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Relevant bibliographies by topics / Computational designing of HIV immunogens

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Journal articles

Academic literature on the topic 'Computational designing of HIV immunogens'

Author: Grafiati

Published: 11 September 2023

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Journal articles on the topic "Computational designing of HIV immunogens"

1

Ahmed, Syed Faraz, Ahmed A. Quadeer, David Morales-Jimenez, and Matthew R. McKay. "Sub-dominant principal components inform new vaccine targets for HIV Gag." Bioinformatics 35, no. 20 (2019): 3884–89. http://dx.doi.org/10.1093/bioinformatics/btz524.

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Abstract Motivation Patterns of mutational correlations, learnt from patient-derived sequences of human immunodeficiency virus (HIV) proteins, are informative of biochemically linked networks of interacting sites that may enable viral escape from the host immune system. Accurate identification of these networks is important for rationally designing vaccines which can effectively block immune escape pathways. Previous computational methods have partly identified such networks by examining the principal components (PCs) of the mutational correlation matrix of HIV Gag proteins. However, driven by

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2

Jiang, Xunqing, Max Totrov, Wei Li, et al. "Rationally Designed Immunogens Targeting HIV-1 gp120 V1V2 Induce Distinct Conformation-Specific Antibody Responses in Rabbits." Journal of Virology 90, no. 24 (2016): 11007–19. http://dx.doi.org/10.1128/jvi.01409-16.

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ABSTRACTThe V1V2 region of HIV-1 gp120 harbors a major vulnerable site targeted by a group of broadly neutralizing monoclonal antibodies (MAbs) such as PG9 through strand-strand recognition. However, this epitope region is structurally polymorphic as it can also form a helical conformation recognized by RV144 vaccine-induced MAb CH58. This structural polymorphism is a potential mechanism for masking the V1V2 vulnerable site. Designing immunogens that can induce conformation-specific antibody (Ab) responses may lead to vaccines targeting this vulnerable site. We designed a panel of immunogens e

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3

DeLaitsch, Andrew T., Nathaniel Liendo, and Pamela J. Bjorkman. "Designing occluded-open Env-based immunogens for HIV-1." Biophysical Journal 122, no. 3 (2023): 472a. http://dx.doi.org/10.1016/j.bpj.2022.11.2532.

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4

Moyo, Nathifa, Edmund G. Wee, Bette Korber, et al. "Tetravalent Immunogen Assembled from Conserved Regions of HIV-1 and Delivered as mRNA Demonstrates Potent Preclinical T-Cell Immunogenicity and Breadth." Vaccines 8, no. 3 (2020): 360. http://dx.doi.org/10.3390/vaccines8030360.

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A vaccine will likely be one of the key tools for ending the HIV-1/AIDS epidemic by preventing HIV-1 spread within uninfected populations and achieving a cure for people living with HIV-1. The currently prevailing view of the vaccine field is to introduce protective antibodies, nevertheless, a vaccine to be effective may need to harness protective T cells. We postulated that focusing a T-cell response on the most vulnerable regions of the HIV-1 proteome while maximizing a perfect match between the vaccine and circulating viruses will control HIV-1 replication. We currently use a combination of

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5

Lin, George, and Peter Nara. "Designing Immunogens to Elicit Broadly Neutralizing Antibodies to the HIV-1 Envelope Glycoprotein." Current HIV Research 5, no. 6 (2007): 514–41. http://dx.doi.org/10.2174/157016207782418489.

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6

Das, Supratik, Rajesh Kumar, Shubbir Ahmed, Hilal Ahmad Parray, and Sweety Samal. "Efficiently cleaved HIV-1 envelopes: can they be important for vaccine immunogen development?" Therapeutic Advances in Vaccines and Immunotherapy 8 (January 2020): 251513552095776. http://dx.doi.org/10.1177/2515135520957763.

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The enormous diversity of HIV-1 is a significant impediment in selecting envelopes (Envs) that can be suitable for designing vaccine immunogens. While tremendous progress has been made in developing soluble, trimeric, native-like Env proteins, those that have elicited neutralizing antibodies (Abs) in animal models are relatively few. A strategy of selecting naturally occurring Envs suitable for immunogen design by studying the correlation between efficient cleavage on the cell surface and their selective binding to broadly neutralizing Abs (bNAbs) and not to non-neutralizing Abs (non-NAbs), pr

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7

Mehandru, Saurabh, Terri Wrin, Justin Galovich, et al. "Neutralization Profiles of Newly Transmitted Human Immunodeficiency Virus Type 1 by Monoclonal Antibodies 2G12, 2F5, and 4E10." Journal of Virology 78, no. 24 (2004): 14039–42. http://dx.doi.org/10.1128/jvi.78.24.14039-14042.2004.

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ABSTRACT As the AIDS epidemic continues unabated, the development of a human immunodeficiency virus (HIV) vaccine is critical. Ideally, an effective vaccine should elicit cell-mediated and neutralizing humoral immune responses. We have determined the in vitro susceptibility profile of sexually transmitted viruses from 91 patients with acute and early HIV-1 infection to three monoclonal antibodies, 2G12, 2F5, and 4E10. Using a recombinant virus assay to measure neutralization, we found all transmitted viruses were neutralized by 4E10, 80% were neutralized by 2F5, and only 37% were neutralized b

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8

Nabel, Gary J., Peter D. Kwong, and John R. Mascola. "Progress in the rational design of an AIDS vaccine." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1579 (2011): 2759–65. http://dx.doi.org/10.1098/rstb.2011.0096.

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Human immunodeficiency virus-1 (HIV-1) has a high degree of genetic and antigenic diversity that has impeded the development of an effective vaccine using traditional methods. We are attempting to develop an AIDS vaccine by employing strategies that include structural biology and computational modelling, in an effort to develop immunogens capable of eliciting neutralizing antibodies of the requisite breadth and potency against circulating strains of HIV-1.

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9

Iroegbu, Johanna, Markus Birk, Una Lazdina, Anders Sönnerborg, and Matti Sällberg. "Variability and Immunogenicity of Human Immunodeficiency Virus Type 1 p24 Gene Quasispecies." Clinical Diagnostic Laboratory Immunology 7, no. 3 (2000): 377–83. http://dx.doi.org/10.1128/cdli.7.3.377-383.2000.

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ABSTRACT Despite the conserved nature of the human immunodeficiency virus type 1 (HIV-1) gag gene, multiple quasispecies of the p24 gene coexist in HIV-1-infected patients. We cloned and sequenced 31 p24 genes from four HIV-1-infected patients. The intrapatient homology between the p24 genes ranged from 97.1 to 99.1%, whereas the interpatient homology ranged from 91.5 to 93.8%, suggesting a host-specific evolution. Synonymous and nonsynonymous nucleotide changes were evenly distributed in the p24 gene, with 27 and 28%, respectively, located within host human leukocyte antigen class I recogniti

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10

Swanson, Olivia, Joshua S. Martin Beem, Brianna Rhodes, et al. "Identification of CDRH3 loops in the B cell receptor repertoire that can be engaged by candidate immunogens." PLOS Pathogens 19, no. 5 (2023): e1011401. http://dx.doi.org/10.1371/journal.ppat.1011401.

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A major goal for the development of vaccines against rapidly mutating viruses, such as influenza or HIV, is to elicit antibodies with broad neutralization capacity. However, B cell precursors capable of maturing into broadly neutralizing antibodies (bnAbs) can be rare in the immune repertoire. Due to the stochastic nature of B cell receptor (BCR) rearrangement, a limited number of third heavy chain complementary determining region (CDRH3) sequences are identical between different individuals. Thus, in order to successfully engage broadly neutralizing antibody precursors that rely on their CDRH

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