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HIV in silico

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https://www.readbyqxmd.com/read/28709077/phytonanotherapy-for-management-of-diabetes-using-green-synthesis-nanoparticles
#1
K Anand, C Tiloke, Pragalathan Naidoo, A A Chuturgoon
The world has a rich diversity of indigenous medicinal plants. The World Health Organization (WHO) gives high priority to eco-friendly, non-hazardous and cost effective healthcare such as the use of medicinal plants to treat various illnesses, including Human immunodeficiency virus (HIV) infection and Acquired immune deficiency syndrome (AIDS), tuberculosis (TB), diabetes mellitus (DM), malaria, and cancer. In developing countries, a high proportion of the population tends to use complementary and alternative medicines (CAM) together with conventional prescription drugs...
June 27, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28659246/discovery-of-novel-dapy-ias-hybrid-derivatives-as-potential-hiv-1-inhibitors-using-molecular-hybridization-based-on-crystallographic-overlays
#2
Boshi Huang, Xueshun Wang, Xinhao Liu, Zihui Chen, Wanzhuo Li, Songkai Sun, Huiqing Liu, Dirk Daelemans, Erik De Clercq, Christophe Pannecouque, Peng Zhan, Xinyong Liu
Crystallographic overlap studies and pharmacophoric analysis indicated that diarylpyrimidine (DAPY)-based HIV-1 NNRTIs showed a similar binding mode and pharmacophoric features as indolylarylsulfones (IASs), another class of potent NNRTIs. Thus, a novel series of DAPY-IAS hybrid derivatives were identified as newer NNRTIs using structure-based molecular hybridization. Some target compounds exhibited moderate activities against HIV-1 IIIB strain, among which the two most potent inhibitors possessed EC50 values of 1...
June 15, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28648081/in-silico-and-in-vitro-screening-for-p-glycoprotein-interaction-with-tenofovir-darunavir-and-dapivirine-an-anti-retroviral-drug-combination-for-topical-prevention-of-colorectal-hiv-transmission
#3
Magda Swedrowska, Shirin Jamshidi, Abhinav Kumar, Charles Kelly, K Miraz Rahman, Ben Forbes
The aim of the study was to use in-silico and in vitro techniques to evaluate whether a triple formulation of antiretroviral drugs (tenofovir, darunavir and dapivirine) interacted with p-glycoprotein (P-gp) or exhibited any other permeability-altering drug-drug interactions in the colorectal mucosa. Potential drug interactions with P-gp were screened initially using molecular docking, followed by molecular dynamics simulations to analyse the identified drug-transporter interaction more mechanistically. The transport of tenofovir, darunavir and dapivirine was investigated in the Caco-2 cells models and colorectal tissue and their apparent permeability coefficient (Papp), efflux ratio (ER) and the effect of transporter inhibitors were evaluated...
June 25, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28641512/molecular-docking-and-molecular-dynamics-simulation-based-approach-to-explore-the-dual-inhibitor-against-hiv-1-reverse-transcriptase-and-integrase
#4
Subhash Chander, Rajan Kumar Pandey, Ashok Penta, Bhanwar Singh Choudhary, Manish Sharma, Ruchi Malik, Vijay Kumar Prajapati, Sankaranarayanan Murugesan
HIV integrase (IN) and reverse transcriptase (RT) are key enzymes for the replication of HIV-1. DNA polymerase and ribonuclease H (RNase H) are the two catalytic domains of HIV-1 RT which are validated as drug targets because of their essence for replication. IN and RNase H domain of RT share the striking structural similarity; it contains conserved DDE triad (two aspartates and one glutamate) and a pair of divalent Mg2+/Mn2+ ions at their catalytic core domain. Therefore, the search of compounds with dual inhibition of IN and RNase H can be the viable and more efficacious approach for the drug development against both wild and drug resistance strains of HIV...
June 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28624190/expression-of-herpes-simplex-virus-thymidine-kinase-ganciclovir-by-rna-trans-splicing-induces-selective-killing-of-hiv-producing-cells
#5
Carin K Ingemarsdotter, Sushmita Poddar, Sarah Mercier, Volker Patzel, Andrew M L Lever
Antiviral strategies targeting hijacked cellular processes are less easily evaded by the virus than viral targets. If selective for viral functions, they can have a high therapeutic index. We used RNA trans-splicing to deliver the herpes simplex virus thymidine kinase-ganciclovir (HSV-tk/GCV) cell suicide system into HIV-producing cells. Using an extensive in silico bioinformatics and RNA structural analysis approach, ten HIV RNA trans-splicing constructs were designed targeting eight different HIV splice donor or acceptor sites and were tested in cells expressing HIV...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28616684/influence-of-ethanol-on-darunavir-hepatic-clearance-and-intracellular-pk-pd-in-hiv-infected-monocytes-and-cyp3a4-darunavir-interactions-using-inhibition-and-in-silico-binding-studies
#6
Narasimha M Midde, Yuqing Gong, Theodore J Cory, Junhao Li, Bernd Meibohm, Weihua Li, Santosh Kumar
PURPOSE: Although the prevalence of alcohol consumption is higher in HIV+ people than general public, limited information is available on how alcohol affects the metabolism and bioavailability of darunavir (DRV). METHODS: DRV was quantified by using LC-MS/MS method. All in vitro experiments were performed using human liver microsomes and HIV-infected monocytic cells. CYP3A4 and DRV/Ritonavir (RTV) docking was performed using GOLD suite 5.8. RESULTS: Ethanol (20 mM) significantly decreased apparent half-life and increased degradation rate constant of RTV-boosted DRV but not for DRV alone...
June 14, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28591513/unravelling-the-molecular-basis-of-high-affinity-nanobodies-against-hiv-p24-in-vitro-functional-structural-and-in-silico-insights
#7
Eleanor R Gray, Jennifer C Brookes, Christophe Caillat, Valérian Turbé, Benjamin L J Webb, Luke A Granger, Benjamin S Miller, Laura E McCoy, Mohamed El Khattabi, C Theo Verrips, Robin A Weiss, Dorothy M Duffy, Winfried Weissenhorn, Rachel A McKendry
Preventing the spread of infectious diseases remains an urgent priority worldwide, and this is driving the development of advanced nanotechnology to diagnose infections at the point of care. Herein, we report the creation of a library of novel nanobody capture ligands to detect p24, one of the earliest markers of HIV infection. We demonstrate that these nanobodies, one tenth the size of conventional antibodies, exhibit high sensitivity and broad specificity to global HIV-1 subtypes. Biophysical characterization indicates strong 690 pM binding constants and fast kinetic on-rates, 1 to 2 orders of magnitude better than monoclonal antibody comparators...
July 14, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28556627/a-mathematical-model-to-predict-hiv-virological-failure-and-elucidate-the-role-of-lymph-node-drug-penetration
#8
S Sanche, N Sheehan, T Mesplède, M A Wainberg, J Li, F Nekka
Preventing virological failure following HIV treatment remains a difficult task that is further complicated by the emergence of drug resistance. We have developed a mathematical model able to explain and predict HIV virological outcomes for various compounds and patients' drug intake patterns. Compared to current approaches, this model considers, altogether, drug penetration into lymph nodes, a refined adherence representation accounting for the propensity for long drug holidays, population pharmacokinetic and pharmacodynamic variability, drug interaction, and crossresistance...
May 27, 2017: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/28482272/screening-of-commercial-cyclic-peptide-conjugated-to-hiv-1-tat-peptide-as-inhibitor-of-n-terminal-heptad-repeat-glycoprotein-2-ectodomain-ebola-virus-through-in-silico-analysis
#9
Usman Sumo Friend Tambunan, Ahmad Husein Alkaff, Mochammad Arfin Fardiansyah Nasution, Arli Aditya Parikesit, Djati Kerami
Ebola Hemorrhagic Fever (EHF) is a disease caused by viruses from genus Ebolavirus. Zaire ebolavirus (EBOV) is the deadliest species which has 76% case fatality rate. Up until now, there is no U.S. Food and Drug Administration (FDA) approved drugs to treat EHF. Antiviral drug based on EBOV N-terminal heptad repeat glycoprotein-2 (NHR GP2) Ectodomain inhibitor is one kind of treatment that has not well developed. NHR GP2 Ectodomain has an important role in the process of EBOV entry into the cell through endocytosis mechanism...
April 21, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28472201/predicting-hiv-1-transmission-and-antibody-neutralization-efficacy-in-vivo-from-stoichiometric-parameters
#10
Oliver F Brandenberg, Carsten Magnus, Peter Rusert, Huldrych F Günthard, Roland R Regoes, Alexandra Trkola
The potential of broadly neutralizing antibodies targeting the HIV-1 envelope trimer to prevent HIV-1 transmission has opened new avenues for therapies and vaccines. However, their implementation remains challenging and would profit from a deepened mechanistic understanding of HIV-antibody interactions and the mucosal transmission process. In this study we experimentally determined stoichiometric parameters of the HIV-1 trimer-antibody interaction, confirming that binding of one antibody is sufficient for trimer neutralization...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28442262/an-integrated-chemical-biology-approach-reveals-the-mechanism-of-action-of-hiv-replication-inhibitors
#11
Nicholas Pagano, Peter Teriete, Margrith E Mattmann, Li Yang, Beth A Snyder, Zhaohui Cai, Marintha L Heil, Nicholas D P Cosford
Continuous flow (microfluidic) chemistry was employed to prepare a small focused library of dihydropyrimidinone (DHPM) derivatives. Compounds in this class have been reported to exhibit activity against the human immunodeficiency virus (HIV), but their molecular target had not been identified. We tested the initial set of DHPMs in phenotypic assays providing a hit (1i) that inhibited the replication of the human immunodeficiency virus HIV in cells. Flow chemistry-driven optimization of 1i led to the identification of HIV replication inhibitors such as 1l with cellular potency comparable with the clinical drug nevirapine (NVP)...
April 8, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28399797/a-machine-learning-approach-for-viral-genome-classification
#12
Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani, Abdoulaye Baniré Diallo
BACKGROUND: Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28392143/development-of-a-dna-vaccine-expressing-a-secreted-hiv-1-gp41-ectodomain-that-includes-the-membrane-proximal-external-region
#13
Luca Melnychuk, Lara Ajamian, Patrick Jean-Pierre, Jiaming Liang, Romina Gheorghe, Mark A Wainberg, Gerasimos J Zaharatos
A limited number of sites on the HIV-1 Envelope protein are vulnerable to broadly neutralizing antibodies (bnAbs). One of these sites, the membrane proximal external region (MPER), is located at the C-terminus of the gp41 ectodomain (gp41ecto). This highly conserved sequence is bound by several well-characterized bnAbs. Efforts to produce a gp41 immunogen are in part hampered by the MPER's hydrophobicity and propensity to induce aggregation. We sought to produce a DNA vaccine expressing a gp41ecto that is both secreted from mammalian cells and maintains binding by bnAbs to the MPER...
May 9, 2017: Vaccine
https://www.readbyqxmd.com/read/28341614/anti-tubercular-drug-discovery-in-silico-implications-and-challenges
#14
REVIEW
Rukmankesh Mehra, Inshad Ali Khan, Amit Nargotra
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them...
June 15, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28303346/high-throughput-sequencing-identifies-hiv-1-replication-and-latency-related-mirnas-in-cd4-t-cell-lines
#15
Xiangyun Lu, Jin Yang, Haibo Wu, Zongxing Yang, Changzhong Jin, Juan Wang, Linfang Cheng, Xiaorong Peng, Fumin Liu, Xiuming Peng, Sujing Ji, Huilin Ou, Tiansheng Xie, Hangping Yao, Nanping Wu
MicroRNAs are potent gene expression regulators involved in regulating various biological processes, including host-pathogen interactions. In this study, we used high-throughput sequencing to investigate cellular miRNA signatures related to HIV-1 replication and latent infection in CD4(+) T cell lines, which included HIV-1-replicating H9/HTLV-IIIB, HIV-1-latently-infected CEM-Bru cells, and their parental uninfected H9 and CEM-SS cells. Relatively few miRNAs were found to be modulated by HIV-1 replication or latent infection, while the cell-lineage-specific miRNA difference was more pronounced, irrespective of HIV-1 infection...
July 2017: Archives of Virology
https://www.readbyqxmd.com/read/28294572/n-hydroxy-substituted-2-aryl-acetamide-analogues-a-novel-class-of-hiv-1-integrase-inhibitors
#16
Utsab Debnath, Prachi Kumar, Aakanksha Agarwal, Ajay Kesharwani, Satish K Gupta, Seturam B Katti
An in silico method has been used to discover N-hydroxy substituted 2-aryl acetamide analogues as a new class of HIV-1 integrase inhibitors. Based on the molecular requirements of the binding pocket of catalytic active site, two molecules (compounds 2 and 4b) were designed as fragments. These were further synthesized and biologically evaluated. In vitro potency along with docking studies highlighted compound 4b as an active fragment which was further used to synthesize new leads as HIV-1 integrase inhibitors...
March 13, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28236450/evaluation-of-4-thiazolidinone-derivatives-as-potential-reverse-transcriptase-inhibitors-against-hiv-1-drug-resistant-strains
#17
Rahul Suryawanshi, Sushama Jadhav, Nandini Makwana, Dipen Desai, Devidas Chaturbhuj, Archana Sonawani, Susan Idicula-Thomas, Vanangamudi Murugesan, Seturam B Katti, Srikanth Tripathy, Ramesh Paranjape, Smita Kulkarni
Rapid emergence of drug resistance is crucial in management of HIV infection limiting implementation of efficacious drugs in the ART regimen. Designing new molecules against HIV drug resistant strains is utmost essential. Based on the anti-HIV-1 activity, we selected four 4-thiazolidinone derivatives (S009-1908, S009-1909, S009-1911, S009-1912) and studied their interaction with reverse transcriptase (RT) from a panel of 10 clinical isolates (8 nevirapine resistant and two susceptible) using in silico methods, and inhibition pattern using in vitro cell based assays...
April 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28197631/repositioning-of-amprenavir-as-a-novel-extracellular-signal-regulated-kinase-2-inhibitor-and-apoptosis-inducer-in-mcf-7-human-breast-cancer
#18
Wenchun Jiang, Xin Li, Tongyu Li, Hailian Wang, Wei Shi, Ping Qi, Chunyang Li, Jie Chen, Jinku Bao, Guodong Huang, Yi Wang
Computational drug repositioning by virtually screening existing drugs for additional therapeutic usage could efficiently accelerate anticancer drug discovery. Herein, a library of 1447 Food and Drug Administration (FDA)-approved small molecule drugs was screened in silico for inhibitors of extracellular signal-regulated kinase 2 (ERK2). Then, in vitro kinase assay demonstrated amprenavir, a HIV-1 protease inhibitor, as a potential kinase inhibitor of ERK2. The in vivo kinase assay indicated that amprenavir could inhibit ERK2-mediated phosphorylation of BimEL at Ser69...
March 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28097165/in-silico-comparison-of-iranian-hiv-1-envelop-glycoprotein-with-five-nearby-countries
#19
Maryam Ghafari, Mandana Behbahani, Hassan Mohabatkar
HIV-1 envelope (env) glycoprotein mediates an important role in entry of the virus into the susceptible target cells. As env glycoprotein of HIV-1 is highly variable in the different geographical regions, in the present study, different properties of this protein in Iran are compared with five nearby countries. The sequences of HIV-1 env glycoproteins of Iran, Afghanistan, Russia, Turkey, Pakistan and Saudi Arabia databases were collected from databases. Amino acid composition and physical and chemical properties of the proteins from these countries were studied using Protparam and COPid tools...
June 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28069446/rich2-is-implicated-in-viraemic-control-of-hiv-1-in-black-south-african-individuals
#20
Maria Paximadis, Refilwe N Ngqobe, Richard E Chaisson, Neil A Martinson, Caroline T Tiemessen
An intronic single nucleotide polymorphism (SNP) in RICH2 (rs2072255; 255(i)), in complete linkage disequilibrium (LD) with an exonic SNP (rs2072254; 254(e)), has been identified in a genome wide association study to be associated with progression to AIDS in Caucasian individuals. RICH2 links tetherin to the cortical actin network and the RICH2/tetherin interaction has been shown to be important for the downstream activation of NF-κβ and the consequential promotion of proinflammatory responses. We investigated the role of these two SNPs in natural control of HIV-1 in black South Africans including healthy controls (HCs; N=102) and antiretroviral-naive HIV-1-infected controllers (HICs; N=52) and progressors (N=74)...
April 2017: Infection, Genetics and Evolution
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