The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site

Abstract

The HIV-1 envelope glycoproteins (Env) undergo conformational changes upon interaction of the gp120 exterior glycoprotein with the CD4 receptor. The gp120 inner domain topological layers facilitate the transition of Env to the CD4-bound conformation. CD4 engages gp120 by introducing its phenylalanine 43 (Phe43) in a cavity (“the Phe43 cavity”) located at the interface between the inner and outer gp120 domains. Small CD4-mimetic compounds (CD4mc) can bind within the Phe43 cavity and trigger conformational changes similar to those induced by CD4. Crystal structures of CD4mc in complex with a modified CRF01_AE gp120 core revealed the importance of these gp120 inner domain layers in stabilizing the Phe43 cavity and shaping the CD4 binding site. Our studies reveal a complex interplay between the gp120 inner domain and the Phe43 cavity and generate useful information for the development of more-potent CD4mc. IMPORTANCE The Phe43 cavity of HIV-1 envelope glycoproteins (Env) is an attractive druggable target. New promising compounds, including small CD4 mimetics (CD4mc), were shown to insert deeply into this cavity. Here, we identify a new network of residues that helps to shape this highly conserved CD4 binding pocket and characterize the structural determinants responsible for Env sensitivity to small CD4 mimetics.

Cryo-EM Structures of HIV-1 trimer bound to CD4-mimetics M48U1 and BNM-III-170 adopt a CD4-bound open conformation

“…As expected, BG505 did not bind17b or 21c IgGs in the absence of sCD4 or BNM-III-170 and M48U1 inhibitors, indicating the Env trimers were well-folded. When incubated with BNM-III-170, M38U1, or sCD4, BG505 bound to 17b IgG, confirming previous results 29,30 and demonstrating accessibility of the V3 loop in an open state ( Supplementary Fig. 1b-d).…”

“…17b, a CD4-induced (CD4i) antibody that binds Env only when the gp120 V3 loop is exposed after V1V2 loop displacement characteristic of CD4-induced Env opening, has been used as a measure of trimer opening [3][4][5][6]27,28 . We first recapitulated and extended studies showing that binding of BNM-III-170 and M48U1 CD4m compounds open Env trimers 29,30 as assessed by a 17b binding assay 31 . D7324-tagged BG505 trimers 8 were immobilized on ELISA plates by binding to the JR-52 antibody as described 8 and then incubated with either buffer, BNM-III-170, M48U1, BMS-626529, or soluble CD4 (sCD4), and the binding of CD4-induced antibodies 17b and 21c, V1V2 bNAbs BG1 and PG16, and V3 bNAb 10-1074 was measured.…”

New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure

“…We noted from studies by Finzi and Sodroski (30) that residue 375 in the CD4 binding pocket of primate lentiviral Envs was under strong positive evolutionary pressure across the broad spectrum of primate lentiviruses. These investigators further showed that substitution of 375-Ser (found in most HIV-1 group M viruses) by 375-Trp (found in most SIV strains from lower primates) favored an HIV-1 Env conformation that was closer to the CD4-bound state (31–34). Based on these findings, we hypothesized that residue 375 might act as a “molecular switch” conferring enhanced Env affinity to rhesus CD4 (35) and a lower energetic barrier to conformational change following CD4 binding (31, 34, 36, 37) when the naturally-occurring Ser or Thr residues were substituted by bulky aromatic residues like Trp.…”

“…Based on these findings, we hypothesized that residue 375 might act as a "molecular switch" conferring enhanced Env affinity to rhesus CD4 (35) and a lower energetic barrier to conformational change following CD4 binding (31,34,36,37) when the naturally-occurring Ser 6 or Thr residues were substituted by bulky aromatic residues like Trp. In testing this hypothesis, we discovered that substitution of a single residue, 375-Ser, in primary or T/F HIV-1 Envs by Trp, Phe, Tyr, His or Met resulted in SHIVs that exhibited enhanced binding to rhesus CD4, increased infection of primary rhesus CD4 + T cells in culture, and consistent infection and replication by SHIVs in RMs in vivo (35).…”

New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention, and Cure

“…We noted from studies by Finzi and Sodroski (30) that residue 375 in the CD4 binding pocket of primate lentiviral Envs was under strong positive evolutionary pressure across the broad spectrum of primate lentiviruses. These investigators further showed that substitution of 375-Ser (found in most HIV-1 group M viruses) by 375-Trp (found in most SIV strains from lower primates) favored an HIV-1 Env conformation that was closer to the CD4-bound state (31)(32)(33)(34).…”