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

Author: Grafiati

Published: 11 September 2023

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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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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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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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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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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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11

Sanou, Missa P., Anne S. De Groot, Michael Murphey-Corb, Jay A. Levy, and Janet K. Yamamoto. "HIV-1 Vaccine Trials: Evolving Concepts and Designs." Open AIDS Journal 6, no. 1 (2012): 274–88. http://dx.doi.org/10.2174/1874613601206010274.

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An effective prophylactic HIV-1 vaccine is needed to eradicate the HIV/AIDS pandemic but designing such a vaccine is a challenge. Despite many advances in vaccine technology and approaches to generate both humoral and cellular immune responses, major phase-II and -III vaccine trials against HIV/AIDS have resulted in only moderate successes. The modest achievement of the phase-III RV144 prime-boost trial in Thailand re-emphasized the importance of generating robust humoral and cellular responses against HIV. While antibody-directed approaches are being pursued by some groups, others are attempt

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Chan-hui, Po-Ying, Terri Wrin, Melissa Simek, et al. "Isolation of Cross-Clade HIV-Neutralizing Human Antibodies from Memory B Cell Repertoires Using Short Term Culture and High-Throughput Primary Neutralization Screens (38.17)." Journal of Immunology 184, no. 1_Supplement (2010): 38.17. http://dx.doi.org/10.4049/jimmunol.184.supp.38.17.

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Abstract Background. We have recently isolated 2 broadly neutralizing monoclonal antibodies (bNAbs), PG9 and PG16, from an HIV-infected subject in an African Protocol G cohort that are more potent than the bNAbs discovered in the past decade. The discovery highlights our human antibody (Ab) discovery approach based on short-term memory B cell culture, high-throughput primary microneutralization screening, and recombinant monoclonal antibody (mAb) reconstitution (Walker LM, et al, 2009, Science, 326:285-9). The epitope specificities of PG9 and PG16 reveal a novel target for designing vaccine im

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Kumar, Rajnish, Ruimin Pan, Chitra Upadhyay, et al. "Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL." Journal of Virology 89, no. 17 (2015): 9090–102. http://dx.doi.org/10.1128/jvi.01280-15.

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ABSTRACTThe V3 region of HIV-1 gp120 is important for virus-coreceptor interaction and highly immunogenic. Although most anti-V3 antibodies neutralize only the sensitive tier 1 viruses, anti-V3 antibodies effective against the more resistant viruses exist, and a better understanding of these antibodies and their epitopes would be beneficial for the development of novel vaccine immunogens against HIV. The HIV-1 isolate JRFL with its cryptic V3 is resistant to most V3-specific monoclonal antibodies (MAbs). However, the V3 MAb 2424 achieves 100% neutralization against JRFL. 2424 is encoded by IGH

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Acharya, Priyamvada, Robert Edwards, Rory Henderson, et al. "How Does HIV Env Structure Informs Vaccine Design?" Microscopy and Microanalysis 26, S2 (2020): 574–75. http://dx.doi.org/10.1017/s1431927620015135.

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BackgroundThe DHVI Division of Structural Biology seeks to use atomic level structural information for design of an effective HIV-1 vaccine. Through visualization of the HIV-1 envelope (Env) and its interactions with the human immune system, we obtain structural information that we translate into the rational development vaccine immunogensMethodsWe use negative stain electron microscopy (NSEM), cryo-electron microscopy (cryo-EM), and x-ray crystallography as the major structural techniques for visualization of HIV-1 Env, and combine these with biochemical and biophysical studies, as well as co

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Cain, Derek Wilson, Ming Tian, Torben Schiffner, et al. "Immunogenicity of a germline-targeting nanoparticle in knock-in mice expressing human B cell receptors of the HIV gp41 neutralizing antibody, DH511." Journal of Immunology 208, no. 1_Supplement (2022): 64.22. http://dx.doi.org/10.4049/jimmunol.208.supp.64.22.

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Abstract The Membrane Proximal External Region (MPER) of HIV Envelope represents a key target for vaccine development due to high neutralization breadth and potency of MPER-specific broadly neutralizing antibodies (bnAbs). However, neutralizing antibody responses to MPER epitopes are restricted by tolerance control and the MPER epitope is absent from many HIV immunogens under clinical investigation. Using computational design and yeast display, a candidate germline-targeting (GT5) immunogen was developed that bound strongly to the inferred human unmutated common ancestor (UCA) of the distal MP

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Lin, George, Andrea Bertolotti-Ciarlet, Beth Haggarty, et al. "Replication-Competent Variants of Human Immunodeficiency Virus Type 2 Lacking the V3 Loop Exhibit Resistance to Chemokine Receptor Antagonists." Journal of Virology 81, no. 18 (2007): 9956–66. http://dx.doi.org/10.1128/jvi.00385-07.

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ABSTRACT Entry of human immunodeficiency virus type 1 (HIV-1) and HIV-2 requires interactions between the envelope glycoprotein (Env) on the virus and CD4 and a chemokine receptor, either CCR5 or CXCR4, on the cell surface. The V3 loop of the HIV gp120 glycoprotein plays a critical role in this process, determining tropism for CCR5- or CXCR4-expressing cells, but details of how V3 interacts with these receptors have not been defined. Using an iterative process of deletion mutagenesis and in vitro adaptation of infectious viruses, variants of HIV-2 were derived that could replicate without V3,

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Louie, Raymond H. Y., Kevin J. Kaczorowski, John P. Barton, Arup K. Chakraborty, and Matthew R. McKay. "Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies." Proceedings of the National Academy of Sciences 115, no. 4 (2018): E564—E573. http://dx.doi.org/10.1073/pnas.1717765115.

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HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected patients has led to renewed hope for a prophylactic vaccine capable of combating the scourge of HIV. A major challenge is the design of immunogens and vaccination protocols that can elicit bnAbs that target regions of the virus’s spike proteins where the likelihood of mutational escape is low due to the high fitness cost of mutations. Related challenges include the choice of combinations of bnAbs for therapy.

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18

Geraghty, Daniel, Jodie P. Gooodridge, Kevin Wang, et al. "HLA-F and MHC open conformers in a novel HIV-1 immunization strategy." Journal of Immunology 196, no. 1_Supplement (2016): 116.10. http://dx.doi.org/10.4049/jimmunol.196.supp.116.10.

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Abstract HLA-F is expressed as a protein independent of bound peptide or b2-microglobulin and surface expression is upregulated in dendritic cells, monocytes and most lymphocyte subsets upon activation. Classical MHC class I (MHCI) is also expressed on proliferating lymphoid cells as so-called ‘open conformers (OCs)’, in addition to the ubiquitously expressed form complexed with peptide and b2-microglobulin. Previous studies showed that HLA-F binds most MHCI proteins as open conformers without peptide but not as peptide bound complex. These studies were extended to show that both HLA-F and MHC

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19

Dar, Khalid Bashir, Aashiq Hussain Bhat, Shajrul Amin, et al. "Modern Computational Strategies for Designing Drugs to Curb Human Diseases: A Prospect." Current Topics in Medicinal Chemistry 18, no. 31 (2019): 2702–19. http://dx.doi.org/10.2174/1568026619666190119150741.

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Drug discovery is an exhaustive and time-consuming process involving numerous stages like target identification, validation, lead optimization, preclinical trials, clinical trials and finally postmarketing vigilance for drug safety. The application of computer-aided drug designing (CADD) is an indispensable approach for developing safe and effective drugs. Previous methods based on combinatorial chemistry (CC) and high throughput screening (HTS) consumed a lot of time as well as expenditure. CADD based approaches including pharmacophore modeling (PM), molecular docking (MD), inverse docking, c

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Geraghty, Daniel, Kevin L. Wang, Ni Lee, et al. "HLA-F and MHC open conformers cooperate in antigen presentation during the inflammatory response." Journal of Immunology 198, no. 1_Supplement (2017): 146.13. http://dx.doi.org/10.4049/jimmunol.198.supp.146.13.

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Abstract HLA-F is expressed as a protein independent of bound peptide or β2-microglobulin and surface expression is upregulated upon activation in dendritic cells, monocytes and most lymphocyte subsets. MHC class I (MHCI) is also expressed on proliferating lymphoid cells as open conformers (OCs), in addition to the ubiquitously expressed complexed form. Previous studies showed that HLA-F binds most MHCI proteins as open conformers without peptide but not as peptide bound complex. These studies were extended to show both HLA-F and MHCI OC are ligands for a subset of killer Ig-like receptors (KI

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BAO, JU, JIN F. LIU, XIAO HE, and JOHN Z. H. ZHANG. "COMPUTATIONAL STUDY OF HIV-1 gp41 NHR TRIMER: INHIBITION MECHANISMS OF N-SUBSTITUTED PYRROLE DERIVATIVES AND FRAGMENT-BASED VIRTUAL SCREENING." Journal of Theoretical and Computational Chemistry 12, no. 08 (2013): 1341001. http://dx.doi.org/10.1142/s0219633613410010.

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Fusion of HIV-1 viral and host cellular membranes is an important step for HIV infection. The HIV-1 envelope glycoprotein mediating the membrane fusion consists of subunits gp120 and gp41 whereas gp120 recognizes the cell-surface receptors and gp41 promotes viral-cell membrane fusion. The trimeric helical complex composed of heterodimer of N-terminal and C-terminal extraviral segments has been used for the gp41 function study, and the trimeric N-terminal teptad repeat (NHR) is considered as an antiviral drug target for developing HIV-1 membrane fusion inhibitors. By using computational solvent

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22

Elalouf, Amir. "In-silico Structural Modeling of Human Immunodeficiency Virus Proteins." Biomedical Engineering and Computational Biology 14 (January 2023): 117959722311544. http://dx.doi.org/10.1177/11795972231154402.

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Human immunodeficiency virus (HIV) is an infectious virus that depletes the CD4+ T lymphocytes of the immune system and causes a chronic life-treating disease—acquired immunodeficiency syndrome (AIDS). The HIV genome encodes different structural and accessory proteins involved in viral entry and life cycle. Determining the 3D structure of HIV proteins is essential for new target position finding, structure-based drug designing, and future planning for computational and laboratory experimentations. Hence, the study aims to predict the 3D structures of all the HIV structural and accessory protei

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Wu, Xueling, Tongqing Zhou, Sijy O'Dell, Richard T. Wyatt, Peter D. Kwong, and John R. Mascola. "Mechanism of Human Immunodeficiency Virus Type 1 Resistance to Monoclonal Antibody b12 That Effectively Targets the Site of CD4 Attachment." Journal of Virology 83, no. 21 (2009): 10892–907. http://dx.doi.org/10.1128/jvi.01142-09.

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ABSTRACT The region of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 that engages its primary cellular receptor CD4 forms a site of vulnerability to neutralizing antibodies. The monoclonal antibody b12 exploits the conservation and accessibility of the CD4-binding site to neutralize many, though not all, HIV-1 isolates. To understand the basis of viral resistance to b12, we used the atomic-level definition of b12-gp120 contact sites to study a panel of diverse circulating viruses. A combination of sequence analysis, computational modeling, and site-directed mutage

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Ahmad, Ashfaq, Rashid Ali, Ijaz Ahmad, Fuad A. Awwad, and Emad A. A. Ismail. "Global Stability of Fractional Order HIV/AIDS Epidemic Model under Caputo Operator and Its Computational Modeling." Fractal and Fractional 7, no. 9 (2023): 643. http://dx.doi.org/10.3390/fractalfract7090643.

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The human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), which is a chronic and sometimes fatal illness. HIV reduces an individual’s capability against infection and illness by demolishing his or her immunity. This paper presents a new model that governs the dynamical behavior of HIV/AIDS by integrating new compartments, i.e., the treatment class T. The steady-state solutions of the model are investigated, and accordingly, the threshold quantity R0 is calculated, which describes the global dynamics of the proposed model. It is proved that for R0 less than one, t

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Edwards, Terri G., Trevor L. Hoffman, Frédéric Baribaud, et al. "Relationships between CD4 Independence, Neutralization Sensitivity, and Exposure of a CD4-Induced Epitope in a Human Immunodeficiency Virus Type 1 Envelope Protein." Journal of Virology 75, no. 11 (2001): 5230–39. http://dx.doi.org/10.1128/jvi.75.11.5230-5239.2001.

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ABSTRACT A CD4-independent version of the X4 human immunodeficiency virus type 1 (HIV-1) HXBc2 envelope (Env) protein, termed 8x, mediates infection of CD4-negative, CXCR4-positive cells, binds directly to CXCR4 in the absence of CD4 due to constitutive exposure of a conserved coreceptor binding site in the gp120 subunit, and is more sensitive to antibody-mediated neutralization. To study the relationships between CD4 independence, neutralization sensitivity, and exposure of CD4-induced epitopes associated with the coreceptor binding site, we generated a large panel of Env mutants and chimeras

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Welbourn, Sarah, Srirupa Chakraborty, Jie E. Yang, et al. "A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence." PLOS Pathogens 18, no. 5 (2022): e1010488. http://dx.doi.org/10.1371/journal.ppat.1010488.

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Transmitted/founder (T/F) HIV-1 envelope proteins (Envs) from infected individuals that developed neutralization breadth are likely to possess inherent features desirable for vaccine immunogen design. To explore this premise, we conducted an immunization study in rhesus macaques (RM) using T/F Env sequences from two human subjects, one of which developed potent and broad neutralizing antibodies (Z1800M) while the other developed little to no neutralizing antibody responses (R66M) during HIV-1 infection. Using a DNA/MVA/protein immunization protocol, 10 RM were immunized with each T/F Env. With

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Baassi, Mouna, Mohamed Moussaoui, Hatim Soufi, et al. "Towards designing of a potential new HIV-1 protease inhibitor using QSAR study in combination with Molecular docking and Molecular dynamics simulations." PLOS ONE 18, no. 4 (2023): e0284539. http://dx.doi.org/10.1371/journal.pone.0284539.

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Human Immunodeficiency Virus type 1 protease (HIV-1 PR) is one of the most challenging targets of antiretroviral therapy used in the treatment of AIDS-infected people. The performance of protease inhibitors (PIs) is limited by the development of protease mutations that can promote resistance to the treatment. The current study was carried out using statistics and bioinformatics tools. A series of thirty-three compounds with known enzymatic inhibitory activities against HIV-1 protease was used in this paper to build a mathematical model relating the structure to the biological activity. These c

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Meuser, Megan, Michael Murphy, Adel Rashad, and Simon Cocklin. "Kinetic Characterization of Novel HIV-1 Entry Inhibitors: Discovery of a Relationship between Off-Rate and Potency." Molecules 23, no. 8 (2018): 1940. http://dx.doi.org/10.3390/molecules23081940.

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The entry of HIV-1 into permissible cells remains an extremely attractive and underexploited therapeutic intervention point. We have previously demonstrated the ability to extend the chemotypes available for optimization in the entry inhibitor class using computational means. Here, we continue this effort, designing and testing three novel compounds with the ability to inhibit HIV-1 entry. We demonstrate that alteration of the core moiety of these entry inhibitors directly influences the potency of the compounds, despite common proximal and distal groups. Moreover, by establishing for the firs

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Meuser, Megan E., Michael B. Murphy, Adel A. Rashad, and Simon Cocklin. "Kinetic Characterization of Novel HIV-1 Entry Inhibitors: Discovery of a Relationship between Off-Rate and Potency." Proceedings 22, no. 1 (2019): 77. http://dx.doi.org/10.3390/proceedings2019022077.

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The entry of HIV-1 into permissible cells remains an extremely attractive and underexploited therapeutic intervention point. We have previously demonstrated the ability to extend the chemotypes available for optimization in the entry inhibitor class using computational means. Here, we continue this effort, designing and testing three novel compounds with the ability to inhibit HIV-1 entry. We demonstrate that alteration of the core moiety of these entry inhibitors directly influences the potency of the compounds, despite common proximal and distal groups. Moreover, by establishing for the firs

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Lee, Tae Jin, Jose A. Vazquez, and Arni S. R. Srinivasa Rao. "Mathematical modeling of impact of eCD4-Ig molecule in control and management of HIV within a host." Mathematical Biosciences and Engineering 18, no. 5 (2021): 6887–906. http://dx.doi.org/10.3934/mbe.2021342.

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<abstract><p>Eradication and eventually cure of the HIV virus from the infected individual should be the primary goal in all HIV therapy. This has yet to be achieved, however development of broadly neutralizing antibodies (bNabs) and eCD4-Ig and its related particles are promising therapeutic alternatives to eliminate the HIV virus from the host. Past studies have found superior protectivity and efficacy eradicating the HIV virus with the use of eCD4-Igs over bNabs, which has proposed the antibody-dependent cell-mediated cytotoxicity (ADCC) effect as one of the key-factors for anti

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Wang, Yueping, Jie Chang, Jiangyuan Wang, et al. "3D-QSAR Studies of S-DABO Derivatives as Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors." Letters in Drug Design & Discovery 16, no. 8 (2019): 868–81. http://dx.doi.org/10.2174/1570180815666180810112321.

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Background: S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside reverse transcriptase inhibitors have received considerable attention during the last decade due to their high potency against HIV-1. Methods: In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2) was used t

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Birse, Kenzie, Kelly B. Arnold, Richard M. Novak, et al. "Molecular Signatures of Immune Activation and Epithelial Barrier Remodeling Are Enhanced during the Luteal Phase of the Menstrual Cycle: Implications for HIV Susceptibility." Journal of Virology 89, no. 17 (2015): 8793–805. http://dx.doi.org/10.1128/jvi.00756-15.

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ABSTRACTThe variable infectivity and transmissibility of HIV/SHIV has been recently associated with the menstrual cycle, with particular susceptibility observed during the luteal phase in nonhuman primate models andex vivohuman explant cultures, but the mechanism is poorly understood. Here, we performed an unbiased, mass spectrometry-based proteomic analysis to better understand the mucosal immunological processes underpinning this observed susceptibility to HIV infection. Cervicovaginal lavage samples (n= 19) were collected, characterized as follicular or luteal phase using days since last me

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Barukab, Omar, Farman Ali, and Sher Afzal Khan. "DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning." Journal of Bioinformatics and Computational Biology 19, no. 04 (2021): 2150018. http://dx.doi.org/10.1142/s0219720021500189.

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DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver cancer) and chronic diseases (i.e. AIDS/HIV, asthma), while other kinds are involved in antibiotics, steroids, and anti-inflammatory drugs designing. These crucial processes are closely related to DBPs types. DBPs are categorized into single-stranded DNA-binding proteins (ssDBPs) and double-stranded DNA-binding proteins (dsDBPs). Few computational

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Karthic, Anandakrishnan, Veerbhan Kesarwani, Rahul Kunwar Singh, et al. "Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp)." Molecules 27, no. 3 (2022): 801. http://dx.doi.org/10.3390/molecules27030801.

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The human population is still facing appalling conditions due to several outbreaks of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus. The absence of specific drugs, appropriate vaccines for mutants, and knowledge of potential therapeutic agents makes this situation more difficult. Several 1, 2, 4-triazolo [1, 5-a] pyrimidine (TP)-derivative compounds were comprehensively studied for antiviral activities against RNA polymerase of HIV, HCV, and influenza viruses, and showed immense pharmacological interest. Therefore, TP-derivative compounds can be repurposed against the RNA-

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Saha, Ananya, and Narendra M. Dixit. "Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection." PLOS Computational Biology 16, no. 11 (2020): e1008434. http://dx.doi.org/10.1371/journal.pcbi.1008434.

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Passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 appears a promising strategy for eliciting long-term HIV-1 remission. When administered concomitantly with the cessation of antiretroviral therapy (ART) to patients with established viremic control, bNAb therapy is expected to prolong remission. Surprisingly, in clinical trials on chronic HIV-1 patients, the bNAb VRC01 failed to prolong remission substantially. Identifying the cause of this failure is important for improving VRC01-based therapies and unraveling potential vulnerabilities of other bNAbs. In the trials, vi

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Yang, Yuhe R., Laura E. McCoy, Marit J. van Gils, et al. "Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits." Journal of Virology 94, no. 7 (2020). http://dx.doi.org/10.1128/jvi.01861-19.

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ABSTRACT Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of the heavily glycosylated trimer that lacks potential N-linked glycosylation sites at positions 230, 241, and 289. The Env derived from B41, a subtype B virus, shares a glycan hole centered on positions 230 and 289. To test whether broader neutralization to the common glycan hole can be achieved, we immunized rabbits with B41 SOSIP (gp120-gp41 disulfide [SOS] with an isoleucine-to-proline

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Pande, Prajakt P. "Computational Approach Towards Designing Potential HIV Inhibitors." Journal of Antivirals & Antiretrovirals 01, no. 02 (2010). http://dx.doi.org/10.4172/jaa.1000012.

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Powell, Rebecca L., Svenja Weiss, Alisa Fox, et al. "An HIV Vaccine Targeting the V2 Region of the HIV Envelope Induces a Highly Durable Polyfunctional Fc-Mediated Antibody Response in Rhesus Macaques." Journal of Virology 94, no. 17 (2020). http://dx.doi.org/10.1128/jvi.01175-20.

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ABSTRACT The HIV vaccine field now recognizes the potential importance of generating polyfunctional antibodies (Abs). The only clinical HIV vaccine trial to date to show significant efficacy (RV144) found that reduced infection rates correlated with the level of nonneutralizing Abs specific for the V2 region of the envelope glycoprotein. We have conducted a comprehensive preclinical reverse vaccinology-based vaccine program that has included the design and production and testing of numerous scaffolded V2 region immunogens. The most immunogenic vaccine regimen in nonhuman primates among those s

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Burton, Samantha, Lori M. Spicer, Tysheena P. Charles, et al. "Clade C HIV-1 Envelope Vaccination Regimens Differ in Their Ability To Elicit Antibodies with Moderate Neutralization Breadth against Genetically Diverse Tier 2 HIV-1 Envelope Variants." Journal of Virology 93, no. 7 (2019). http://dx.doi.org/10.1128/jvi.01846-18.

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ABSTRACTThe goals of preclinical HIV vaccine studies in nonhuman primates are to develop and test different approaches for their ability to generate protective immunity. Here, we compared the impact of 7 different vaccine modalities, all expressing the HIV-1 1086.C clade C envelope (Env), on (i) the magnitude and durability of antigen-specific serum antibody responses and (ii) autologous and heterologous neutralizing antibody capacity. These vaccination regimens included immunization with different combinations of DNA, modified vaccinia virus Ankara (MVA), soluble gp140 protein, and different

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Sher, Hamza, Hafsa Sharif, Tahreem Zaheer, et al. "Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1)." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09330-4.

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Abstract Background Despite being in the 21st century, the world has still not been able to vanquish the global AIDS epidemic, and the only foreseeable solution seems to be a safe and effective vaccine. Unfortunately, vaccine trials so far have returned unfruitful results, possibly due to their inability to induce effective cellular, humoral and innate immune responses. The current study aims to tackle these limitations and propose the desired vaccine utilizing immunoinformatic approaches that have returned promising results in designing vaccines against various rapidly mutating organisms. For

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Che, Ye, Alexey V. Gribenko, Xi Song, et al. "Rational Design of a Highly Immunogenic Prefusion-Stabilized F Glycoprotein Antigen for a Respiratory Syncytial Virus Vaccine." Science Translational Medicine, April 6, 2023. http://dx.doi.org/10.1126/scitranslmed.ade6422.

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Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently available. The RSV fusion (F) glycoprotein is a key antigen for vaccine development, and its prefusion conformation is the target of the most potent neutralizing antibodies. Here, we describe a computational and experimental strategy for designing immunogens that enhance the conformational stability and immunogenicity of RSV prefusion F. We obtained an optimized vaccine antigen after screening near

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Malherbe, Delphine C., Jason Mendy, Lo Vang, et al. "Combination Adenovirus and Protein Vaccines Prevent Infection or Reduce Viral Burden after Heterologous Clade C Simian-Human Immunodeficiency Virus Mucosal Challenge." Journal of Virology 92, no. 2 (2017). http://dx.doi.org/10.1128/jvi.01092-17.

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ABSTRACT HIV vaccine development is focused on designing immunogens and delivery methods that elicit protective immunity. We evaluated a combination of adenovirus (Ad) vectors expressing HIV 1086.C (clade C) envelope glycoprotein (Env), SIV Gag p55, and human pegivirus GBV-C E2 glycoprotein. We compared replicating simian (SAd7) with nonreplicating human (Ad4) adenovirus-vectored vaccines paired with recombinant proteins in a novel prime-boost regimen in rhesus macaques, with the goal of eliciting protective immunity against SHIV challenge. In both vaccine groups, plasma and buccal Env-specifi

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Yang, Fengyuan, Jingyi Yang, Zhao Zhang, et al. "Recent Advances in Computer-aided Antiviral Drug Design Targeting HIV-1 Integrase and Reverse Transcriptase Associated Ribonuclease H." Current Medicinal Chemistry 28 (July 8, 2021). http://dx.doi.org/10.2174/0929867328666210708090123.

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: Acquired immunodeficiency syndrome (AIDS) has been a chronic, life-threatening disease for a long time. However, a broad range of antiretroviral drug regimens are applicable for the successful suppression of virus replication in human immunodeficiency virus type 1 (HIV-1) infected people. The mutation-induced drug resistance problems during the treatment of AIDS forced people to continuously look for new antiviral agents. HIV-1 integrase (IN) and reverse transcriptase associated ribonuclease (RT-RNase H), two pivotal enzymes in HIV-1 replication progress, has gain popularity as drug-able tar

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Li, Zhenfeng, Lun Hu, Zehai Tang, and Cheng Zhao. "Predicting HIV-1 Protease Cleavage Sites With Positive-Unlabeled Learning." Frontiers in Genetics 12 (March 26, 2021). http://dx.doi.org/10.3389/fgene.2021.658078.

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Understanding the substrate specificity of HIV-1 protease plays an essential role in the prevention of HIV infection. A variety of computational models have thus been developed to predict substrate sites that are cleaved by HIV-1 protease, but most of them normally follow a supervised learning scheme to build classifiers by considering experimentally verified cleavable sites as positive samples and unknown sites as negative samples. However, certain noisy can be contained in the negative set, as false negative samples are possibly existed. Hence, the performance of the classifiers is not as ac

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Malherbe, Delphine C., Lo Vang, Jason Mendy, et al. "Modified Adenovirus Prime-Protein Boost Clade C HIV Vaccine Strategy Results in Reduced Viral DNA in Blood and Tissues Following Tier 2 SHIV Challenge." Frontiers in Immunology 11 (February 15, 2021). http://dx.doi.org/10.3389/fimmu.2020.626464.

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Designing immunogens and improving delivery methods eliciting protective immunity is a paramount goal of HIV vaccine development. A comparative vaccine challenge study was performed in rhesus macaques using clade C HIV Envelope (Env) and SIV Gag antigens. One group was vaccinated using co-immunization with DNA Gag and Env expression plasmids cloned from a single timepoint and trimeric Env gp140 glycoprotein from one of these clones (DNA+Protein). The other group was a prime-boost regimen composed of two replicating simian (SAd7) adenovirus-vectored vaccines expressing Gag and one Env clone fro

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Bag, Arijit. "DFT based computational methodology of IC50 prediction." Current Computer-Aided Drug Design 16 (February 19, 2020). http://dx.doi.org/10.2174/1573409916666200219115112.

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Background: IC50 is one of the most important parameters of a drug. But, it is very difficult to predict this value of a new compound without experiment. There are only a few QSAR based methods available for IC50 prediction which is also highly dependable on huge number of known data. Thus, there is an immense demand for a sophisticated computational method of IC50 prediction, in the field of in-silico drug designing. Objective: Recently developed quantum computation based method of IC50 prediction by Bag and Ghorai requires an affordable known data. In present research work further developmen

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Pan, Ruimin, Yali Qin, Marisa Banasik, et al. "Increased Epitope Complexity Correlated with Antibody Affinity Maturation and a Novel Binding Mode Revealed by Structures of Rabbit Antibodies against the Third Variable Loop (V3) of HIV-1 gp120." Journal of Virology 92, no. 7 (2018). http://dx.doi.org/10.1128/jvi.01894-17.

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ABSTRACT The third variable (V3) loop of HIV-1 gp120 is an immunodominant region targeted by neutralizing antibodies (nAbs). Despite limited breadth, better characterization of the structural details of the interactions between these nAbs and their target epitopes would enhance our understanding of the mechanism of neutralization and facilitate designing better immunogens to induce nAbs with greater breadth. Recently, we isolated two anti-V3 neutralizing monoclonal antibodies (MAbs), 10A3 and 10A37, from a rabbit immunized with gp120 of the M group consensus sequence. In this study, crystal st

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Al-Kubati, Anwar A. G., Mahmoud Kandeel, Jamal Hussen, Maged Gomaa Hemida, and Abdullah I. A. Al-Mubarak. "Immunoinformatic prediction of the pathogenicity of bovine viral diarrhea virus genotypes: implications for viral virulence determinants, designing novel diagnostic assays and vaccines development." Frontiers in Veterinary Science 10 (July 6, 2023). http://dx.doi.org/10.3389/fvets.2023.1130147.

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IntroductionBovine viral diarrhea virus (BVDV) significantly impacts the bovine industries, both dairy and beef sectors. BVDV can infect various domestic and wild animals, most notably cattle. The dynamic variations among BVDV serotypes due to the continuous genetic diversity, especially in BVDV1 (BVDV1), reduce the effectiveness of the currently available vaccines and reduce the specificity/sensitivity of the diagnostic assays. The development of novel, safe, and effective vaccines against BVDV requires deep knowledge of the antigenicity and virulence of the virus. Previous studies on the ant

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Kumar, Sanjay, Geethu S. Kumar, Subhrangsu Sundar Maitra, et al. "Viral informatics: bioinformatics-based solution for managing viral infections." Briefings in Bioinformatics, August 10, 2022. http://dx.doi.org/10.1093/bib/bbac326.

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Abstract Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because

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Waqas, Muhammad, Shahkaar Aziz, Pietro Liò, et al. "Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets." Frontiers in Immunology 14 (January 26, 2023). http://dx.doi.org/10.3389/fimmu.2023.1091941.

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IntroductionThe current monkeypox (MPX) outbreak, caused by the monkeypox virus (MPXV), has turned into a global concern, with over 59,000 infection cases and 23 deaths worldwide.ObjectivesHerein, we aimed to exploit robust immunoinformatics approach, targeting membrane-bound, enveloped, and extracellular proteins of MPXV to formulate a chimeric antigen. Such a strategy could similarly be applied for identifying immunodominant epitopes and designing multi-epitope vaccine ensembles in other pathogens responsible for chronic pathologies that are difficult to intervene against.MethodsA reverse va

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