Klebsiella pneumoniae o3 specific antibodies

Abstract

A cross-neutralizing monoclonal antibody that specifically recognizes a cross-reactive epitope of the lipopolysaccharide (LPS) antigen structure of Klebsiella pneumoniae , which is an O3b epitope, cross-reacting with an O3a epitope and an O3 epitope, wherein the antibody is characterized by specific CDR sequences or VH and VL sequences.

1 . A cross-neutralizing monoclonal antibody that specifically recognizes a cross-reactive epitope of the lipopolysaccharide (LPS) antigen structure of  Klebsiella pneumoniae , which is an O3b epitope, cross-reacting with an O3a epitope and an O3 epitope, which antibody is selected from any of
 a) an antibody comprising the CDR1-CDR6 sequences of any one of the antibodies listed in Table 1a or Table 1b; or   b) an antibody comprising the VH and VL sequences of any one of the antibodies depicted in  FIG. 2 b   ; or   c) an antibody which is a functionally active variant of a parent antibody that is any one of the antibodies of a) or b), which functionally active variant has a specificity to bind the same epitope as the parent antibody, and comprises at least one point mutation in any of the CDR, wherein the number of point mutations is either 0, 1, 2, or 3 point mutations in each of the CDR sequences, wherein the sequence identity in each of the CDR sequences is at least 60% compared to the respective CDR sequences of the parent antibody.   
     
     
         2 . The antibody of  claim 1 , which is
 A)   selected from the group consisting of group members i) to v), wherein   i)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 21; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 22; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 23; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 33; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 34; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 35; 
   ii)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 24; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 25; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 26; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 36; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 37; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 38; 
   iii)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 27; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 28; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 29; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 39; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 40; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 41; 
   iv)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 30; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 31; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 32; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 42; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 34; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 43; 
   and   v)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 21; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 22; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 74; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 33; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 34; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 35; 
   wherein CDR sequences are designated according to the numbering system of Kabat;   or   B) an antibody which is the functionally active variant of a parent antibody that is any of the group members of A.   
     
     
         3 . The antibody of  claim 1 , which is
 A)   selected from the group consisting of group members i) to v), wherein   i)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 44; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 45; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 46; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 56; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 57; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 58; 
   ii)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 47; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 48; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 49; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 59; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 60; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 61; 
   iii)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 50; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 51; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 52; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 62; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 63; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 64; 
   iv)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 53; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 54; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 55; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 65; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 57; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 66; 
   and   v)   is an antibody which comprises
 a) CDR1 consisting of the amino acid sequence SEQ ID 44; 
 b) CDR2 consisting of the amino acid sequence SEQ ID 45; 
 c) CDR3 consisting of the amino acid sequence of SEQ ID 67; 
 d) CDR4 consisting of the amino acid sequence SEQ ID 56; 
 e) CDR5 consisting of the amino acid sequence SEQ ID 57; and 
 f) CDR6 consisting of the amino acid sequence of SEQ ID 58; 
   wherein CDR sequences are designated according to the numbering system of IMGT;   or   B) an antibody which is the functionally active variant of a parent antibody that is any of the group members of A.   
     
     
         4 . The antibody of  claim 3 , wherein the functionally active variant comprises CDR1-6, wherein
 a) the CDR1 comprises SEQ ID 75;   b) the CDR2 comprises SEQ ID 76;   c) the CDR3 comprises SEQ ID 77;   d) the CDR4 comprises SEQ ID 78;   e) the CDR5 comprises SEQ ID 57; and   f) the CDR6 comprises SEQ ID 79,   which CDR sequences are according to IMGT,   and wherein each of the CDR sequences has at least 60% sequence identity to the respective CDR sequence of said parent antibody.   
     
     
         5 . The antibody of  claim 1 , which is
 A)   selected from the group consisting of group members i) to viii), wherein   i)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 11; and 
 b) VL consisting of the amino acid sequence SEQ ID 16; 
   ii)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 12; and 
 b) VL consisting of the amino acid sequence SEQ ID 17; 
   iii)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 13; and 
 b) VL consisting of the amino acid sequence SEQ ID 18; 
   iv)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 14; and 
 b) VL consisting of the amino acid sequence SEQ ID 19; 
   v)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 15; and 
 b) VL consisting of the amino acid sequence SEQ ID 20; 
   vi)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 68; and 
 b) VL consisting of the amino acid sequence SEQ ID 16; 
   vii)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 69; and 
 b) VL consisting of the amino acid sequence SEQ ID 16; 
   and   viii)   is an antibody which comprises
 a) VH consisting of the amino acid sequence SEQ ID 70; and 
 b) VL consisting of the amino acid sequence SEQ ID 16; 
   or   B) an antibody which is the functionally active variant of a parent antibody that is any of the group members of A.   
     
     
         6 . The antibody of  claim 1 , wherein
 a) the O3b epitope is incorporated in the LPS O3b antigen of  Klebsiella pneumoniae  comprising the structure of Formula (I), including one or more O3b antigen trimannose homopolymer repeating units, wherein Formula (I) is:
   MeP→3)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→3)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→] n ;
 
   b) the O3a epitope is incorporated in the LPS O3a antigen of  Klebsiella pneumoniae  comprising the structure of Formula (II), including one or more O3a antigen tetramannose homopolymer repeating units, wherein Formula (II) is:
   MeP→3)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→[3)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→] n ;
 
   and   c) the O3 epitope is incorporated in the LPS O3 antigen of  Klebsiella pneumoniae  comprising the structure of Formula (III), including one or more O3 antigen pentamannose homopolymer repeating units, wherein Formula (III) is:
   MeP→3)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→[3)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→2)-α- D -Man p -(1→3)-α- D -Man p -(1→] n  
 
   wherein   MeP is methyl phosphate; and   n is 0-50.   
     
     
         7 . The antibody of  claim 1 , which has an affinity to bind the O3a epitope with a K D  of less than 10 −6 M, preferably less than 10 −7 M, as determined by biolayer interferometry for bivalent binding. 
     
     
         8 . The antibody of  claim 1 , which is neutralizing endotoxin of  Klebsiella pneumoniae  strains expressing LPS molecules comprising any of the O3b, O3a, or O3 epitopes. 
     
     
         9 . The antibody of  claim 1 , which is any one of a full-length antibody, an antibody fragment thereof, or a fusion protein, each comprising at least VH and VL antibody domains incorporating a binding site recognizing the cross-reactive epitope. 
     
     
         10 . The antibody of  claim 1 , which is of human origin, or an affinity matured variant thereof, specifically wherein the antibody is a non-naturally occurring antibody which comprises an artificial amino acid sequence, specifically, wherein the antibody is an IgA antibody or an IgA to IgG isotype switch variant thereof. 
     
     
         11 . The antibody of  claim 1 , for use in treating a subject at risk of or suffering from  K. pneumoniae  infection or colonization to limit the infection in the subject or to ameliorate a disease condition resulting from said infection, preferably for treatment or prophylaxis of any of primary and secondary bacteremia, pneumonia, urinary tract infection, liver abscess, peritonitis, or meningitis, specifically wherein the subject is an immunocompromised or immunosuppressed patient, or a contact thereof. 
     
     
         12 . A pharmaceutical preparation comprising the antibody of  claim 1 , and a pharmaceutically acceptable carrier or excipient in a parenteral formulation. 
     
     
         13 . An isolated nucleic acid encoding the antibody of  claim 1 . 
     
     
         14 . An expression cassette or a plasmid comprising a coding sequence to express a proteinaceous construct comprising a VH and/or VL of the antibody of  claim 1 . 
     
     
         15 . A host cell comprising the expression cassette or a plasmid of  claim 14 . 
     
     
         16 . A method of producing the antibody of  claim 1 , wherein the host cell of  claim 15  is cultivated or maintained under conditions to produce said antibody.