQ ID NO: 2 which has been developed in context of the present invention and which has been shown to have a good killing activity against S.aureus (see Example 4) was employed as a starting point for the directed evolution method described herein below.
- L0482ag variants obtained by the directed evolution approach are further described and characterized in Example 6 below.
- adaptation of lysins to the eukaryotic secretory pathway is highly desirable, for example, in a situation when a lysin is administered in form of a plasmid or mRNA (“ribolysin”) to a patient.
- the lysin is expressed in the patient’s cells with high efficiency and secreted from the cells in an active and soluble form.
- the adaptation to the eukaryotic secretory pathway is also important when a lysin is to be produced recombinantly in a mammalian system which may have certain advantages, e.g. over a prokaryotic expression system. These advantages include the higher protein folding capacity of mammalian cells in comparison to prokaryotic cells.
- lysins targeted against gram-negative bacteria may be toxic to their prokaryotic expression host, e.g. E.coli.
- yeast display method (Boder (2000). Proc Natl Acad Sci USA 97(20)) adapted to P.pastoris, where lysin variants are secreted and anchored to the yeast cell wall via N- terminal fusion to a fragment of the Sag1-protein (De Schutter (2021). Methods Mol Biol 911).
- yeast cells secreting high levels of such fusion proteins can be enriched by flow cytometry-based cell sorting.
- YODA or YODB
- L0482ag SEQ ID NO: 2
- Library generation A variant library of L0482ag was generated by the DNA shuffling method (Stemmer (1994). Nature 370(6488)), in which DNA sequences are subjected to DNA fragmentation by DNAseI treatment and randomly recombined by the polymerase chain reaction ( Figure 7A).
- L0482ag and 11 homologues of L0482 identified bioinformatically and confirmed for activity in a growth inhibition assay (in lysates of E.coli expressing the respective variants) were chosen (see Example 1).
- the pool of possible mutations was enriched by including six variants of L0482ag, which had been designed for improved stability by the ROSETTA algorithm (Leman (2020). Nat Methods 17(7)).
- the residue variations at each position present in the parental library are listed in Table 1: Table 1.
- Sequence variants of L0482ag per position Parental amino acid sequences were aligned to L0482ag and amino acids found at each position in the alignment are listed (columns 2 and 3, respectively). L0482ag was further aligned to its close natural homologues (all sequences with at least 80% sequence coverage and 60% sequence identity). The fraction of amino acids identical to L0482ag at each position was calculated, as detailed in Example 7, and is shown in the third column “conservation”.
- the LYSM domain is from positions 1 to 51; the linker is from positions 52 to 71; the CHAP domain is from positions 72 to 215.
- DNA encoding the variant libraries fused to an N-terminal signal peptide and a C-terminal V5-epitope tag, followed by the sequence of the SAG1 membrane anchor domain were subsequently produced in E.coli and transformed into P.pastoris GS115 cells.
- Screening procedure As a first step in the screening procedure (i.e. the yeast display step), P.pastoris cells (representing the L0482ag variant library) were selected for high surface display levels of lysins.
- the P. pastoris cells containing the library of sorted L0482ag variants obtained by the yeast display step are then plated on YODA agar (about 10000 colonies per round of directed evolution). Clones with halos were picked (22 clones with the biggest halos in Round 1, 196 clones with the biggest halos in Round 2 and Round 3). Then, the yeast display was repeated with the P. pastoris cells containing the L0482ag variants (enriched for well active and well expressed and secreted lysins) obtained by the initial yeast display and YODA steps as library.
- P. pastoris cells expressing the enriched L0482ag variants fused to the SAG1 membrane anchor domain were then grown and the cells with the highest surface display levels of lysins were sorted by FACS, followed by plating of the sorted cells on YNB agar plates. Colonies were picked (96 for round 1, 196 for rounds 2 and 3) and lysin DNA was sequenced. A hit table was generated in which the frequency of each lysin sequence was counted.
- G1-G4 and H1-H10 obtained after rounds 1 and 2, respectively, as described in Example 5) were expressed in E.coli followed by purification to assess their stability and enzymatic activity.
- E.coli BL21(DE3) cells were transformed with the lysin variants cloned with an N-terminal hexahistidine tag and a 3C- protease cleavage site into the pET29b vector (SEQ ID NO: 305; Novagen).
- the pET29b vector shown in SEQ ID NO: 305 contains, as an example, the sequence encoding the lysin variant “G1” at positions 146 to 790.
- lysins e.g., G2-G4 and H1-H10
- the pET29b vector contained, inter alia, the following elements in SEQ ID NO: 305: a T7 promoter/ Lac Operator at positions 1 to 42, the start codon (for the polypeptide containing the lysin) at positions 89 to 91 and the corresponding stop codon at positions 791 to 793, an hexahistidine tag at positions 95 to 112, a 3C protease cleavage site at positions 113 to 145, and an T7 terminator at positions 892 to 931.
- Transformed cultures were grown in 150ml LB medium supplemented with Kanamycin (for antibiotic selection of the pET29b vector) to an optical density at 600nm of 0.6. At this point, protein production was induced by addition of 0.5mM IPTG. Expression was continued at 18°C for 24h, followed by harvest of the cells by centrifugation. Purification of L0482 variants from E. coli The cells were then resuspended in 100ml lysis buffer (20mM Hepes, pH 7.0, 10mM MgCl2), supplemented with 1mM PMSF and 5ul benzonase (VWR, 70746-3), followed by sonication (20% duty cycle, 4min, 4°C).
- Bound protein was eluted with elution buffer (20mM Hepes, pH 7.0, 300mM NaCl, 300mM Imidazole; 10ml final volume) and concentrated using 10kDa molecular weight cutoff spin filters (Amicon). The protein concentration was determined using the Bradford reagent and eluates were supplemented with one molar percent of precision protease in order to remove the 6H tag.3C treated eluates were then dialyzed for 16h at room temperature against 2L of final storage buffer (20mM Hepes, pH 7.0, 150mM NaCl). Precipitates were removed using spin filters with a pore size of 0.22 ⁇ m. Final protein concentrations were determined using the Bradford assay.
- Protein stability was determined using the Thermofluor assay. 19 ⁇ l lysin solutions were mixed with 1 ⁇ l of a 20x solution of SYPRO Orange (Thermo, S6651) in DMSO. The mixtures were transferred to the wells of a 384 well plate. Changes in fluorescence of the SYPRO Orange fluorophore were measured in a qPCR machine (Roche, LightCycler 480) while applying a temperature ramp protocol between 23°C and 95°C. These melting curves were then analyzed in Prism 9.0 (GraphPad) in the following way: The first derivatives were determined with data smoothing across 35 consecutive data points.
- the minimal inhibitory concentration (MIC) was determined as the lowest lysin concentration, at which the OD of the reaction at 620 nm stayed below 0.1 over the course of the 24h incubation at 37°C. These experiments showed a MIC for L0482ag of 8 ⁇ g/ml. All variants showed absence of S.aureus growth at 2 to 16 fold lower lysin concentrations. The lowest MICs were observed at 0.5 ⁇ g/ml for variants H5 (SEQ ID NO: 11) and H7 (SEQ ID NO: 13) ( Figure 8C).
- the pCDNA3.4 vector shown in SEQ ID NO: 306 contains, as an example, the sequence encoding the lysin variant “G1” at positions 871 to 1515. Further lysins (e.g., G2-G4 and H1-H10) can be and were cloned into the pCDNA3.4 vector instead of G1 as indicated.
- the pCDNA3.4 vector contains, inter alia, the following elements in SEQ ID NO: 306: a CMV promoter at positions 47 to 727, a Kozak sequence at positions 742 to 751, a start codon at position 748 to 750, a signal peptide (mouse IgKappa) at positions 748 to 813, the sequence containing the lysin at positions 871 to 1515 and a corresponding stop codon at positions 1516 to 1518, an hexahistidine tag at positions 820 to 837, a 3C protease site at positions 838 to 870, and a WPRE (Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element) at positions 1559 to 2155.
- a CMV promoter at positions 47 to 727
- a Kozak sequence at positions 742 to 751
- a start codon at position 748 to 750
- a signal peptide mime IgKappa
- Plasmids i.e. pCDNA3.4 vectors
- pCDNA3.4 vectors were transfected at a final concentration of 1 ⁇ g/ml in 3.2x10 ⁇ 6 cells per ml of an Expi293 culture in Expi293 medium (Thermo, A14527 and A1435101, respectively) using the Expifectamine transfection kit as described by the manufacturer. Cells were grown shaking at 5% CO2 and at 37°C. Transfected cultures were supplemented with Enhancer solutions 1 and 224h after transfection according to the manufacturers instructions. Cells were removed after 72h by centrifugation (300xg, 5min) and the supernatants used for further analysis. Supernatants were analyzed by SDS-PAGE followed by Western blotting.
- Lysin variants were stained using a primary antibody raised against the 3C tag (Abcam, ab183574), followed by staining with a secondary antibody coupled to HRP (Thermo, G-21234). Stained proteins were detected using the ECL reagent (Thermo, 32106). Band intensities were background corrected and then quantified using ImageJ (NIH). Analysis of the levels of protein secretion from HEK (i.e. EXPI293) cells showed that parental L0482ag (SEQ ID NO: 2) was either not secreted or secreted at levels that could not be detected ( Figure 8D). In contrast, variant G1 (SEQ ID NO: 3) could be detected in the supernatants, albeit at low levels.
- the free-floating biofilm-like aggregate in synovial fluid assay mimics the situation in joint infections (e.g. prosthetic joint infections).
- Peg biofilm in plasma assay Disruption of staphylococcal biofilms was assessed using the MBEC Assay® Kit (Innovotech). Overnight cultures of S.
- aureus strain ATCC 43300 were grown in cation-adjusted Müller-Hinton broth (caMHB, Sigma) at 37°C, 220rpm shaking and adjusted the next morning to an optical density of 0.1 in caMHB supplemented with 10% human Li- Heparin plasma (Innovative Research), previously dialysed in PBS (Thermo Scientific) using a 10 kDa dialyses cassette (Pierce). 100 ⁇ l of this bacterial suspension was dispensed into each well of the 96 well plate. The plate lid with 96 pegs attached, was immersed into these wells and biofilms were grown statically for 24 hours at 37°C.
- the pegs were immersed into 100 ⁇ l of treatment solutions containing lysins or appropriate controls. Lysins at 50 ⁇ g/ml or vancomycin at 256 ⁇ g/ml in caMHB supplemented with 50% human Li-Heparin plasma, were incubated for a duration of 2 hours (static at 37°C). The treatment solution was removed and fresh treatment was applied and incubated again for 2 hours at 37°C after which the pegs were washed 3 times with PBS. Biofilm dislodgment was performed by immersing the pegs in 100 ⁇ l of TrypLETM (Gibco) for 20 min and stopping the reaction by the addition of 100 ⁇ l of PBS.
- TrypLETM Gibco
- Quantification of bacterial counts was performed by plating serial dilutions (in saline) on tryptic soy agar plates. Free-floating biofilm-like aggregate in synovial fluid assay (FBA) The ability to disrupt floating biofilm-like aggregates in bovine synovial fluid was assessed. Overnight cultures of S. aureus strain ATCC 43300 were grown in BHI (Carl Roth) at 37°C, 220 rpm shaking.
- optical density of the bacterial culture was adjusted to 0.1 in caMHB (Sigma) supplemented with 50% bovine synovial fluid (Dunn Labortechnik) and 200 ⁇ l of this bacterial suspension was dispensed into single wells in a 96 deep well plate (NuncTM Non-Treated Multidishes). The plate was incubated for 24 hours @37°C, 500 rpm to allow for the formation of floating biofilm-like aggregates. Treatment was performed by the addition of 22 ⁇ l of a 10 fold concentrated stock of lysin or controls, providing a final lysin concentration of 50 ⁇ g/ml and a final vancomycin concentration of 256 ⁇ g/ml, respectively.
- Vancomycin an antibiotic that is used in the clinics against S. aureus infections and which is active against planktonic bacteria (with a MIC around 1 ⁇ g/ml depending on the strain), showed very little or no activity against S. aureus biofilms or free-floating aggregates, respectively, even at a very high concentration of 256 ⁇ g/ml.
- both L0482 variants tested i.e., G1 (SEQ ID NO: 3) and H5 (SEQ ID NO: 11), effectively killed S. aureus biofilms or biofilm-like free-floating aggregates; see Figure 12.
- the L0482 variant H5 showed a 2.32-log (i.e.99.52%) reduction of bacterial cell counts vs.
- the L0482 variant H5 showed a 3.17-log (i.e.99.93%) reduction of bacterial cell counts vs. vancomycin and a 3.03 log reduction vs untreated aggregates, (i.e.99.9%) in the FBA assay which, again, was both statistically highly significant.
- the L0482 variant G1 showed a 1.54-log (i.e.97.11% killing) reduction vs vancomycin and a 2.91 (99.98% killing) log reduction vs untreated reactions which was also both statistically highly significant.
- Example 7 Identification of conserved positions and segments and beneficial mutations in L0482 variants Homologues of L0482ag were identified in the following manner: A BLAST search against the amino acid sequence of L0482ag (lacking the initiating amino acid methionine) was performed against the NCBI nucleotide database. The 5000 closest homologues of L0482ag were downloaded. Sequences with a coverage below 80% and a sequence identity below 60% were excluded from this selection.
- amino acid sequences of all variants identified in directed evolution rounds 1 to 3, which had been confirmed to be active by YODA were aligned to L0482ag using Clustal Omega and analyzed by Excel to list the amino acids at each position in the lysin sequence.
- a combination of the two lists with addition of beneficial aglycosylation mutations identified in Example 4 allowed identification of mutations that can be considered as “beneficial”, or at least “permissive”, when present in isolation or in combination (Table 3).
- the list of beneficial/permissive mutations was compared with the fraction identities to L0482ag per amino acid position (i.e., the % of the analyzed 621 natural variants having the same amino acid residue at a certain position as WT L0482). It was found that none of the considered variants (either generated upon directed evolution, used as input variant for the directed evolution, or one of the other assessed 621 natural variants) had a variation/mutation at the following positions of L0482 (SEQ ID NO: 1 or 2): 12, 80, 87, 88, 98, 99, 103, 106, 110, 114, 122, 126, 128, 137, 182, 202, and 208 (marked by black fields in Table 3).
- SEQ ID NO: 1 positions of SEQ ID NO: 1 are thus considered as conserved positions. Notably, 16/17 of these conserved positions are within the CHAP domain (i.e. positions 72 to 215). Moreover, it has been found that 11/16 of these conserved positions in the CHAP domain are within positions 87 to 128 in SEQ ID NO: 1 and that this CHAP segment contains many further relatively conserved positions (marked by grey fields in Table 3). Said CHAP segment (i.e. positions 87 to 128 in SEQ ID NO: 1) is thus considered as a particularly conserved CHAP segment. Table 3.
- the column “conservation” shows the % of 621 assessed natural variants of L0482 having the same amino acid residue per position as L0482ag (SEQ ID NO: 2), as also shown in Table 1.
- the column “conserved position” shows in black fields positions where no mutation/variation was identified at all, and in grey fields positions where no mutation/variation was identified in the input variants or active and secreted variants generated experimentally herein and no variation was observed in at least 99.0% of the 621 natural variants assessed.
- the LYSM domain is from positions 1 to 51; the linker is from positions 52 to 71; the CHAP domain is from positions 72 to 215. A particularly conserved segment has been found within positions 87 to 128.
- the inventors identified all mutations occurring in the selected hit variants obtained in rounds 1 to 3 of the directed evolution, i.e., G1 to G4, H1 to H10 and I1 to I30; see Table 2 and SEQ ID NO: 3 to 46. These particularly beneficial mutations are shown in Table 4. Furthermore, to identify the most beneficial mutations, a consensus sequence was generated using Geneious (Dotmatics, version 2022.2.2) by determining the most frequent residues at each position in the alignment of all selected hit variants (see Figure 9 and black highlights in Table 4). In this analysis, the variant H3 (SEQ ID NO: 9) was found to reflect the consensus sequence.
- variant H3 surprisingly contained certain amino acid substitution pairs and individual amino acid substitutions that were present in different combinations in the selected hits. These substitutions pairs or individual substitutions are considered herein as the consensus mutation units.
- the following consensus mutation units were found: 1. R86K 2. T82S and N85G in combination 3. S130N and H136K in combination; alternatively, S130N and H136R in combination 4. D169N 5. N185Y and N186G in combination
- all selected hit variants contained the mutation R86K.
- the mutation R86K was further found in 96.08% of all sequenced active and secreted L0482ag variants obtained by the three rounds of directed evolution.
- mutation R86K in reference to SEQ ID NO: 1 or 2 is a particularly important amino acid substitution among the most beneficial mutations in order to improve the pharmaceutical properties of L0482 variants.
- variants H3 (SEQ ID NO: 9) and H5 (SEQ ID NO: 11) were among the variants which showed the best properties in terms of stability, enzymatic activity and secretion in mammalian cells and since all selected and further characterized variants showed strong improvements in these aspects relative to L0482ag (see Figure 8B- E)
- the individual mutations, and in particular the consensus mutation units, identified above can be deemed to have additive or synergistic beneficial effects on the lysin variants.
- variant H5 (SEQ ID NO: 11) contained the additional mutation F155Y, which is deemed highly beneficial since F155Y is the only difference between H3 and H5, the latter of which showed better enzymatic activity after secretion from EXPI293 cells (see Figure 10 and the grey highlight in Table 4).
- Table 4 Identification of particularly beneficial mutations contained in the selected hit variants obtained in rounds 1 to 3 of the directed evolution. Shown are mutations per position contained in at least one of the variants G1 to G4, H1 to H10 and I1 to I30, i.e. the hits, as described in Table 2 and SEQ ID NO: 3 to 46.
- Mutations found in G1 to G4 refer to round 1 (R1) mutations, mutations found in H1 to H10 refer to round 2 (R2) mutations and mutations found in I1 to I 30 refer to round 3 (R3) mutations. Positions which were not modified in G1 to G4, H1 to H10 and I1 to I30 are not shown. Highlighted in black are the most beneficial mutations contained in the consensus sequence, as reflected by H3 (SEQ ID NO: 9). Highlighted in grey is another one of the most beneficial mutations, namely the only amino acid substitution in the best performing variant characterized, i.e. H5 (SEQ ID NO: 11), vis à vis H3.
- variants G1 to G4, H1 to H10 and I1 to I30 contained a “K” at position 68 and a “G” or “S” at position 73. Most variants, including H3 and H5, contained a “K” at position 68 and a “G” at position 73, like the parental L0482ag.
- the LYSM domain is from positions 1 to 51; the linker is from positions 52 to 71; the CHAP domain is from positions 72 to 215. Furthermore, the inventors checked whether the particularly beneficial mutations occurred at the active site of L0482, i.e., the active site surface around the catalytic cysteine.
- the inventors inspected a published X-ray structure of a CHAP domain in a lysin of the CHAP-AMI-SH3 architecture (LysK) which cleaves S.aureus peptidoglycan; Sanz-Gaitero et al. Virology Journal 2014, 11:133.
- This individual active site mutation is also contained in the H5 variant (SEQ ID NO: 11) obtained in round 2 of the directed evolution and is therefore among the most beneficial amino acid substitutions found in context of the present invention.
- the third round of the directed evolution did not yield any further mutation within the active site of the L0482 variants.
- the amino acid substitution N186G is the only tolerated mutation within the active site of L0482 lysins which enhances the killing activity against S. aureus, the protein stability and/or the secretion of the lysin from eukaryotic cells.
- almost all (31/32) positions which were mutated in the CHAP domain of the hit variants found by three rounds of directed evolution are outside the active site.
- the active site is a region of the CHAP domain of L0482 variants that is barely amenable as a target for improving the killing activity and/or other pharmaceutical properties like the secretion from eukaryotic cells.
- Example 8 Re-glycosylation of lysin variants Protein glycosylation has been shown to increase protein stability and solubility for eukaryotic proteins (Shental- Bechor (2009). Curr Opin Struct Biol 19(5)). Therefore, one or more identified hit variants from in vitro evolution will be subjected to rational re-glycosylation engineering using a structural model obtained with AlphaFold 2.0 (Jumper, Evans et al. 2021) as the template.
- Single amino acid substitutions of surface exposed residues will be mutated to either N or S/T to generate NXS/T glycosylation motifs (where X corresponds to any amino acid but proline).
- the variants will be interrogated for HEK293 expression/secretion levels, stability and functional activity (e.g., as described in Example 6 above).
- Variants with engineered single N-glycosylation motifs may be combined and validated in the same manner.
- Example 9 Half-life extension of lysin variants Endolysins are small proteins of bacterial or phage origin with relatively short half-lifes in humans (minutes to hours; Cassino (2016), “Results of the First in Human Study of Lysin CF-301 Evaluating the Safety, Tolerability, and Pharmacokinetic (PK) Profile in Healthy Human Volunteers”, presented at 26th European Congress of Clinical Microbiology and Infectious Diseases Apr 9-12, 2016). It is contemplated in the context of the present invention that half-life extension modules (i.e. an “extended pharmacokinetic (PK) peptide” / “PK tag”), such as human Fc fragment (e.g.
- PK extended pharmacokinetic
- glycosylated peptide tags e.g. C-terminal peptide of human chorionic gonadotropin (CTP), for example, as shown in SEQ ID NO: 295
- human lysozyme e.g. as shown in SEQ ID NO: 296
- the half-life extension module and the lysin are preferably connected by a peptide linker, e.g.
- a flexible glycin-serine linker for example as shown in SEQ ID NO: 297 to 299.
- the fusion proteins will then be interrogated for HEK293 expression/secretion level, stability and functional activity (e.g., as described in Example 6 above).
- the pharmacokinetics in mice will be determined.
- Example 10 Deimmunization of lysin variants Phage and bacteria derived endolysins may pose immunogenicity risks, particularly for chronic or repeated systemic applications, due to presence of T-cell epitopes in their amino acid sequences (Zhao (2015). Chem Biol 22(5)). It is therefore contemplated in the context of the present invention that one or more identified lysin hit variants (e.g.
- T-cell epitopes will be determined experimentally via MAPPs and/or T-cell activation assays with human PBMCs selected to represent the global HLA distribution. Alternatively or in addition, T-cell epitopes will be predicted using in silico algorithms such as NetMHCII Pan (Reynisson (2020). J Proteome Res 19(6)). 2. A de-immunized endolysin sequence library will be obtained using a Rosetta based algorithm (Rosetta MHC, Yachnin (2021).
- the Rosetta based algorithm allows to design deimmunizing mutations that maintain the calculated stability of the protein. It is thus credible that other advantageous properties the lysin (e.g. H5) had before deimmunization, e.g. the bactericidal activity, stability and ability of being secreted from eukaryotic cells, are maintained upon deimmunization according to the invention.
- silico generated deimmunized variants of H5 are shown in SEQ ID NO: 52 to 251.
- In silico determined deimmunizing amino acid residues per position are shown in Table 5. Table 5.
- Table 5 In silico determined deimmunizing amino acid residues. The three dimensional structure of variant H5 was predicted using Alphafold 2.0.
- the structure and the multiple sequence alignment generated by Alphafold 2.0 were used as the input for ROSETTA-MHC design runs, in which HLA type 1 and HLA type 2 epitopes were mutated while maintaining the overall stability of the protein. Shown are amino acids found at each position which were introduced as deimmunizing mutations in a library of 200 designed variants (“deimmun”).
- the column “H5” shows the amino acid sequence of H5 (i.e. SEQ ID NO: 11).
- the LYSM domain is from positions 1 to 51; the linker is from positions 52 to 71; the CHAP domain is from positions 72 to 215.
- Example 11 Ribolysin construct design and mRNA production In vitro transcription of lysin encoding mRNAs was based on the pST1-T7-AGA-dEarI-hAg-MCS-FI-A30LA70 plasmid- backbone and derivative DNA-constructs.
- These plasmid constructs contain a 5 ⁇ UTR (untranslated region, a derivate of the 5 ⁇ -UTR of homo sapiens hemoglobin subunit alpha 1 (hAg)), a 3’ FI element (where F is a 136 nucleotide long 3 ⁇ -UTR fragment of amino-terminal enhancer of split, mRNA and I is a 142 nucleotide long fragment of mitochondrially encoded 12S RNA both identified in Homo sapiens; WO 2017/060314) and a poly(A) tail of 100 nucleotides, with a linker after 70 nucleotides.
- Several top-displaying hits from the directed evolution screens (Example 6; Figure 8) were selected for mRNA expression.
- the insulin signal sequence (SEQ ID NO: 378; derived from human insulin, UniProtKB entry P01308_INS_HUMAN) as well as a DYKDDDDK tag (SEQ ID NO: 307) was added N-terminally, a hexa-histidine tag was added C-terminally; see Tables 6 to 8 and SEQ ID NO: 252 to 275 for the corresponding RNAs and proteins.
- the signal sequence targets the lysin constructs to the secretory pathway and is cleaved off at the signal peptidase site after translocation into the ER.
- the DYKDDDDK and the hexa-histidine tags were introduced to facilitate the quantification of translated lysin.
- mRNA was generated by in vitro transcription as described by Kreiter et al. (Kreiter, S. et al. Cancer Immunol. Immunother. 56, 1577–87 (2007)) with substitution of the normal nucleoside uridine by 1-methyl-pseudouridine. Resulting mRNAs are equipped with a Cap1-structure and double-stranded (dsRNA) molecules were depleted. Purified mRNA was eluted in H 2 O and stored at -80 °C until further use. In vitro transcription of all described mRNA constructs was carried out at BioNTech SE.
- Table 6 Full amino acid and nucleotide sequences of mRNA-encoded hits from directed evolution screens of L0482.
- the nucleotide sequences shown refer to the mRNAs generated from codon-optimized DNA constructs and encoding various lysins including signal peptide and tags, and further containing a 5’ UTR (comprising the deltaEarI-hAg- Kozak sequence shown in SEQ ID NO: 371), a 3’ UTR (comprising the 3’ FI element shown in SEQ ID NO: 374) and a poly(A) tail (SEQ ID NO: 375), wherein each uridine (shown as “T”) in these mRNA sequences was replaced by 1-methyl-pseudouridine.
- ribolysin variants of L0482 was analyzed by lipofection of mRNA into HEK293T/17 cells and subsequent quantification of secreted His- tagged protein by Western Blot (see Table 8).
- 0.9x10 6 HEK293T/17 cells were seeded in 3 mL DMEM (Life Technologies GmbH, cat. no.31966-021) + 10 % fetal bovine serum (FBS, Biochrom GmbH, cat. No. S0115) in 6-well plates.
- FBS fetal bovine serum
- mRNA was formulated using the RiboJuiceTM mRNA Transfection Kit (Sigma Aldrich, cat.
- RNA-encoded L0482 variants Protein expression from mRNA was visible at the expected size of approximately 27 kDa and was demonstrated for all L0482 variants (Figure 10); however, the distribution between cell lysate and supernatant differed significantly between variants. While wt and aglycosylated (ag) L0482 displayed only faint bands in the supernatants, all variants obtained by the directed evolution tested could be found at considerable levels in the supernatant and thus were well secreted by the HEK293T/17 cells. In particular, variants G1, G3, G4, H3 and H5 showed more than 20x higher protein levels in the supernatant compared to wt. In summary, secretion of mRNA-encoded L0482 by human cells was successfully improved by using the directed evolution approach.
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- 2024-03-08 CN CN202480023743.2A patent/CN121127584A/en active Pending
- 2024-03-08 WO PCT/EP2024/056254 patent/WO2024184533A1/en not_active Ceased
- 2024-03-08 JP JP2025552235A patent/JP2026507918A/en active Pending
- 2024-03-08 IL IL322837A patent/IL322837A/en unknown
- 2024-03-08 EP EP24709418.8A patent/EP4676598A1/en active Pending
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Also Published As
| Publication number | Publication date |
|---|---|
| IL322837A (en) | 2025-10-01 |
| JP2026507918A (en) | 2026-03-06 |
| CN121127584A (en) | 2025-12-12 |
| WO2024184533A1 (en) | 2024-09-12 |
| AU2024234022A1 (en) | 2025-08-28 |
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