Classifications

• • 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
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/08—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from viruses
  • C07K16/10—RNA viruses
  • C07K16/102—Coronaviridae (F)
  • C07K16/104—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2]
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/55—Fab or Fab'
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding

Definitions

• Coronaviridae family comprises a large number of virus species that are further classified in four genera. Seven species are of human interest and are highly diversified in terms of adaptation, pathogenicity and diffusion. Indeed, four species are endemic and highly adapted to humans (HCoV-229E, HCoV-NL63, HCoV- OC43 and HCoV-HKUl), two are epidemic (MERS-CoV and the extinct SARS- CoV) and one pandemic, the recently emerged and currently circulating SARS-CoV and SARS-CoV-2 belong to the same genus (Betacoronavirus) and subgenus (Sarbecovirus) but are phylogenetically distinct and have strikingly different features in terms of infectivity and clinical signs. These aspects demonstrate the difficulties in thoroughly sampling the entire Coronaviridae family necessary to implement an effective surveillance program and therefore stress the need to have therapeutic strategies with broad activity on Co Vs.
• the ideal target to inhibit a virus replication is represented by the proteins that mediate entry because this prevents cell infection. Entry inhibitors can thus be used as effective therapeutics and, whether endowed with long half-life, in prophylaxis.
• the relevance of inhibiting virus entry is demonstrated by the fact that most neutralizing antibodies elicited by natural infection or vaccination recognizes fundamental regions of the viral proteins involved in entry.
• mAbs monoclonal antibodies
• immunization will be the most effective approach to limit and possibly eradicate SARS-CoV-2
• the identification of neutralizing mAbs (nAbs) will be fundamental to address vaccines intrinsic limitations regarding the delayed response, the fraction of non-responders and the impossibility to vaccinate immunocompromised individuals.
• nAbs neutralizing mAbs
• the entire entry process of all CoVs into host cells is mediated by the spike (S), a large transmembrane glycoprotein protruding from the virus envelope.
• the spike is a homotrimer in which each monomer is produced as a single protein (SO) that is cleaved by host proteases into the SI and S2 subunits.
• SI is located apically and contains the receptor binding domain (RBD), therefore it mediates the attachment phase by interacting with host proteins.
• S2 forms the spike stalk that contains the fusion peptide, the transmembrane domain, and the heptad repeats (HR1 and HR2), all necessary to fuse the virus envelope to the host membranes.
• CoVs entry is a multistep process that involves receptor engagement of all three RBDs in each spike trimer, the proteolytic cleavage of at least one specific spike site and the subsequent fusion.
• SARS-CoV-2 in analogy with SARS-CoV and several animal CoVs, specifically binds to the angiotensin-converting enzyme 2 (ACE2).
• ACE2 angiotensin-converting enzyme 2
• the binding event is necessary but not sufficient to mediate entry, as SARS-CoV-2 S requires to be processed by host proteases that also specifically determine the virus entry site. Indeed, if the spike is cleaved by furin and TMPRSS2, SARS-CoV-2 fusion happens at the plasma membrane, conversely it enters from the endosomal compartment, where the spike is cleaved by cathepsins. Once the spike is completely engaged and cleaved, S 1 dissociates from S2 allowing the exposure of the fusion peptide and its insertion in the host membranes.
• the spike protein of CoVs is the most prominent protein exposed on virions surface and the main target of the humoral response. Characterization of sera from SARS-CoV-2 infected individuals has identified several neutralizing epitopes located on the spike protein that either overlap with domains fundamental for its function or indirectly inhibit the conformational changes required to mediate attachment and fusion.
• the broadly neutralizing mAb ADG-2 recognizes an epitope partially shared with class 1 nAbs, highlighting how even minor differences in terms of residues involved and angle of approach can dramatically impact the biologic activity of a nAb.
• nAbs recognizing other epitopes have been identified as well. Indeed, strong neutralization has been documented to a mAb that binds to a region (N-terminal domain -NTD) in SI not directly involved in entry.
• RBD the neutralizing response in patient sera is dominated by antibodies specific for the RBD
• S 1 the spike most variable domains, both considering SARS-CoV-2 variants continuously emerging and among CoVs belonging to the same sub-genus.
• bamlanivimab LY-CoV555
• LY-CoV555 a combination of bamlanivimab
• LY-C0VOI6 or JS016 a combination of casirivimab
• REGN10987 a combination of casirivimab
• REGN10987 an element of Regeneron
• a combination cilgavimab COV2-2130 or AZD1061
• tixagevimab COV2-2196 or AZD8955
• monotherapy-based nAbs sotrovimab VIR-7831
• CT-P59 regdanvimab
• VOC World Health Organization
• a “variant of interest” is a variant with a new mutation capable of affecting disease severity, transmissibility, immune and diagnostic escape.
• the current variants of concern are Alpha (B .1.1.7, identified in the United Kingdom) [12], Beta (B.1.351, identified in South Africa) [13], Gamma (P.1, identified in Brazil) [14], Delta (B.1.617.2, identified in India) [15] and Omicron sublineages and descendent lineages (Omicron (B.1.1.529) [16], Omicron BA.2 (B.1.1.529+BA.2) Omicron BAA (B.1.1.529+BA.4) and Omicron BA.5.2 (B.1.1.529+BA.5)).
• an effective antiviral therapeutic strategy should have the ability to prevent infection/disease by new variants while simultaneously maintaining breadth against existing multiple viral strains/variants.
• Recent studies have reported that many NTD- specific NAbs are relatively less effective to all emerging variants, whereas RBD- specific NAbs are variably effective against emerging variants and VOCs.
• the majority of the potent therapeutic nAbs as monotherapy showed complete abrogation or reduced neutralizing activity against SARS-CoV-2 emerging variants that contain the E484K/Q or L452R mutations.
• Bamlanivimab (LY-CoV555) was ineffective against all VOCs and thus was no longer considered for EUA.
• combination therapies comprising a cocktail of nAbs targeting distinct nonoverlapping epitopes on RBD have demonstrated exceptional potency and promising correlates of protection against SARS-CoV-2 and its variants. See for reference Additionally, newly identified RBD core-binding nAbs SARS2-38 and LY- CoV1404 as monotherapy potently neutralize all variants of concern of SARS-CoV- 2.
• an isolated antibody or antibody fragment binding a conserved region of the spike protein of Sarbecoviruses characterized by an antigen binding site comprising: a) a heavy chain variable sequence comprising: i) a CDR1 comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3 , SEQ ID NO:4 and SEQ ID NO: 93; ii) a CDR2 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7,SEQ ID NO:8 and SEQ ID NO:94; iii) a CDR3 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO:95; and/or b) a light chain variable sequence comprising: i) a CDR1 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:
• CDRs Complementary determining regions (CDRs; CDR1-CDR3) of the variable domain of heavy and constant regions and framework regions (FRs; FR1-FR4) characterizing the sequence of the isolated antibody or antibody fragment of the invention have been determined according to IMGT nomenclature.
• the heavy chain variable sequence the antibody or antibody fragment of the invention further comprises: a) a framework region (FR1) comprising an amino acid sequence selected from the group consisting of SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28 and SEQ ID NO:98; b) a framework region (FR2) comprising an amino acid sequence selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32 and SEQ ID NO:99; c) a framework region (FR3) comprising an amino acid sequence selected from the group consisting of SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36 and SEQ ID NO: 100; d) a framework region (FR4) comprising an amino acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, and SEQ ID NO: 101; and
• the antibody or antibody fragment is characterized by an antigen binding site comprising: a) a heavy chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO:1; a CDR2 comprising the amino acid sequence SEQ ID NO:5; a CDR3 comprising the amino acid sequence SEQ ID NO:9 and/or a light chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO: 13; a CDR2 comprising the amino acid sequence GAS; a CDR3 comprising the amino acid sequence SEQ ID NO:20.
• said heavy chain variable sequence may further comprises: a framework region FR1 comprising SEQ ID NO:25; a framework region FR2 comprising SEQ ID NO:29; a framework region FR3 comprising SEQ ID NO:33 and a framework region FR4 comprising SEQ ID NO:37; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:41, a framework region FR2 comprising SEQ ID NO:46, a framework region FR3 comprising SEQ ID NO:51, and a framework region FR4 comprising SEQ ID NO:56; b) a heavy chain variable sequence comprising: a CDR1 comprising the amino acid sequence SEQ ID NO:1; a CDR2 comprising the amino acid sequence SEQ ID NO:5; a CDR3 comprising the amino acid sequence SEQ ID NO:9 and/or a light chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO: 13; a CDR2 comprising the amino acid
• said heavy chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:25; a framework region FR2 comprising SEQ ID NO:29; a framework region FR3 comprising SEQ ID NO:33 and a framework region FR4 comprising SEQ ID NO:38; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:42; a framework region FR2 comprising SEQ ID NO:47; a framework region FR3 comprising SEQ ID NO:52, and a framework region FR4 comprising SEQ ID NO:57; c) a heavy chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO:2; a CDR2 comprising the amino acid sequence SEQ ID NO:6; a CDR3 comprising the amino acid sequence SEQ ID NO: 10 and/or a light chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO: 14; a CDR2 comprising the amino acid sequence A
• said heavy chain variable sequence may further comprises a framework region FR1 consisting of SEQ ID NO:26; a framework region FR2 consisting of SEQ ID NO:30 a framework region FR3 comprising SEQ ID NO:34, and a framework region FR4 comprising SEQ ID NO:39; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:43; a framework region FR2 comprising SEQ ID NO:48; a framework region FR3 comprising SEQ ID NO:53 and a framework region FR4 comprising SEQ ID NO:58; d) a heavy chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO:3; a CDR2 comprising the amino acid sequence SEQ ID NO:7; a CDR3 comprising the amino acid sequence SEQ ID NO: 11 and/or a light chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO: 15; a CDR2 comprising the amino acid sequence
• said heavy chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:27; a framework region FR2 comprising SEQ ID NO:31 a framework region FR3 comprising SEQ ID NO:35 and a framework region FR4 consisting of SEQ ID NO:40; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:44; a framework region FR2 comprising SEQ ID NO:49; a framework region FR3 comprising SEQ ID NO:54 and a framework region FR4 comprising SEQ ID NO:56; e) a heavy chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO:4; a CDR2 comprising the amino acid sequence SEQ ID NO:8; a CDR3 comprising the amino acid sequence SEQ ID NO: 12; and/or a light chain variable sequence comprising: a CDR1 comprising the amino acid sequence SEQ ID NO: 16; a CDR2 comprising the amino acid sequence
• said heavy chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:28; a framework region FR2 comprising SEQ ID NO:32; a framework region FR3 comprising SEQ ID NO:36 and a framework region FR4 comprising SEQ ID NO:39; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:45; a framework region FR2 comprising SEQ ID NO:50; a framework region FR3 comprising SEQ ID NO:55; and a framework region FR4 comprising SEQ ID NO:59; f) a heavy chain variable sequence comprising a CDR1 comprising the amino acid sequence SEQ ID NO:93; a CDR2 comprising the amino acid sequence SEQ ID NO:94; a CDR3 comprising the amino acid sequence SEQ ID NO:95; and/or a light chain variable sequence comprising: a CDR1 comprising the amino acid sequence SEQ ID NO:96; a CDR2 comprising the amino acid
• said heavy chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO:98; a framework region FR2 comprising SEQ ID NO:99; a framework region FR3 comprising SEQ ID NO: 100 and a framework region FR4 comprising SEQ ID NO: 101; said light chain variable sequence may further comprises a framework region FR1 comprising SEQ ID NO: 102; a framework region FR2 comprising SEQ ID NO: 103; a framework region FR3 comprising SEQ ID NO: 104; and a framework region FR4 comprising SEQ ID NO: 105.
• the antibody or antibody fragment (clone Fab 5#) of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and/or a light chain variable sequence comprising the amino acid sequence:
• the antibody or antibody fragment (clone Fab BU.2) of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and a light chain variable sequence comprising the amino acid sequence:
• the isolated antibody or antibody fragment (clone Fab BU.7) of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and/or a light chain variable sequence comprising the amino acid sequence:
• the isolated antibody or antibody fragment of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and/or a light chain variable sequence comprising the amino acid sequence:
• the isolated antibody or antibody fragment of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and/or a light chain variable sequence comprising the amino acid sequence:
• the isolated antibody or antibody fragment (clone Fab BS.70) of the invention comprises an heavy chain variable sequence comprising the amino acid sequence: and a light chain variable sequence comprising the amino acid sequence:
• nucleotide sequence encoding for the heavy chain variable region and/or the light chain variable region of the antibody or antibody fragment of the invention above listed.
• the invention reates to an expression vector comprising at least one of the nucleotide sequence encoding for the heavy chain and/or the light chain variable region of the antibody or antibody fragment of the invention.
• a further object of the invention contemplates an host cell comprising the vector above outlined. It is another object of the invention an hybridoma comprising at least one of the nucleotide sequence encoding for the heavy chain and/or the light chain variable region of the antibody or antibody fragment of the invention.
• the invention contemplates a formulation for molecular/vector-based passive immunoprophylaxis comprising at least one of the nucleotide sequence or expression vector of the invention together with one or more pharmaceutically acceptable excipients and/or adjuvants.
• the vaccine formulation may be advantageously be used in the prevention of Sarbecoviruses-mediated diseases in a subject, in particular of the Severe Acute Respiratory Syndrome mediated by SARS- CoV-1 or SARS-CoV-2.
• the antibody or antibody fragment of the invention is a monoclonal antibody.
• the antibody fragment is a Fab fragment.
• the antibody or antibody fragment of the invention is a human antibody.
• the antibody or antibody fragment is a human IgG or an IgG fragment selected from the group consisting of IgGl, IgG2, IgG3, IgG4 or a recombinant IgG comprising a mutated Fc portion to improve their binding and neutralization activity or all the Fc-mediated immune functions.
• the antibody or antibody fragment of the invention are in a format selected among the group comprising single chain antibodies (scFv), nanobodies, bispecific antibodies, monoclonal antibodies conjugated with drugs and/or molecules influencing their pharmacokinetics and/or their delivery.
• scFv single chain antibodies
• nanobodies nanobodies
• bispecific antibodies monoclonal antibodies conjugated with drugs and/or molecules influencing their pharmacokinetics and/or their delivery.
• the antibody or antibody fragment of the invention is labelled with a marker or conjugated with a drug.
• antitumour activity has been accomplished by conjugating antibodies with different effector molecules that accomplish cell death after antibody binding and internalisation.
• effector molecules include cytotoxic agents [19, 20], bacterial or plant protein toxins (immunotoxins) [21, 22], and radiopharmaceutical agents [23].
• a further object of the present invention is the use of the antibody or antibody fragment of the invention to detect the presence of a Sarbecovirus, preferably of SARS-CoV-1 or SARS-CoV-2 in a biological sample.
• the present invention further contemplates the antibody or antibody fragment of the invention for use in medical field for the treatment and/or prophylaxis of Sarbecoviruses-mediated diseases in a subject, in particular of the Severe Acute Respiratory Syndrome mediated by SARS-CoV-1 or SARS-CoV-2.
• SARS-Cov-2 encompasses anyone of the variants of concern (VOCs) Alpha (B.1.1.7), Beta (B.1.351) Gamma (P.1), Delta (B.1.617.2), D614 G (Universita di Pavia) and Omicron (B.1.1.529) or of the variants of interest (VOIs) Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1) and Lambda (C.37), known sofar.
• the antibody or antibody fragment of the present invention may be used alone or in combination with another antibody or antibody fragment directed against different conserved regions of the spike protein.
• the combined use of the antibody or antibody fragment of the invention enhances the cross reactivity of the therapeutic treatment towards the different VOCs of SARS-CoV-2.
• the second antibody may be also a different antibody with respect to the claimed ones. Combinations of antibodies targeting different epitopes can translate into enhanced therapeutic efficacy, i.e., overcoming drug-related side effects of already approved molecules or clearing drug resistance of possible novel circulating variants.
• the subject is an immunocompromised patient or a patient with an history of cardiovascular and/or respiratory diseases.
• the patient may be an elderly patient (that is older than 70 years) or a vaccine -hesitant subject.
• the antibody or antibody fragment according to the invention may be advantageously therapeutically administered in a human being also in a combination antibody cocktail.
• the antibody or antibody fragment of the invention is administered after 5- 10 days from occurrence of SARS-CoV-1 or SARS-CoV-2 infection.
• a pharmaceutical composition comprising at least one of the antibody or antibody fragment of the invention as the active ingredient, together with one or more pharmaceutically acceptable excipients and/or adjuvants.
• the antibody or antibody fragment is adapted to systemic administration by intravenous route.
• the invention alternatively contemplates intramuscular or subcutaneous administration route.
• the present invention further relates to a pharmaceutical composition
• a pharmaceutical composition comprising at least one of the antibody or antibody fragment of the invention for use in the treatment or prophylaxis of Sarbecoviruses-mediated diseases in a subject, in particular of the Severe Acute Respiratory Syndrome mediated by SARS-CoV-1 or SARS-CoV-2.
• composition or kit of parts comprising a first antibody or antibody fragment that binds a targeted conserved region of the spike protein of SARS-CoV-1 or SARS-CoV-2 of the invention and a second antibody or antibody fragment that binds a different targeted conserved region of the spike protein of SARS CoV-1 or SARS-CoV-2, for the simultaneous, separate or sequential administration in a subject affected by Sarbecoviruses-mediated diseases, in particular by the Severe Acute Respiratory Syndrome mediated by SARS CoV-1 or SARS-CoV-2.
• the first antibody or antibody fragment and the second antibody or antibody fragment are in separate containers.
• FIG. 1 shows a general scheme for the preparation and selection of a naive recombinant antibody library. This figure indicates the general steps involved in the construction and selection of a recombinant antibody from a phage display library.
• the B -lymphocytes are first isolated from the blood of the donors. The total mRNA is extracted from the isolated lymphocyte cells and reverse-transcribed to complementary DNA (cDNA).
• the variable heavy (VH) and variable light (VL) chain antibody genes are amplified by polymerase chain reaction with gene-specific primers and assembled before cloning into a phage display vector. The resulting phages display antibody fragments on their surfaces.
• filamentous phage display libraries are incubated with antigens immobilized on a solid phase.
• the antigen-binding phages remains attached to the antigen, whereas the unbound phages are washed away.
• the bound phages are then eluted and amplified by infection with bacterial cells.
• the expression host By changing the expression host to a non- suppressor bacterial strain, the soluble antibody fragment can be expressed and secreted to the culture medium.
• Figure 2 shows the whole amino acid (panel A) and nucleotide sequences (panel B) of the heavy chain variable region and of the light chain variable region for each clone, specifying both the framework regions FR1-FR4 and the complementary determining regions CDR1-CDR3.
• Figure 3 shows the binding activity of the selected clones (#5, BU.2, BU.7, BU.11, BU.54, BS.70) both as Fab and IgGl format assessed by ELISA assay.
• the selected Fabs and IgG were tested for their binding to the recombinant protein of the different VOCs.
• Figure 4 shows the results of immunofluorescence analysis of the binding activity of the selected clones, both as Fab and IgGl format.
• the selected Fabs can detect the VeroE6 cells infected by D614G, Alpha_B.1.1.7, Beta_B.1.135, Gamma P.1, Delta_B.1.617.1, Omicron_B.1.529 (BA.1), Omicron_B.1.529 (BA.2), Omicron_B.1.529 (BAA) and Omicron_B.1.529 (BA.5) viral variants.
• Figure 5 shows neutralizing activities of clone Fab#5, both as Fab and IgGl format against the tested VOCs (D614G, B.1.1.7, P.1 and B.1.135) (panel A) and of clones Fab BU.2, BU.7, BU.11, BU.54 and BS.70 both as Fab and IgGl format (panel B) against the tested VOCs (D614G, Alpha_B.1.1.7, Beta_B.1.135, Delta B.1.617.1, Gamma_P.1, Omicron B.1.1.529 (BA.1), Omicron B.1.1.529 (BA.2)).
• Figure 6 shows neutralizing activity using pseudovirus of clones Fab BU.7 and BU.54 againt SARS-CoV-1 and Omicron VOC of SARS-CoV-2.
• the neutralizing nAbs of the invention have been identified on the basis of the binding affinity to SARS-CoV1 and SARS-CoV-2 spike or specific domains and characterized in terms of neutralizing activity and epitope specificity as described in the following examples. These aspects are fundamental to select the most promising nAbs as those endowed with the highest potency and/or recognizing conserved spike epitopes, the main parameters determining a potential cross reactive treatment effective against all the VOIs and VOIc of SARS-Cov-2 known sofar or emerging in the future.
• EXAMPLE 1 Generation of new human antibody Phage Display Libraries and selection of antibodies able to bind with high affinity the spike protein of SARS-CoV- 2 through Bio-panning procedures
• the technique focuses on the construction of a library of peptides or antibody variants, which are then selected for their affinity to the target of interest since they are fused to a phage-coat protein (see for reference Figure 1).
• All surface proteins of bacteriophages can be engineered for display, but the most used are pVIII and pill from M13 filamentous phages.
• Each virion contains about 2700 copies of the former protein, representing almost 87% of its mass, and they are half-exposed to the environment, thus allowing an efficient display of only short- sequence peptides due to virion architecture.
• pill can be used for larger peptides, such as the “functional portion” of antibodies, resulting only in a slight loss of infectivity in a few cases.
• Each library is composed by phagemid vectors containing only the sequence of a phage-coat protein fused to the peptide of interest; therefore, a helper phage with a reduced packaging efficiency is needed to obtain a population of phages both infectious and composed by modified coating proteins.
• the bio-panning procedure is then performed, and phages are selected for their ability to bind the antigen of interest. Many factors must be considered: library variability, target conformation, affinity, and avidity of the molecules exposed on phages. As mentioned, phage display has been widely used to find novel therapeutics against pathogens, particularly mAbs.
• Peripheral (for Fab #5) and bone marrow (for Fabs BU.2, BU.7, BU.11, BU.54) blood samples was collected from subjects previously infected by SARS-CoV-2 and subsequently vaccinated with COVID- 19 vaccine (2 doses of Comirnaty, Pfizer) and used for the collection of PBMC and B-cell precursors, respectively.
• the extraction of PBMCs was carried out following the Histopaque®-1077 (SIGMA- ALDRICH) protocol. At the end of the procedure 10 6 cells were lysed using Trizol Reagent (SIGMA- ALDRICH) to allow the subsequent extraction of cellular RNA using RNeasy Mini Kit (QIAGEN).
• Antibody phagemidic IgG libraries were generated through B-cell-mRNA reverse transcription to cDNA using SuperScriptTM IV Reverse Transcriptase (ThermoFisher Scientific). Heavy and light chains were amplified from the obtained cDNA by using the PFU Native Polymerase enzyme (Agilent) and the primer pairs described in the following Table.
• Phagemidic libraries were then converted into phage libraries by transforming electrocompetent Gram-negative cells expressing sexual pilus (XLl-Blue, Agilent) and superinfecting them with a helper-phage (M13K07, NEB).
• the new libraries were screened by using different Bio-panning procedures with the aim of maximizing the selection of cross-reactive antibodies (antibodies recognizing more SARS-CoV-2 clinical isolates) in their Fab format.
• S proteins of different SARS-CoV-2 variants were used: D614G (University of Pavia) for Fab #5, and B.1.1.7 (40589-V08B6, Sino Biological), P.1 (40589-V08B 10, Sino Biological) or B.1.135 (40589-V08B7, Sino Biological) for Fab BU.2, BU.7, BU.11, BU.54.
• Bacteriophages carrying on their capsid monoclonal antibodies (expressed as Fab fragments) selected through bio-panning were used to obtain the DNA codifying the antibody expressed on their surface.
• DNAs codifying for the variable antibody regions present on the phage surface was sequenced and used for protein purification using E. coli expression system (XE1- Blue, Agilent) and immune-affinity chromatography (HiTrap® Protein L, Merck).
• IgGl format of Fab #5 was obtained from Genscript through High Throughput Antibody Production Service (GenScript).
• amino acidic sequences of the heavy and light chain variable regions are the following:
• Lc The nucleotide sequences encoding the same are the following:
• Figure 2 shows the whole amino acid and nucleotide sequence of the heavy chain variable region and of the light chain variable region for each clone, specifying both the framework regions FR1-FR4 and the complementary determining regions CDR1- CDR3.
• EXAMPLE 2 Study on the binding activity of the neutralizing mAbs of the invention Binding evaluation of the Fabs a) Enzyme Linked Immunosorbent Assay (ELISA)
• the binding efficiency of the Fabs was tested using ELISA assay.
• Fabs were detected with goat anti-human IgG (Fab specific)-peroxidase antibody (A0293; Sigma- Aldrich), with His-tagged proteins with anti-His6-peroxidase antibody (11 2416001; Sigma- Aldrich) as a coating control and using the Pierce TMB substrate kit (ThermoFisher Scientific).
• the OD450 was measured using Multiskan GO (ThermoFisher Scientific).
• Fab #5 binds the S protein of Alpha, Gamma, and Omicron
• IgG #5 binds the S protein of D614G, Alpha, Beta, Gamma, Delta, Omicron, and SARS-CoV-1
• Fab BU.7 binds the S protein of Alpha, SARS-CoV-1, and less Gamma,
• IgG BU.54 binds the S protein of Alpha, Delta, Omicron, and SARS-CoV-1
• Fab BS.70 binds the S protein of Alpha, Delta, Omicron, and SARS-CoV-1
• Results are depicted in Figure 3.
• Data showed that Fab #5 can recognize the B.1.1.7 recombinant protein even when used at low concentrations, but also P.1 spike when used at higher concentrations.
• IgG #5 binds well the recombinant spike of all tested SARS-CoV-2 variants (D614G, B.1.1.7, B.1.351, P.1, B.1.1.529, B.1.617.1).
• the BU.7 binds P.1 protein, and even better B.1.1.7 spike protein. Its IgG format shows a weak binding activity also on B.1.617.1 and B.1.1.529 proteins.
• B.1.1.7 spike is well recognized also by BU.11 and BU.2 Fabs
• IgG BU.54 recognizes well B.11.7, B.1.617.1, P.1, B.1.1.529 and SARS-CoV-1 recombinat proteins.
• Fab BS.70 binds even at low concentrations B.1.1.7, B.1.617.1, B.1.1.529 proteins.
• SARS-CoV-1 spike protein is very well recognized by IgG #5, BU.7 in both Fab and IgG formats, IgG BU.54, and Fab BS.70.
• Vero E6 Vero C1008, clone E6 — CRL-1586; ATCC cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with non-essential amino acids (NEAA), penicillin/streptomycin (P/S), Hepes buffer, and 10% (v/v) fetal bovine serum (FBS).
• DMEM Dulbecco's modified Eagle's medium
• NEAA non-essential amino acids
• P/S penicillin/streptomycin
• Hepes buffer Hepes buffer
• 10% v/v fetal bovine serum
• Virus stocks were titrated using both Plaque Reduction Assay (PRA, PFU/ml) and Endpoint Dilutions Assay (EDA, TCID50/ml).
• PRA Plaque Reduction Assay
• EDA Endpoint Dilutions Assay
• Vero E6 cells were seeded into 96 wells plates 24 h before the experiment performed at 95% cell confluency for each well, and then infected with SARS-CoV-2 at 0.01 multiplicity of infection (MOI) for 1 h at 37°C. Then, the cells were washed with PBS lx to remove cell-free virus particles and virus-containing mixtures and controls were replaced with complete DMEM supplemented with 2% FBS. The plates were incubated at 37°C in the presence of CO 2 for 72 h. Then were washed with PBS lx and fixed with MeOH:Ac (1:1) for 15 minutes, and stored at -20°C.
• MOI multiplicity of infection
• Fabs (1:200 dilution) were applied to cells as primary antibody.
• Anti-Spike Antibody (0150-R007, Sino Biological) was added as control.
• Fabs were detected with goat anti-rabbit IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 488 (A-11008, Thermo Scientifc).
• Hoechst 33258 (Sigma-Aldrich) was used for nuclear staining.
• Fab #5 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), and Omicron (BA.2)
• IgG #5 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), Omicron (BA.2), Omicron (BA.5), and less Omicron (BAA)
• Fab BU.2 binds cells infected with D614G, Alpha, Gamma, Delta, Omicron (BA.2), less Beta, and no Omicron (BA.1)
• Fab BU.7 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), and Omicron (BA.2)
• IgG BU.7 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), Omicron (BA.2), Omicron (BA.5), and Omicron (BAA).
• Fab BU.11 binds cells infected with D614G, Alpha, Gamma, Delta, Beta, less Omicron (BA.2), and no Omicron (BA.1)
• IgG BU.54 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), Omicron (BA.2), Omicron (BA.5), and less Omicron (BAA)
• Fab BS.70 binds cells infected with D614G, Alpha, Beta, Gamma, Delta, Omicron (BA.1), and Omicron (BA.2), (BAA) and less (BA.5)
• B .1.1.7 variant is recognized better by Fab #5, BU.2, BU.11 and IgG BU.54, and less well by BS.70 and BU.7 Fabs.
• the IgG format of BU.7 shows an improved binding activity against this variant.
• B.1.135 variant is recognized well only by clone #5 in both Fab and IgG formats, IgG BU.7, IgG BU.54, and Fab BS.70, while only a slight green signal is observed using the other Fabs.
• the binding to the P.1 variant is well observed with all the tested Fabs, but the Fab #5 signal had the least intensity.
• Delta variant is well recognized by all Fabs and IgGs tested, while Omicron (BA.1) is not recognized only by BU.2 and BU.11 Fabs. Last, Omicron (BA.2) is recognized, albeit with a less intense signal than BA.1, by all but Fab BU.11.
• Fab BS.70 is the clone showing the strongest binding signals against all tested variants, followed by IgG #5, IgG BU.7, IgG BU.54. Both Omicron BAA and BA.5 are well recognized by IgGBU.7 on infected cells. IgG#5 and IgG BU.54 strongly recognize Omicron BA.5 sublineage and recognize with lower binding signal the BAA.
• Vero E6 cells were seeded into 96 wells plates 24 h before the experiment performed at 95% cell confluency for each well. Two-fold serial dilutions of the selected clones were incubated with SARS-CoV-2 at 0.01 MOI for 1 h at 37°C. Virus-serum mixtures and positive infection control were applied to Vero E6 monolayers after washing cells with PBS lx, and virus adsorption was carried out at 37°C for 1 h. Then, the cells were washed with PBS lx to remove cell-free virus particles and virus-containing mixtures and controls were replaced with complete DMEM supplemented with 2% FBS. The plates were incubated at 37°C in the presence of CO 2 for 72 h. The experiments were performed in triplicate. Neutralization activity was evaluated by comparing cytopathic effect (CPE) presence detected in the presence of virus-serum mixtures to positive infection control.
• CPE cytopathic effect
• the clone #5 showed an important neutralizing activity against D614G variant both as Fab format and IgGl. However, IgGl showed enhanced activity against the other tested VOCs compared to the Fab fragment, except for B.1.135 variant ( Figure 5A). All tested BU clones can inhibit efficiently D614G, but only BU.7 retains its activity against all the tested VOCs. Fab BU.2 can neutralize better B.1.1.7 variant than the other two, while BU.11 showed a significant activity against P.1 ( Figure 5B).
• IgG #5 neutralizes D614G, Alpha, Gamma, and less Beta
• IgG BU.7 neutralizes D614G, Alpha, Gamma, Beta, Delta, Omicron, and
• IgG BU.54 neutralizes D614G, Alpha, Gamma, Beta, Delta, Omicron, and Omicron (BA.2)
• Tables 2-3-4 summarize the neutralizing activity expressed as IC50 pg/ml shown by the selected clones Fab #5, IgG #5, Fab BU.2, Fab BU.7, Fab BU.11, Fab BS.70, IgG BU.7, IgG BU.54 against different VOCs of SARS-CoV-2.
• SARS-CoV-2-pseudotyped particles were produced and titrated.
• HEK293 T were co-transfected with the S plasmids from either SARS-CoV- 1 or SARS-CoV-2 Omicron, HIV gag-pol and the Luc-reporter plasmid.
• Neutralization assays were performed by incubating pseudoviruses (106 RLU) with endpoint twofold serial dilutions of monoclonal antibodies (37°C in the presence of 5% CO 2 ) for 1 h before adding the neutralization mix of 104 HEK 293T-ACE2- TMPRSS2 cells per well. 72h post-infection (37°C), luciferase activity was quantified.
• the neutralization assay according to this alternative strategy show that the monoclonal antibodies of the invention IgG BU.7 and IgG BU.54 neutralize SARS- CoV-1 and Omicron variant of SARS CoV-2.
• Figure 6 shows the results of the neutralization assays using pseudovirus.
• Table 5 summarize the neutralizing activity expressed as IC 50 ⁇ g/ml shown by the selected clones IgG BU.7 and IgG BU.54 against SARS-CoV-1 and Omicron variant of SARS CoV-2.
• VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2. bioRxiv; doi: 10.1101/2021.03.09.434607

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