Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design

Isolation of HIV-1-Neutralizing Mucosal Monoclonal Antibodies from Human Colostrum

BACKGROUND: Generation of potent anti-HIV antibody responses in mucosal compartments is a potential requirement of a transmission-blocking HIV vaccine. HIV-specific, functional antibody responses are present in breast milk, and these mucosal antibody responses may play a role in protection of the majority of HIV-exposed, breastfeeding infants. Therefore, characterization of HIV-specific antibodies produced by B cells in milk could guide the development of vaccines that elicit protective mucosal antibody responses. METHODS: We isolated B cells from colostrum of an HIV-infected lactating woman with a detectable neutralization response in milk and recombinantly produced and characterized the resulting HIV-1 Envelope (Env)-specific monoclonal antibodies (mAbs). RESULTS: The identified HIV-1 Env-specific colostrum mAbs, CH07 and CH08, represent two of the first mucosally-derived anti-HIV antibodies yet to be reported. Colostrum mAb CH07 is a highly-autoreactive, weakly-neutralizing gp140-specific mAb that binds to linear epitopes in the gp120 C5 region and gp41 fusion domain. In contrast, colostrum mAb CH08 is a nonpolyreactive CD4-inducible (CD4i) gp120-specific mAb with moderate breadth of neutralization. CONCLUSIONS: These novel HIV-neutralizing mAbs isolated from a mucosal compartment provide insight into the ability of mucosal B cell populations to produce functional anti-HIV antibodies that may contribute to protection against virus acquisition at mucosal surfaces

Induction of Antibodies in Rhesus Macaques That Recognize a Fusion-Intermediate Conformation of HIV-1 gp41

A component to the problem of inducing broad neutralizing HIV-1 gp41 membrane proximal external region (MPER) antibodies is the need to focus the antibody response to the transiently exposed MPER pre-hairpin intermediate neutralization epitope. Here we describe a HIV-1 envelope (Env) gp140 oligomer prime followed by MPER peptide-liposomes boost strategy for eliciting serum antibody responses in rhesus macaques that bind to a gp41 fusion intermediate protein. This Env-liposome immunization strategy induced antibodies to the 2F5 neutralizing epitope 664DKW residues, and these antibodies preferentially bound to a gp41 fusion intermediate construct as well as to MPER scaffolds stabilized in the 2F5-bound conformation. However, no serum lipid binding activity was observed nor was serum neutralizing activity for HIV-1 pseudoviruses present. Nonetheless, the Env-liposome prime-boost immunization strategy induced antibodies that recognized a gp41 fusion intermediate protein and was successful in focusing the antibody response to the desired epitope

Structural constraints of vaccine-induced tier-2 autologous HIV neutralizing antibodies targeting the receptor-binding site.

CAPRISA, 2017.Abstract available in pdf

A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice

Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV, bat coronaviruses WIV-1, RsSHC014, and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor-binding domain (RBD)-specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccin

Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.

CAPRISA, 2017.Abstract available in pdf

Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide.

CAPRISA, 2017.Abstract available in pdf

Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies.

CAPRISA, 2014.Abstract available in pdf

Recent Advances in Mathematical Programming with Semi-continuous Variables and Cardinality Constraint

Abstract Mathematical programming problems with semi-continuous variables and cardinality constraint have many applications, including production planning, portfolio selection, compressed sensing and subset selection in regression. This class of problems can be modeled as mixed-integer programs with special structures and are in general NP-hard. In the past few years, based on new reformulations, approximation and relaxation techniques, promising exact and approximate methods have been developed. We survey in this paper these recent developments for this challenging class of mathematical programming problems.

Dominant p11C-specific population contained lower frequency of cytokine- and chemokine-producing cells than subdominant epitope-specific populations.

<p>PBMCs from monkeys chronically-infected with either SIVmac251 (n = 4) or SIVsmE660 (n = 5) were stimulated with either p11C, p54AS/E660, or p68A peptides and intracellular staining was used to assess production of the chemokine MIP-1β and cytokines IFNγ, TNFα, and IL-2. Bars represent mean ± SEM. A) Individual cytokine and chemokine production. Top, SIVmac251. Bottom, SIVsmE660. B) Polyfunctional analysis. Positivity for each cytokine/chemokine is indicated by the dots below the bar graph. Vertical bars are grouped into 4, 3, 2 or 1 function (indicated by the pink, light blue, purple, and orange horizontal bars, respectively). C) Polyfunctionality charts. Left, SIVmac251. Right, SIVsmE660. Each slice represents the percentage of tetramer-positive cells expressing between 1 and 4 functions. Data were collected between weeks 36–42 for SIVmac251 and 14–25 for SIVsmE660.</p