IP Library › Granted Patent US 12704514
Granted Patent B2
US 12704514 · App. 18/028,195 · Granted Aug 11, 2026

Engineered binding proteins for recognition of bacteria

Inventors: Hadley Sikes Johnson (Arlington, MA); Ki-Joo Sung (Minneapolis, MN); Yining Hao (Cambridge, MA)
Assignee: Massachusetts Institute of Technology
G01N33/56916C07K16/1232C07K16/1235C07K16/126C07K16/1296C07K2317/31C07K2318/20C07K2319/40C07K2319/60C07K2319/61G01N2469/10
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Quick Facts
Patent No.
US 12704514
App. No.
18/028,195
Granted
Aug 11, 2026
Kind
B2
Abstract

Described herein are antigen-binding molecules that bind to bacteria (e.g., Listeria monocytogenes ) and methods of use thereof. Also described herein are compositions and kits comprising these antigen-binding molecules.

Claims (45)

1 . An antigen-binding molecule comprising a reduced charge Sso7d (rcSso7d) antigen-binding protein,

wherein the antigen-binding molecule comprises a reduced charge Sso7d (rcSso7d) antigen-binding protein that binds:

a) Listeria monocytogenes protein LMOf2365_0639, wherein the antigen-binding protein comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 1-8;

or

b) Salmonella typhi Native Omp, said Native Omp comprising the amino acid sequence of Salmonella typhi membrane proteins OmpA, OmpW, OmpC, OmpF, OmpD, and phoE, wherein the antigen-binding protein comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 58-71;

or

c) Escherichia coli OmpW, wherein the antigen-binding protein comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 73-80;

or

d) Escherichia coli OmpA, wherein the antigen-binding protein comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 81-83.

2 . The antigen-binding molecule of claim 1 , wherein the antigen-binding molecule binds Listeria monocytogenes protein LMOf2365_0639 and comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 1-8.

3 . The antigen-binding molecule of claim 2 , wherein the rcSso7d antigen-binding protein comprises:

(i) the amino acid sequence of any one of SEQ ID NOs: 13-15; or

(ii) an amino acid sequence having no more than ten conserved amino acid substitutions with any one of SEQ ID NOs: 13-15, wherein any conserved amino acid substitutions do not occur in the variable region.

4 . The antigen-binding molecule of claim 2 , wherein the rcSso7d antigen-binding protein comprises:

(i) the amino acid sequence of any one of SEQ ID NOs: 16-19; or

(ii) an amino acid sequence having no more than seven conserved amino acid substitutions with any one of SEQ ID NOs: 16-19, wherein any conserved amino acid substitutions do not occur in the variable region.

5 . The antigen-binding molecule of claim 1 , wherein the antigen-binding molecule binds Salmonella typhi Native Omp, said Native Omp comprising the amino acid sequence of Salmonella typhi membrane proteins OmpA, OmpW, OmpC, OmpF, OmpD, and phoE, and wherein the antigen-binding protein comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 58-71.

6 . The antigen-binding molecule of claim 5 , wherein the rcSso7d antigen-binding protein comprises:

(i) the amino acid sequence of any one of SEQ ID NOs: 33-46; or

(ii) an amino acid sequence having no more than ten conserved amino acid substitutions with any one of SEQ ID NOs: 33-46, wherein any conserved amino acid substitutions do not occur in the variable region.

7 . The antigen-binding molecule of claim 1 , wherein the antigen-binding molecule binds Escherichia coli OmpW and comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 73-80.

8 . The antigen-binding molecule of claim 7 , wherein the rcSso7d antigen-binding protein comprises:

(i) the amino acid sequence of any one of SEQ ID NOs: 47-54; or

(ii) an amino acid sequence having no more than ten conserved amino acid substitutions with any one of SEQ ID NOs: 47-54, wherein any conserved amino acid substitutions do not occur in the variable region.

9 . The antigen-binding molecule of claim 1 , wherein the antigen-binding molecule binds Escherichia coli OmpA and comprises a variable region having the amino acid sequence of any one of SEQ ID NOs: 81-83.

10 . The antigen-binding molecule of claim 9 , wherein the rcSso7d antigen-binding protein comprises:

(i) the amino acid sequence of any one of SEQ ID NOs: 55-57; or

(ii) an amino acid sequence having no more than ten conserved amino acid substitutions with any one of SEQ ID NOs: 55-57, wherein any conserved amino acid substitutions do not occur in the variable region.

11 . An antigen-binding molecule comprising a reduced charge Sso7d (rcSso7d) antigen-binding protein, wherein the rcSso7d antigen-binding protein comprises the amino acid sequence of any one of SEQ ID NOs: 13-19 or 33-57.

12 . The antigen-binding molecule of claim 1 , further comprising an enzyme, a fluorescent protein, an immunoglobulin, a peptide tag, a small molecule, or a combination thereof.

13 . The antigen-binding molecule of claim 12 , wherein the antigen-binding molecule comprises:

an enzyme selected from the group consisting of alkaline phosphatase, horseradish peroxidase, and β-galactosidase;

a fluorescent protein selected from the group consisting of TagBFP, mTagBFP2, Azurite, EBFP2, EBFP2, Sirius, Sapphire, T-Sapphire, ECFP, Cerulean, SCFP3A, mTurquoise, mTurquoise2, monomeric Midoriishi-Cyan, TagCFP, mTFP1, EGFP, Emerald, Superfolder GFP, Monomeric Azami Green, TagGFP2, mUKG, mWasabi, Clover, mNeonGreen, EYFP, Citrine, Venus, SYFP2, TagYFP, Monomeric Kusabira-Orange, mKOκ, mKO2, mOrange, mOrange2, mRaspberry, mCherry, mStrawberry, mTangerine, tdTomato, TagRFP, TagRFP-T, mApple, mRuby, mRuby2, mPlum, HcRed-Tandem, mKate2, mNeptune, and NirFP;

a peptide tag selected from the group consisting of a His tag, a biotin acceptor tag, an HA tag, a c-Myc tag, a streptavidin tag, and a FLAG tag;

biotin; or

a combination thereof.

14 . A composition comprising an antigen-binding molecule according to claim 1 and a buffer, wherein the buffer has a pH≤6.0, optionally wherein the buffer has a pH of 5.0-6.0.

15 . A method of detecting a protein in a sample, the method comprising:

(a) contacting the sample with an antigen-binding molecule of claim 1 ; and

(b) detecting, if present, protein bound by the antigen-binding molecule.

16 . A method of detecting bacteria in a sample comprising:

(a) contacting the sample with an antigen-binding molecule of claim 1 ; and

(b) detecting, if present, bacteria bound by the antigen-binding molecule.

17 . A kit comprising the antigen-binding molecule of claim 1 .

18 . An antigen-binding molecule comprising a reduced charge Sso7d (rcSso7d) antigen-binding protein, wherein the rcSso7d antigen-binding protein comprises the amino acid sequence of any one of SEQ ID NOs: 13-19 or 33-57 or an amino acid sequence having no more than seven conserved amino acid substitutions with any one of SEQ ID NOs: 55-57, wherein any conserved amino acid substitutions do not occur in a variable region of the rcSso7d antigen-binding protein.