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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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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 (November 30, 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 attempting to develop vaccines targeting cell-mediated immunity, since evidence show CTLs to be important for the control of HIV replication. Phase-I and -IIa multi-epitope vaccine trials have already been conducted with vaccine immunogens consisting of known CTL epitopes conserved across HIV subtypes, but have so far fallen short of inducing robust and consistent anti-HIV CTL responses. The concepts leading to the development of T-cell epitope-based vaccines, the outcomes of related clinical vaccine trials and efforts to enhance the immunogenicity of cell-mediated approaches are summarized in this review. Moreover, we describe a novel approach based on the identification of SIV and FIV antigens which contain conserved HIV-specific T-cell epitopes and represent an alternative method for developing an effective HIV vaccine against global HIV isolates.
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Chan-hui, Po-Ying, Terri Wrin, Melissa Simek, Sanjay Phogat, Ole Olsen, Phil Hammond, Pascal Poignard, 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 (April 1, 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 immunogens that may elicit broad anti-HIV protection. To identify additional epitopes for vaccine design, we extended the bNAb discovery to more HIV-infected subjects. Method. We selected several HIV-infected subjects with broad neutralization activity in serum. Memory B cells from these elite neutralizers were activated and the IgG-containing culture media were screened for neutralizing activity against multiple pseudotyped viruses. mAbs were rescued from selected B cell culture wells by RT-PCR and subcloning. Results. From an HIV-infected elite neutralizer, we have identified in the primary screen multiple human Abs that cross-neutralize MGRM-C-26 of clade C, and 93BR020 and JR-CSF of clade B. Antibodies that neutralize either MGRM-C-26 alone or 94UG103 of clade A alone were also detected. Recombinant mAbs are currently being rescued for further characterization. (Supported by IAVI and USAID)
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Kumar, Rajnish, Ruimin Pan, Chitra Upadhyay, Luzia Mayr, Sandra Cohen, Xiao-Hong Wang, Preetha Balasubramanian, 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 (June 24, 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 IGHV3-53 and IGLV2-28 genes, a pairing rarely used by the other V3 MAbs. 2424 also has distinct binding and neutralization profiles. Studies of 2424-mediated neutralization of JRFL produced with a mannosidase inhibitor further revealed that its neutralizing activity is unaffected by the glycan composition of the virus envelope. To understand the distinct activity of 2424, we determined the crystal structure of 2424 Fab in complex with a JRFL V3 peptide and showed that the 2424 epitope is located at the tip of the V3 crown (307IHIGPGRAFYT319), dominated by interactions with HisP308, ProP313, and ArgP315. The binding mode of 2424 is similar to that of the well-characterized MAb 447-52D, although 2424 is more side chain dependent. The 2424 epitope is focused on the very apex of V3, away from nearby glycans, facilitating antibody access. This feature distinguishes the 2424 epitope from the other V3 crown epitopes and indicates that the tip of V3 is a potential site to target and incorporate into HIV vaccine immunogens.IMPORTANCEHIV/AIDS vaccines are crucial for controlling the HIV epidemics that continue to afflict millions of people worldwide. However, HIV vaccine development has been hampered by significant scientific challenges, one of which is the inability of HIV vaccine candidates evaluated thus far to elicit production of potent and broadly neutralizing antibodies. The V3 loop is one of the few immunogenic targets on the virus envelope glycoprotein that can induce neutralizing antibodies, but in many viruses, parts of V3 are inaccessible for antibody recognition. This study examined a V3-specific monoclonal antibody that can completely neutralize HIV-1 JRFL, a virus isolate resistant to most V3 antibodies. Our data reveal that this antibody recognizes the most distal tip of V3, which is not as occluded as other parts of V3. Hence, the epitope of 2424 is in one of the vulnerable sites on the virus that may be exploited in designing HIV vaccine immunogens.
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Acharya, Priyamvada, Robert Edwards, Rory Henderson, Kartik Manne, Katayoun Mansouri, Katarzyna Janowska, Shana McDowell, Victoria Stalls, Megan Kopp, and Barton Haynes. "How Does HIV Env Structure Informs Vaccine Design?" Microscopy and Microanalysis 26, S2 (July 30, 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 computational methods to obtain a basic understanding of the functions and interactions of the HIV-1 Env.Results:1.The DHVI NSEM pipeline runs on a daily basis to quality control vaccine immunogens for animal studies and other applications. Offering rapid sample turnover and economical operations, the NSEM pipeline is the most widely utilized resource of the DHVI Division of Structural Biology. Over the last year, the NSEM team has focused efforts on improving operational speed and data processing allowing high-quality visualization of a large variety of samples including HIV-1 Env immunogens, antibodies, nanoparticles, and VLPs. In the last year we have also expanded our NSEM studies to the analyses of serum samples and mucosal fluids.2.To understand the mechanism of HIV-1 entry we have determined structures of HIV-1 entry intermediates. We have determined a 3.8 Å resolution structure of a single CD4 bound to a closed HIV-1 Env trimer revealing new contacts of CD4 with Env. We have also structurally characterized an Env designed to prevent CD4-induced rearrangements by targeted disruption of an allosteric network modulating Env conformational changes.3.We have structurally characterized the HIV-1 glycan-V3 targeting DH270 Broadly Neutralizing Antibody Lineage. The structures revealed movements in the V1 loop and interactive glycans, shifts in antibody orientations, antibody VH-VL orientations, and antibody elbow angles, as the lineage progressed to maturation.4.We have solved a structure in complex with the HIV-1 Env immunogen Man5-enriched CH505.N279K.G458Y.SOSIP.664 of the unmutated common ancestor (UCA) of the HIV-1 CD4-binding site targeting CH235 Broadly Neutralizing Antibody Lineage. The structure revealed interactions of the N279K and G458Y mutations with the CDR L3 loop of CH235 UCA thus providing a structural understanding of the role of these mutations in facilitating binding to the CH235 UCA. (see also Henderson et al abstract)5.Using NSEM and cryo-EM we have characterized the structural properties of a novel class of 2G12-mimetic, yet non domain-swapped Fab dimer glycan-reactive (FDG) antibodies. These studies showed that the Fab-dimerized 2G12-like motif is more common than previously thought, and that creation of a Fab-dimerized paratope for an HIV-1 neutralizing antibody does not require VH domain-swapping.6.Finally, the structural team is an integral part of the CHAVD Kalma Immunogen Design Team, wherein we are defining the structural basis of bnAb affinity maturation to guide sequential immunogen design.Conclusions:These results highlight the power of structural information on HIV-1 vaccine design, from leveraging a basic understanding of HIV-1 entry mechanism for immunogen design, to rapid visualization of Env immunogens by NSEM for quality control, discovery of novel antibody interactions, and atomic level visualization of antibody/Env interactions.
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Cain, Derek Wilson, Ming Tian, Torben Schiffner, Kimmo Rantalainen, Kevin O. Saunders, Kevin Wiehe, Brian Watts, 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 (May 1, 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 MPER bnAb DH511, as well as to several human DH511-like potential precursor antibodies. We studied the immunogenicity of a multimeric nanoparticle of the GT5 immunogen in a knock-in mouse line expressing human DH511.UCA B cell receptors (BCRs). Naïve DH511.UCA knock-in mice exhibited a reduction in overall B cell numbers, and DH511.UCA-bearing B cells expressed low levels of surface IgM and IgD, suggesting that DH511.UCA expression is subject to immune tolerance control. Nonetheless, following immunization with GT5 nanoparticles mixed with a saponin/monophosphoryl lipid A adjuvant, knock-in mice mounted robust anti-GT5 humoral responses, including anti-GT5 IgG in serum and GT5-specific germinal center B cells and T follicular helper cells in lymphoid tissues. Sequencing analysis of IgG+ GT5-specific B cells revealed improbable mutations in knock-in immunoglobulin genes of DH511.UCA. These studies will guide further optimization of immunogens with potential to select for development of bnAbs against MPER epitopes. Supported by a grant from NIH (P01-AI138211)
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Lin, George, Andrea Bertolotti-Ciarlet, Beth Haggarty, Josephine Romano, Katrina M. Nolan, George J. Leslie, Andrea P. O. Jordan, 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 (July 3, 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, either with or without a deletion of the V1/V2 variable loops. The generation of these functional but markedly minimized Envs required adaptive changes on the gp120 core and gp41 transmembrane glycoprotein. V3-deleted Envs exhibited tropism for both CCR5- and CXCR4-expressing cells, suggesting that domains on the gp120 core were mediating interactions with determinants shared by both coreceptors. Remarkably, HIV-2 Envs with V3 deletions became resistant to small-molecule inhibitors of CCR5 and CXCR4, suggesting that these drugs inhibit wild-type viruses by disrupting a specific V3 interaction with the coreceptor. This study represents a proof of concept that HIV Envs lacking V3 alone or in combination with V1/V2 that retain functional domains required for viral entry can be derived. Such minimized Envs may be useful in understanding Env function, screening for new inhibitors of gp120 core interactions with chemokine receptors, and designing novel immunogens for vaccines.
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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 (January 8, 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. An accurate representation of viral fitness as a function of its protein sequences (a fitness landscape), with explicit accounting of the effects of coupling between mutations, could help address these challenges. We describe a computational approach that has allowed us to infer a fitness landscape for gp160, the HIV polyprotein that comprises the viral spike that is targeted by antibodies. We validate the inferred landscape through comparisons with experimental fitness measurements, and various other metrics. We show that an effective antibody that prevents immune escape must selectively bind to high escape cost residues that are surrounded by those where mutations incur a low fitness cost, motivating future applications of our landscape for immunogen design.
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Geraghty, Daniel, Jodie P. Gooodridge, Kevin Wang, Aura Burian, John McNevin, Margaret J. McElrath, and Ni Lee. "HLA-F and MHC open conformers in a novel HIV-1 immunization strategy." Journal of Immunology 196, no. 1_Supplement (May 1, 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 MHCI OC are ligands for a specific subset of killer Ig-like receptors (KIRs). The HLA-F/MHCI physical interaction was further implicated in the function of HLA-F and MHCI open conformers in a general mode of exogenous MHCI antigen uptake and antigen presentation by activated immune cells that differs from the canonical MHCI endogenous antigen presentation. We are currently testing the hypothesis that antigen entry is governed by a synergy between specific structural characteristics of the exogenous antigen and the MHC-I allele types of target cells. New evidence is presented using HIV-1 p24 gag derived long polypeptides suggesting a requirement for HLA class I peptide epitope specificity in antigen uptake, upstream of antigen presentation, which subsequently can be presented by either or both of MHCI and MHCII. These experiments suggested that the physical proximity of HIV-1 class I and class II peptide epitopes within a p24 polypeptide can govern antigen presentation of epitopes through either MHCI or MHCII or both. A goal is to manipulate these features in designing effective immunogens for directed stimulation of antigen-specific host responses.
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Dar, Khalid Bashir, Aashiq Hussain Bhat, Shajrul Amin, Rabia Hamid, Suhail Anees, Syed Anjum, Bilal Ahmad Reshi, Mohammad Afzal Zargar, Akbar Masood, and Showkat Ahmad Ganie. "Modern Computational Strategies for Designing Drugs to Curb Human Diseases: A Prospect." Current Topics in Medicinal Chemistry 18, no. 31 (February 22, 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, chemical similarity (CS), quantitative structure-activity relationship (QSAR), virtual screening (VS) and molecular dynamics simulations have been quite productive in predicting the therapeutic outcome of candidate drugs/compounds besides saving precious time. CADD tools exploit structural and other information available regarding the target (enzyme/receptor) and the ligands to identify the compounds with the ability to treat diseases notably cancer, neurodegenerative disorders, malaria, Ebola, HIV-AIDS and many more. Computational approaches have led to the discovery of many drugs that have passed preclinical and clinical trials and become novel therapeutics in the treatment of a variety of diseases. Some notable examples of CADD derived novel drugs include dorzolamide, saquinavir, ritonavir, indinavir, captopril and tirofiban. CADD plays important role in predicting absorption, distribution, metabolism, excretion and toxicity (ADME/T) of candidate drugs. Overall, CADD represents an effective and much-needed strategy for designing therapeutically effective drugs to combat human diseases.
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Geraghty, Daniel, Kevin L. Wang, Ni Lee, Aura Burian, Jodie P. Goodridge, Akiko Ishitani, John McNevin, and Margaret J. McElrath. "HLA-F and MHC open conformers cooperate in antigen presentation during the inflammatory response." Journal of Immunology 198, no. 1_Supplement (May 1, 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 (KIRs), defining a new paradigm for MHCI function in the innate and acquired immune responses. The HLA-F/MHCI physical interaction was further implicated in the function of HLA-F and MHCI OCs in a general mode of exogenous MHCI antigen uptake and antigen presentation by activated immune cells that differs from the canonical MHCI endogenous antigen presentation. We are currently testing the hypothesis that antigen entry is governed by a synergy between specific structural characteristics of the exogenous antigen and the MHC-I allele types of target cells. New evidence is presented using HIV-1 p24 gag derived long polypeptides suggesting a requirement for HLA class I peptide epitope specificity in antigen uptake, upstream of antigen presentation, which subsequently can be presented by either or both of MHCI and MHCII. These experiments suggested that the physical proximity of HIV-1 class I and class II peptide epitopes within a p24 polypeptide can influence antigen presentation of epitopes through either MHCI or MHCII or both. A goal is to manipulate these features in designing effective immunogens for directed stimulation of antigen-specific host responses.
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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 (December 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 probe mapping, we have explored druggable sites on the trimeric NHR peptides, and identified residues K574 and R579 as the hot spots for inhibitor designing. We further demonstrated that although NB-2 and NB-64 are all N-substituted Pyrrole derivatives and have very similar chemical structures, it is possible that diverse inhibitory mechanisms targeting different negative electrostatic residues (K574 and R579) exist. Results from fragment-based virtual screening identified series of potential lead compounds which could be used for further design of fusion inhibitors.
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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 proteins using computational homology modeling to understand better the structural basis of HIV proteins interacting with host cells and viral replication. The sequences of HIV capsid, matrix, nucleocapsid, p6, reverse transcriptase, invertase, protease, gp120, gp41, virus protein r, viral infectivity factor, virus protein unique, RNA splicing regulator, transactivator protein, negative regulating factor, and virus protein x proteins were retrieved from UniProt. The primary and secondary structures of HIV proteins were predicted by Expasy ProtParam and SOPMA web servers. For the homology modeling, the MODELLER predicted the 3D structures of HIV proteins using templates. Then, the modeled structures were validated by the Ramachandran plot, local and global quality estimation scores, QMEAN scores, and Z-scores. Most of the amino acid residues of HIV proteins were present in the most favored and generously allowed regions in the Ramachandran plots. The local and global quality scores and Z-scores of the HIV proteins confirmed the good quality of modeled structures. The 3D modeled structures of HIV proteins might help further investigate the possible treatment.
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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 (August 19, 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 mutagenesis was used to determine the influence of amino acid variants on binding and neutralization by b12. We found that several substitutions within the dominant b12 contact surface, called the CD4-binding loop, mediated b12 resistance, and that these substitutions resided just proximal to the known CD4 contact surface. Hence, viruses varied in key b12 contact residues that are proximal to, but not part of, the CD4 contact surface. This explained how viral isolates were able to evade b12 neutralization while maintaining functional binding to CD4. In addition, some viruses were resistant to b12 despite minimal sequence variation at b12 contact sites. Such neutralization resistance usually could be reversed by alterations at residues thought to influence the quaternary configuration of the viral envelope spike. To design immunogens that elicit neutralizing antibodies directed to the CD4-binding site, researchers need to address the antigenic variation within this region of gp120 and the restricted access to the CD4-binding site imposed by the native configuration of the trimeric viral envelope spike.
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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 (August 23, 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, the infection-free state of the model is globally asymptotically stable. However, as the threshold number increases by one, the endemic equilibrium becomes globally asymptotically stable, and in such case, the disease-free state is unstable. At the end of the paper, the analytic conclusions obtained from the analysis of the ordinary differential equation (ODE) model are supported through numerical simulations. The paper also addresses a comprehensive analysis of a fractional-order HIV model utilizing the Caputo fractional differential operator. The model’s qualitative analysis is investigated, and computational modeling is used to examine the system’s long-term behavior. The existence/uniqueness of the solution to the model is determined by applying some results from the fixed points of the theory. The stability results for the system are established by incorporating the Ulam–Hyers method. For numerical treatment and simulations, we apply Newton’s polynomial and the Toufik–Atangana numerical method. Results demonstrate the effectiveness of the fractional-order approach in capturing the dynamics of the HIV/AIDS epidemic and provide valuable insights for designing effective control strategies.
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Edwards, Terri G., Trevor L. Hoffman, Frédéric Baribaud, Stéphanie Wyss, Celia C. LaBranche, Josephine Romano, Joshua Adkinson, Matthew Sharron, James A. Hoxie, and Robert W. Doms. "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 (June 1, 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 between 8x and its CD4-dependent parent, HXBc2. We found that a frameshift mutation just proximal to the gp41 cytoplasmic domain in 8x Env was necessary but not sufficient for CD4 independence and led to increased exposure of the coreceptor binding site. In the presence of this altered cytoplasmic domain, single amino acid changes in either the 8x V3 (V320I) or V4/C4 (N386K) regions imparted CD4 independence, with other changes playing a modulatory role. The N386K mutation resulted in loss of an N-linked glycosylation site, but additional mutagenesis showed that it was the presence of a lysine rather than loss of the glycosylation site that contributed to CD4 independence. However, loss of the glycosylation site alone was sufficient to render Env neutralization sensitive, providing additional evidence that carbohydrate structures shield important neutralization determinants. Exposure of the CD4-induced epitope recognized by monoclonal antibody 17b and which overlaps the coreceptor binding site was highly sensitive to an R298K mutation at the base of the V3 loop and was often but not always associated with CD4 independence. Finally, while not all neutralization-sensitive Envs were CD4 independent, all CD4-independent Envs exhibited enhanced sensitivity to neutralization by HIV-1-positive human sera, indicating that the humoral immune response can exert strong selective pressure against the CD4-independent phenotype in vivo. Whether this can be used to advantage in designing more effective immunogens remains to be seen.
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Welbourn, Sarah, Srirupa Chakraborty, Jie E. Yang, Anne S. Gleinich, Sailaja Gangadhara, Salar Khan, Courtney Ferrebee, 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 (May 3, 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. Within each T/F Env group, the protein boosts were administered as either monomeric gp120 or stabilized trimeric gp140 protein. All vaccination regimens elicited high titers of antigen-specific IgG, and two animals that received monomeric Z1800M Env gp120 developed autologous neutralizing activity. Using early Env escape variants isolated from subject Z1800M as guides, the serum neutralizing activity of the two immunized RM was found to be dependent on the gp120 V5 region. Interestingly, the exact same residues of V5 were also targeted by a neutralizing monoclonal antibody (nmAb) isolated from the subject Z1800M early in infection. Glycan profiling and computational modeling of the Z1800M Env gp120 immunogen provided further evidence that the V5 loop is exposed in this T/F Env and was a dominant feature that drove neutralizing antibody targeting during infection and immunization. An expanded B cell clonotype was isolated from one of the neutralization-positive RM and nmAbs corresponding to this group demonstrated V5-dependent neutralization similar to both the RM serum and the human Z1800M nmAb. The results demonstrate that neutralizing antibody responses elicited by the Z1800M T/F Env in RM converged with those in the HIV-1 infected human subject, illustrating the potential of using immunogens based on this or other T/F Envs with well-defined immunogenicity as a starting point to drive breadth.
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Baassi, Mouna, Mohamed Moussaoui, Hatim Soufi, Sanchaita Rajkhowa, Ashwani Sharma, Subrata Sinha, and Said Belaaouad. "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 (April 20, 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 compounds were designed by software; their descriptors were computed using various tools, such as Gaussian, Chem3D, ChemSketch and MarvinSketch. Computational methods generated the best model based on its statistical parameters. The model’s applicability domain (AD) was elaborated. Furthermore, one compound has been proposed as efficient against HIV-1 protease with comparable biological activity to the existing ones; this drug candidate was evaluated using ADMET properties and Lipinski’s rule. Molecular Docking performed on Wild Type, and Mutant Type HIV-1 proteases allowed the investigation of the interaction types displayed between the proteases and the ligands, Darunavir (DRV) and the new drug (ND). Molecular dynamics simulation was also used in order to investigate the complexes’ stability allowing a comparative study on the performance of both ligands (DRV & ND). Our study suggested that the new molecule showed comparable results to that of darunavir and maybe used for further experimental studies. Our study may also be used as pipeline to search and design new potential inhibitors of HIV-1 proteases.
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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 (August 3, 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 first time a surface plasmon resonance (SPR)-based interaction assay with soluble recombinant SOSIP Env trimers, we demonstrate that the off-rate (kd) parameter shows the strongest correlation with potency in an antiviral assay. Finally, we establish an underappreciated relationship between the potency of a ligand and its degree of electrostatic complementarity (EC) with its target, the Env complex. These findings not only broaden the chemical space in this inhibitor class, but also establish a rapid and simple assay to evaluate future HIV-1 entry inhibitors.
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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 (August 15, 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 first time a surface plasmon resonance (SPR)-based interaction assay with soluble recombinant SOSIP Env trimers, we demonstrate that the off-rate (kd) parameter shows the strongest correlation with potency in an antiviral assay. Finally, we establish an underappreciated relationship between the potency of a ligand and its degree of electrostatic complementarity (EC) with its target, the Env complex. These findings not only broaden the chemical space in this inhibitor class, but also establish a rapid and simple assay to evaluate future HIV-1 entry inhibitors.
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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 antibody design. In this study, we evaluated the dynamics of the HIV virus, CD4 T-cells, and eCD4-Ig in humans using a gene-therapy approach which has been evaluated in primates previously. We utilized a mathematical model to investigate the relationship between eCD4-Ig levels, ADCC effects, and the neutralization effect on HIV elimination. In addition, a balance between ADCC and viral neutralization effect of eCD4-Ig has been investigated in order to understand the condition of which HIV eliminating antibodies needs to satisfy. Our analysis indicated some level of ADCC effect, which was missing from ART, was required for viral elimination. The results will be helpful in designing future drugs or therapeutic strategies.</p></abstract>
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Wang, Yueping, Jie Chang, Jiangyuan Wang, Peng Zhong, Yufang Zhang, Christopher Cong Lai, and Yanping He. "3D-QSAR Studies of S-DABO Derivatives as Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors." Letters in Drug Design & Discovery 16, no. 8 (August 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 to determine the most probable binding mode and to obtain reliable conformations for molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA (q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis of hybrid docking-based and ligand-based alignment. Results: The predictive ability of CoMFA and CoMSIA models was further validated using a test set of eight compounds with predictive r2 pred values of 0.843 and 0.723, respectively. Conclusion: The information obtained from the 3D contour maps can be used in designing new SDABO derivatives with improved HIV-1 inhibitory activity.
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Birse, Kenzie, Kelly B. Arnold, Richard M. Novak, Stuart McCorrister, Souradet Shaw, Garrett R. Westmacott, Terry B. Ball, Douglas A. Lauffenburger, and Adam Burgener. "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 (June 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 menstrual period, and analyzed by tandem mass spectrometry. Biological insights from these data were gained using a spectrum of computational methods, including hierarchical clustering, pathway analysis, gene set enrichment analysis, and partial least-squares discriminant analysis with LASSO feature selection. Of the 384 proteins identified, 43 were differentially abundant between phases (P< 0.05, ≥2-fold change). Cell-cell adhesion proteins and antiproteases were reduced, and leukocyte recruitment (interleukin-8 pathway,P= 1.41E–5) and extravasation proteins (P= 5.62E–4) were elevated during the luteal phase. LASSO/PLSDA identified a minimal profile of 18 proteins that best distinguished the luteal phase. This profile included cytoskeletal elements and proteases known to be involved in cellular movement. Gene set enrichment analysis associated CD4+T cell and neutrophil gene set signatures with the luteal phase (P< 0.05). Taken together, our findings indicate a strong association between proteins involved in tissue remodeling and leukocyte infiltration with the luteal phase, which may represent potential hormone-associated mechanisms of increased susceptibility to HIV.IMPORTANCERecent studies have discovered an enhanced susceptibility to HIV infection during the progesterone-dominant luteal phase of the menstrual cycle. However, the mechanism responsible for this enhanced susceptibility has not yet been determined. Understanding the source of this vulnerability will be important for designing efficacious HIV prevention technologies for women. Furthermore, these findings may also be extrapolated to better understand the impact of exogenous hormone application, such as the use of hormonal contraceptives, on HIV acquisition risk. Hormonal contraceptives are the most widely used contraceptive method in sub-Saharan Africa, the most HIV-burdened area of the world. For this reason, research conducted to better understand how hormones impact host immunity and susceptibility factors important for HIV infection is a global health priority.
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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 (July 21, 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 predictors have been reported for discriminating ssDBPs and dsDBPs. However, due to the limitations of the existing methods, an intelligent computational system is still highly desirable. In this work, features from protein sequences are discovered by extending the notion of dipeptide composition (DPC), evolutionary difference formula (EDF), and K-separated bigram (KSB) into the position-specific scoring matrix (PSSM). The highly intrinsic information was encoded by a compression approach named discrete cosine transform (DCT) and the model was trained with support vector machine (SVM). The prediction performance was further boosted by the genetic algorithm (GA) ensemble strategy. The novel predictor (DBP-GAPred) acquired 1.89%, 0.28%, and 6.63% higher accuracies on jackknife, 10-fold, and independent dataset tests, respectively than the best predictor. These outcomes confirm the superiority of our method over the existing predictors.
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Karthic, Anandakrishnan, Veerbhan Kesarwani, Rahul Kunwar Singh, Pavan Kumar Yadav, Navaneet Chaturvedi, Pallavi Chauhan, Brijesh Singh Yadav, and Sandeep Kumar Kushwaha. "Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp)." Molecules 27, no. 3 (January 26, 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-dependent RNA polymerase (RdRp) protein of SARS-CoV-2. In this study, a meta-analysis was performed to ensure the genomic variability and stability of the SARS-CoV-2 RdRp protein. The molecular docking of natural and synthetic TP compounds to RdRp and molecular dynamic (MD) simulations were performed to analyse the dynamic behaviour of TP compounds at the active site of the RdRp protein. TP compounds were also docked against other non-structural proteins (NSP1, NSP2, NSP3, NSP5, NSP8, NSP13, and NSP15) of SARS-CoV-2. Furthermore, the inhibition potential of TP compounds was compared with Remdesivir and Favipiravir drugs as a positive control. Additionally, TP compounds were analysed for inhibitory activity against SARS-CoV RdRp protein. This study demonstrates that TP analogues (monomethylated triazolopyrimidine and essramycin) represent potential lead molecules for designing an effective inhibitor to control viral replication. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-CoV-2.
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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 (November 30, 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, viremia resurged rapidly in most patients despite suppressive VRC01 concentrations in circulation, suggesting that VRC01 resistance was the likely cause of failure. ART swiftly halts viral replication, precluding the development of resistance during ART. If resistance were to emerge post ART, virological breakthrough would have taken longer than without VRC01 therapy. We hypothesized therefore that VRC01-resistant strains must have been formed before ART initiation, survived ART in latently infected cells, and been activated during VRC01 therapy, causing treatment failure. Current assays preclude testing this hypothesis experimentally. We developed a mathematical model based on the hypothesis and challenged it with available clinical data. The model integrated within-host HIV-1 evolution, stochastic latency reactivation, and viral dynamics with multiple-dose VRC01 pharmacokinetics. The model predicted that single but not higher VRC01-resistant mutants would pre-exist in the latent reservoir. We constructed a virtual patient population that parsimoniously recapitulated inter-patient variations. Model predictions with this population quantitatively captured data of VRC01 failure from clinical trials, presenting strong evidence supporting the hypothesis. We attributed VRC01 failure to single-mutant VRC01-resistant proviruses in the latent reservoir triggering viral recrudescence, particularly when VRC01 was at trough levels. Pre-existing resistant proviruses in the latent reservoir may similarly compromise other bNAbs. Our study provides a framework for designing bNAb-based therapeutic protocols that would avert such failure and maximize HIV-1 remission.
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Yang, Yuhe R., Laura E. McCoy, Marit J. van Gils, Raiees Andrabi, Hannah L. Turner, Meng Yuan, Christopher A. Cottrell, et al. "Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits." Journal of Virology 94, no. 7 (January 15, 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 mutation [IP] in gp41) alone, as well as B41 and BG505 coimmunization. We isolated autologous neutralizing antibodies (nAbs) and described their structure in complex with the B41 Env. Our data suggest that distinct autologous nAb lineages are induced by BG505 and B41 immunogens, even when both were administered together. In contrast to previously described BG505 glycan hole antibodies, the B41-specific nAbs accommodate the >97% conserved N241 glycan, which is present in B41. Single-particle cryo-electron microscopy studies confirmed that B41- and BG505-specific nAbs bind to overlapping glycan hole epitopes. We then used our high-resolution data to guide mutations in the BG505 glycan hole epitope in an attempt to broaden the reactivity of a B41-specific nAb, but we recovered only partial binding. Our data demonstrate that the lack of cross-reactivity in glycan hole antibodies is due to amino acid differences within the epitope, and our attempts to rationally design cross-reactive trimers resulted in only limited success. Thus, even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult. IMPORTANCE A glycan hole is one of the most dominant autologous neutralizing epitopes targeted on BG505 and B41 SOSIP trimer-immunized rabbits. Our high-resolution cryo-electron microscopy (cryoEM) studies of B41 in complex with a B41-specific antibody complex elucidate the molecular basis of this strain-specific glycan hole response. We conclude that even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult.
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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, Xiaomei Liu, Vincenza Itri, Xunqing Jiang, Christina C. Luo, 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 (June 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 studied as part of this program consisted of a cocktail of three immunogens presenting V2 from different viruses and clades in the context of different scaffolds. Presently we demonstrate that the V2-specific Ab response from this regimen was highly durable and functionally diverse for the duration of the study (25 weeks after the final immunization). The total IgG binding response at this late time point exhibited only an ∼5× reduction in potency. Three immunizations appeared essential for the elicitation of a strong Ab-dependent cellular cytotoxicity (ADCC) response for all animals, as opposed to the Ab-dependent cellular phagocytosis (ADCP) and virus capture responses, which were comparably potent after only 2 immunizations. All functionalities measured were highly durable through the study period. Therefore, testing this vaccine candidate for its protective capacity is warranted. IMPORTANCE The only HIV vaccine trial for which protective efficacy was detected correlated this efficacy with V2-specific Abs that were effectively nonneutralizing. This result has fueled a decade of HIV vaccine research focused on designing an HIV vaccine capable of eliciting V2-focused, polyfunctional Abs that effectively bind HIV and trigger various leukocytes to kill the virus and restrict viral spread. From the numerous vaccine candidates designed and tested as part of our V2-focused preclinical vaccine program, we have identified immunogens and a vaccine regimen that induces a highly durable and polyfunctional V2-focused Ab response in rhesus macaques, described herein.
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Burton, Samantha, Lori M. Spicer, Tysheena P. Charles, Sailaja Gangadhara, Pradeep B. J. Reddy, Tiffany M. Styles, Vijayakumar Velu, 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 (January 16, 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 adjuvants. Serum samples collected from 130 immunized monkeys at two key time points were analyzed using the TZM-bl cell assay: at 2 weeks after the final immunization (week 40/41) and on the day of challenge (week 58). Key initial findings were that inclusion of a gp140 protein boost had a significant impact on the magnitude and durability of Env-specific IgG antibodies, and addition of 3M-052 adjuvant was associated with better neutralizing activity against the SHIV1157ipd3N4 challenge virus and a heterologous HIV-1 CRF01 Env, CNE8. We measured neutralization against a panel of 12 tier 2 Envs using a newly described computational tool to quantify serum neutralization potency by factoring in the predetermined neutralization tier of each reference Env. This analysis revealed modest neutralization breadth, with DNA/MVA immunization followed by gp140 protein boosts in 3M-052 adjuvant producing the best scores. This study highlights that protein-containing regimens provide a solid foundation for the further development of novel adjuvants and inclusion of trimeric Env immunogens that could eventually elicit a higher level of neutralizing antibody breadth.IMPORTANCEDespite much progress, we still do not have a clear understanding of how to elicit a protective neutralizing antibody response against HIV-1 through vaccination. There have been great strides in the development of envelope immunogens that mimic the virus particle, but less is known about how different vaccination modalities and adjuvants contribute to shaping the antibody response. We compared seven different vaccines that were administered to rhesus macaques and that delivered the same envelope protein through various modalities and with different adjuvants. The results demonstrate that some vaccine components are better than others at eliciting neutralizing antibodies with breadth.
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Sher, Hamza, Hafsa Sharif, Tahreem Zaheer, Sarmad Ahmad Khan, Amjad Ali, Hasnain Javed, and Aneela Javed. "Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1)." BMC Genomics 24, no. 1 (May 24, 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 this, all polyprotein and protein sequences of HIV-1 were retrieved from the LANL (Los Alamos National Laboratory) database. The consensus sequence was generated after alignment and used to predict epitopes. Conserved, antigenic, non-allergenic, T-cell inducing, B-cell inducing, IFN-ɣ inducing, non-human homologous epitopes were selected and combined to propose two vaccine constructs i.e., HIV-1a (without adjuvant) and HIV-1b (with adjuvant). Results HIV-1a and HIV-1b were subjected to antigenicity, allergenicity, structural quality analysis, immune simulations, and MD (molecular dynamics) simulations. Both proposed multi-epitope vaccines were found to be antigenic, non-allergenic, stable, and induce cellular, humoral, and innate immune responses. TLR-3 docking and in-silico cloning of both constructs were also performed. Conclusion Our results indicate HIV-1b to be more promising than HIV-1a; experimental validations can confirm the efficacy and safety of both constructs and in-vivo efficacy in animal models. Graphical Abstract
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Che, Ye, Alexey V. Gribenko, Xi Song, Luke D. Handke, Kari S. Efferen, Kristin Tompkins, Srinivas Kodali, 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 nearly 400 engineered F constructs. Through in vitro and in vivo characterization studies, we identified F constructs that are more stable in the prefusion conformation and elicit ~10-fold higher serum neutralizing titers in cotton rats than DS-Cav1. The stabilizing mutations of the lead construct (847) were introduced onto F glycoprotein backbones of strains representing the dominant circulating genotypes of the two major RSV subgroups, A and B. Immunization of cotton rats with a bivalent vaccine formulation of these antigens conferred complete protection against RSV challenge, with no evidence of disease enhancement. The resulting bivalent RSV prefusion F investigational vaccine has recently been shown to be efficacious against RSV disease in two pivotal phase 3 efficacy trials, one for passive protection of infants by immunization of pregnant women and the second for active protection of older adults by direct immunization.
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Malherbe, Delphine C., Jason Mendy, Lo Vang, Philip T. Barnette, Jason Reed, Samir K. Lakhashe, Joshua Owuor, 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 (November 1, 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-specific IgG, tier 1 heterologous neutralizing antibodies, and antibody-dependent cell-mediated viral inhibition were readily generated. High Env-specific T cell responses elicited in all vaccinees were significantly greater than responses targeting Gag. After three intrarectal exposures to heterologous tier 1 clade C SHIV, all 10 sham-vaccinated controls were infected, whereas 4/10 SAd7- and 3/10 Ad4-vaccinated macaques remained uninfected or maintained tightly controlled plasma viremia. Time to infection was significantly delayed in SAd7-vaccinated macaques compared to the controls. Cell-associated and plasma virus levels were significantly lower in each group of vaccinated macaques compared to controls; the lowest plasma viral burden was found in animals vaccinated with the SAd7 vectors, suggesting superior immunity conferred by the replicating simian vectors. Furthermore, higher V1V2-specific binding antibody titers correlated with viral control in the SAd7 vaccine group. Thus, recombinant Ad plus protein vaccines generated humoral and cellular immunity that was effective in either protecting from SHIV acquisition or significantly reducing viremia in animals that became infected, consequently supporting additional development of replicating Ad vectors as HIV vaccines. IMPORTANCE There is a well-acknowledged need for an effective AIDS vaccine that protects against HIV infection and limits in vivo viral replication and associated pathogenesis. Although replicating virus vectors have been advanced as HIV vaccine platforms, there have not been any direct comparisons of the replicating to the nonreplicating format. The present study directly compared the replicating SAd7 to nonreplicating Ad4 vectors in macaques and demonstrated that in the SAd7 vaccine group, the time to infection was significantly delayed compared to the control group, and V1V2 Env-specific binding antibodies correlated with viral outcomes. Viral control was significantly enhanced in vaccinated macaques compared to controls, and in infected SAd7-vaccinated macaques compared to Ad4-vaccinated macaques, suggesting that this vector may have conferred more effective immunity. Because blocking infection is so difficult with current vaccines, development of a vaccine that can limit viremia if infection occurs would be valuable. These data support further development of replicating adenovirus vectors.
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Yang, Fengyuan, Jingyi Yang, Zhao Zhang, Gao Tu, Xiaojun Yao, Weiwei Xue, and Feng Zhu. "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 targets for designing novel HIV-1 antiviral drugs. During the development of HIV-1 IN and/or RT-RNase H inhibitors, computer-aided drug design (CADD), including homology modeling, pharmacophore, docking, molecular dynamics (MD) simulation, and binding free energy calculation, represents a significant tool to accelerate the discovery of new drug candidates and reduce costs in antiviral drug development. In this review, we summarized the recent advances in the design of single-and dual-target inhibitors against HIV-1 IN or/and RT-RNase H as well as the prediction of mutation-induced drug resistance based on computational methods. We highlighted the results of the reported literature and proposed some perspectives on the design of novel and more effective antiviral drugs in the future.
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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 accurate as they could be due to the biased prediction results. In this work, unknown substrate sites are regarded as unlabeled samples instead of negative ones. We propose a novel positive-unlabeled learning algorithm, namely PU-HIV, for an effective prediction of HIV-1 protease cleavage sites. Features used by PU-HIV are encoded from different perspectives of substrate sequences, including amino acid identities, coevolutionary patterns and chemical properties. By adjusting the weights of errors generated by positive and unlabeled samples, a biased support vector machine classifier can be built to complete the prediction task. In comparison with state-of-the-art prediction models, benchmarking experiments using cross-validation and independent tests demonstrated the superior performance of PU-HIV in terms of AUC, PR-AUC, and F-measure. Thus, with PU-HIV, it is possible to identify previously unknown, but physiologically existed substrate sites that are able to be cleaved by HIV-1 protease, thus providing valuable insights into designing novel HIV-1 protease inhibitors for HIV treatment.
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Malherbe, Delphine C., Lo Vang, Jason Mendy, Philip T. Barnette, David A. Spencer, Jason Reed, Bettie W. Kareko, 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 from the same timepoint as the DNA+Protein group paired with the same Env gp140 trimer (SAd7+Protein). The env genes were isolated from a single pre-peak neutralization timepoint approximately 1 year post infection in CAP257, an individual with a high degree of neutralization breadth. Both DNA+Protein and SAd7+Protein vaccine strategies elicited significant Env-specific T cell responses, lesser Gag-specific responses, and moderate frequencies of Env-specific TFH cells. Both vaccine modalities readily elicited systemic and mucosal Env-specific IgG but not IgA. There was a higher frequency and magnitude of ADCC activity in the SAd7+Protein than the DNA+Protein arm. All macaques developed moderate Tier 1 heterologous neutralizing antibodies, while neutralization of Tier 1B or Tier 2 viruses was sporadic and found primarily in macaques in the SAd7+Protein group. Neither vaccine approach provided significant protection from viral acquisition against repeated titered mucosal challenges with a heterologous Tier 2 clade C SHIV. However, lymphoid and gut tissues collected at necropsy showed that animals in both vaccine groups each had significantly lower copies of viral DNA in individual tissues compared to levels in controls. In the SAd7+Protein-vaccinated macaques, total and peak PBMC viral DNA were significantly lower compared with controls. Taken together, this heterologous Tier 2 SHIV challenge study shows that combination vaccination with SAd7+Protein was superior to combination DNA+Protein in reducing viral seeding in tissues in the absence of protection from infection, thus emphasizing the priming role of replication-competent SAd7 vector. Despite the absence of correlates of protection, because antibody responses were significantly higher in this vaccine group, we hypothesize that vaccine-elicited antibodies contribute to limiting tissue viral seeding.
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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 development of this method is carried out such that the requisite number of known data being minimal. Methods: To retrench the cardinal data span and shrink the effects of variant biological parameters on the computed value of IC50, a relative approach of IC50 computation is pursued in the present method. To predict an approximate value of IC50 of a small molecule, only the IC50 of a similar kind of molecule is required for this method. Results: The present method of IC50 computation is tested for both organic and organometallic compounds as HIV-1 capsid A inhibitor and cancer drugs. Computed results match very well with the experiment. Conclusion: This method is easily applicable to both organic and organometallic com- pounds with acceptable accuracy. Since this method requires only the dipole moments of an unknown compound and the reference compound, IC50 based drug search is possible with this method. An algorithm is proposed here for IC50 based drug search.
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Pan, Ruimin, Yali Qin, Marisa Banasik, William Lees, Adrian J. Shepherd, Michael W. Cho, and Xiang-Peng Kong. "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 (January 17, 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 structures of these MAbs bound to target epitopes were determined. 10A3 binds to the V3 crown ( 303 TRKSIHIGPGRAF 317 ) using the cradle binding mode, similar to human V3 MAbs encoded by IGHV5-51 germ line genes, and its epitope structure resembles that bound to the human antibodies. In contrast, 10A37, which exhibits greater breadth and potency than 10A3, binds the V3 crown and the succeeding stem region ( 308 HIGPGRAFYTTGEI 323 ). Unexpectedly, the 315 RAFYTT 320 portion of the epitope existed as helical turns, a V3 structure that has not been observed previously. Its main chain-dominated antigen-antibody interactions not only explain the broad neutralization of 10A37 but also show that its epitope is a potential vaccine target to be further evaluated. In conclusion, our study provides novel insights about neutralization-susceptible epitope structures of the V3 loop of HIV-1 gp120 and demonstrates that, despite low amino acid sequence similarity to human antibody germ line genes, rabbits can serve as a useful animal model to evaluate human vaccine candidates. IMPORTANCE The apex crown of V3 of HIV-1 gp120 is the most immunogenic region of the surface glycoprotein, and many MAbs targeting this region have been developed. Structural understanding of V3 crown MAbs not only can help understand how antibody responses target this unique region but also contribute to immunogen design for vaccine development. We present here crystal structures of two neutralizing V3 MAbs, 10A3 and 10A37, developed from a rabbit immunized with gp120. Our analysis of 10A3 in complex with V3 provided a detailed example of how epitope complexity can evolve with affinity maturation, while that of 10A37 revealed a novel V3 binding mode targeting the C-terminal side of the V3 crown and showed that this region can form a helical structure. Our study provides novel insights about neutralization-susceptible V3 epitope structures and demonstrates that rabbits can serve as a useful animal model to evaluate human vaccine candidates.
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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 antigenicity and the virulence of BVDV serotypes have been mainly focused on one or a few BVDV proteins. While however, little is known about the orchestration of all BVDV in the context of viral virulence and immunogenicity. The main aim of the current study was to do a comparative computational evaluation of the immunogenicity, and virulence for all the encoded proteins of both BVDV1 and BVDV2 and their sub-genotypes.MethodsTo achieve this goal, 11,737 protein sequences were retrieved from Virus Pathogen Resource. The analysis involved a total of 4,583 sequences after the removal of short sequences and those with unknown collection time. We used the MP3 tool to map the pathogenic proteins across different BVDV strains. The potential protective and the epitope motifs were predicted using the VaxiJen and EMBOSS antigen tools, respectively.Results and discussionThe virulence prediction revealed that the NS4B proteins of both BVDV1 and BVDV2 likely have essential roles in BVDV virulence. Similarly, both the capsid (C) and the NS4-A proteins of BVDV1 and the Npro and P7 proteins of BVDV2 are likely important virulent factors. There was a clear trend of increasing predicted virulence with the progression of time in the case of BVDV1 proteins, but that was not the case for the BVDV2 proteins. Most of the proteins of the two BVDV serotypes possess antigens predicted immunogens except Npro, P7, and NS4B. However, the predicted antigenicity of the BVDV1 was significantly higher than that of BVDV2. Meanwhile, the predicted immunogenicity of the immunodominant-E2 protein has been decreasing over time. Based on our predicted antigenicity and pathogenicity studies of the two BVDV serotypes, the sub-genotypes (1a, 1f, 1k, 2a, and 2b) may represent ideal candidates for the development of future vaccines against BVDV infection in cattle. In summary, we identified some common differences between the two BVDV genotypes (BVDV1 and BVDV2) and their sub-genotypes regarding their protein antigenicity and pathogenicity. The data presented here will increase our understanding of the molecular pathogenesis of BVDV infection in cattle. It will also pave the way for developing some novel diagnostic assays and novel vaccines against BVDV in the near future.
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Kumar, Sanjay, Geethu S. Kumar, Subhrangsu Sundar Maitra, Petr Malý, Shiv Bharadwaj, Pradeep Sharma, and Vivek Dhar Dwivedi. "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 of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Waqas, Muhammad, Shahkaar Aziz, Pietro Liò, Yumna Khan, Amjad Ali, Aqib Iqbal, Faizullah Khan, and Fahad Nasser Almajhdi. "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 vaccinology pipeline was used to select 11 potential vaccine candidates, which were screened and mapped to predict immunodominant B-cell and T-cell epitopes. The finalized epitopes were merged with the aid of suitable linkers, an adjuvant (Resuscitation-promoting factor), a PADRE sequence (13 aa), and an HIV TAT sequence (11 aa) to formulate a multivalent epitope vaccine. Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. C-ImmSim server was implemented to examine the immune response against the designed multi-epitope antigen.Results and discussionThe designed chimeric vaccine construct included 21 immunodominant epitopes (six B-cell, eight cytotoxic T lymphocyte, and seven helper T-lymphocyte) and is predicted non-allergen, antigenic, soluble, with suitable physicochemical features, that can promote cross-protection among the MPXV strains. The selected epitopes indicated a wide global population coverage (93.62%). Most finalized epitopes have 70%–100% sequence similarity with the experimentally validated immune epitopes of the vaccinia virus, which can be helpful in the speedy progression of vaccine design. Lastly, molecular docking and molecular dynamics simulation computed stable and energetically favourable interaction between the putative antigen and TLR4.ConclusionOur results show that the multi-epitope vaccine might elicit cellular and humoral immune responses and could be a potential vaccine candidate against the MPXV infection. Further experimental testing of the proposed vaccine is warranted to validate its safety and efficacy profile.