Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
  • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
  • C07K14/4723—Cationic antimicrobial peptides, e.g. defensins
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
  • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
  • C07K14/4726—Lectins
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K9/00—Medicinal preparations characterised by special physical form
  • A61K9/0012—Galenical forms characterised by the site of application
  • A61K9/0043—Nose
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K9/00—Medicinal preparations characterised by special physical form
  • A61K9/0012—Galenical forms characterised by the site of application
  • A61K9/007—Pulmonary tract; Aromatherapy
  • A61K9/0073—Sprays or powders for inhalation; Aerolised or nebulised preparations generated by other means than thermal energy
• • 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
  • A61P31/12—Antivirals
  • A61P31/14—Antivirals for RNA viruses
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/575—Hormones
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Y—ENZYMES
  • C12Y304/00—Hydrolases acting on peptide bonds, i.e. peptidases (3.4)
  • C12Y304/17—Metallocarboxypeptidases (3.4.17)
  • C12Y304/17023—Angiotensin-converting enzyme 2 (3.4.17.23)
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif

Definitions

• the present invention relates to a bifunctional peptide according to the preamble of claim 1 , to the medical use of such a peptide according to the preamble of claim 9, to a medicament comprising such a peptide according to the preamble of claim 1 1 , and to a method for manufacturing such a peptide according to the preamble of claim 13.
• a peptide having the claim elements of claim 1 is a bifunctional peptide that comprises a virus binding moiety and a mucin binding moiety that is covalently bound to the virus binding moiety.
• the binding between the virus binding moiety and the mucin binding moiety can be a direct covalent binding or a binding via a linker.
• the virus binding moiety comprises or is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11 , SEQ ID NO.
• SEQ ID NO. 27 SEQ ID NO. 28, SEQ ID NO. 29, SEQ ID NO. 30, SEQ ID NO. 31 , SEQ ID NO. 32, SEQ ID NO. 33, SEQ ID NO. 34, SEQ ID NO. 35, SEQ ID NO. 36, SEQ ID NO. 37, SEQ ID NO.
• SEQ ID NO. 48 SEQ ID NO. 49, SEQ ID NO. 50, SEQ ID NO. 51 , SEQ ID NO. 52, SEQ ID NO.
• SEQ ID NO. 59 SEQ ID NO. 60, SEQ ID NO. 61 , SEQ ID NO. 62, or SEQ ID NO. 63.
• SEQ ID NO. 2 to 13 and 23 to 43 relate to virus binding moieties that are particularly appropriate for binding the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While SEQ ID NO. 2, 3, and 23 to 41 relate to linear virus binding peptides, SEQ ID NO. 4 to
• stapled peptides relate to partially cyclized peptides, so-called stapled peptides. They comprise at least one bridge between two not directly subsequent (but yet nearby) amino acids. This bridge acts like a staple and serves for a stabilization of the respective peptide.
• the bridge can be established by the two side chains of the respective amino acid residues or by a chemical moiety being covalently bound to the respective amino acid residues in addition to their regular side chains. In case of SEQ ID NO. 42 and 43, the bridge is a disulfide bridge formed between two cysteine residues.
• SEQ ID NO. 48 describes a peptide particularly appropriate for binding the influenza A virus (in particular strains H1 , H3, H7). This peptide targets the hemagglutinin (HA protein) of the influenza A virus and is described by Memczak et al. and Miriam Hoffmann et al.
• SEQ ID NO. 49 and 50 describe peptides particularly appropriate for binding the influenza A virus (in particular strain H5N1 clade 2.3.4, bird strain). These peptides target the hemagglutinin (HA protein) of the influenza A virus and are derived from sequences of antibody 65C6 described by Zuo et al.
• SEQ ID NO. 51 and 52 describe peptides particularly appropriate for binding the influenza A virus (in particular strain H5N1 clade 2.3.2.1 , bird strain). These peptides target specific sequences of the hemagglutinin (HA protein) found in general in HA protein of variants of this strain, for example in the sequences of the HA protein described by Bui et al.
• SEQ ID NO. 53 and 54 describe peptides particularly appropriate for binding the influenza B virus. These peptides target the neuraminidase of the influenza B virus and are described by Madsen et al.
• SEQ ID NO. 55 and 56 describe peptides particularly appropriate for binding rhinoviruses (RVs) and other enteroviruses (EV). These peptides are derived from anti-RV antibodies that are described by Hrebik et aL, Khan et aL, and Smith et al.
• SEQ ID NO. 57 describes a peptide particularly appropriate for binding the human parainfluenza virus (HPIV) (in particular strains HIPV1 and HIPV3).
• HPIV human parainfluenza virus
• This peptide targets the fusion protein (F protein) of HPIV and is derived from anti-HPIV antibodies described by Caban et al.
• SEQ ID NO. 58, 59, and 60 describe peptides particularly appropriate for binding the metapneuvirus (MPV) and the respiratory syncytial virus (RSV) (in particular subtype A and/or subtype B). These peptides target the fusion protein (F protein) of MPV and of RSV. They are derived from anti-HPIV antibodies and are described by Caban et al.
• SEQ ID NO. 61 , 62, and 63 describe peptides particularly appropriate for binding RSV (in particular subtype A and/or subtype B). These peptides also target the fusion protein (F protein) of RSV and are described by Issmail et al, Zhu et aL, and McLellan et al.
• the mucin binding moiety comprises or is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 1 (modified trefoil factor 3, TFF3 (C57K)), SEQ ID NO. 14 (native TFF3), SEQ ID NO. 20 (native TFF1 ), SEQ ID NO. 21 (native TFF2), or SEQ ID NO. 22 (jacalin) .
• TFF3 is a naturally produced protein in the airways (Thim et al. 2002).
• the presently claimed peptide is able to strengthen the natural barrier function of respiratory mucus.
• Respiratory mucus is the first physical barrier encountered by respiratory pathogens approaching their target cells of the respiratory epithelium. With its high viscosity and microbial- binding properties, mucus is an important part of our body’s antimicrobial defense system and efficiently clears adsorbed pathogens through ciliary movement.
• the presently claimed peptide can be used to strengthen the mucus by increasing its antimicrobial properties through the incorporation of binding sites for viral pathogens (mucus augmentation). Retained pathogens can then be cleared before reaching the epithelial cell layer, thus preventing infection.
• the present approach is thus to use modular biomimetic peptides to increase and support the antiviral efficacy of mucus.
• Mucus augmentation is a new concept for protecting people against respiratory infections.
• the present approach can be combined with other (non)-pharmacological measures to reduce the risk of infection in uninfected individuals and the risk of transmission and severe disease in already infected ones.
• the presently claimed peptide constitutes the core of an adjustable peptide-based system with a molecule that can adhere to airway mucins and specifically absorb viruses. Both parts of the peptide can be adapted to respond to a quickly changing situation.
• This biomimetic approach reinforces the natural antiviral properties of mucus, and as the peptide components are derived from human proteins, side-effects are considered to be low.
• the bifunctional peptide can also be used therapeutically in infected patients, as it will also trap viruses released from infected cells, thereby reducing the viral titer and shedding into the environment.
• the present approach can be combined with established antiviral measures, together helping to reduce the risk of infection and minimizing the risk of disease.
• both functional moieties of the peptide can be adapted for the desired application.
• An appropriate linker for establishing a covalent binding between the mucin binding moiety and the virus binding moiety is a polyethylene glycol (PEG) linker or an amino acid linker comprising 1 to 20 amino acids, in particular 2 to 19 amino acids, in particular 3 to 18 amino acids, in particular 4 to 17 amino acids, in particular 5 to 16 amino acids, in particular 6 to 15 amino acids, in particular 7 to 14 amino acids, in particular 8 to 13 amino acids, in particular 9 to 12 amino acids, in particular 10 to 11 amino acids.
• a dipeptide, such as a GT dipeptide is a particularly appropriate linker.
• a linker comprising or consisting of an amino acid sequence being at least 95 %%, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 % identical to SEQ ID NO. 44, SEQ ID NO. 45, SEQ ID NO. 46, or SEQ ID NO. 47 it is a particularly appropriate linker, too.
• SEQ ID NO. 44 is an example for a flexible linker.
• SEQ ID NO. 45 is an example for a rigid linker.
• SEQ ID NO. 46 represents a linking peptide resulting from a chemo-enzymatic coupling reaction via Sortase A.
• the virus binding moiety or the mucin binding moiety peptide is coupled to the glutamyl residue (Q7) via a y-glutamyl-e-lysyl isopeptide bond.
• the mucin binding moiety comprises a glycotope binding domain and binds to an N-acetylglucosamine-alpha-1 ,4-galactose (GlcNAc-a-1 ,4-Gal) disaccharide with an affinity of at least 150 pM, in particular of at least 100 pM, in particular of at least 75 pM, in particular of at least 50 pM, in particular of at least 25 pM, in particular with an affinity lying in a range of from 25 pM to 150 pM, in particular from 50 pM to 125 pM, in particular from 75 pM to 100 pM.
• GlcNAc-a-1 ,4-Gal N-acetylglucosamine-alpha-1 ,4-galactose
• the GlcNAc-a-1 ,4-Gal disaccharide is a glycotope that is specifically present in mucins such as mucin 2 (Muc2), mucin 5AC (Muc5AC), and mucin 6 (Muc6).
• mucins such as mucin 2 (Muc2), mucin 5AC (Muc5AC), and mucin 6 (Muc6).
• mucin 2 mucin 2
• Moc5AC mucin 5AC
• Mucin 6 mucin 6
• the virus binding moiety is covalently bound to the mucin binding moiety at amino acid 57 of the mucin binding moiety.
• amino acid 57 is a cysteine residue.
• amino acid 57 is a lysine residue.
• the virus binding moiety is covalently bound to the mucin binding moiety at the C terminus of the mucin binding moiety. In particular in the latter embodiment, it is of no special importance for the binding ability to the virus binding moiety which amino acid is present at position 57 (or at any other position) of the mucin binding moiety.
• the peptide comprises at least two virus binding moieties.
• the mucin binding moiety is directly or via a linker covalently bound to at least one of the at least two virus binding moieties.
• the mucin binding moiety may also be bound to more than one virus binding moieties.
• a bifurcated linker is, in an embodiment, particularly helpful. Such a bifurcated linker may be used to couple a single mucin binding moiety to a plurality of virus binding moieties that are, after coupling, arranged more or less equally distant from the mucin binding moiety.
• the virus binding moiety is a moiety that is adapted to bind a viral spike protein.
• the virus binding moiety is a peptide.
• the virus binding moiety is an antimicrobial peptide, such as a defensin. Retrocyclin is a particular appropriate defensin.
• the virus binding moiety is a non-peptidic antiviral residue, such as a dendritic or linear polysulfate or polycarbohydrate.
• the virus binding moiety comprises or is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11 , SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25,
• SEQ ID NO. 26 SEQ ID NO. 27, SEQ ID NO. 28, SEQ ID NO. 29, SEQ ID NO. 30, SEQ ID NO.
• SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
• the virus binding moiety is a peptide, wherein at least one of the residues of this peptide carries a substitution.
• the C terminus of the peptide is substituted with an amino group.
• the N terminus of the peptide is substituted with an acetyl group.
• the C terminus of the peptide is substituted with an amino group and the N terminus of the peptide is substituted with an acetyl group.
• the virus binding moiety is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 2 and the mucin binding moiety (1 ) is a trefoil factor 3 peptide being at least 95 %%, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 1 .
• SARS-CoV-1 severe acute respiratory syndrome coronavirus 1
• Han et aL high affinity
• the virus binding moiety is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 3 and the mucin binding moiety (1 ) is a trefoil factor 3 peptide being at least 95 %%, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 1 .
• SARS-CoV-1 severe acute respiratory syndrome coronavirus 1
• Han et aL 2006
• the p6 peptide is also very appropriate to bind to SARS-CoV-2.
• the binding affinity of the p6 peptide with respect to SARS-CoV-2 is approximately twice as high as the affinity of the p4 peptide.
• p6 is also able to bind SARS-CoV-2 variants alpha and delta with an even higher affinity than the SARS-CoV-2 Wuhan wild type (cf. Table 1)-
• the virus binding moiety is a peptide being at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 10.
• This peptide is a stapled variant of the p6 peptide. In the following, it is also referred to as p6-cyc or p6 (R8)I 5 (S5) 22 .
• the binding affinity of different virus binding moieties towards SARS-CoV-2 (expressed as the dissociation constant Kd) is summarized in the following Table 1. It was determined by microscale thermophoresis (MST). It can be well seen that the p4 and the p6 peptides (the latter both in its linear in its cyclized form) bind to several receptor binding domains of currently circulating SARS-CoV-2 variants with nanomolar binding constants.
• Table 1 Properties of different virus binding moieties.
• X in position 15 (X15) of p6-cyc is an alkenylated (R)-Ala residue
• X in position 22 (X22) of p6-cyc is an alkenylated (S)-Ala residue
• the peptide has a cyclization between X15 and X22 via a 7- undecenyl residue.
• the peptide is at least 95 %, in particular at least 96 %, in particular at least 97 %, in particular at least 98 %, in particular at least 99 %, in particular 100 %, identical to SEQ ID NO. 18 or SEQ ID NO. 19.
• SEQ ID NO. relate to synthetic and recombinant TFF-3-p6 peptides that turned out to have very appropriate properties for solving the present object.
• the present invention relates to the use of the peptide according to the preceding explanations as medicament.
• the present invention relates to the medical use of the peptide according to the preceding explanations in preventing or treating a viral infection.
• the viral infection to be treated or prevented is an infection with SARS-CoV- 2.
• the present invention relates to a medical method for treating or preventing a viral infection in a patient in need of such treatment.
• patient as used herein relates to a human or animal patient. Mammals are particularly appropriate animal patients.
• the method comprises the step of administering the peptide according to the preceding explanations to the patient (e.g., in form of a medicament comprising this peptide). This administration is done, in an embodiment, by providing the peptide to the nose or to the mouth of the patient. This can be particularly easy achieved by providing the peptide in a dosage form of a spray. Then, the peptide can be administered, e.g., as an aerosol like a nasal spray or an inhalation spray.
• the peptide Upon administration, it will then contact the patient’s mucosa and will allow a binding of the peptide to the mucosa via the mucin binding moiety. Afterwards, the peptide will stay in its bound form at the patient’s mucosa and will be able to “filter” viruses out of the air inhaled by the patient due to its virus binding moiety.
• the present invention relates to a medical method for mucus augmentation in a patient in need thereof.
• This method comprises the step of administering the peptide according to the preceding explanations to the patient (e.g., in form of a medicament comprising this peptide).
• the present invention relates to a medicament that comprises a peptide according to the preceding explanations as pharmaceutically active ingredient.
• This medicament can comprise other pharmaceutically active ingredients.
• the peptide is the only pharmaceutically active ingredient.
• the medicament is formulated such that it can be administered as an aerosol, such as a nasal spray or as an inhalation spray. Then, the medicament (and therewith the peptide as pharmaceutically active ingredient) directly contacts the mucosa in the nasopharyngeal zone upon its administration. This, in turn, leads to a mucus augmentation as explained above. As a result, the patient’s mucus is better prepared to bind and subsequently eliminate viruses with which the patient is confronted (either by inhaling them from the environment or by exhaling them from virus-infected cells of the patient’s body).
• the present invention relates to a method for manufacturing a peptide according to the preceding explanations.
• This method comprises the steps explained in the following. First, a virus binding moiety precursor is reacted with a first mucin binding moiety precursor.
• the first mucin binding moiety precursor comprises a first part of the final mucin binding moiety. This reaction leads to the formation of a peptide precursor.
• the peptide precursor is reacted with a second mucin binding moiety precursor.
• the second mucin binding moiety precursor comprises a second part of the mucin binding moiety.
• the final peptide is formed.
• other intermediate reaction steps may also be accomplished.
• the individual mucin binding moiety precursors are reacted one after the other with the already formed peptide precursor to finally result in the peptide.
• the virus binding moiety precursor comprises a 4-pentynoic moiety that establishes a covalent bond to the mucin binding moiety of the final peptide.
• This 4-pentynoic moiety may still be present (either fully or in part) in the final peptide. It may act as linker between the virus binding moiety and the mucin binding moiety in an embodiment.
• the peptide comprises a triazole residue acting as linker between the virus binding moiety and the mucin binding moiety.
• the peptide comprises a polyethylene glycol residue acting as linker between the virus binding moiety and the mucin binding moiety. Such polyethylene glycol residue is combined with a triazole residue to form a linker in an embodiment.
• the first mucin binding moiety precursor comprises less than half of all amino acids of the mucin binding moiety. If only two mucin binding moiety precursors are used, then the second mucin binding moiety precursor comprises more than the half of all amino acids of the mucin binding moiety.
• the first mucin binding moiety precursor comprises amino acids 36 to 59 of the mucin binding moiety, which is a trefoil factor 3 peptide in this embodiment.
• the second mucin binding moiety precursor comprises amino acids 1 to 35 of the mucin bending moiety.
• All embodiments of the peptide can be combined in any desired way and can be transferred either individually or in any arbitrary manner to the uses, to the medicament, and to the different methods.
• all embodiments of the different uses can be combined in any desired way and can be transferred either individually or in any arbitrary manner to the peptide, to the respective other uses, to the medicament, and to the different methods.
• all embodiments of the medicament can be combined in any desired way and can be transferred either individually or in any arbitrary manner to the peptide, to the different uses, and to the different methods.
• all embodiments of the different methods can be combined in any desired way and can be transferred either individually or in any arbitrary manner to the peptide, to the different uses, and to the respective other methods.
• Figure 1 A schematically shows the structure of a first embodiment of a bifunctional peptide
• Figure 1 B schematically shows the structure of a second embodiment of a bifunctional peptide
• Figure 2A shows the primary structure of an embodiment of a first mucin binding moiety precursor corresponding to SEQ ID NO. 15;
• Figure 2B shows the primary structure of an embodiment of a second mucin binding moiety precursor corresponding to SEQ ID NO. 16
• Figure 2C shows the primary structure of an embodiment of a virus binding moiety precursor corresponding to SEQ ID NO. 17;
• Figure 3 shows the primary structure of an embodiment of a peptide corresponding to SEQ ID NO. 18 comprising a mucin binding moiety made from the first and second mucin binding moiety precursors of Figures 2A and 2B and a virus binding moiety made from the virus binding moiety precursor of Figure 2C;
• Figure 4 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 4;
• Figure 5 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 5;
• Figure 6 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 6;
• Figure 7 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 7;
• Figure 8 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 8;
• Figure 9 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 9;
• Figure 10 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 10;
• Figure 1 1 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 1 1 ;
• Figure 12 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 12
• Figure 13 shows the primary structure of an embodiment of a virus binding moiety corresponding to SEQ ID NO. 13;
• Figure 14 shows a plot illustrating the binding affinity between the p6 peptide and different SARS-CoV-2 variants
• Figure 15 shows a plot illustrating the binding affinity between the bifunctional synthetic TFF3-p6 peptide corresponding to SEQ ID NO. 18 and different SARS-CoV-2 variants;
• Figure 16 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 23 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 17 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 24 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 18 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 25 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 19 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 26 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 20 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 28 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 21 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 29 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 22 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 30 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 23 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 31 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 24 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 32 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 25 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 33 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 26 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 34 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 27 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 35 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 28 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 36 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 29 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 37 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 30 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 38 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 31 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 39 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 32 shows a plot illustrating the binding affinity between the p4 peptide variant corresponding to SEQ ID NO. 40 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 33 shows a plot illustrating the binding affinity between the p6 peptide variant corresponding to SEQ ID NO. 41 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 34 shows a plot illustrating the binding affinity between the p6 peptide variant corresponding to SEQ ID NO. 42 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 35 shows a plot illustrating the binding affinity between the p6 peptide variant corresponding to SEQ ID NO. 43 and the receptor binding domain of SARS-CoV- 2 (2019-nCoV);
• Figure 36 shows a plot illustrating the binding affinity between the bifunctional recombinant TFF3-p6 peptide corresponding to SEQ ID NO. 19 and different SARS-CoV-2 variants.
• FIG. 1A schematically illustrates the structure of the first embodiment of a bifunctional peptide, namely TFF3-p6.
• TFF3-p6 This is a peptide in which a trefoil factor 3 (TFF3) peptide 1 is the mucin binding moiety, wherein the p6 peptide 2 is the virus binding moiety.
• the TFF3 peptide 1 has a primary sequence corresponding to SEQ ID NO. 1 .
• the p6 peptide 2 has a primary sequence corresponding to SEQ ID NO. 3.
• the p6 peptide 2 is covalently bound to lysine 57 of the TFF3 peptide.
• Figure 1 A shows an alternative embodiment of a bifunctional peptide.
• similar elements will be denoted with the same numeral reference.
• the p6 peptide 2 is covalently bound to the C terminus of the TFF3 peptide 1 .
• TFF3-p6 The synthesis of TFF3-p6 will be explained in the following in more detail.
• TFF3 For the production of TFF3, the protocol of Braga Emidio et al. 2021 was followed. In contrast to the synthesis routes published by Braga Emidio et aL, azido lysine was introduced into TFF3 by replacing cysteine at position 57.
• TFF3(36-59)(C57AzK) representing an embodiment of a first virus binding moiety precursor was made totally by SPPS on Rink Amide Resin, using the corresponding building block for azido lysine (AzK) for position 57.
• the primary structure is illustrated in Figure 2A.
• TFF3(1-35)-Nbz representing an embodiment of a second virus binding moiety precursor was synthesized on Rink Amide Resin, which was initially functionalized with 3- fluorenylmethoxycarbonyl-4-diaminobenzoic acid (Fmoc-Dbz) by normal coupling methodologies (5 equivalents (eq) Fmoc-Dbz, 4.9 eq hexafluorophosphate azabenzotriazole tetramethyl uronium (HATU), 10 eq N,N-diisopropylethylamine (Dipea), in dimethylformamide (DMF) enough to make the solution 0.2 M regarding the 3-Fmoc-4-diaminobenzoic acid (Fmoc- Dbz).
• Fmoc-Dbz 3- fluorenylmethoxycarbonyl-4-diaminobenzoic acid
• TFF3(1-35)-Nbz and TFF3(36-59)(C57K-Pentyp6) 0.8 eq
• reaction buffer 6M guanidinium hydrochloride, 100 mM of Na 2 HPO 4 , and 30 mM TCEP, the pH was adjusted to 7.0 with HCI/NaOH).
• MeSNa 2-mercaptoethanesulfonate
• Controls were made by dissolving 1 pL of reaction crude in 20 pL 30% acetonitrile (MeCN)/H 2 O, and then adding TCEP to reach a 30 mM concentration. After incubation at 37 °C for 5 minutes, the samples were analyzed by HPLC-MS. When no more trace of the thioester were left, the volume of the reaction was increased to 3 mL by adding 30% MeCN/H 2 O with 0.1% TFA, filtered, and injected on a preparative HPLC system for purification.
• MeCN acetonitrile
• Native TFF3 was also produced in a recombinant way. To achieve this, the protocol of Jarva et aL, 2020 was followed and adjusted.
• E. coli BL21 CodonPlus(DE3) RIPL cells were transformed with the according plasmid. The cells were streaked out on lysogeny broth (LB) agar plates containing 50 pg/mL Streptomycin, 25 pg/pL Chloramphenicol and 50 pg/mL Kanamycin and incubated in an incubator at 37 °C over night. One colony was picked and a LB medium containing 50 pg/mL Streptomycin, 25 pg/pL Chloramphenicol and 50 pg/mL Kanamycin was inoculated and incubated in a rotary shaker incubator at 250 rpm, at 37 °C over night.
• LB lysogeny broth
• TB medium was inoculated with the LB culture with a starting optical density measured at 600 nm (OD 6 oo) of 0.02 and incubated in a rotary shaker incubator at 250 rpm and 37 °C. The culture was grown to an OD 6 OO of >2.867. 7.527% DMSO were added to this culture, and the mixture (pre-culture) was snap-frozen in liquid nitrogen and stored at -80 °C for further use.
• TB medium was inoculated with an OD 6 oo of 0.04 with the pre-culture.
• the culture was incubated in a rotary shaker incubator at 250 rpm, 26 °C for 24 hours. After 24 hours, the bacterial culture was cooled down on ice for 15 minutes and spun down with a centrifuge at 3000 g for 15 minutes. The supernatant was discarded and the cells were resuspended in washing buffer (HEPES based, pH 7) + DNase I + phenylmethylsulfonylfluorid (PMSF). The suspension was spun down at 3000 g for 15 min and the supernatant was discarded. The washing step was repeated.
• washing buffer HPES based, pH 7
• PMSF phenylmethylsulfonylfluorid
• the target proteins were purified upon tandem affinity purification with His-tag, and Strep-tag (binding motif for streptavidin) purification. Protease cleavage sites allow the elution of proteins from the columns. The eluted protein was dialyzed and verified upon SDS-PAGE.
• lactam-stapled peptides were made on Rink-amide resin.
• the building blocks for the isopeptide bond formation were N-a-Fmoc-N-£-4-methyltrityl-L-lysine (hereinafter denoted as MttK) and N-a-Fmoc-L-aspartic acid p-2-phenylisopropyl ester (hereinafter denoted as PhiPr).
• MttK N-a-Fmoc-N-£-4-methyltrityl-L-lysine
• PhiPr N-a-Fmoc-L-aspartic acid p-2-phenylisopropyl ester
• SPPS the peptide bound in the resin was treated with 2 % TFA in dichloromethane (DCM) to induce 4-methyltrityl and 2- phenylisopropyl deprotection.
• DCM dichloromethane
• isopeptide bond formation was allowed to take place, followed by adding 0.9 equivalents of HATU and 2 equivalents DIPEA, in DMF. After extensive rinsing in DMF and DCM, a second addition of coupling cocktail was done. The peptides were cleaved from the resin using 95:2.5:2.5 of TFA:H 2 O:TIPS and precipitated with cold ether. The peptides were then filtered, dried, and redissolved in 30 % MeCN/H2O with 0.1 % TFA to a final volume of 3 mL. After filtration, the samples were injected in a preparative HPLC system for purification.
• the binding affinity of different cyclic virus binding moieties towards SARS-CoV-2 (expressed as the dissociation constant Kd) is summarized in the following Table 2. It was determined by microscale thermophoresis (MST). It can be well seen that the cyclic p6 peptides bind to SARS- CoV-2 with micromolar binding constants.
• the coupling conditions were: 3.0 equivalents AA, 2.9 eq HATU, 6 eq DIPEA. DMF was added to reach a 0.2 M concentration with respect to the AA.
• the coupling conditions were: 5.0 equivalents AA, 4.9 eq HATU, 10 eq DIPEA. DMF was added to reach a 0.2 M concentration with respect to the AA.
• the resin was washed with 1 ml of DCE (3 x 1 min) and then with 1 ml of DCM (3 x 1 min) and then dried under a stream of nitrogen. Peptide cleavage from the resin was done using 95:2.5:2.5 of TFA:H 2 O:TIPS.
• the crude was precipitated with cold ether, filtered, and dried.
• the product was redissolved in 30% MeCN/H2O with 0.1 % TFA to a final volume of 3 mL. After filtration, the samples was injected in a preparative HPLC system for purification.
• Acetylation was performed on the RCM products by swelling the Fmoc-deprotected resin in 1 ml of N-methyl-2-pyrrolidone (NMP) for 10 min and draining the solvent. Then, 2 ml of a solution of acetic anhydride and DIPEA in NMP (85:315:1 ,600 in volume) was prepared and added to the resin. Gently agitation of the mixture with bubbling under nitrogen was performed for 45 min and then the solvent was drained. Extensive washings followed with DCM and DMF. Finally, cleavage and purification was performed as outlined above.
• NMP N-methyl-2-pyrrolidone
• the peptides contained i) an S5 residue (an alkenylated S-alanine) and an R8 residue (an alkenylated R-alanine) or ii) two S5 residues.
• An alkenyl bridge was formed between i) an S5 residue and an R8 residue or ii) between two S5 residues.
• This alkenyl bridge is a 7-undecenyl residue in case of an S5 residue and an R8 residue.
• the alkenyl bridge is a 4-octenyl residue in case of two S5 residues.
• thermophoresis microscale thermophoresis
• RBD labelled compound
• bound ligands here: peptides
• MST microscale thermophoresis
• an infrared laser induces a local heat spot and subsequently a temperature gradient. Molecules move along this gradient depending on their characteristics at the water-protein interface.
• a bound ligand leads to changes of the ordered water shell at the observed protein, and may change or add also the effective surface potential. This leads to changes in the thermophoretic behavior indicated by an either increasing or decreasing thermophoresis amplitude.
• the change in fluorescence can be plotted (y-axis) against the ligand concentration. From the half-maximum change in fluorescence (inflexion point from saturation curve), the Kd of the protein-ligand interaction can be derived upon application of the mass-action law (Jerabek-Willemsen et al. 2014).
• RBD labeling and purification was performed using a 2 nd generation NHS-Red labeling kit (NanoTemper). RBD solution was diluted with water to 10 pM, rebuffered in sodium carbonate aqueous solution at pH 8.0, and incubated in the dark at 300 pM of the red dye.
• Size exclusion chromatography allowed obtaining the labeled RBD free of unreacted dye.
• the labeling efficiency was analyzed from spectroscopy measurements to be approximately 1 :1 (protein :dye). Affinity measurements were conducted in Dulbecco's Phosphate Buffered Saline (DPBS) (without Ca 2+ and Mg 2+ ) supplemented with 0.05 % (v/v) Tween20, and premium capillaries (NanoTemper).
• DPBS Dulbecco's Phosphate Buffered Saline
• MST was then measured by making 16 sequential 1 :1 dilutions of each peptide, using PBS + 0.05 % Tween 20 as diluent, each with a final volume of 10 pL. Each diluted sample was then incubated with 10 pL of the 10 nM labeled RBD stock solution, therefore always keeping a 5 nM concentration of the labeled target protein in every sample.
• MST signal was then acquired in a NanoTemper Technologies Monolith NT.1 15 Pico instrument, at an excitation power of 20% and a MST power of 40%.
• the signal was analyzed 1 .5 seconds after the start of the IR-laser, and the obtained data was fitted as shown previously (Bhatia et al. 2017). These conditions were kept the same for all the measured samples.
• a plurality of additional p4 and p6 derivatives was synthesized and the affinity of these p4 and p6 derivatives against the receptor binding domain was tested in MST experiments as explained above for the p6 peptide.
• All p4 derivatives were synthesized as described in Sarto et al. 2022.
• the p6 derivatives p6- rigid, p6-dis and p6-rigid-dis were ordered from PSL (Peptide Specialty Laboratories GmbH, Heidelberg) as TFA-salt. Upon arrival, the peptides were reconstituted in PBS, snap-frozen in liquid nitrogen and stored at -80°C until further usage.
• Table 4 lists the different tested p4 derivatives as well as the dissociation constants obtained from the affinity measurements.
• the cysteine residues of all peptides are in their normal, reduced state.
• the results of the affinity measurements are also illustrated in Figures 16 to 32.
• Table 4 Properties of p4 derivatives (virus binding moieties).
• All p4 derivatives showing a dissociation constant against the SARS-CoV-2 RBD of less than 0.3, in particular less than 0.2, in particular less than 0.1 , in particular less than 0.05, in particular less than 0.04, in particular less than 0.03, in particular less than 0.02, are particular appropriate virus binding moieties.
• Table 5 lists the different tested p6 derivatives as well as the dissociation constants obtained from the affinity measurements.
• the cysteine residues of all peptides are in their oxidized state so that they form an intramolecular disulfide bond.
• the results of the affinity measurements are also illustrated in Figures 33 to 35.
• Table 5 Properties of p6 derivatives (virus binding moieties).
• TFF3-p6 was also produced in a recombinant way. To achieve this, the protocol of Jarva et aL, 2020 was followed and adjusted.
• the TFF3 sequence was then extended to introduce purification tags and a TEV (Tobacco Etch Virus) protease cleavage site at the 5’ end and p6 at the 3’ end.
• TEV tobacco Etch Virus
• the product was integrated into the plasmid pET28b for bacterial expression using sequence- and ligationindependent cloning (SLIC).
• SLIC sequence- and ligationindependent cloning
• the final plasmid was approved by sequencing and transformed into BL21 CodonPlus(DE3) RIPL cells for bacterial expression. This was done as explained above in detail in the paragraph “Preparation of Exponential Growth Stock-Culture of Transformed E. coli BL21 CodonPlus(DE3) RIPL”.
• TB medium was inoculated with an OD 6 oo of 0.04 with the pre-culture.
• the culture was incubated in a rotary shaker incubator at 250 rpm, 26 °C for 24 hours. After 24 hours, the bacterial culture was cooled down on ice for 15 minutes and spun down with a centrifuge at 3000 g for 15 minutes. The supernatant was discarded and the cells were resuspended in washing buffer (HEPES based, pH 8). The suspension was spun down at 3000 g for 15 min and the supernatant was discarded. The washing step was repeated. The bacteria cells were lysed in lysis buffer (HEPES based, pH 8) by sonication. The lysate was spun down at 12.000 g for 45 minutes, the pellet discarded, and the supernatant filtered through a 0.2 pm filter.
• the target proteins were purified upon tandem affinity purification with His-tag, and Strep-tag (binding motif for streptavidin) purification.
• Imidazole (ImH) was added to the filtered bacterial lysate to a final concentration of 40 mM.
• the lysate was applied to a HisTrap column (Cytiva) using an Akta Pure 25 (Cytiva) fast protein liquid chromatography (FPLC) device.
• the column was washed with wash buffer (300 mM NaCI, 50 mM Tris-base, 40 mM ImH, pH 7.5), the proteins eluted with elution buffer (300 mM NaCI, 50 mM Tris-base, 400 mM ImH, pH 7.5) and the elute collected in fractions. Fractions containing the product of interest were identified via SDS-PAGE and pooled.
• the pooled fractions were applied to a Strep-Tactin XT 4Flow column (IBA Lifesciences) using an Akta Pure 25.
• the column was washed with wash buffer (100 mM Tris-HCI, 150 mM NaCI, 1 mM ETDA, pH 8), the proteins eluted with elution buffer (100 mM Tris-HCI, 150 mM NaCI, 1 mM ETDA, 50 mM biotin, pH 8) and the elute collected in fractions.
• Fractions containing the product of interest were identified via SDS-PAGE and pooled prior to dialysis against PBS (pH 7.4).
• the protein content was determined via the absorption spectrum at 280 nM using a NanoDrop2000 spectrophotometer (Thermo Fisher Scientific).
• the purified products were incubated over night at 30 °C with ProTEV Plus (Promega) according to the manufacturer’s recommendations with 1 U ProTEV Plus per 15 pg of purified product.
• ImH was added to the reaction mix to a final concentration of 40 mM before applying it to a HisTrap column using an Akta Pure 25 and washing the column with wash buffer (300 mM NaCI, 50 mM Tris-base, 40 mM ImH, pH 7.5)
• wash buffer 300 mM NaCI, 50 mM Tris-base, 40 mM ImH, pH 7.5
• the flow through with the final product (TFF3- p6) was collected in fractions, while the cleaved purification tags and the ProTEV Plus (also containing a His-tag) remained in the column.
• Fractions containing the final product were identified via SDS-PAGE, pooled and dialyzed against PBS (pH 7.4).
• the volume was reduced using a Vivaspin PES Centrifugal Concentrator (Sartorius) to a final protein concentration between 1 mg/ml and 3 mg/ml as determined by NanoDrop2000.
• the solution was snap-frozen in liquid nitrogen and stored at -20 °C until further usage.
• the correct final product and the purity was controlled by SDS-PAGE and Ultra-Performance-Liquid-Chromatography-Mass- Spectrometry (UPLC/MS).
• TFF3-p6 TFF3-C57K(Penty-p6) or TFF3-p6 syn; the primary structure of which is illustrated in Figure 3 and reproduced in SEQ ID NO. 18
• recombinant TFF3-p6 TFF3-p6 rec
• SEQ ID NO. 19 recombinant TFF3-p6 (TFF3-p6 rec) according to SEQ ID NO. 19 were titrated against a constant concentration (5 nM) fluorescently labelled RBD of the wildtype SARS-CoV2 (also denoted as nCov2019) and o the Delta variant of SARS-CoV2 (also denoted as Delta (B.1 .617.2)).
• the resulting dissociation constants (Kd) are listed in Table 6.
• the results of this affinity measurement are shown in Figure 15 for TFF3-p6 syn and in Figure 36 for TFF3-p6 rec.
• Table 6 Dissociation constants of affinity measurements of TFF-p6 versus RBD of SARS- CoV-2.
• Cell viability was determined using a Cell Counting Kit (Hycultec, HY-K0301 ) according to the manufacturer’s instructions.
• A549, HBE and Calu-3 cells were cultured in DMEM supplemented with 10% (v/v) FBS, 100 U/mL penicillin and 100 pg/mL streptomycin. Cells were seeded in a 96-well plate at a density of 5 x 10 4 cells/mL in 90pl DMEM Medium per well over night at 37°C and 5% CO2.
• VSV vesicular stomatitis virus
• VSVAG-CoV-2 SARS-CoV-2 spike protein
• TFF3-p6 or PBS (control) was incubated with VSVAG-CoV-2 for 30 min at a final concentration of 50 pM TFF3-p6 and 2.625 x 10 4 ffu/mL virus in 100 pl.
• the mixture was added to VeroE6 cells and incubated for 24 h at 37 °C in a cell culture incubator. Pictures were taken using a fluorescence microscope and the number of infected cells was determined.
• TFF3-p6 could reduce the infection of VeroE6 cells with VSVAG-CoV2 pseudovirus by about 40 % as compared to the PBS control.

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