Antigen Binding Molecules Targeting SARS-CoV-2

Abstract

The disclosure provides, in various embodiments, polypeptides (e.g., antibodies and antigen binding fragments thereof) that specifically bind to S2 domains of betacoronavirus Spike glycoproteins, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoproteins. The disclosure also provides, in various embodiments, fusion proteins comprising one or more of polypeptides, polynucleotides encoding polypeptides, vectors and host cells suitable for expressing polypeptides, and methods for treating viral infections (e.g., COVID-19).

What is claimed is: 
     
         1 . A polypeptide that specifically binds a severe acute respiratory syndrome coronavirus 2 Spike glycoprotein (SARS-CoV-2-Spike), comprising:
 a) an immunoglobulin heavy chain variable domain (V H ) amino acid sequence comprising a heavy chain complementarity determining region 1 (HCDR1), a heavy chain complementarity determining region 2 (HCDR2) and a heavy chain complementarity determining region 3 (HCDR3) that are substantially similar to a HCDR1, HCDR2 and HCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:4-48; and   b) an immunoglobulin light chain variable domain (V L ) amino acid sequence comprising a light chain complementarity determining region 1 (LCDR1), a light chain complementarity determining region 2 (LCDR2) and a light chain complementarity determining region 3 (LCDR3) that are substantially similar to a LCDR1, LCDR2 and LCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:51-76.   
     
     
         2 . The polypeptide of  claim 1 , comprising the HCDR1, HCDR2 and HCDR3, and LCDR1, LCDR2 and LCDR3, of an antibody comprising an amino acid sequence selected from:
 a) SEQ ID NO:4 and SEQ ID NO:51 (AB-1);   b) SEQ ID NO:5 and SEQ ID NO:52 (AB-2);   c) SEQ ID NO:6 and SEQ ID NO:53 (AB-3);   d) SEQ ID NO:7 and SEQ ID NO:54 (AB-4);   e) SEQ ID NO:8 and SEQ ID NO:51 (AB-5);   f) SEQ ID NO:9 and SEQ ID NO:55 (AB-6);   g) SEQ ID NO:10 and SEQ ID NO:56 (AB-7);   h) SEQ ID NO:11 and SEQ ID NO:57 (AB-8);   i) SEQ ID NO:12 and SEQ ID NO:58 (AB-9);   j) SEQ ID NO:13 and SEQ ID NO:59 (AB-10);   k) SEQ ID NO:14 and SEQ ID NO:60 (AB-11);   l) SEQ ID NO:15 and SEQ ID NO:56 (AB-12);   m) SEQ ID NO:16 and SEQ ID NO:51 (AB-13);   n) SEQ ID NO:10 and SEQ ID NO:50 (AB-14);   o) SEQ ID NO:17 and SEQ ID NO:61 (AB-15);   p) SEQ ID NO:18 and SEQ ID NO:62 (AB-16);   q) SEQ ID NO:6 and SEQ ID NO:63 (AB-17);   r) SEQ ID NO:19 and SEQ ID NO:64 (AB-18);   s) SEQ ID NO:4 and SEQ ID NO:61 (AB-19);   t) SEQ ID NO:20 and SEQ ID NO:61 (AB-20);   u) SEQ ID NO:21 and SEQ ID NO:65 (AB-21);   v) SEQ ID NO:22 and SEQ ID NO:66 (AB-22);   w) SEQ ID NO:4 and SEQ ID NO:67 (AB-23);   x) SEQ ID NO:23 and SEQ ID NO:56 (AB-24);   y) SEQ ID NO:24 and SEQ ID NO:68 (AB-25);   z) SEQ ID NO:25 and SEQ ID NO:51 (AB-26);   aa) SEQ ID NO:26 and SEQ ID NO:56 (AB-27);   bb) SEQ ID NO:27 and SEQ ID NO:61 (AB-28);   cc) SEQ ID NO:28 and SEQ ID NO:56 (AB-29);   dd) SEQ ID NO:28 and SEQ ID NO:69 (AB-30);   ee) SEQ ID NO:29 and SEQ ID NO:70 (AB-31);   ff) SEQ ID NO:30 and SEQ ID NO:71 (AB-32);   gg) SEQ ID NO:31 and SEQ ID NO:72 (AB-33);   hh) SEQ ID NO:32 and SEQ ID NO:67 (AB-34);   ii) SEQ ID NO:33 and SEQ ID NO:56 (AB-35);   jj) SEQ ID NO:34 and SEQ ID NO:73 (AB-36);   kk) SEQ ID NO:35 and SEQ ID NO:51 (AB-37);   ll) SEQ ID NO:36 and SEQ ID NO:56 (AB-38);   mm) SEQ ID NO:37 and SEQ ID NO:63 (AB-39);   nn) SEQ ID NO:38 and SEQ ID NO:69 (AB-40);   oo) SEQ ID NO:39 and SEQ ID NO:74 (AB-41);   pp) SEQ ID NO:40 and SEQ ID NO:52 (AB-42);   qq) SEQ ID NO:41 and SEQ ID NO:51 (AB-43);   rr) SEQ ID NO:42 and SEQ ID NO:75 (AB-44);   ss) SEQ ID NO:43 and SEQ ID NO:56 (AB-45);   tt) SEQ ID NO:44 and SEQ ID NO:51 (AB-46);   uu) SEQ ID NO:45 and SEQ ID NO:75 (AB-47);   vv) SEQ ID NO:46 and SEQ ID NO:53 (AB-48);   ww) SEQ ID NO:47 and SEQ ID NO:52 (AB-49);   xx) SEQ ID NO:48 and SEQ ID NO:76 (AB-50); or   yy) SEQ ID NO:3 and SEQ ID NO:56 (AB-51).   
     
     
         3 . The polypeptide of  claim 1 , wherein the V H  has at least 85% sequence identity to the amino acid sequence of any one or more of SEQ ID NOs:4-48. 
     
     
         4 . The polypeptide of  claim 1 , wherein the V L  has at least 85% sequence identity to the amino acid sequence of any one or more of SEQ ID NOs: 51-76. 
     
     
         5 . The polypeptide of  claim 1 , comprising the HCDR1, HCDR2 and HCDR3, and LCDR1, LCDR2 and LCDR3, of an antibody comprising the amino acid sequence of SEQ ID NO:4 and SEQ ID NO:51 (AB-1). 
     
     
         6 . The polypeptide of  claim 5 , comprising the HCDR1, HCDR2 and HCDR3, and LCDR1, LCDR2 and LCDR3 amino acid sequences of SEQ ID NOs: 77, 80, 91, 133, 141 and 144, respectively. 
     
     
         7 . The polypeptide of  claim 1 , wherein the V H  has at least 85% sequence identity to the amino acid sequence of SEQ ID NO:4. 
     
     
         8 . The polypeptide of  claim 1 , wherein the V L  has at least 85% sequence identity to the amino acid sequence of SEQ ID NO:51. 
     
     
         9 . The polypeptide of  claim 1 , wherein:
 a) the V H  comprises the amino acid sequence of SEQ ID NO:4; and   b) the V L  comprises the amino acid sequence of SEQ ID NO:51.   
     
     
         10 . The polypeptide of any one of  claim 1 , wherein the VH and VL are humanized, contain human framework regions, or a combination thereof. 
     
     
         11 . The polypeptide of  claim 1 , wherein the polypeptide is an antibody or an antigen-binding fragment thereof. 
     
     
         12 . The polypeptide of  claim 11 , wherein the antigen binding fragment is selected from Fab, F(ab′) 2 , Fab′, scFv, or Fv. 
     
     
         13 . The polypeptide of  claim 11 , comprising an antibody heavy chain constant domain sequence, an antibody light chain constant domain sequence, or both an antibody heavy chain constant domain sequence and an antibody light chain constant domain sequence. 
     
     
         14 . The polypeptide of  claim 13 , wherein the antibody heavy chain constant domain is selected from the group consisting of an IgA constant domain, an IgD constant domain, an IgE constant domain, an IgG constant domain and an IgM constant domain. 
     
     
         15 . The polypeptide of  claim 13 , wherein the antibody heavy chain constant domain is an IgG1 heavy chain constant domain. 
     
     
         16 . A polypeptide that specifically binds a severe acute respiratory syndrome coronavirus 2 Spike glycoprotein (SARS-CoV-2-Spike), comprising an immunoglobulin heavy chain variable domain (V H ) comprising the amino acid sequence of SEQ ID NO:2, wherein:
 a) X 1  is S, N, A, R, L or F;   b) X 2  is D or E;   c) X 3  is T or V;   d) X 4  is L or V;   e) X 5  is S, Q, R, K, Y, D or E;   f) X 6  is N, K, A, S, R or E;   g) X 7  is G, N or L;   h) X 8  is V, I, S or K; or   i) X 9  is Q, Y, K, F or H,   j) or any combination of the foregoing.   
     
     
         17 . The polypeptide of  claim 16 , wherein:
 a) X 1  is N, A, R, L or F;   b) X 2  is E;   c) X 3  is V;   d) X 4  is V;   e) X 5  is Q, R, K, Y, D or E;   f) X 6  is K, A, S, R or E;   g) X 7  is N or L;   h) X 8  is I, S or K; or   i) X 9  is Y, K, F or H,   j) or any combination of the foregoing.   
     
     
         18 . The polypeptide of  claim 16 , comprising an immunoglobulin light chain variable domain (V L ) comprising the amino acid sequence of SEQ ID NO:49, wherein:
 a) X 10  is Q, K or I;   b) X 11  is G or S;   c) X 12  is S, R or V;   d) X 13  is S or N;   e) X 14  is N, H, D, Y or S;   f) X 15  is S or Q;   g) X 16  is F, Y, L, V, Tor D; or   h) X 17  is Y or L,   i) or any combination of the foregoing.   
     
     
         19 . The polypeptide of  claim 18 , wherein:
 a) X 10  is K or I;   b) X 11  is S;   c) X 12  is R or V;   d) X 13  is N;   e) X 14  is H, D, Y or S;   f) X 15  is Q;   g) X 16  is Y, L, V, T or D; or   h) X 17  is L,   i) or any combination of the foregoing.   
     
     
         20 . A composition comprising the polypeptide of  claim 1 . 
     
     
         21 . The composition of  claim 20 , comprising one or more pharmaceutical excipients, diluents, or carriers. 
     
     
         22 . A fusion protein comprising the polypeptide of  claim 1 . 
     
     
         23 . A polynucleotide comprising a sequence encoding the polypeptide of  claim 1 . 
     
     
         24 . A vector comprising the polynucleotide of  claim 23 . 
     
     
         25 . A host cell comprising the polynucleotide of  claim 23 . 
     
     
         26 . A method of treating a subject having, or suspected of having, a betacoronavirus infection, comprising administering an effective amount of a polypeptide that specifically binds a severe acute respiratory syndrome coronavirus 2 Spike glycoprotein (SARS-CoV-2-Spike) to the subject, wherein the polypeptide comprises:
 a) an immunoglobulin heavy chain variable domain (V H ) amino acid sequence comprising a heavy chain complementarity determining region 1 (HCDR1), a heavy chain complementarity determining region 2 (HCDR2) and a heavy chain complementarity determining region 3 (HCDR3) that are substantially similar to a HCDR1, HCDR2 and HCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:4-48; and   b) an immunoglobulin light chain variable domain (V L ) amino acid sequence comprising a light chain complementarity determining region 1 (LCDR1), a light chain complementarity determining region 2 (LCDR2) and a light chain complementarity determining region 3 (LCDR3) that are substantially similar to a LCDR1, LCDR2 and LCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:51-76.   
     
     
         27 . The method of  claim 26 , comprising administering a therapeutically effective amount of an additional therapeutic or prophylactic agent to the subject. 
     
     
         28 . The method of  claim 27 , wherein the additional therapeutic agent is selected from the group consisting of an antiviral agent, an ACE2 inhibitors, an additional SARS-CoV-2-Spike-binding antibody, an antibiotic, an antimalarial agent, a vaccine, and combinations thereof. 
     
     
         29 . The method of  claim 28 , wherein:
 a) the additional SARS-CoV-2-Spike-binding antibody is selected from the group consisting of bamlanivimab, etesevimab, bebtelovimab, casirivimab, imdevimab, Cilgavimab, Tixagevimab, AZD7442 (Tixagevimab-Cilgavimab), Regdanvimab, Sotrovimab and combinations thereof;   b) the antiviral agent is selected from the group consisting of Molnupiravir (LAGEVRIO, Merck), PF-07817883 (Pfizer), STI-1558 (Sorrento Therapeutics), PBI-0451 (Pardes Biosciences), EDP-235 (Enanta Pharmaceuticals), oseltamivir (Tamiflu), favipiravir, amantadine, remdesivir, rimantadine, pleconaril, an anti-sense RNA to SARS-CoV-2, a siRNA to SARS-CoV-2, and combinations thereof;   c) the ACE2 inhibitor is selected from the group consisting of an RNAi to ACE2, a siRNA to ACE2, CRISPR-based inhibitor of ACE2, a soluble ACE2, a soluble ACE2 variant, an anti-ACE2 antibody, and combinations thereof;   d) the antibiotic comprises azithromycin;   e) the antimalarial agent comprises a chloroquine;   f) the vaccine is a nucleic acid vaccine or an inactivated virus vaccine; or   g) a combination thereof.   
     
     
         30 . A method of reducing infectivity of a betacoronavirus in a subject in need thereof, comprising administering an effective amount of a polypeptide that specifically binds a severe acute respiratory syndrome coronavirus 2 Spike glycoprotein (SARS-CoV-2-Spike) to the subject, wherein the polypeptide comprises:
 a) an immunoglobulin heavy chain variable domain (V H ) amino acid sequence comprising a heavy chain complementarity determining region 1 (HCDR1), a heavy chain complementarity determining region 2 (HCDR2) and a heavy chain complementarity determining region 3 (HCDR3) that are substantially similar to a HCDR1, HCDR2 and HCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:4-48; and   b) an immunoglobulin light chain variable domain (V L ) amino acid sequence comprising a light chain complementarity determining region 1 (LCDR1), a light chain complementarity determining region 2 (LCDR2) and a light chain complementarity determining region 3 (LCDR3) that are substantially similar to a LCDR1, LCDR2 and LCDR3, respectively, of the amino acid sequence of any one of SEQ ID NOs:51-76.