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Current Computer-aided Drug Design

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https://www.readbyqxmd.com/read/27903217/rational-drug-discovery-of-hcv-helicase-inhibitor-improved-docking-accuracy-with-multiple-seedings-of-autodock-vina-and-in-situ-minimization
#1
SeeKhai Lim, Rozana Othman, Rohana Yusof, ChoonHan Heh
BACKGROUND: Hepatitis C is a significant cause for end-stage liver diseases and liver transplantation which affects approximate 3% of the global populations. Despite the present of several direct antiviral agents in the treatment of hepatitis C, the standard treatment for HCV is accompanied by several drawbacks such as adverse side effects, high pricing of medications and the rapid emerging rate of resistant HCV variants. OBJECTIVES: To discover potential inhibitors for HCV helicase through an optimized in silico approach...
November 30, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27897106/predicting-isoform-specific-binding-selectivities-of-benzenesulfonamides-using-qsar-and-3d-qsar
#2
Vytautas Raskevicius, Visvaldas Kairys
BACKGROUND: Design of isoform-specific inhibitors is a major challenge in the new therapeutic agents development. METHODS: The article describes the development of a robust selectivity for CA XII QSAR and 3D-QSAR models of 40 benzenesulfonamide derivatives bearing pyrimidine moieties using PHASE module of Schrödinger for 3D-QSAR or E-DRAGON and R software for 2D-QSAR. Two QSAR protocols were explored: traditional (affinity) and selectivity (affinity ratio) based...
November 29, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27890013/in-silico-characterization-of-a-hypothetical-protein-rv1288-of-mycobacterium-tuberculosis-containing-an-esterase-signature-and-an-uncommon-lyte-domain
#3
Arbind Kumar, Pratibha Maan, Gurpreet Singh, Jagdeep Kaur
BACKGROUND: Death toll due to tuberculosis is still rising day by day. Whole genome sequence of Mycobacterium tuberculosis has provided a platform to conduct research in order to identify the probable drug target. OBJECTIVES: Out of 4000 gene products of M. tuberculosis, approximately 40% of proteins are annotated as hypothetical. Identifying and characterizing these proteins could provide a new prescriptive for developing new TB drugs. Rv1288, a protein of M. tuberculosis H37Rv has been annotated as a hypothetical protein in database...
November 24, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27781937/a-new-computational-approach-to-the-classification-of-fluoroquinolones-according-to-the-biopharmaceutical-classification-system
#4
Kłosińska-Szmurło Ewa, Mazurek Aleksander Paweł, Grudzień Monika, Betlejewska-Kielak Katarzyna
BACKGROUND: Two main factors, which have an influence on oral absorption from solid, immediate release dosage form, are solubility and permeability. These are considered the main fundamental properties that govern the rate and extent of oral absorption. The significance of these properties has been highlighted in the Biopharmaceutics Classification System (BCS). OBJECTIVE: The concept of this paper was to predict the solubility and permeability of fluoroquinolones using in silico methods based on the assumptions of the BCS...
October 14, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27748170/screening-of-potential-lead-molecule-as-novel-mure-inhibitor-virtual-screening-molecular-dynamics-and-in-vitro-studies
#5
Kunal Zaveri, Kiranmayi Patnala
BACKGROUND: The prevalence of multi-drug resistance S. aureus is one most challenging task for treatment of nosocomial infections. Proteins and enzymes of peptidoglycan biosynthesis pathway are one among the well-studied targets, but many of the enzymes are unexplored as targets. MurE is one such enzyme featured to be a promising target. As MurE plays an important role in ligating the L-lys to stem peptide at third position that is crucial for peptidoglycan synthesis. OBJECTIVE: To screen the potential MurE inhibitor...
October 10, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27719631/understanding-the-action-of-indolizines-as-biologically-active-moieties-a-molecular-dynamics-study
#6
Mircea V Diudea, Beata Szefler, Przemysław Czeleń
BACKGROUND: Indolizines represent a class of heteroaromatic compounds, of pharmacological importance, containing two condensed 5- and 6-memebered rings bridged by a nitrogen atom. Despite indolizine is an important medicinal moiety, a detailed view on the mechanism of action of biologically active indolizines is unavailable. OBJECTIVE: The study of ligand-enzyme affinity is of high interest; description of characteristics (energetic and geometric ones) of ligand binding to the active sites of an enzyme could be useful in understanding the action mechanism of a given ligand on the concerned enzyme...
October 4, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27682644/editorial-spilled-over-emerging-infectious-diseases-necessitate-an-accelerated-drug-design-and-discovery-program-some-comments-with-special-reference-to-chemoinformatics-and-the-current-zika-virus-crisis
#7
Apurba K Bhattacharjee, Subhash C Basak
No abstract text is available yet for this article.
September 27, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27654309/lemont-b-kier-art-science-and-green-cheese
#8
Guillermo Restrepo
No abstract text is available yet for this article.
September 20, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27632987/molecular-modeling-investigation-of-some-new-2-mercaptoimidazoles
#9
Nidhi Rani Prajapat, Randhir Singh
Molecular docking study has become a standard tool for the investigation of drug- receptor interaction. In the present study 18 new imidazole derivatives having mercapto group (4a-r) were synthesized. Structures of the newly synthesized compounds were characterized by spectral studies. Compounds were screened for their antimicrobial potency. Compounds 4j and 4k were found to be the most potent compounds of the series against al the tested strains with MIC ranging from 2-8µg/ml. All the compounds were subjected to molecular docking studies for the inhibition of the enzyme 14α-demethylase...
September 15, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27632988/computational-analysis-of-physicochemical-factors-driving-cyp2d6-ligand-interaction
#10
Olujide Oludayo Olubiyi, Maryam O Olagunju, Abiola O Obisesan
The metabolic action of CYP2D6 remains a crucial factor influencing the therapeutic outcomes for some drug molecules while others are largely or only slightly affected. To understand the basis for the metabolic discrimination, the structural and physicochemical details of its interaction with established drug substrates were investigated at atomistic resolution. The otherwise relatively extensive binding surface was found to present subtle but important topological features that explain the enzyme's highly efficient capability for processing diverse chemical classes of drugs and endogenous substrates...
September 8, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27600878/exploring-intrinsic-dimensionality-of-chemical-spaces-for-robust-qsar-model-development-a-comparison-of-several-statistical-approaches
#11
Subhabrata Majumdar, Subhash C Basak
Background- Computed mathematical descriptors of molecules are used for the prediction of their property/ bioactivity. In the 1970s only a few descriptors could be calculated, currently available software can calculate a large number of descriptors for molecules or biomolecules like DNA/ RNA, proteins. Objective- When p molecular descriptors are calculated for n molecules, the data set can be viewed as n vectors in p dimensions, each chemical being represented as a point in R^p. Because many of the descriptors are strongly correlated, the n points in R^p will lie on a subspace of dimension lower than p...
September 6, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27600879/rational-design-and-engineering-of-a-mutant-variant-of-urate-oxidase-as-a-therapeutic-enzyme-a-molecular-dynamics-simulation-approach
#12
Sajjad Ahrari, Fatemeh Dabbagh, Sobhan Ahrari, Younes Ghasemi, Navid Mogharrab, Yasser Riazalhosseini
BACKGROUND: Urate oxidase is absent in humans so the enzyme is considered as an important therapeutic agent to control hyperuricemic disorders. Currently available enzymes with pharmaceutical applications have adverse effects associated with allergic reactions and anaphylactic shocks, in case of chronic treatment. Therefore, developing variant forms of the enzyme, with lower immunogenicity and similar or higher activity, is of great importance. AIM: Here, we tried to improve the structure of a recently resurrected ancestral mammalian urate oxidase (which is claimed to have higher enzymatic activity compared to other mammalian counterparts) by introducing eight rational mutations and verified the consequence of these mutations on immunogenicity, stability and the affinity of protein to uric acid by computational techniques...
September 5, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27585602/design-of-novel-chemotherapeutic-agents-targeting-checkpoint-kinase-1-using-3d-qsar-modeling-and-molecular-docking-methods
#13
Anand Balupuri, Pavithra K Balasubramanian, Seung Joo Cho
BACKGROUND: Checkpoint kinase 1 (Chk1) has emerged as a potential therapeutic target for design and development of novel anticancer drugs. OBJECTIVE: Herein, we have performed three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking analyses on a series of diazacarbazoles to design potent Chk1 inhibitors. METHODS: 3D-QSAR models were developed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques...
September 1, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27559000/mathematical-nanotoxicoproteomics-quantitative-characterization-of-effects-of-multi-walled-carbon-nanotubes-mwcnt-and-tio2-nanobelts-tio2-nb-on-protein-expression-patterns-in-human-intestinal-cells
#14
Subhash Basak, Marjan Vracko, Frank A Witzmann
BACKGROUND: Various applications of nanosubstances in industrial and consumer goods sectors are growing rapidly because of their useful chemical and physical properties. OBJECTIVES: Assessment of hazard posed by exposure to nanosubstances is essential for the protection of human and ecological health. METHODS: We analyzed the proteomics patterns of Caco-2/HT29-MTX cells in co-culture exposed for three and twenty four hours to two kinds of nanoparticles: multi-walled carbon nanotubes (MWCNT) and TiO2 nanobelts (TiO2-NB)...
August 24, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27503744/proton-hopping-as-the-nerve-conduction-message
#15
Lemont B Kier
A new theory has emerged in the recent literature proposing a mechanism of the transfer of information along a neuron. The method of this transfer is proposed to be proton hopping through water present in all parts of a nerve system. A series of studies, considering this process have been published and are reviewed here.
August 7, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27457083/nerve-conduction-through-dendrites-via-proton-hopping
#16
Lemont B Kier
Our previous studies of the role of proton hopping in nerve conduction have dealt with the axon, soma, synapse, and nodes of Ranvier. We complete the study and application of the theory of proton hopping being the system of nerve conduction by examining the dendrites and their accompanying spines as they function within the nerve system. The role of proton hopping continues to be a very probable mechanism within this intermediate system linking two nerves at the synapse.
July 25, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27449897/screening-and-in-vitro-evaluation-of-potential-plasmodium-falciparum-leucyl-aminopeptidase-inhibitors
#17
Meenakshi Chaudhary, Vineeta Singh, Anup R Anvikar, Shakti Sahi
Plasmodium falciparum leucyl aminopeptidase (PfA-M17) regulates the intracellular pool of amino acids required for the growth and development of parasites. Thus, PfA-M17 is a promising target for anti-malarial drug development. In the present study, structure-based drug design was used to identify novel PfA-M17 inhibitors, which were subsequently validated by in vitro PfA-M17 and human LAP3 enzyme inhibition assay. A library of 3,147,882 compounds was screened using receptor-based virtual screening against the active site of PfA-M17, and three levels of accuracy were used: high-throughput virtual screening, grid-based ligand docking with energetics (Glide) standard precision and Glide extra precision...
July 22, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27439721/quantitative-analysis-of-essential-molecular-features-of-coumarin-derivatives-with-antioxidant-activity-using-chemometric-tools
#18
Biplab De, Indrani Adhikari, Ashis Nandy, Achintya Saha, Binoy Behari Goswami
BACKGROUND: The endogeneous antioxidant mechanism often fails to combat the huge free radical overload necessitating external antioxidant supplementation. Thus identification and definite structural manipulation of the naturally available antioxidant derivatives using in silico methodology helps in design of new moieties with improved therapeutic potential. OBJECTIVE: The present work has been performed with the aim to identify the essential molecular fragments that contribute to the antioxidant property of the coumarin derivatives...
July 21, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27439722/withdrawn-identification-of-inhibitors-for-the-lutheran-blood-group-glycoprotein-laminin-511-521-interaction-by-molecular-modeling-and-simulation-techniques
#19
Noelly Madeleine, Fabrice Gardebien
Ahead of Print article withdrawn by publisher
July 18, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27412704/a-computational-model-for-docking-of-noncompetitive-neuraminidase-inhibitors-and-probing-their-binding-interactions-with-neuraminidase-of-influenza-virus-h5n1
#20
Anand S Chintakrindi, Elvis A F Martis, Devanshi J Gohil, Sweta T Kothari, Abhay S Chowdhary, Evans C Coutinho, Meena A Kanyalkar
With cases of emergence of drug resistance to the current competitive inhibitors of neuraminidase (NA) such as oseltamivir and zanamavir, there is a present need for an alternative approach in the treatment of avian influenza. With this in view, some flavones and chalcones were designed based on quercetin, the most active naturally occurring noncompetitive inhibitor. Molecular docking was used as a tool to filter out the flavones and chalcones. This yielded two compounds i.e., 4'-methoxyflavone and 2'-hydroxy-4-methoxychalcone, as promising leads...
July 13, 2016: Current Computer-aided Drug Design
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