Transplanting supersites of HIV-1 vulnerability.

Tongqing Zhou,Wayne C Koff,Gilad Ofek,Jonathan Stuckey,Mark Connors,Christopher R Lees,Sanjay Srivatsan,Dennis R Burton,Jiang Zhu,Aliaksandr Druz,Jason Gorman,Gabriel Lu,Yongping Yang,Cinque Soto,Peter D Kwon

doi:10.1371/journal.pone.0099881

Abstract

One strategy for isolating or eliciting antibodies against a specific target region on the envelope glycoprotein trimer (Env) of the human immunodeficiency virus type 1 (HIV-1) involves the creation of site transplants, which present the target region on a heterologous protein scaffold with preserved antibody-binding properties. If the target region is a supersite of HIV-1 vulnerability, recognized by a collection of broadly neutralizing antibodies, this strategy affords the creation of “supersite transplants”, capable of binding (and potentially eliciting) antibodies similar to the template collection of effective antibodies. Here we transplant three supersites of HIV-1 vulnerability, each targeted by effective neutralizing antibodies from multiple donors. To implement our strategy, we chose a single representative antibody against each of the target supersites: antibody 10E8, which recognizes the membrane-proximal external region (MPER) on the HIV-1 gp41 glycoprotein; antibody PG9, which recognizes variable regions one and two (V1V2) on the HIV-1 gp120 glycoprotein; and antibody PGT128 which recognizes a glycopeptide supersite in variable region 3 (glycan V3) on gp120. We used a structural alignment algorithm to identify suitable acceptor proteins, and then designed, expressed, and tested antigenically over 100-supersite transplants in a 96-well microtiter-plate format. The majority of the supersite transplants failed to maintain the antigenic properties of their respective template supersite. However, seven of the glycan V3-supersite transplants exhibited nanomolar affinity to effective neutralizing antibodies from at least three donors and recapitulated the mannose9-N-linked glycan requirement of the template supersite. The binding of these transplants could be further enhanced by placement into self-assembling nanoparticles. Essential elements of the glycan V3 supersite, embodied by as few as 3 N-linked glycans and ∼25 Env residues, can be segregated into acceptor scaffolds away from the immune-evading capabilities of the rest of HIV-1 Env, thereby providing a means to focus the immune response on the scaffolded supersite.

Highlights

Antibody isolation and immunogen design are critical components in the current global effort to design an effective vaccine against the human immunodeficiency virus type 1 (HIV-1)
AListed items include supersite index, Protein Databank (PDB) identifier, chain name, percent secondary structure composition, number of residues in the supersite, number of residues aligned to the epitope, Ca root-mean-square deviation (RMSD) of aligned residues, TM-score from TMalign output, solvent accessibility ratio between the epitope-matching region in the transplant context versus the epitope alone, transplant-antibody clash score, and number of variants designed based on each transplant. doi:10.1371/journal.pone.0099881.t001
V1V2-supersite transplant aListed items include scaffold index, PDB identifier, chain name, percent secondary structure composition, number of residues in the scaffold structure, number of residues aligned to the epitope, Ca RMSD of aligned residues, TM-score from TMalign output, solvent accessibility ratio between the epitope-matching region in the scaffold context versus the epitope alone, scaffold-antibody clash score, and number of variants designed based on each scaffold. doi:10.1371/journal.pone.0099881.t002

Summary

Introduction

Antibody isolation and immunogen design are critical components in the current global effort to design an effective vaccine against the human immunodeficiency virus type 1 (HIV-1) (reviewed in [1,2]). The HIV-1 viral spike is metastable and protected from antibody recognition by multiple overlapping mechanisms of immune evasion [3,4,5,6,7,8]. A plethora of antibodies are elicited against the viral spike or its component subunits, gp120 and gp, early in natural infection or after vaccination, but virtually none are capable of broad and potent neutralization. Substantial effort has been mounted to isolate such antibodies (to understand their immune mechanisms of effective HIV-1 recognition) and to elicit similar antibodies (to protect prophylactically against HIV-1 infection). There is a need for probes to bind to desired effective antibodies and for immunogens to elicit them

Methods

Results

Conclusion