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HIV in silico

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https://www.readbyqxmd.com/read/27915028/catalytic-synthesis-of-%C3%AE-amino-chromone-phosphonates-and-their-antimicrobial-toxicity-and-potential-hiv-1-rt-inhibitors-based-on-silico-screening
#1
Abosede Oluwabukola Jaiyeola, K Anand, K Kasumbwe, M Ramesh, R M Gengan
The α-amino phosphonates exhibit a wide range of biological properties which create demand for simple and efficient synthetic routes of new molecules. In this study synthesis of a new series of derivatives of α-amino chromone phosphonates (ACPs) was reported using RhBT catalyst. The RhBT was first prepared by simply mixing boron nitride in a solution of rhodium acetate, under inert atmosphere for a week followed by filtration (yield: 92%). The catalyst can be re-used for up to four times and showed minimal loss of activity...
November 23, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27894873/design-synthesis-and-anti-hiv-1-rt-evaluation-of-2-benzyl-4-chlorophenyl-amino-1-piperazin-1-yl-ethanone-derivatives
#2
Subhash Chander, Ping Wang, Penta Ashok, Liu-Meng Yang, Yong-Tang Zheng, Murugesan Sankaranarayanan
In this study, using molecular hybridization approach, fourteen novel 2-(benzyl(4-chlorophenyl)amino)-1-(piperazin-1-yl)ethanone derivatives (7a-n) were designed as inhibitor of HIV-1 RT. The binding affinity of the designed compounds with HIV-1 RT as well as their drug-likeness behavior was predicted using in-silico studies. All the designed compounds were synthesized, characterized and in-vitro evaluated for HIV-1 RT inhibitory activity, in which tested compounds displayed significant to weak potency against the selected target...
November 14, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27844017/design-of-new-potent-htlv-1-protease-inhibitors-in-silico-study
#3
Mitra Kheirabadi, Javad Maleki, Safieh Soufian, Samaneh Hosseini
HTLV-1 and HIV-1 are two major causes for severe T-cell leukemia disease and acquired immune deficiency syndrome (AIDS). HTLV-1 protease, a member of aspartic acid protease family, plays important roles in maturation during virus replication cycle. The impairment of these proteases results in uninfectious HTLV-1virions.Similar to HIV-1protease deliberate mutations that confer drug resistance on HTLV-1 are frequently seen in this protease. Therefore, inhibition of HTLV-1 protease activity is expected to disrupt HTLV-1's ability to replicate and infect additional cells...
March 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/27788396/in-silico-analysis-of-hepatitis-c-virus-hcv-polyprotein-domains-and-their-comparison-with-other-pathogens-and-allergens-to-gain-insight-on-pathogenicity-mechanisms
#4
Seema Patel
Hepatitis C (HCV) is a deadly virus from family Flaviviridae, causing acute or chronic liver inflammation. Given its lethality and no known vaccine to curb it, understanding its pathogenic mechanism is critical. By analyzing the domains in its protein sequence, a plethora can be learnt about its immune manipulation strategies. In this regard, current in silico study compares publicly-available HCV polyprotein sequences and their domain profiles. Apart from using UniProt sequences and SMART (Simple modular architecture research tool) platform for domain profiling, a set of customized scripts were developed to extract the patterns of protein domain distribution...
October 15, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27764177/development-validation-and-field-testing-of-an-instrument-for-clinical-assessment-of-hiv-associated-neuropathy-and-neuropathic-pain-in-resource-restricted-and-large-population-study-settings
#5
Yohannes W Woldeamanuel, Peter R Kamerman, Demetri G A Veliotes, Tudor J Phillips, David Asboe, Marta Boffito, Andrew S C Rice
HIV-associated sensory peripheral neuropathy (HIV-SN) afflicts approximately 50% of patients on antiretroviral therapy, and is associated with significant neuropathic pain. Simple accurate diagnostic instruments are required for clinical research and daily practice in both high- and low-resource setting. A 4-item clinical tool (CHANT: Clinical HIV-associated Neuropathy Tool) assessing symptoms (pain and numbness) and signs (ankle reflexes and vibration sense) was developed by selecting and combining the most accurate measurands from a deep phenotyping study of HIV positive people (Pain In Neuropathy Study-HIV-PINS)...
2016: PloS One
https://www.readbyqxmd.com/read/27730744/anti-hiv-1-activity-prediction-of-novel-gp41-inhibitors-using-structure-based-virtual-screening-and-molecular-dynamics-simulation
#6
Saghi Sepehri, Lotfollah Saghaie, Afshin Fassihi
The fusion of viral and host cell membranes is mediated using gp41 subunit of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein. As the HIV-1 enters the host cells, the two helical regions (HR1 and HR2) in the ectodomain of gp41 form a six-helix bundle, which carries the target and viral cell membranes to close proximity. Steps of this process serve as attractive targets for developing HIV-1 fusion inhibitors. Identification of some novel HIV fusion inhibitors with the goal of blocking the formation of the six-helix bundle was accomplished by computer-aided drug design techniques...
October 12, 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27730231/enhanced-conformational-sampling-technique-provides-an-energy-landscape-view-of-large-scale-protein-conformational-transitions
#7
Qiang Shao
Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27721439/hiv-1-vpr-n-terminal-tagging-affects-alternative-splicing-of-the-viral-genome
#8
Ann Baeyens, Evelien Naessens, Anouk Van Nuffel, Karin E Weening, Anne-Marie Reilly, Eva Claeys, Wim Trypsteen, Linos Vandekerckhove, Sven Eyckerman, Kris Gevaert, Bruno Verhasselt
To facilitate studies on Vpr function in replicating HIV-1, we aimed to tag the protein in an infectious virus. First we showed that N-, but not C-terminal HA/FLAG tagging of Vpr protein preserves Vpr cytopathicity. Cloning the tags into proviral DNA however ablated viral production and replication. By construction of additional viral variants we could show this defect was not protein- but RNA-dependent and sequence specific, and characterized by oversplicing of the genomic RNA. Simulation of genomic RNA folding suggested that introduction of the tag sequence induced an alternative folding structure in a region enriched in splice sites and splicing regulatory sequences...
October 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27602436/computational-evaluation-of-hiv-1-gp120-conformations-of-soluble-trimeric-gp140-structures-as-targets-for-de-novo-docking-of-first-and-second-generation-small-molecule-cd4-mimics
#9
Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B Smith Iii, Irwin M Chaiken, Cameron F Abrams
Small-molecule CD4 mimics (SMCM's) bind to gp120 subunit of the HIV-1 envelope glycoprotein (Env) and have been optimized to block cell infection in vitro. The lack of the V1/2 and V3 loops and the presence of the β2/3 and β20/21 strands (bridging sheet) in the available structures of the monomeric gp120 core may limit its applicability as a target for further synthetic optimization of SMCM potency and/or breadth. Here, we employ a combination of binding-site search, docking, estimation of protein-ligand interaction energy, all-atom molecular dynamics, and ELISA-based CD4-binding competition assays to create, characterize, and rationalize models of first- and second-generation of SMCM's bound to the distinct, trimeric BG505 SOSIP...
September 7, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/27546042/software-infrastructure-for-computer-aided-drug-discovery-and-development-a-practical-example-with-guidelines
#10
Loris Moretti, Luca Sartori
In the field of Computer-Aided Drug Discovery and Development (CADDD) the proper software infrastructure is essential for everyday investigations. The creation of such an environment should be carefully planned and implemented with certain features in order to be productive and efficient. Here we describe a solution to integrate standard computational services into a functional unit that empowers modelling applications for drug discovery. This system allows users with various level of expertise to run in silico experiments automatically and without the burden of file formatting for different software, managing the actual computation, keeping track of the activities and graphical rendering of the structural outcomes...
September 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27517812/computational-and-synthetic-approaches-for-developing-lavendustin-b-derivatives-as-allosteric-inhibitors-of-hiv-1-integrase
#11
Fatima E Agharbaoui, Ashley C Hoyte, Stefania Ferro, Rosaria Gitto, Maria Rosa Buemi, James R Fuchs, Mamuka Kvaratskhelia, Laura De Luca
Through structure-based virtual screening and subsequent activity assays of selected natural products, Lavendustin B was previously identified as an inhibitor of HIV-1 integrase (IN) interaction with its cognate cellular cofactor, lens epithelium-derived growth factor (LEDGF/p75). In order to improve the inhibitory potency we have employed in silico-based approaches. Particularly, a series of new analogues was designed and docked into the LEDGF/p75 binding pocket of HIV-1 IN. To identify promising leads we used the Molecular Mechanics energies combined with the Generalized Born and Surface Area continuum solvation (MM-GBSA) method, molecular dynamics simulations and analysis of hydrogen bond occupancies...
November 10, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27310139/prothymosin-%C3%AE-variants-elicit-anti-hiv-1-response-via-tlr4-dependent-and-independent-pathways
#12
G Luca Gusella, Avelino Teixeira, Judith Aberg, Vladimir N Uversky, Arevik Mosoian
BACKGROUND: Prothymosin α (ProTα) (isoform 2: iso2) is a widely distributed, small acidic protein with intracellular and extracellular-associated functions. Recently, we identified two new ProTα variants with potent anti-HIV activity from CD8+ T cells and cervicovaginal lavage. The first is a splice variant of the ProTα gene known as isoB and the second is the product of ProTα pseudogene 7 (p7). Similarly to iso2, the anti-HIV activity of both variants is mediated by type I IFN. Here we tested whether the immunomodulatory activity of isoB and p7 are also TLR4 dependent and determined their kinetic of release in response to HIV-1 infection...
2016: PloS One
https://www.readbyqxmd.com/read/27294106/integration-of-hiv-in-the-human-genome-which-sites-are-preferential-a-genetic-and-statistical-assessment
#13
Juliana Gonçalves, Elsa Moreira, Inês J Sequeira, António S Rodrigues, José Rueff, Aldina Brás
Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs)...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27291589/cheminformatics-based-machine-learning-approaches-for-assessing-glycolytic-pathway-antagonists-of-mycobacterium-tuberculosis
#14
Kanupriya Tiwari, Salma Jamal, Sonam Grover, Sukriti Goyal, Aditi Singh, Abhinav Grover
BACKGROUND: Tuberculosis is the second leading cause of death from an infectious disease worldwide after HIV, thus reasoning the expeditions in anti-tuberculosis research. The rising number of cases of infection by resistant forms of M. tuberculosis has given impetus to the development of novel drugs that have different targets and mechanisms of action against the bacterium. METHODS: In this study, we have used machine learning algorithms on the available high throughput screening data of inhibitors of fructose bisphosphate aldolase, an enzyme central to the glycolysis pathway in M...
June 9, 2016: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/27165479/identification-of-novel-potential-gp120-of-hiv-1-antagonist-using-per-residue-energy-contribution-based-pharmacophore-modelling
#15
Emiliene Berinyuy, Mahmoud E S Soliman
Inhibition of HIV-1 target cell entry, by targeting gp120, has been identified as a promising approach for the identification and development of prophylactic and salvage HIV infection inhibitors. A small molecule compound 18A is an important chemotype in the development of novel and diverse viral cell entry inhibitors, as it inhibits a wide variety of HIV strains by disrupting allosteric structuring on gp120. This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120...
May 10, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27108399/design-discovery-modelling-synthesis-and-biological-evaluation-of-novel-and-small-low-toxicity-s-triazine-derivatives-as-hiv-1-non-nucleoside-reverse-transcriptase-inhibitors
#16
Birgit Viira, Anastasia Selyutina, Alfonso T García-Sosa, Maarit Karonen, Jari Sinkkonen, Andres Merits, Uko Maran
A set of top-ranked compounds from a multi-objective in silico screen was experimentally tested for toxicity and the ability to inhibit the activity of HIV-1 reverse transcriptase (RT) in cell-free assay and in cell-based assay using HIV-1 based virus-like particles. Detailed analysis of a commercial sample that indicated specific inhibition of HIV-1 reverse transcription revealed that a minor component that was structurally similar to that of the main compound was responsible for the strongest inhibition. As a result, novel s-triazine derivatives were proposed, modelled, discovered, and synthesised, and their antiviral activity and cellular toxicity were tested...
June 1, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/27105027/design-synthesis-and-anti-hiv-activity-of-novel-quinoxaline-derivatives
#17
Saloni B Patel, Bhumika D Patel, Christophe Pannecouque, Hardik G Bhatt
In order to design novel anti-HIV agents, pharmacophore modelling, virtual screening, 3D-QSAR and molecular docking studies were performed. Pharmacophore model was generated using 17 structurally diverse molecules using DISCOtech followed by refinement with GASP module of Sybyl X. The best model containing four features; two donor sites, one acceptor atom and one hydrophobic region; was used as a query for virtual screening in NCI database and 6 compounds with Qfit value ≥98 were retrieved. The quinoxaline ring which is the bio-isostere of pteridine ring, retrieved as a hit in virtual screening, was selected as a core moiety...
July 19, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27054280/kill-boosting-hiv-specific-immune-responses
#18
Lydie Trautmann
PURPOSE OF REVIEW: Increasing evidence suggests that purging the latent HIV reservoir in virally suppressed individuals will require both the induction of viral replication from its latent state and the elimination of these reactivated HIV-infected cells ('Shock and Kill' strategy). Boosting potent HIV-specific CD8 T cells is a promising way to achieve an HIV cure. RECENT FINDINGS: Recent studies provided the rationale for developing immune interventions to increase the numbers, function and location of HIV-specific CD8 T cells to purge HIV reservoirs...
July 2016: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/26927806/molecular-characterization-of-hiv-1-nef-and-acot8-interaction-insights-from-in-silico-structural-predictions-and-in-vitro-functional-assays
#19
Michela Serena, Alejandro Giorgetti, Mirko Busato, Francesca Gasparini, Erica Diani, Maria Grazia Romanelli, Donato Zipeto
HIV-1 Nef interacts with several cellular proteins, among which the human peroxisomal thioesterase 8 (ACOT8). This interaction may be involved in the endocytosis regulation of membrane proteins and might modulate lipid composition in membrane rafts. Nef regions involved in the interaction have been experimentally characterized, whereas structural details of the ACOT8 protein are unknown. The lack of structural information hampers the comprehension of the functional consequences of the complex formation during HIV-1 infection...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26903989/in-silico-analysis-of-hiv-1-env-gp120-reveals-structural-bases-for-viral-adaptation-in-growth-restrictive-cells
#20
Masaru Yokoyama, Masako Nomaguchi, Naoya Doi, Tadahito Kanda, Akio Adachi, Hironori Sato
Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope...
2016: Frontiers in Microbiology
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