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HIV in silico

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https://www.readbyqxmd.com/read/29928568/sulfonated-compounds-bind-with-prostatic-acid-phosphatase-pap-248-286-to-inhibit-the-formation-of-amyloid-fibrils
#1
Tingting Zhang, Haikui Yang, Zichao Yang, Suiyi Tan, Jiabin Jin, Shuwen Liu, Jiajie Zhang
The peptide segment of prostatic acid phosphatase (PAP248-286 ) aggregates to form SEVI (semen-derived enhancer of virus infection) amyloid fibrils. These are characteristic seminal amyloids that have the ability to promote the effect of HIV infection. In this paper, we explore the binding of sulfonated compounds with PAP248-286 through an in silico study. Three derivatives of suramin, NF110, NF279, and NF340, are selected. All of these sulfonated molecules bind to PAP248-286 and alter the conformation of the peptide, even though they have various structures, sizes, and configurations...
June 2018: ChemistryOpen
https://www.readbyqxmd.com/read/29847134/predicting-binding-free-energies-in-a-large-combinatorial-chemical-space-using-multisite-lambda-dynamics
#2
Jonah Z Vilseck, Kira A Armacost, Ryan Lee Hayes, Garrett B Goh, Charles L Brooks
In this study, we demonstrate the extensive scalability of the biasing potential replica exchange multisite λ-dynamics (BP-REX MSλD) free energy method by calculating binding affinities for 512 inhibitors to HIV Reverse Transcriptase (HIV-RT). This is the largest exploration of chemical space using free energy methods known to date, requires only a few simulations, and identifies 55 new inhibitor designs against HIV-RT predicted to be at least as potent as a tight binding reference compound (i.e., as potent as 56 nM)...
May 30, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29766800/antifungal-activity-gas-chromatographic-mass-spectrometric-analysis-and-in-silico-study-of-punica-granatum-peel-extracts-against-fluconazole-resistant-strains-of-candida-species
#3
Sony Paul, M Kalyani, I Kannan
AIMS: Candida species is the common cause of opportunistic fungal infections all over the world with increased mortality and morbidity especially in immunosuppressed patients. Fluconazole is the first line therapy for candidiasis. The antifungal resistance pattern in high-risk patients is a major concern. The present study was aimed to assess the anticandidal activity of Punica granatum peel against fluconazole resistant Candida species isolated from HIV patients. MATERIALS & METHODS: Ethanol, chloroform, petroleum ether and aqueous extracts of the peel of P...
May 14, 2018: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/29705491/structural-discordance-in-hiv-1-vpu-from-brain-isolate-alarms-amyloid-fibril-forming-behavior-a-computational-perspective
#4
Patil Sneha, Pritam Kumar Panda, Fatemeh Rahimi Gharemirshamlu, Kourosh Bamdad, Seetharaman Balaji
HIV-1 being the most widespread type worldwide, its accounts for almost 95% of all infections including HIV associated dementia (HAD) that triggers neurological dysfunction and neurodegeneration in patients. The common features associated with HAD and other neurodegenerative diseases are accumulation of amyloid plaques, neuronal loss and deterioration of cognitive abilities, amongst which amyloid fibrillation is considered to be a hallmark. The success of effective therapeutics lies in the understanding of mechanisms leading to neurotoxicity...
August 14, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29686657/naphthoquinone-derivatives-as-scaffold-to-develop-new-drugs-for-tuberculosis-treatment
#5
Priscila C B Halicki, Laís A Ferreira, Kelly C G De Moura, Paula F Carneiro, Karina P Del Rio, Tatiane Dos S C Carvalho, Maria do C F R Pinto, Pedro E A da Silva, Daniela F Ramos
Despite being a curable disease, tuberculosis (TB) remains a public health problem worldwide mainly due to lengthy treatment, as well as its toxic effects, TB/HIV co-infection and the emergence of resistant Mycobacterium tuberculosis strains. These barriers reinforcing the need for development of new antimicrobial agents, that ideally should reduce the time of treatment and be active against susceptible and resistant strains. Quinones are compounds found in natural sources and among them, the naphthoquinones show antifungal, antiparasitic, and antimycobacterial activity...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29651941/identification-of-adjacent-nnrti-binding-pocket-in-multi-mutated-hiv1-rt-enzyme-model-an-in-silico-study
#6
R F Kamil, U Debnath, S Verma, Y S Prabhakar
Introduction: A possible strategy to combat mutant strains is to have a thorough structural evaluation before and after mutations to identify the diversity in the non-nucleoside inhibitor binding pocket and their effects on enzyme-ligand interactions to generate novel NNRTI’s accordingly. Objective: The primary objective of this study was to find effects of multiple point mutations on NNRTI binding pocket. This study included the contribution of each individual mutation in NNIBP that propose an adjacent binding pocket which can be used to discover novel NNRTI derivatives...
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
#7
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
#8
Jagadeesan 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 in neonatals and also increase the transmission of HIV. Acyclovir is widely used drug to treat HSV-2 infection but it 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
#9
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
#10
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...
April 19, 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
#11
Carlos Guerrero-Beltran, Ignacio Rodriguez-Izquierdo, Ma Jesus Serramia, Ingrid Araya-Durán, Valeria Márquez-Miranda, Rafael Gomez, Francisco Javier de la Mata, Manuel Leal, Fernando González-Nilo, M Angeles Muñoz-Fernández
Cell-to-cell transmission is the most effective pathway for the spread of human immunodeficiency virus (HIV-1). Infected cells expose virus-encoded fusion proteins on their surface as a consequence of HIV-1 replicative cycle that interacts with noninfected cells through CD4 receptor and CXCR4 coreceptor leading to the formation of giant multinucleated cells known as syncytia. Our group previously described the potent activity of dendrimers against CCR5-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...
May 16, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29567319/in-silico-design-of-mycobacterium-tuberculosis-epitope-ensemble-vaccines
#12
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...
May 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
#13
(no author information available yet)
No abstract text is available yet for this article.
March 20, 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
#14
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
#15
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...
April 1, 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
#16
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
#17
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 < ...
March 2018: Virology
https://www.readbyqxmd.com/read/29414440/induction-of-broadly-neutralizing-antibodies-in-germinal-centre-simulations
#18
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
#19
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
#20
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
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