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HIV in silico

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https://www.readbyqxmd.com/read/28399797/a-machine-learning-approach-for-viral-genome-classification
#1
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
#2
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...
April 6, 2017: Vaccine
https://www.readbyqxmd.com/read/28341614/anti-tubercular-drug-discovery-in-silico-implications-and-challenges
#3
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...
March 21, 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
#4
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...
March 16, 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
#5
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
#6
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...
February 15, 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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28062682/genome-wide-association-study-of-nevirapine-hypersensitivity-in-a-sub-saharan-african-hiv-infected-population
#10
Daniel F Carr, Stephane Bourgeois, Mas Chaponda, Louise Y Takeshita, Andrew P Morris, Elena M Cornejo Castro, Ana Alfirevic, Andrew R Jones, Daniel J Rigden, Sam Haldenby, Saye Khoo, David G Lalloo, Robert S Heyderman, Collet Dandara, Elizabeth Kampira, Joep J van Oosterhout, Francis Ssali, Paula Munderi, Giuseppe Novelli, Paola Borgiani, Matthew R Nelson, Arthur Holden, Panos Deloukas, Munir Pirmohamed
Background: The antiretroviral nevirapine is associated with hypersensitivity reactions in 6%-10% of patients, including hepatotoxicity, maculopapular exanthema, Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Objectives: To undertake a genome-wide association study (GWAS) to identify genetic predisposing factors for the different clinical phenotypes associated with nevirapine hypersensitivity. Methods: A GWAS was undertaken in a discovery cohort of 151 nevirapine-hypersensitive and 182 tolerant, HIV-infected Malawian adults...
April 1, 2017: Journal of Antimicrobial Chemotherapy
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
#11
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...
January 2017: 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
#12
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...
January 1, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27844017/design-of-new-potent-htlv-1-protease-inhibitors-in-silico-study
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B Smith, Irwin Chaiken, Cameron F Abrams
Small-molecule CD4 mimics (SMCM's) bind to the 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...
October 24, 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
#20
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
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