Готові списки джерел за темами / Computational designing of HIV immunogens

Добірка наукової літератури з теми "Computational designing of HIV immunogens"

Автор: Grafiati

Опубліковано: 11 вересня 2023

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Статті в журналах з теми "Computational designing of HIV immunogens"

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 (June 28, 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 a conservative approach, these methods analyze the few dominant (strongest) PCs, potentially missing information embedded within the sub-dominant (relatively weaker) ones that may be important for vaccine design. Results By using sequence data for HIV Gag, complemented by model-based simulations, we revealed that certain networks of interacting sites that appear important for vaccine design purposes are not accurately reflected by the dominant PCs. Rather, these networks are encoded jointly by both dominant and sub-dominant PCs. By incorporating information from the sub-dominant PCs, we identified a network of interacting sites of HIV Gag that associated very strongly with viral control. Based on this network, we propose several new candidates for a potent T-cell-based HIV vaccine. Availability and implementation Accession numbers of all sequences used and the source code scripts for all analysis and figures reported in this work are available online at https://github.com/faraz107/HIV-Gag-Immunogens. Supplementary information Supplementary data are available at Bioinformatics online.

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Jiang, Xunqing, Max Totrov, Wei Li, Jared M. Sampson, Constance Williams, Hong Lu, Xueling Wu, et al. "Rationally Designed Immunogens Targeting HIV-1 gp120 V1V2 Induce Distinct Conformation-Specific Antibody Responses in Rabbits." Journal of Virology 90, no. 24 (October 5, 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 engrafting the V1V2 domain into trimeric and pentameric scaffolds in structurally constrained conformations. We also fused V1V2 to an Fc fragment to mimic the unconstrained V1V2 conformation. We tested these V1V2-scaffold proteins for immunogenicity in rabbits and assessed the responses by enzyme-linked immunosorbent assay (ELISA) and competition assays. Our V1V2 immunogens induced distinct conformation-specific Ab responses. Abs induced by structurally unconstrained immunogens reacted preferentially with unconstrained V1V2 antigens, suggesting recognition of the helical configuration, while Abs induced by the structurally constrained immunogens reacted preferentially with constrained V1V2 antigens, suggesting recognition of the β-strand conformation. The Ab responses induced by the structurally constrained immunogens were more broadly reactive and had higher titers than those induced by the structurally unconstrained immunogens. Our results demonstrate that immunogens presenting the different structural conformations of the gp120 V1V2 vulnerable site can be designed and that these immunogens induce distinct Ab responses with epitope conformation specificity. Therefore, these structurally constrained V1V2 immunogens are vaccine prototypes targeting the V1V2 domain of the HIV-1 envelope.IMPORTANCEThe correlates analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the V1V2 region of HIV-1 gp120 was responsible for the modest protection observed in the trial. In addition, V1V2 harbors one of the key vulnerable sites of HIV-1 Env recognized by a family of broadly neutralizing MAbs such as PG9. Thus, V1V2 is a key target for vaccine development. However, this vulnerable site is structurally polymorphic, and designing immunogens that present different conformations is crucial for targeting this site. We show here that such immunogens can be designed and that they induced conformation-specific antibody responses in rabbits. Our immunogens are therefore prototypes of vaccine candidates targeting the V1V2 region of HIV-1 Env.

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

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Moyo, Nathifa, Edmund G. Wee, Bette Korber, Kapil Bahl, Samantha Falcone, Sunny Himansu, Adrianne L. Wong, Antu K. Dey, Mark Feinberg, and Tomáš Hanke. "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 (July 6, 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 replication-deficient simian (chimpanzee) adenovirus and poxvirus modified vaccinia virus Ankara to deliver bivalent conserved-mosaic immunogens to human volunteers. Here, we exploit the mRNA platform by designing tetravalent immunogens designated as HIVconsvM, and demonstrate that mRNA formulated in lipid nanoparticles induces potent, broad and polyfunctional T-cell responses in a pre-clinical model. These results support optimization and further development of this vaccine strategy in experimental medicine trials in humans.

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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 (November 1, 2007): 514–41. http://dx.doi.org/10.2174/157016207782418489.

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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), properties essential in immunogens, may be useful. Here we discuss some of the challenges of developing an efficacious HIV-1 vaccine and the work done in generating soluble immunogens. We also discuss the study of naturally occurring, membrane-bound, efficiently cleaved (naturally more sensitive to furin) Envs and how they may positively add to the repertoire of HIV-1 Envs that can be used for vaccine immunogen design. However, even with such Envs, the challenges of developing well-folded, native-like trimers as soluble proteins or using other immunogen strategies such as virus-like particles with desirable antigenic properties remain, and are formidable. In spite of the progress that has been made in the HIV-1 vaccine field, an immunogen that elicits neutralizing Abs with significant breadth and potency in vaccines has still not been developed. Efficiently cleaved Envs may increase the number of available Envs suitable for immunogen design and should be studied further.

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Mehandru, Saurabh, Terri Wrin, Justin Galovich, Gabriela Stiegler, Brigitta Vcelar, Arlene Hurley, Christine Hogan, 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 (December 15, 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 by 2G12. We propose that the induction of 4E10-like antibodies should be a priority in designing immunogens to prevent HIV-1 infection.

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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 (October 12, 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 (May 1, 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 recognition sites. This would suggest only a minor influence from the host cytotoxic T-cell response on the evolution of the p24 gene. The importance of minor variations within p24 was analyzed by designing DNA-based immunogens from two distinct p24 quasispecies genes simultaneously derived from one patient. In plasmid-immunizedH-2b , H-2d , andH-2k haplotype mice, a clear influence from the host major histocompatibility complex was noted on the immune responses, fully consistent with those noted when a recombinant p24 protein is used as the immunogen. The two p24 DNA immunogens did not differ in their immunogenicity, indicating that the limited genetic variability (<1%) had little influence on the immune responses.

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Swanson, Olivia, Joshua S. Martin Beem, Brianna Rhodes, Avivah Wang, Maggie Barr, Haiyan Chen, Robert Parks, et al. "Identification of CDRH3 loops in the B cell receptor repertoire that can be engaged by candidate immunogens." PLOS Pathogens 19, no. 5 (May 17, 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 CDRH3 loop for antigen recognition, immunogens must be able to tolerate sequence diversity in the B cell receptor repertoire across an entire vaccinated population. Here, we present a combined experimental and computational approach to identify BCRs in the human repertoire with CDRH3 loops predicted to be engaged by a target immunogen. For a given antibody/antigen pair, deep mutational scanning was first used to measure the effect of CDRH3 loop substitution on binding. BCR sequences, isolated experimentally or generated in silico, were subsequently evaluated to identify CDRH3 loops expected to be bound by the candidate immunogen. We applied this method to characterize two HIV-1 germline-targeting immunogens and found differences in the frequencies with which they are expected to engage target B cells, thus illustrating how this approach can be used to evaluate candidate immunogens towards B cell precursors engagement and to inform immunogen optimization strategies for more effective vaccine design.

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Більше джерел

Дисертації з теми "Computational designing of HIV immunogens"

Derby, Nina Rafterman. "Designing immunogens to elicit broadly reactive neutralizing antibodies to the HIV envelope /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9302.

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KATHPALIA, ANISHA. "APPLICATION OF DATA MODELLING IN BUILDING STRUCTURE-ACTIVITY CLASSIFIERS FROM Plasmodium falciparum BIOASSAY SCREENS." Thesis, 2013. http://dspace.dtu.ac.in:8080/jspui/handle/repository/14270.

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Certain elite controllers have very potent broadly neutralizing antibodies that neutralize a range of HIV viruses by targeting certain conserved regions on the virus. Designing immunogens to elicit such broadly neutralizing antibodies capable of neutralizing all HIV variants and types that are found globally has proven extremely challenging. This finding has not only provided novel strategies of rational vaccine design but has also led to the emergence of epitope driven vaccines. In the same direction we performed the computational grafting of discontinuous Bcell epitopes of gp120 on suitable scaffolds. 431 scaffolds were screened for sites capable of carrying the epitopes of interest. Out of the 431 candidates, four structures were the successfully designed which would be used by the wet lab experimentalists for further work and analysis. The main idea behind the work is that given the appropriate immunogen, it should be possible to elicit these broadly neutralizing antibody responses by vaccination.
Dr. Asmita Das Dr. Andrew M. Lynn DTU (formerly DCE) JNU, New Delhi DEPARTMENT OF BIOTECHNOLOGY DELHI TECHNOLOGICAL UNIVERSITY (FORMERLY DELHI COLLEGE OF ENGINEERING)

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Частини книг з теми "Computational designing of HIV immunogens"

Kassa, Aemro, Zohar Biron-Sorek, Pampi Sarkar, and Indresh K. Srivastava. "Designing Immunogens for Vaccine Development in Reference to HIV." In Development of Vaccines, 141–84. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118023648.ch6.

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Biron, Zohar, and Indresh K. Srivastava. "A Modern Biopharmaceutical to Treat AIDS - Challenges in Designing HIV Env Immunogens for Developing a Vaccine." In Modern Biopharmaceuticals, 297–347. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2013. http://dx.doi.org/10.1002/9783527669417.ch15.

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Srivastava, Indresh K., and R. Holland Cheng. "Challenges in Designing HIV Env Immunogens for Developing a Vaccine." In Structure-Based Study of Viral Replication, 327–79. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812790859_0013.

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Nascimento, Igor José dos Santos, Thiago Mendonça de Aquino, and Edeildo Ferreira da Silva-Júnior. "Molecular Dynamics Applied to Discover Antiviral Agents." In Frontiers in Computational Chemistry: Volume 6, 62–131. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815036848122060005.

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In recent years, the world has faced several outbreaks caused by viral diseases, resulting in deaths and comorbidities, harming the health of the population. Due to the “constant” discovery of new antivirals, vaccines, hygiene habits, and basic sanitation, society had the false impression of being free from these diseases. However, since the 1980s, various outbreaks have occurred, such as HIV (Human immunodeficiency virus) and recently, ZIKV (Zika virus), CHIKV (Chikungunya virus), and EBOV (Ebola virus) have increased the concern about such pathogens, resulting in advances in drug discovery. In addition, the SARS-CoV-2 outbreak responsible for 27,417,497 cases, and 894,241 deaths (to date, September 9th, 2020), showed how scientists should advance to end this disease so damaging to the global health and economy. In this context, researches focused on drug development have been improved in recent years. Thus, it is essential to use computational approaches to accelerate drug discovery in laboratories. Based on this, structure-based drug design (SBDD) techniques constitute the most used computer-aided approaches for discovering and developing new drugs. Among these techniques, molecular dynamics (MD) simulations have been essential steps and their use in virtual screening studies is considered indispensable. The MD considers the macromolecule flexibility using Newtonian principles applied to proteins, enzymes, membranes, nucleic acids, and other systems. Thus, it is possible to analyze protein-ligand interactions, and also the affinity energy that a determined ligand exhibits towards its target. Such information is indispensable for designing and optimizing new active agents. This chapter will be addressed to concepts and applications of MD simulations, as well as their applications in the discovery of drugs against Coronaviruses (SARS-, MERS-CoV, and SARSCoV-2); Influenza (INFV); Chikungunya (CHIKV); Zika (ZIKV); Dengue (DENV); Ebola (EBOV); and human immunodeficiency virus (HIV), constituting a great source of helpful information that could be utilized for designing new compounds against these diseases.

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Manhas, Anu, Siddhi Kediya, and Prakash C. Jha. "Pharmacophore Modeling Approach in Drug Discovery Against the Tropical Infectious Disease Malaria." In Frontiers in Computational Chemistry: Volume 6, 132–92. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/9789815036848122060006.

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