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RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules

J. Zaretzki, C. Bergeron, T.-w. Huang, P. Rydberg, S. J. Swamidass, C. M. Breneman
2012 Bioinformatics  
Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules.  ...  RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes.  ...  ACKNOWLEDGEMENT The authors thank Dr Michael Krein for systems support and the Rensselaer Center for Biotechnology and Interdisciplinary Studies (CBIS).  ... 
doi:10.1093/bioinformatics/bts705 pmid:23242264 pmcid:PMC3570214 fatcat:oeasseicizebzdo6sd4oe6ylfq

Curcumin Analogues as a Potential Drug against Antibiotic Resistant Protein, β-Lactamases and L, D-Transpeptidases Involved in Toxin Secretion in Salmonella typhi: A Computational Approach

Tanzina Akter, Mahim Chakma, Afsana Yeasmin Tanzina, Meheadi Hasan Rumi, Mst. Sharmin Sultana Shimu, Md. Abu Saleh, Shafi Mahmud, Saad Ahmed Sami, Talha Bin Emran
2021 BioMedInformatics  
The screened drug candidates were further evaluated in ADMET, and pharmacological properties along with positive drug-likeness properties were observed for these ligand molecules.  ...  A molecular modeling study of these targeted proteins was carried out by various methods, such as homology modeling, active site prediction, prediction of disease-causing regions, and by analyzing the  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biomedinformatics2010005 fatcat:sohnjftapraalgkxvr7qv3dcre

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics

Anastasia V. Rudik, Alexander V. Dmitriev, Alexey A. Lagunin, Dmitry A. Filimonov, Vladimir V. Poroikov
2016 Journal of Cheminformatics  
The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification.  ...  The prediction of the reacting atom(s) in a molecule for the major classes of biotransformation reactions is necessary to generate drug metabolites.  ...  The site of metabolism (SOM) refers to the site of a molecule where a metabolic reaction occurs [3] .  ... 
doi:10.1186/s13321-016-0183-x pmid:27994650 fatcat:mgbsbjr5nrh2fp4lzowxdsqqia

In silico identification of novel chemical compounds with antituberculosis activity for the inhibition of InhA and EthR proteins from Mycobacterium tuberculosis

Sajal Kumar Halder, Fatiha Elma
2021 Journal of Clinical Tuberculosis and Other Mycobacterial Diseases  
, excretion, toxicity) profile evaluation, P450 site of metabolism prediction, and molecular dynamics simulation.  ...  In this study, we have analyzed fifty small molecules with antituberculosis properties using in silico approach including molecular docking, drug-likeness assessment, ADMET (absorption, distribution, metabolism  ...  Nine of the isozymes under the CYP system scanned for the prediction of the metabolically vulnerable points using RS-WebPredictor tool [38] .  ... 
doi:10.1016/j.jctube.2021.100246 pmid:34124395 pmcid:PMC8173314 fatcat:jcsgw6jjbbd7rgqnjwmodxqmcq

Curcumin Analogues as the Inhibitors of TLR4 Pathway in Inflammation and Their Drug Like Potentialities: A Computer-based Study [article]

Md. Asad Ullah, Fatema Tuz Johora, Bishajit Sarkar, Yusha Araf, MD. Hasanur Rahman
2020 bioRxiv   pre-print
Multiple analogues showed better binding affinity than the approved drugs for the respective targets.  ...  Then their drug like potentialities were analyzed in different experiments where they also performed sound and similar.  ...  Acknowledgements Authors acknowledge the members of Swift Integrity Computational Lab, Dhaka, Bangladesh, a virtual platform of young researchers for their support during the preparation of the manuscript  ... 
doi:10.1101/2020.01.27.921528 fatcat:d7l7vhqljvblnipf4fosm7kysm

In Silico Analysis of Some Phytochemicals as Potential Anti-cancer Agents Targeting Cyclin Dependent Kinase-2, Human Topoisomerase IIa and Vascular Endothelial Growth Factor Receptor-2 [article]

Bishajit Sarkar, Md. Asad Ullah, Syed Sajidul Islam
2020 bioRxiv   pre-print
study, druglikeness property experiment, ADME/T test, PASS prediction and P450 site of metabolism prediction, pharmacophore modelling, DFT calculations and molecular dynamics simulation study to determine  ...  one best ligand (total three ligands for three enzymes) that have the capability to inhibit each of the mentioned enzymes.  ...  The P450 Site of Metabolism (SOM) of the three best selected ligand molecules were determined by online tool, RS-WebPredictor 1.0 (http://reccr.chem.rpi.edu/Software/RS-WebPredictor/) (103) .  ... 
doi:10.1101/2020.01.10.901660 fatcat:oluk3xqdxbbctpyoursd7khmde

In silico identification of novel chemical compounds with anti-TB potential for the inhibition of InhA and EthR from Mycobacterium tuberculosis [article]

Sajal Kumar Halder, Fatiha Elma
2020 bioRxiv   pre-print
, P450 site of metabolism prediction and molecular dynamics simulation study.  ...  This study involves fifty drug-like compounds with antibacterial activity that inhibit InhA and EthR involved in the synthesis of one of the major lipid components, mycolic acid, which is crucial for the  ...  ACKNOWLEDGEMENTS The authors are thankful to Mohammad Mahfuz Ali Khan Shawan, the Assistant Professor of Dept. of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka for reviewing  ... 
doi:10.1101/2020.12.04.411967 fatcat:cup74o3i7rdlpbo6a43czrt7sm

Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer's disease: a computational approach

Bishajit Sarkar, Sayka Alam, Tiluttoma Khan Rajib, Syed Sajidul Islam, Yusha Araf, Md. Asad Ullah
2021 Egyptian Journal of Medical Human Genetics  
through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.  ...  For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources.  ...  Acknowledgements The authors are thankful to the Swift Integrity Computational Lab, Dhaka, Bangladesh, a virtual platform of young researchers, for providing the support.  ... 
doi:10.1186/s43042-020-00127-8 fatcat:gye7ozhpbfan3e3ouxhdi4fmpy

A Computational Approach for Exploring Herbal Inhibitors of Acetylcholinesterase in Alzheimer's Disease [article]

Bishajit Sarkar, Md. Asad Ullah, Nazmul Islam Prottoy
2020 medRxiv   pre-print
To determine the safety and efficacy of the three best ligands, a set of tests: the druglikeness property test, ADME/T test, PASS & P450 site of metabolism prediction, pharmacophore mapping and modelling  ...  Alzheimers disease (AD) is the most common type of age related dementia. Many hypotheses shed light on several reasons that lead to AD development.  ...  The P450 site of metabolism (SOM) of the three best selected ligand molecules were determined by online tool, RS-WebPredictor 1.0 (http://reccr.chem.rpi.edu/Software/RS-WebPredictor/) [51] .  ... 
doi:10.1101/2020.01.04.20016535 fatcat:xgbjjvvnjzfsbmfxeh5rzxfxwu

Computational methods for drug design and discovery: focus on China

Mingyue Zheng, Xian Liu, Yuan Xu, Honglin Li, Cheng Luo, Hualiang Jiang
2013 TIPS - Trends in Pharmacological Sciences  
For each selected method, a short background precedes an assessment of the method with respect to the needs of drug discovery, and, in particular, work from China is highlighted.  ...  Application of these methods spans a wide range, from drug target identification to hit discovery and lead optimization.  ...  Recently, Zaretzki et al. developed a server named RS-WebPredictor that can predict the isozyme-specific regioselectivity for CYP450mediated reaction [65] .  ... 
doi:10.1016/j.tips.2013.08.004 pmid:24035675 pmcid:PMC7126378 fatcat:beegy5gxh5ex5nv2kablrzzqb4