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HIV in silico

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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
#1
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
https://www.readbyqxmd.com/read/29136775/high-parathyroid-hormone-concentration-in-tenofovir-treated-patients-are-due-to-inhibition-of-calcium-sensing-receptor-activity
#2
Alessandra Mingione, Katia Maruca, Federica Chiappori, Francesca Pivari, Caterina Brasacchio, Tiziana Quirino, Ivan Merelli, Laura Soldati, Paolo Bonfanti, Stefano Mora
Bone health impairment is a common finding in HIV-infected patients on antiretroviral treatment. High serum parathyroid hormone (PTH) concentration in patients on antiretroviral treatment containing tenofovir disoproxil fumarate (TDF) has been reported. Hyperparathyroidism was not always sustained by a reduction in vitamin D concentration. We thus hypothesized a direct inhibitory effect of TDF on the Calcium-sensing receptor (CaSR), leading to hyperparathyroidism. Human embryonic kidney cells were transfected with CASR wild-type gene or mutated in different sites (N124K, T1051G, C788T, T888M)...
November 7, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29135580/wake-me-up-before-you-go-a-strategy-to-reduce-the-latent-hiv-reservoir
#3
Nicolas Chomont, Afam A Okoye, David Favre, Lydie Trautmann
: In the quest to eliminate or reduce the HIV reservoir, shock and kill strategies require the combined administration of a latency reversing agent (LRA) to reactivate the latent reservoir and an intervention to boost effector functions to clear this reservoir. Both parts of this strategy are quite inefficient when LRAs are administered to HIV-infected individuals on suppressive ART for several years, possibly due to low levels of induced antigen expression, negative impact of LRAs on clearance mechanisms, and very low number of effective cytotoxic T cells (CTLs)...
November 10, 2017: AIDS
https://www.readbyqxmd.com/read/29117524/cholesterol-promotes-protein-binding-by-affecting-membrane-electrostatics-and-solvation-properties
#4
Milka Doktorova, Frederick A Heberle, Richard L Kingston, George Khelashvili, Michel A Cuendet, Yi Wen, John Katsaras, Gerald W Feigenson, Volker M Vogt, Robert A Dick
Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29068470/aspartate-%C3%AE-semialdeyhyde-dehydrogenase-as-a-potential-therapeutic-target-of-mycobacterium-tuberculosis-h37rv-evidence-from-in-silico-elementary-mode-analysis-of-biological-network-model
#5
Saif Khan, Pallavi Somvanshi, Tulika Bhardwaj, Raju K Mandal, Sajad A Dar, Mohd Wahid, Arshad Jawed, Mohtashim Lohani, Mahvish Khan, Mohammed Y Areeshi, Shafiul Haque
The emergence of multi-drug resistant strains and co-occurrence of tuberculosis with HIV creates a major burden to the human health globally. Failure of primary antibacterial therapy necessitates the identification of new mycobacterial drugs. In this study, a comprehensive analysis involving bottom-up systems biology approach was applied wherein we have identified potential therapeutic targets of Mycobacterium tuberculosis infections. Our study prioritized M. tuberculosis therapeutic targets [aspartate-β-semialdeyhde dehydrogenase (ASD), dihydrodipicolinate reductase and diaminopimelate decarboxylase] based on flux and elementary mode analysis using direct mathematical modeling of the relevant metabolic pathways...
October 25, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28955936/is-unphosphorylated-rex-as-multifunctional-protein-of-htlv-1-a-fully-intrinsically-disordered-protein-an-in-silico-study
#6
Mitra Kheirabadi, Majid Taghdir
Intracellularlocation of a viral unspliced mRNA in host cell is a crucial factor for normal life of the virus. Rex is a neucleo-cytoplasmic shuffling protein of Human T-cell Leukemia Virus-1(HTLV-1)which has important role in active transport of cargo-containing RNA from nucleus to cytoplasm. Therefore, it plays a crucial role in the disease development by the virus. In spite of its importance, the 3d-structurephosphorylated and unphosphorylated of this protein has not been determined. In this study, first we predicted whether Rex protein is an ordered or disordered protein...
December 2016: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28940894/the-antiretroviral-nelfinavir-mesylate-a-potential-therapy-for-systemic-scleroderma
#7
Cecilia G Sanchez, Steven V Molinski, Rafael Gongora, Meredith Sosulski, Taylor Fuselier, Stephen S MacKinnon, Debasis Mondal, Joseph A Lasky
Transforming growth factor (TGF)-β1 is considered a key factor in fibrogenesis, and blocking TGF-β1 signaling pathways diminishes fibrogenesis in animal models. The objective of this study was to determine whether nelfinavir mesylate (NFV), a drug approved by the Food and Drug Administration (FDA) for treating HIV infection can be repurposed to treat pulmonary fibrosis in systemic scleroderma (SSc) METHODS: Normal human lung, ventricular, and skin fibroblasts, as well as lung fibroblasts from SSc patients, were used to determine the effects of NFV on fibroblast to myofibroblast differentiation (FMD) mediated by TGF-β1...
September 21, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28885709/prenylation-of-viral-proteins-by-enzymes-of-the-host-virus-driven-rationale-for-therapy-with-statins-and-ft-ggt1-inhibitors
#8
REVIEW
Ekaterina S Marakasova, Birgit Eisenhaber, Sebastian Maurer-Stroh, Frank Eisenhaber, Ancha Baranova
Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 (CMV) and few other proteins encoded by Herpesviridae, Nef (HIV-1), E1A (human adenovirus 1), NS5A (HCV), PB2 (influenza), HN (human parainfluenza virus 3), L83L (African swine fever), MC155R (molluscum contagiosum virus), other Poxviridae proteins, and some bacteriophages of human associated bacteria...
September 8, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28820066/mutational-impact-on-the-interaction-between-human-il27-and-gp130-in-silico-approach-for-defending-hiv-infection
#9
Arundhati Banerjee, Rakhi Dasgupta, Sujay Ray
INTRODUCTION: With advances in proteomics, it is essential to investigate the molecular-level participation of IL27 and gp130 to hinder HIV infection. Their interaction causes cell-cycle arrest in HIV+ cells by activating the receptor-associated JAK signaling and causing apoptosis of cancerous cells. METHODOLOGY: The best human wild-type WT_IL27 model was prepared after varied molecular modeling techniques. The vital tyrosine residues in WT_IL27 were identified, mutated and IL27 was re-modeled...
August 17, 2017: Current HIV Research
https://www.readbyqxmd.com/read/28809439/in-silico-profiling-of-the-biological-activities-of-amaryllidaceae-alkaloids
#10
Eman Shawky
OBJECTIVES: The large number of publications about Amaryllidaceae alkaloids reflects the abundance and variety in biological activity of these alkaloids. An in-silico approach was implemented in this work to rationalize the individual alkaloids to molecular biological activity. METHODS: A database was generated containing 313 Amaryllidaceae alkaloids which were then subjected to in-silico-validated structure-based virtual screening using extra precision (XP) approach of Glide docking program...
August 15, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28792504/common-gene-network-signature-of-different-neurological-disorders-and-their-potential-implications-to-neuroaids
#11
Vidya Sagar, S Pilakka-Kanthikeel, Paola C Martinez, V S R Atluri, M Nair
The neurological complications of AIDS (neuroAIDS) during the infection of human immunodeficiency virus (HIV) are symptomized by non-specific, multifaceted neurological conditions and therefore, defining a specific diagnosis/treatment mechanism(s) for this neuro-complexity at the molecular level remains elusive. Using an in silico based integrated gene network analysis we discovered that HIV infection shares convergent gene networks with each of twelve neurological disorders selected in this study. Importantly, a common gene network was identified among HIV infection, Alzheimer's disease, Parkinson's disease, multiple sclerosis, and age macular degeneration...
2017: PloS One
https://www.readbyqxmd.com/read/28780227/insights-into-the-immune-manipulation-mechanisms-of-pollen-allergens-by-protein-domain-profiling
#12
Seema Patel, Aruna Rani, Arun Goyal
Plant pollens are airborne allergens, as their inhalation causes immune activation, leading to rhinitis, conjunctivitis, sinusitis and oral allergy syndrome. A myriad of pollen proteins belonging to profilin, expansin, polygalacturonase, glucan endoglucosidase, pectin esterase, and lipid transfer protein class have been identified. In the present in silico study, the protein domains of fifteen pollen sequences were extracted from the UniProt database and submitted to the interactive web tool SMART (Simple Modular Architecture Research Tool), for finding the protein domain profiles...
July 29, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28756560/in-silico-analysis-of-the-cyanobacterial-lectin-scytovirin-new-insights-into-binding-properties
#13
Andrei Santos Siqueira, Alex Ranieri Jerônimo Lima, Rafael Conceição de Souza, Alberdan Silva Santos, João Lídio da Silva Gonçalves Vianez Júnior, Evonnildo Costa Gonçalves
Scytovirin is a lectin isolated from the cyanobacterium Scytonema varium that has shown activity against HIV, SARS coronavirus and Zaire Ebola virus. Its 95 amino acids are divided into two structural domains (SD), the first spanning amino acids 1-48 (SD1) and the second 49-95 (SD2). Interestingly, the domains are nearly identical but differ in their affinities for carbohydrates. With the aim of enhancing understanding of the binding properties of scytovirin, we performed molecular dynamics (MD) simulations of scytovirin complexed with Man4...
August 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28709077/phytonanotherapy-for-management-of-diabetes-using-green-synthesis-nanoparticles
#14
REVIEW
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...
August 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
#15
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...
August 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-antiretroviral-drug-combination-for-topical-prevention-of-colorectal-hiv-transmission
#16
Magda Swedrowska, Shirin Jamshidi, Abhinav Kumar, Charles Kelly, Khondaker 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 analyze the identified drug-transporter interaction more mechanistically. The transport of tenofovir, darunavir, and dapivirine was investigated in the Caco-2 cell models and colorectal tissue, and their apparent permeability coefficient (Papp), efflux ratio (ER), and the effect of transporter inhibitors were evaluated...
August 7, 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
#17
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
#18
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
#19
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...
September 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
#20
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
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