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HIV in silico

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https://www.readbyqxmd.com/read/29651941/identification-of-adjacent-nnrti-binding-pocket-in-multi-mutated-hiv1-rt-enzyme-model-an-in-silico-study
#1
R F Kamil, U Debnath, S Verma, Y S Prabhakar
The Acquired Immunodeficiency Syndrome is an immunesuppressant disorder caused by human immunodeficiency virus, the upshot of which can be observed on affected individual's immune system. The salient role of HIV-1RT in progression & development of disease makes it a significant target. In current the study a 3D-model of HIV-1 RT enzyme having following multiple mutations K103N, Y181C and Y188L was developed through homology modeling with the aim to perceive effects of multiple mutations on binding pocket and binding interractions...
April 12, 2018: Current HIV Research
https://www.readbyqxmd.com/read/29619445/in-silico-screening-and-biological-evaluation-of-the-compounds-of-justicia-gendarussa-leaves-extract-as-interferon-gamma-inducer-a-study-of-anti-human-immunodeficiency-virus-hiv-development
#2
Restry Sinansari, Bambang Prajogo Ew, Prihartini Widiyanti
Background: Justicia gendarussa Burm f. (Achanthaceae) has been known as traditional medicine in Indonesia. It contains of flavonoids and alkaloids. This study was conducted to evaluate the effect of J. gendarussa on the profile of IFN-γ on mice (Mus musculus ). Molecular docking test was also conducted to determine the interaction of alkaloids and flavonoids on the J. gendarussa leaves against IFN-γ receptor. It is expected that this research will provide scientific information on the development of J...
2018: African Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29604421/study-on-antiviral-activities-drug-likeness-and-molecular-docking-of-bioactive-compounds-of-punica-granatum-l-to-herpes-simplex-virus-2-hsv-2
#3
Jagadheesan Arunkumar, Swaminathan Rajarajan
Herpes simplex virus - 2 (HSV-2) causes lifelong persisting infection in the immunocompromised host and intermittent in healthy individuals with high morbidity and also increase the transmission of HIV. Acyclovir is widely used drug to treat HSV-2 infection but is unable to control viral latency and recurrent infection and prolonged usage lead to drug resistance. Plant-based bioactive compounds are the lead structural bio-molecules play an inevitable role as a potential antiviral agent with reduced toxicity...
March 28, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29579063/in-silico-identification-of-micrornas-predicted-to-regulate-n-myristoyltransferase-and-methionine-aminopeptidase-2-functions-in-cancer-and-infectious-diseases
#4
Ranjit Chauhan, David Datzkiw, Shailly Varma Shrivastav, Anuraag Shrivastav
Protein myristoylation is a key protein modification carried out by N-Myristoyltransferase (NMT) after Methionine aminopeptidase 2 (MetAP2) removes methionine from the amino-terminus of the target protein. Protein myristoylation by NMT augments several signaling pathways involved in a myriad of cellular processes, including developmental pathways and pathways that when dysregulated lead to cancer or immune dysfunction. The emerging evidence pointing to NMT-mediated myristoylation as a major cellular regulator underscores the importance of understanding the framework of this type of signaling event...
2018: PloS One
https://www.readbyqxmd.com/read/29571972/immunoinformatics-approaches-to-design-a-novel-multi-epitope-subunit-vaccine-against-hiv-infection
#5
Rajan Kumar Pandey, Rupal Ojha, Veeranarayanan Surya Aathmanathan, Muthukalingan Krishnan, Vijay Kumar Prajapati
The end goal of HIV vaccine designing requires novel strategies to elicit a strong humoral and cell-mediated immune response. The emergence of drug resistance and the requirement of next line treatment necessitate the finding of the potential and immunogenic vaccine candidate. This study employed a novel immunoinformatics approach to design multi-epitope subunit vaccine against HIV infection. Here, we designed the subunit vaccine by the combination of CTL, HTL and BCL epitopes along with suitable adjuvant and linkers...
March 20, 2018: Vaccine
https://www.readbyqxmd.com/read/29570280/anionic-carbosilane-dendrimers-destabilize-the-gp120-cd4-complex-blocking-hiv-1-entry-and-cell-to-cell-fusion
#6
Carlos Guerrero-Beltrán, Ignacio Rodríguez-Izquierdo, Mª Jesús Serramía, Ingrid Araya-Duran, Valeria Márquez-Miranda, Rafael Gómez, Francisco Javier de la Mata, Manuel Leal, Fernando Danilo Gonzalez-Nilo, M Ángeles Muñoz-Fernández
Cell-to-cell transmission is the most effective pathway for human immunodeficiency virus (HIV-1) spread. Infected cells expose virus-encoded fusion proteins on their surface as consequence of HIV-1 replicative cycle that interacts with non-infected cells through CD4 receptor and CXCR4 co-receptor leading to the formation of giant multinucleated cells known as syncytia. Our group previously described the potent activity of dendrimers against R5-tropic viruses. Nevertheless, the study of G1-S4, G2-S16 and G3-S16 dendrimers in the context of X4-HIV-1 tropic cell-cell fusion referred to syncytium formation remains still unknown...
March 23, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29567319/in-silico-design-of-mycobacterium-tuberculosis-epitope-ensemble-vaccines
#7
Preksha Shah, Jaymisha Mistry, Pedro A Reche, Derek Gatherer, Darren R Flower
Effective control of Mycobacterium tuberculosis is a global necessity. In 2015, tuberculosis (TB) caused more deaths than HIV. Considering the increasing prevalence of multi-drug resistant forms of M. tuberculosis, the need for effective TB vaccines becomes imperative. Currently, the only licensed TB vaccine is Bacillus Calmette-Guérin (BCG). Yet, BCG has many drawbacks limiting its efficacy and applicability. We applied advanced computational procedures to derive a universal TB vaccine and one targeting East Africa...
March 19, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/29531046/correction-for-kudalkar-et-al-from-in-silico-hit-to-long-acting-late-stage-preclinical-candidate-to-combat-hiv-1-infection
#8
(no author information available yet)
No abstract text is available yet for this article.
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29512823/variable-domain-n-linked-glycosylation-and-negative-surface-charge-are-key-features-of-monoclonal-acpa-implications-for-b-cell-selection
#9
Katy A Lloyd, Johanna Steen, Khaled Amara, Philip J Titcombe, Lena Israelsson, Susanna L Lundström, Diana Zhou, Roman A Zubarev, Evan Reed, Luca Piccoli, Cem Gabay, Antonio Lanzavecchia, Dominique Baeten, Karin Lundberg, Daniel L Mueller, Lars Klareskog, Vivianne Malmström, Caroline Grönwall
Autoreactive B cells have a central role in the pathogenesis of rheumatoid arthritis (RA), and recent findings have proposed that anti-citrullinated protein autoantibodies (ACPA) may be directly pathogenic. Herein, we demonstrate the frequency of variable-region glycosylation in single-cell cloned mAbs. A total of 14 ACPA mAbs were evaluated for predicted N-linked glycosylation motifs in silico, and compared to 452 highly-mutated mAbs from RA patients and controls. Variable region N-linked motifs (N-X-S/T) were strikingly prevalent within ACPA (100%) compared to somatically hypermutated (SHM) RA bone marrow plasma cells (21%), and synovial plasma cells from seropositive (39%) and seronegative RA (7%)...
March 7, 2018: European Journal of Immunology
https://www.readbyqxmd.com/read/29482943/synthesis-and-evaluation-of-substituted-4-arylimino-3-hydroxybutanoic-acids-as-potential-hiv-1-integrase-inhibitors
#10
Faridoon, Dumisani Mnkandhla, Michelle Isaacs, Heinrich C Hoppe, Perry T Kaye
A series of readily accessible 4-arylimino-3-hydroxybutanoic acids have been prepared and evaluated as potential HIV-1 Integrase inhibitors. None of the ligands exhibited significant toxicity against human embryonic kidney (HEK 293) cells, while five of them showed activity against HIV-1 integrase - the most active (6c) with an IC50 value of 3.5 μM. In silico docking studies indicate the capacity of ligand 6c to interact with several amino acid residues and the two Mg2+ cations in the HIV-1 integrase receptor cavity...
February 12, 2018: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29439644/potential-hiv-1-fusion-inhibitors-mimicking-gp41-specific-broadly-neutralizing-antibody-10e8-in-silico-discovery-and-prediction-of-antiviral-potency
#11
Alexander M Andrianov, Ivan A Kashyn, Alexander V Tuzikov
An integrated computational approach to in silico drug design was used to identify novel HIV-1 fusion inhibitor scaffolds mimicking broadly neutralizing antibody (bNab) 10E8 targeting the membrane proximal external region (MPER) of the HIV-1 gp41 protein. This computer-based approach included (i) generation of pharmacophore models representing 3D-arrangements of chemical functionalities that make bNAb 10E8 active towards the gp41 MPER segment, (ii) shape and pharmacophore-based identification of the 10E8-mimetic candidates by a web-oriented virtual screening platform pepMMsMIMIC, (iii) high-throughput docking of the identified compounds with the gp41 MPER peptide, and (iv) molecular dynamics simulations of the docked structures followed by binding free energy calculations...
January 15, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29425767/proteomic-profiling-of-hiv-infected-t-cells-by-swath-mass-spectrometry
#12
Jason DeBoer, Melinda S Wojtkiewicz, Nicole Haverland, Yan Li, Emma Harwood, Emily Leshen, Joseph W George, Pawel Ciborowski, Michael Belshan
Viral pathogenesis results from changes in host cells due to virus usurpation of the host cell and the innate cellular responses to thwart infection. We measured global changes in protein expression and localization in HIV-1 infected T-cells using subcellular fractionation and the Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) proteomic platform. Eight biological replicates were performed in two independent experimental series. In silico merging of both experiments identified 287 proteins with altered expression (p < ...
February 6, 2018: Virology
https://www.readbyqxmd.com/read/29414440/induction-of-broadly-neutralizing-antibodies-in-germinal-centre-simulations
#13
REVIEW
Philippe A Robert, Andrea Lj Marschall, Michael Meyer-Hermann
Vaccines against mutating pathogens such as influenza, HIV, or plasmodium are poorly protective towards new evolving strains. Rare individuals naturally mount broadly neutralizing antibodies covering most strains, but the requirements for their induction are unknown. The antibody response to vaccination has been recapitulated by in silico models that proposed two opposite schemes: A theory of 'frustration' where one epitope at a time leads to optimal antibody breadth through sequential immunizations, that was proven successful for HIV vaccination in primates...
February 1, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29336469/transcriptional-regulation-of-hiv-1-host-factor-commd1-by-the-sp-family
#14
Eriko Kudo, Manabu Taura, Mary Ann Suico, Hiroki Goto, Hirofumi Kai, Seiji Okada
Copper metabolism Murr1 domain containing 1 (COMMD1) has multiple functions in the regulation of protein stability at the plasma membrane and in the cytoplasm. However, the regulation of COMMD1 transcriptional has remained to be elucidated. In the present study, the 5'‑flanking region (‑1,192/+83 bp) of the human COMMD1 gene was cloned. It was observed that the COMMD1 promoter region contains GC‑rich region that has 7 putative Sp1‑binding sites via in silico analysis. The proximal promoter region at ‑289/+83 bp was required for COMMD1 basal promoter activity by deletion constructs of COMMD1 promoter...
April 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29330771/inhibition-of-human-immunodeficiency-type-1-virus-hiv-1-life-cycle-by-different-egg-white-lysozymes
#15
Mandana Behbahani, Mokhtar Nosrati, Hassan Mohabatkar
Lysozyme is a relatively small enzyme with different biological activities, which is found in tears, saliva, egg white, and human milk. In the study, the anti-HIV-1 activity of lysozymes purified from quail, Meleagris, and hen egg white has been determined. For this end, a time-of-drug-addition assay was performed to identify the target of anti-HIV-1 agents and for determination of probable anti HIV-1 mechanism of the studied lysozyme, the binding affinity of the lysozymes to the human CD4 receptor was studied by molecular docking method...
January 13, 2018: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29279368/from-in-silico-hit-to-long-acting-late-stage-preclinical-candidate-to-combat-hiv-1-infection
#16
Shalley N Kudalkar, Jagadish Beloor, Elias Quijano, Krasimir A Spasov, Won-Gil Lee, José A Cisneros, W Mark Saltzman, Priti Kumar, William L Jorgensen, Karen S Anderson
The HIV-1 pandemic affecting over 37 million people worldwide continues, with nearly one-half of the infected population on highly active antiretroviral therapy (HAART). Major therapeutic challenges remain because of the emergence of drug-resistant HIV-1 strains, limitations because of safety and toxicity with current HIV-1 drugs, and patient compliance for lifelong, daily treatment regimens. Nonnucleoside reverse transcriptase inhibitors (NNRTIs) that target the viral polymerase have been a key component of the current HIV-1 combination drug regimens; however, these issues hamper them...
January 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29277258/in-silico-toxicity-profiling-of-natural-product-compound-libraries-from-african-flora-with-anti-malarial-and-anti-hiv-properties
#17
Pascal Amoa Onguéné, Conrad V Simoben, Ghislain W Fotso, Kerstin Andrae-Marobela, Sami A Khalid, Bonaventure T Ngadjui, Luc Meva'a Mbaze, Fidele Ntie-Kang
This paper describes an analysis of the diversity and chemical toxicity assessment of three chemical libraries of compounds from African flora (the p-ANAPL, AfroMalariaDb, and Afro-HIV), respectively containing compounds exhibiting activities against diverse diseases, malaria and HIV. The diversity of the three data sets was done by comparison of the three most important principal components computed from standard molecular descriptors. This was also done by a study of the most common substructures (MCSS keys)...
February 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29244833/genomic-characterization-and-molecular-evolution-analysis-of-subtype-b-and-bf-recombinant-hiv-1-strains-among-argentinean-men-who-have-sex-with-men-reveal-a-complex-scenario
#18
Cintia G Cevallos, Leandro R Jones, Maria A Pando, Jean K Carr, Maria M Avila, Jorge Quarleri
Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM...
2017: PloS One
https://www.readbyqxmd.com/read/29235845/structure-based-identification-of-hiv-1-nucleocapsid-protein-inhibitors-active-against-wild-type-and-drug-resistant-hiv-1-strains
#19
Mattia Mori, Lesia Kovalenko, Savina Malancona, Francesco Saladini, Davide De Forni, Manuel Pires, Nicolas Humbert, Eleonore Real, Thomas Botzanowski, Sarah Cianférani, Alessia Giannini, Maria Chiara Dasso Lang, Giulia Cugia, Barbara Poddesu, Franco Lori, Maurizio Zazzi, Steven Harper, Vincenzo Summa, Yves Mely, Maurizio Botta
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR...
January 19, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29184023/effects-of-mutations-on-replicative-fitness-and-major-histocompatibility-complex-class-i-binding-affinity-are-among-the-determinants-underlying-cytotoxic-t-lymphocyte-escape-of-hiv-1-gag-epitopes
#20
Yushen Du, Tian-Hao Zhang, Lei Dai, Xiaojuan Zheng, Aleksandr M Gorin, John Oishi, Ting-Ting Wu, Janice M Yoshizawa, Xinmin Li, Otto O Yang, Otoniel Martinez-Maza, Roger Detels, Ren Sun
Certain "protective" major histocompatibility complex class I (MHC-I) alleles, such as B*57 and B*27, are associated with long-term control of HIV-1 in vivo mediated by the CD8+ cytotoxic-T-lymphocyte (CTL) response. However, the mechanism of such superior protection is not fully understood. Here we combined high-throughput fitness profiling of mutations in HIV-1 Gag, in silico prediction of MHC-peptide binding affinity, and analysis of intraperson virus evolution to systematically compare differences with respect to CTL escape mutations between epitopes targeted by protective MHC-I alleles and those targeted by nonprotective MHC-I alleles...
November 28, 2017: MBio
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