Papers by Priyamvada Acharya
Nature Communications
Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In s... more Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affi...
Nature Communications
Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In s... more Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affi...
Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously... more Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
Frontiers in Immunology, 2021
Broadly neutralizing antibodies (bNAbs), known to mediate immune control of HIV-1 infection, only... more Broadly neutralizing antibodies (bNAbs), known to mediate immune control of HIV-1 infection, only develop in a small subset of HIV-1 infected individuals. Despite being traditionally associated with patients with high viral loads, bNAbs have also been observed in therapy naïve HIV-1+ patients naturally controlling virus replication [Virus Controllers (VCs)]. Thus, dissecting the bNAb response in VCs will provide key information about what constitutes an effective humoral response to natural HIV-1 infection. In this study, we identified a polyclonal bNAb response to natural HIV-1 infection targeting CD4 binding site (CD4bs), V3-glycan, gp120-gp41 interface and membrane-proximal external region (MPER) epitopes on the HIV-1 envelope (Env). The polyclonal antiviral antibody (Ab) response also included antibody-dependent cellular phagocytosis of clade AE, B and C viruses, consistent with both the Fv and Fc domain contributing to function. Sequence analysis of envs from one of the VCs rev...
This entry contains filtered trajectories for both the WT and Mut (K417N+E484K+N501Y) datasets an... more This entry contains filtered trajectories for both the WT and Mut (K417N+E484K+N501Y) datasets and the scripts used for the vector relationship and Markov modelling work in our paper "Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity" posted on bioRxiv March 12th 2021. The VMD scripts can be run from the tcl console after loading VMD and your structure or via the command line using: vmd -dispdev none -e script_name.tcl your_SARS-CoV-2_structure.pdb Residue numbers in these scripts are specific to SARS-CoV-2 and must be numbered in a manner consistent with the the PDB ID 6VXX structure. Analysis of other Coronavirus Spike structures will require modification of the residue selections. Tcl commands for visulizing the vectors in VMD are provided at the bottom of each VMD script. The HTMD.py script commands can be run in an interactive python session to allow for modification of the model and/or testing alternative projections, etc. Th...
AIDS Research and Human Retroviruses, 2018
Cell Reports, 2021
Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding si... more Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
Science Translational Medicine, 2021
Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-C... more 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 and 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 miti...
Breast milk secretory IgA antibodies provide a first line of defense against enteric infections. ... more Breast milk secretory IgA antibodies provide a first line of defense against enteric infections. Despite this and an effective vaccine, human rotaviruses (RVs) remain the leading cause of severe infectious diarrhea in children in low- and middle-income countries (LMIC) where vaccine efficacy is lower than that of developed nations. Therapeutic strategies that deliver potently neutralizing antibodies into milk could provide protection against enteric pathogens such as RVs. We developed a murine model of maternal protective-transfer using systemic administration of a dimeric IgA (dIgA) monoclonal antibody. We confirmed that systemically-administered dIgA passively transferred into milk and stomach of suckling pups in a dose-dependent manner. We then demonstrated that systemic administration of an engineered potent RV-neutralizing dIgA (mAb41) in lactating dams protected suckling pups from RV-induced diarrhea. This maternal protective-transfer immunization platform could be an effectiv...
Cell Host & Microbe, 2021
Cell Reports Medicine, 2021
Microscopy and Microanalysis, 2020
Single-particle cryo-EM is a powerful imaging modality used to determine the structure of biomedi... more Single-particle cryo-EM is a powerful imaging modality used to determine the structure of biomedically important macromolecular complexes. The underlying principle for three-dimensional reconstruction consists in combining projection views corresponding to multiple copies of the target of interest taken from random orientations. While well-behaved and homogeneous samples can readily yield highresolution reconstructions [1], most realistic targets are often heterogeneous, flexible or dynamic, making it challenging to obtain high-quality density maps. Successful analysis of such datasets relies on the use of laborious protocols for 2D and 3D image classification aimed at identifying homogeneous subpopulations of particles that when combined in 3D can yield high-resolution structures. This supervised process of image sorting is not only prone to bias, difficult to reproduce and computationally inefficient, but also incompatible with modern strategies for high-throughput data collection and analysis used in single-particle cryo-EM. We have previously addressed the problem of unsupervised structure refinement in the case of homogeneous samples [2], and showed that high-resolution structures of even challenging samples like HIV-1 Env can be obtained without user supervision [3]. Here, we extend these ideas to the case of samples that display discrete heterogeneity, i.e., where a finite but unknown number of conformations are present in the data. To address this problem, we propose a strategy to automatically determine the number of distinct conformations present in a mix using a simple statistical test based on particle scores measured against multiple 3D references. Results obtained on several challenging datasets demonstrate that our strategy can be used to successfully recover the correct number of discrete conformations present in heterogeneous datasets without supervision, paving the way for the development of high-throughput strategies for single-particle cryo-EM data analysis.
Organic Letters, 2003
Peptides U 0400 Asymmetric Total Synthesis and Stereochemical Elucidation of the Antitumor Agent ... more Peptides U 0400 Asymmetric Total Synthesis and Stereochemical Elucidation of the Antitumor Agent PM-94128.-The key steps for the synthesis of the dihydroxyamino moiety of the target depsipeptide are a diastereoselective addition of tert-butyl lithiopropiolate to a chiral nitrone, and a 2,3-dihydro[1,2]oxazin-6-one dihydroxylation.-(PATEL, S.
Immunity, 2021
The Plasmodium falciparum circumsporozoite protein (PfCSP) is targeted by neutralizing antibodies... more The Plasmodium falciparum circumsporozoite protein (PfCSP) is targeted by neutralizing antibodies and is a focus of malaria vaccine development. In this issue of Immunity, Kratochvil et al. (2021) combine vaccination and bioinformatics strategies to develop a best-in-class PfCSP-targeting antibody.
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Papers by Priyamvada Acharya