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Current Computer-aided Drug Design

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
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
Apurba K Bhattacharjee, Subhash C Basak
No abstract text is available yet for this article.
September 27, 2016: Current Computer-aided Drug Design
Guillermo Restrepo
No abstract text is available yet for this article.
September 20, 2016: Current Computer-aided Drug Design
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
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
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
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
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
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
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
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
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
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
Noelly Madeleine, Fabrice Gardebien
BACKGROUND: Drepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal, rigid, sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran strongly interacts with the Laminin 511/521. The aim of this study is to identify a PPI inhibitor with a high probability of binding to Lutheran for the inhibition of the Lutheran-Laminin 511/521 interaction...
July 18, 2016: Current Computer-aided Drug Design
Anand S Chintakrindi, Elvis A F Martis, Devanshi J Gohil, Sweta T Kothari, Abhay S Chowdhary, Evans C Coutinho, Meena A Kanyalkar
A computational model was developed using molecular docking methodology coupled with molecular dynamics simulation to study the binding pattern of noncompetitive inhibitors of neuraminidase (NA). Few naturally occurring NA noncompetitive inhibitors were docked in the regulatory site of H5N1-NA and the binding interactions of endogenous ligand sialic acid in the active site was probed using molecular dynamics (MD) studies. Docking and MD simulation studies demonstrated that the sialic acid was docked in non-native pose owing to change in active site...
July 13, 2016: Current Computer-aided Drug Design
S Sugunakala, S Selvaraj
BACKGROUND: Epidermal Growth Factor Receptor tyrosine kinase (EGFR) is an important anticancer drug target. Series of pyridopyrimidine analogs have been reported as EGFR inhibitors and they inhibit by binding to the ATP binding pocket of the tyrosine kinase domain. OBJECTIVE: To identify key properties of pyridopyrimidine analogs involved in the inhibition of the EGFR protein tyrosine kinase by developing 2D QSAR model. METHODS: Variable selection was performed by least absolute shrinkage and selection operator (LASSO) method and multiple linear regression (MLR) method was applied by using Build QSAR software to develop QSAR model...
June 6, 2016: Current Computer-aided Drug Design
Ankita Sharma, Sagarika Biswas, G Soundhara Rajan, Rupsi Kharb
Chlamydia pneumoniae (C. pneumoniae) is a pathogen associated with respiratory tract infection of humans and its viable presence in atherosclerotic plaques is also assumed to play significant function in cardiac diseases. Unavailability of effective antimicrobial drugs has implicated the urgent need of some more disease associated vaccines that may provide relief efficiently. Thus, present study has been undertaken to analyse the whole proteome of C. pneumoniae in order to propose bacterial proteins as candidate vaccine for CAD by taking the aid of 'Reverse Vaccinology'...
May 26, 2016: Current Computer-aided Drug Design
Dwaipayan Sen, Subhadeep Dasgupta, Indrajit Pal, Smarajit Manna, Subhash C Basak, Ashesh Nandy, Gregory D Grunwald
The formulation of a large number of alignment-free techniques of graphical representation and numerical characterization (GRANCH) of bio-molecular sequences necessitate an assessment of the relative efficacy of these methods in determining the degree of similarities and dissimilarities of such sequences. We have undertaken a study on this issue and report here preliminary results on analysis of a selected number of different GRANCH techniques. We find that some of these are strongly correlated implying a commonality of structural information encoded by them while others are distinctly separate...
May 25, 2016: Current Computer-aided Drug Design
Sagarika Sahoo, Chandana Adhikari, Minati Kuanar, Bijay K Mishra
Graph theory has a significant role in encoding the chemical structures to numerical values, which has a broad application in drug designing and quantitative structure property/activity (QSP/AR) relationships. With the evolution of technology chemical science has been swarming of data for which further codification and classification is necessary. In this work, the molecular descriptors developed with time are classified in to different categories based on their genesis with their application in QSP/AR study...
May 25, 2016: Current Computer-aided Drug Design
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