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In Silico Prediction of Drug–Drug Interactions Mediated by Cytochrome P450 Isoforms

Alexander V. Dmitriev, Anastassia V. Rudik, Dmitry A. Karasev, Pavel V. Pogodin, Alexey A. Lagunin, Dmitry A. Filimonov, Vladimir V. Poroikov
2021 Pharmaceutics  
induction of the most important drug-metabolizing cytochrome P450 isoforms.  ...  The SAR models created are publicly available as a web resource and provide predictions of DDIs mediated by the most important cytochromes P450.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pharmaceutics13040538 pmid:33924315 fatcat:e3sm5nnhozfm7mu6bjeo4vs5fa

Structure-Based Virtual Screening of Benzaldehyde Thiosemicarbazone Derivatives against DNA Gyrase B of Mycobacterium tuberculosis

Andiyappan Kistan, Balakrishnan Anna Benedict, Sundaramoorthy Vasanthan, Alphonse PremKumar, Malathi Kullappan, Jenifer Mallavarpu Ambrose, Vishnu Priya Veeraraghavan, Gayathri Rengasamy, Krishna Mohan Surapaneni, Saravanan Ramachandran
2021 Evidence-Based Complementary and Alternative Medicine  
Emergence of antibiotic-resistant Mycobacterium tuberculosis (M. tuberculosis) restricts the availability of drugs for the treatment of tuberculosis, which leads to the increased morbidity and mortality  ...  of the disease worldwide.  ...  Acknowledgments MK, JMA, and SKM would like to thank the management of PMCHRI for providing the necessary facilities to carry out this research work.  ... 
doi:10.1155/2021/6140378 pmid:34938343 pmcid:PMC8687812 fatcat:x2un2hsg4nglpnjb5pah4j55lq

Exploring the Chemical Space of Cytochrome P450 Inhibitors using Integrated Physicochemical Parameters, Drug Efficiency Metrics and Decision Tree Models

Kiani, Jabeen
2019 Computation  
The cytochrome P450s (CYPs) play a central role in the metabolism of various endogenous and exogenous compounds including drugs.  ...  Therefore, insights into the underlying mechanism of CYP450 inhibition and the estimation of overall CYP inhibitor properties might serve as valuable tools during the early phases of drug discovery.  ...  Conflicts of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.  ... 
doi:10.3390/computation7020026 fatcat:gjpz3n2c7vbmhdu7ssitmlkaaq

Computational methods and tools to predict cytochrome P450 metabolism for drug discovery

Jonathan D. Tyzack, Johannes Kirchmair
2019 Chemical Biology and Drug Design  
In this review, we present important, recent developments in the computational prediction of cytochrome P450 (CYP) metabolism in the context of drug discovery.  ...  We discuss in silico models for the various aspects of CYP metabolism prediction, including CYP substrate and inhibitor predictors, site of metabolism predictors (i.e., metabolically labile sites within  ...  ., 2015) is another web service that predicts inhibitors and noninhibitors of the same major CYPs based on the same data.  ... 
doi:10.1111/cbdd.13445 pmid:30471192 fatcat:n63v527reffeblghwdh5v4v4my

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug–Drug Interactions

Maria Karlgren, Anna Vildhede, Ulf Norinder, Jacek R. Wisniewski, Emi Kimoto, Yurong Lai, Ulf Haglund, Per Artursson
2012 Journal of Medicinal Chemistry  
We then used MTA to predict the effects of a subset of inhibitors on atorvastatin uptake in vivo. Using a data set of 225 drug-like compounds, 91 OATP inhibitors were identified.  ...  Here, we developed in vitro and in silico models for identification and prediction of specific and general inhibitors of OATP1B1, OATP1B3, and OATP2B1.  ...  The bars represent the percentage of correctly classified inhibitors (black) and noninhibitors (gray).  ... 
doi:10.1021/jm300212s pmid:22541068 pmcid:PMC3361267 fatcat:vwcyjori75hitgnrsxemchtka4

Artificial neural network cascade identifies multi-P450 inhibitors in natural compounds

Zhangming Li, Yan Li, Lu Sun, Yun Tang, Lanru Liu, Wenliang Zhu
2015 PeerJ  
Experimental data reportingin vitroinhibition of five P450 isoforms (CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4) were obtained for 8,148 compounds from the Cytochrome P450 Inhibitors Database (CPID).  ...  Using our NNC model, 22.2% of the approximately 160,000 natural compounds in TCM Database@Taiwan were identified as potential multi-P450 inhibitors.  ...  MATERIALS AND METHODS Acquisition of in vitro data and chemical re-sorting The dataset of experimentally validated P450 inhibitors and non-inhibitors was downloaded from the LMMD Cytochrome P450 Inhibitors  ... 
doi:10.7717/peerj.1524 pmid:26719820 pmcid:PMC4696407 fatcat:6i3bgalpjzerbdiw7bviaeiy2a

In silico approach for the discovery of new PPARγ modulators among plant-derived polyphenols

Encinar JA, Fernández-Ballester G, Galiano-Ibarra V, Micol V
2015 Drug Design, Development and Therapy  
Full agonists of synthetic thiazolidinediones (TZDs) have been therapeutically used in clinical practice to treat type 2 diabetes for many years.  ...  Additionally, most of the selected compounds have favorable druggability and good ADMET properties.  ...  Classification of cytochrome P450 inhibitors and noninhibitors using combined classifiers. Anzenbacher P, Anzenbacherova E. Cytochromes P450 and metabolism of xenobiotics.  ... 
doaj:4ecb7f4cde774b5eb329de314186c723 fatcat:kiaf64n2xbbqvegve3jjc64pyy

A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms

Maris Lapins, Apilak Worachartcheewan, Ola Spjuth, Valentin Georgiev, Virapong Prachayasittikul, Chanin Nantasenamat, Jarl E. S. Wikberg, Daniel S. Sem
2013 PLoS ONE  
Citation: Lapins M, Worachartcheewan A, Spjuth O, Georgiev V, Prachayasittikul V, et al. (2013) A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms.  ...  The entire training dataset contained 63 391 interactions and the best PCM model was obtained using signature descriptors of height 1, 2 and 3 and inducing the model with a support vector machine.  ...  CYP isoform-inhibitor combinations were assigned the category membership +1, and CYP isoform-noninhibitor combinations were assigned the category membership 21.  ... 
doi:10.1371/journal.pone.0066566 pmid:23799117 pmcid:PMC3684587 fatcat:rnxqtv42kjestgru5pyv3kv72u

MACHINE LEARNING APPROACHES TO IDENTIFY POTENTIAL DNA Gyr B INHIBITORS FOR MYCOBACTERIUM TUBERCULOSIS

2021 International Journal of Biology Pharmacy and Allied Sciences  
We developed four supervised classification models (SMO, Random Forest, Naive Bayes, and MLR) using Weka to classify the molecules as actives and inactives and four regression models to predict the inhibitory  ...  This attracts us to build classifiers for virtual high-throughput screening and to select molecules from large libraries for further analysis.  ...  1 Cytochrome P450 is an enzyme responsible for the metabolism of the drug in a biological system and its clearance from the body.  ... 
doi:10.31032/ijbpas/2021/10.12.5774 fatcat:mdaggu45e5ga3owov7spe72t74

Tamoxifen and CYP2D6: A Contradiction of Data

D. L. Hertz, H. L. McLeod, W. J. Irvin
2012 The Oncologist  
Bioconversion of tamoxifen to endoxifen, its most abundant active metabolite, is primarily dependent on the activity of cytochrome P450 2D6 (CYP2D6), which is highly polymorphic.  ...  Comparison of these factors between the positive and negative studies suggests that tamoxifen combination therapy, genotyping comprehensiveness, and CYP2D6 inhibitor coadministration may account for some  ...  The metabolism of tamoxifen to endoxifen is heavily dependent on cytochrome P450 2D6 activity.  ... 
doi:10.1634/theoncologist.2011-0418 pmid:22531359 pmcid:PMC3360902 fatcat:2p5t6vusbfhcrcgwuc6rrrp2gy

Machine Learning Method To Screen Inhibitors of Virulent Transcription Regulator of Salmonella Typhi

Syed Asif, Atif Hassan, Tabrej Khan
2018 International Journal of Advanced Computer Science and Applications  
In this study, bagging and gradient boosting based ML algorithm was used to build a predictive classification model to perform virtual HTS of active inhibitors of the PhoP regulon of Salmonella enterica  ...  The eXtreme Gradient Boosting (XGBoost) based classification model was comparatively accurate and sensitive in classifying active drug-like inhibitors of PhoP regulon of Salmonella enterica serotype typhi  ...  Omar Barukab of the Faculty of Computing and Information Technology Rabigh (FCITR) of King Abdulaziz University, Jeddah for providing the computational facility to perform current experiments.  ... 
doi:10.14569/ijacsa.2018.090235 fatcat:gthgj5t3qfcxnnofg4duyuyxae

Structure-Based Drug Design for Cytochrome P450 Family 1 Inhibitors

Zbigniew Dutkiewicz, Renata Mikstacka
2018 Bioinorganic Chemistry and Applications  
The superfamily of cytochromes P450 consists of families and subfamilies which are characterized by a specific structure and substrate specificity.  ...  Cytochromes P450 family 1 (CYP1s) play a distinctive role in the metabolism of drugs and chemical procarcinogens.  ...  Substrates and Inhibitors of CYP1s A classification of inhibitors and noninhibitors of CYPs is particularly important in relation to drug design and the prediction of drug-drug interactions.  ... 
doi:10.1155/2018/3924608 pmid:30147715 pmcid:PMC6083639 fatcat:5hdcm4kyo5bd5aqqdhkjy3hpgi

Applications of Support Vector Machines in Chemistry [chapter]

Ovidiu Ivanciuc
2007 Reviews in computational chemistry  
and Gü nther for the discrimination of kinase inhibitors from noninhibitors. 85 Yap and Chen compared two jury SVM procedures for classifying inhibitors and substrates of cytochromes P450 3A4, 2D6 and  ...  Yap and Chen developed a jury SVM method for the classification of inhibitors and substrates of cytochromes P450 3A4 (CYP3A4, 241 inhibitors and 368 substrates), 2D6 (CYP2D6, 180 inhibitors and 198 substrates  ... 
doi:10.1002/9780470116449.ch6 fatcat:aumcn53nvfhhhocxvav32rhwzm

Modeling Chemical Interaction Profiles: I. Spectral Data-Activity Relationship and Structure-Activity Relationship Models for Inhibitors and Non-inhibitors of Cytochrome P450 CYP3A4 and CYP2D6 Isozymes

Brooks McPhail, Yunfeng Tie, Huixiao Hong, Bruce A. Pearce, Laura K. Schnackenberg, Weigong Ge, Luis G. Valerio, James C. Fuscoe, Weida Tong, Dan A. Buzatu, Jon G. Wilkes, Bruce A. Fowler (+2 others)
2012 Molecules  
In the present work, spectral data-activity relationship (SDAR) and structure-activity relationship (SAR) approaches were used to develop machine-learning classifiers of inhibitors and non-inhibitors of  ...  Many of these chemicals--drugs, pesticides, and environmental pollutants--interact at the level of metabolic biotransformations mediated by cytochrome P450 (CYP) enzymes.  ...  and Disease Registry, or those of the U.S.  ... 
doi:10.3390/molecules17033383 pmid:22421792 pmcid:PMC6268752 fatcat:dsrnpaqiafavlejw5kzk5ytuha

A Novel Approach for Predicting P-Glycoprotein (ABCB1) Inhibition Using Molecular Interaction Fields

Fabio Broccatelli, Emanuele Carosati, Annalisa Neri, Maria Frosini, Laura Goracci, Tudor I. Oprea, Gabriele Cruciani
2011 Journal of Medicinal Chemistry  
In addition, inhibitors of Pgp can be used to overcome multidrug resistance. Given this dual-purpose, reliable in silico procedures to predict Pgp inhibition are of great interest.  ...  High accuracy was demonstrated internally, with two different validation sets, and moreover using a number of molecules, for which Pgp inhibition was not experimentally available but was evaluated 'inhouse  ...  Both methods contributed to the prediction of Pgp inhibitors, however Volsurf+ was more selective in classifying compounds as noninhibitors.  ... 
doi:10.1021/jm101421d pmid:21341745 pmcid:PMC3069647 fatcat:rxnqyl5fqvf2dailtxhptgbmvy
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