Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding

Area of Science:

• Immunology
• Virology
• Structural Biology

Background:

• An effective HIV-1 vaccine needs broadly neutralizing antibodies (bnAbs) targeting diverse Envelope glycoproteins (Env).
• Longer hypervariable (HV) loops in Env increase resistance to bnAbs.
• Consensus sequences for HIV-1 subtypes B, C, and CRF01_AE represent circulating strains.

Purpose of the Study:

• To redesign HIV-1 Env hypervariable loops to increase sensitivity to bnAbs.
• To maintain Env structural integrity and glycan shield during HV loop modification.
• To assess the impact of HV loop redesign on Env conformation, binding, and neutralization sensitivity.

Main Methods:

• Utilized AlphaFold2 modeling to guide the reduction of V1, V2, and V5 HV loop lengths.
• Modified the V4 HV loop and introduced spacers to limit strain-specific targeting.
• Generated infectious pseudoviruses with modified Env, analyzed structure, performed binding and neutralization assays.

Main Results:

• Modified Env pseudoviruses maintained structural integrity and infectivity.
• Binding assays showed enhanced binding to modified subtype B and CRF01_AE Env, but not subtype C.
• Neutralization assays demonstrated increased sensitivity to bnAbs, notably rendering resistant CRF01_AE Env sensitive to 10-1074.

Conclusions:

• Redesigning HIV-1 Env HV loops can enhance sensitivity to broadly neutralizing antibodies.
• This strategy offers a potential avenue for developing more effective HIV-1 vaccines.
• HV loop modification can overcome specific resistance mechanisms, even in the absence of key glycans.