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TitleImproved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design.
Journal, issue, pagesCell Rep, Vol. 42, Issue 7, Page 112711, Year 2023
Publish dateJul 10, 2023
AuthorsGraham T Holt / Jason Gorman / Siyu Wang / Anna U Lowegard / Baoshan Zhang / Tracy Liu / Bob C Lin / Mark K Louder / Marcel S Frenkel / Krisha McKee / Sijy O'Dell / Reda Rawi / Chen-Hsiang Shen / Nicole A Doria-Rose / Peter D Kwong / Bruce R Donald /
PubMed AbstractBroadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth and potency of neutralization. We employ ...Broadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth and potency of neutralization. We employ the OSPREY computational protein design software to engineer variants of two apex-directed bNAbs, PGT145 and PG9RSH, resulting in increases in potency of over 100-fold against some viruses. The top designed variants improve neutralization breadth from 39% to 54% at clinically relevant concentrations (IC < 1 μg/mL) and improve median potency (IC) by up to 4-fold over a cross-clade panel of 208 strains. To investigate the mechanisms of improvement, we determine cryoelectron microscopy structures of each variant in complex with the HIV envelope trimer. Surprisingly, we find the largest increases in breadth to be a result of optimizing side-chain interactions with highly variable epitope residues. These results provide insight into mechanisms of neutralization breadth and inform strategies for antibody design and improvement.
External linksCell Rep / PubMed:37436900 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 3.75 Å
Structure data

29248

8fk5

EMDB-29248, PDB-8fk5:
Cryo-EM Structure of PG9RSH DU011 Fab in complex with BG505 DS-SOSIP.664
Method: EM (single particle) / Resolution: 3.4 Å

29264

8fl1

EMDB-29264, PDB-8fl1:
Cryo-EM Structure of PG9RSH DU025 Fab in complex with BG505 DS-SOSIP.664
Method: EM (single particle) / Resolution: 3.75 Å

29288

8flw

EMDB-29288, PDB-8flw:
Cryo-EM Structure of PGT145 DU303 Fab in complex with BG505 DS-SOSIP.664
Method: EM (single particle) / Resolution: 3.58 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / CD4 / HIV-1 / SOSIP / Vaccine / IMMUNE SYSTEM / llama / V2 apex / therapeutic

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