I-101 Quaternary contact improves the potency of broadly neutralizing antibodies to the CD4-binding site of HIV-1

Abstract

Broadly neutralizing antibodies (bNAb) directly cloned from HIV-infected individuals are attracting increasing consideration for the prevention and treatment of HIV-1 infection. We recently reported the identification of a second, quaternary CD4-binding site (CD4-BS) in the native HIV-1 envelope trimer, showing that selected anti-CD4BS NAbs also establish quaternary interactions with a neighboring gp120 protomer through the extended framework 3 (FR3) loop of their heavy chain. In contrast, some potent bNAbs like VRC01 and N6 contain a shorter FR3 loop and appear to interact with a single gp120 protomer. Here, we used structure-based engineering to engraft the extended FR3 loop of VRC03 onto 4 potent anti-CD4 supersite antibodies, namely, VRC01, VRC07, N6 and 3BNC117, with the aim of enabling them to contact an adjacent gp120 promoter. With the exception of 3BNC117, all the chimeric antibodies showed an enhanced neutralizing capacity against the majority of a large HIV-1 envelope panel (208 strains), which correlated with an increased binding affinity for the pre-fusion envelope trimer. The crystal structure of one engineered antibody, N6 FR3-03, was solved in complex with a soluble stabilized trimer, BG505 SOSIP.664, which allowed to visualize the quaternary interaction of the engrafted FR3 loop with residues at the base of the V3 loop of a neighboring gp120 protomer. Thus, engraftment of the VRC03 FR3 loop enabled potent anti-CD4BS antibodies to establish quaternary contact with a neighboring protomer of the HIV-1 Env timer, leading to increased neutralization potency. FR3 loop-chimeric bNAbs may be considered for applications in HIV-1 prevention and treatment.