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Lagunin AA, Sezganova AS, Muraviova ES, Rudik AV, Filimonov DA. BC CLC-Pred: a freely available web-application for quantitative and qualitative predictions of substance cytotoxicity in relation to human breast cancer cell lines. SAR QSAR Environ Res 2024; 35:1-9. [PMID: 38112004 DOI: 10.1080/1062936x.2023.2289050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
In silico prediction of cell line cytotoxicity considerably decreases time and financial costs during drug development of new antineoplastic agents. (Q)SAR models for the prediction of drug-like compound cytotoxicity in relation to nine breast cancer cell lines (T47D, ZR-75-1, MX1, Hs-578T, MCF7-DOX, MCF7, Bcap37, MCF7R, BT-20) were created by GUSAR software based on the data from ChEMBL database (v. 30). The separate datasets related with IC50 and IG50 values were used for the creation of (Q)SAR models for each cell line. Based on leave-one-out and 5F CV procedures, 24 reasonable (Q)SAR models were selected for the creation of a freely available web-application (BC CLC-Pred: https://www.way2drug.com/bc/) to predict substance cytotoxicity in relation to human breast cancer cell lines. The mean accuracies of prediction r2, RMSE, Balance Accuracy for the selected (Q)SAR models calculated by 5F CV were 0.599, 0.679 and 0.875, respectively. As a result, BC CLC-Pred provides simultaneous quantitative and qualitative predictions of IC50 and IG50 values for most of the nine breast cancer cell lines, which may be helpful in selecting promising compounds and optimizing lead compounds during the development of new antineoplastic agents against breast cancer.
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Affiliation(s)
- A A Lagunin
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Sezganova
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - E S Muraviova
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - A V Rudik
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - D A Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Rudik A, Dmitriev A, Lagunin A, Filimonov D, Poroikov V. Computational Prediction of Inhibitors and Inducers of the Major Isoforms of Cytochrome P450. Molecules 2022; 27:5875. [PMID: 36144612 DOI: 10.3390/molecules27185875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022]
Abstract
Human cytochrome P450 enzymes (CYPs) are heme-containing monooxygenases. This superfamily of drug-metabolizing enzymes is responsible for the metabolism of most drugs and other xenobiotics. The inhibition of CYPs may lead to drug–drug interactions and impair the biotransformation of drugs. CYP inducers may decrease the bioavailability and increase the clearance of drugs. Based on the freely available databases ChEMBL and PubChem, we have collected over 70,000 records containing the structures of inhibitors and inducers together with the IC50 values for the inhibitors of the five major human CYPs: 1A2, 3A4, 2D6, 2C9, and 2C19. Based on the collected data, we developed (Q)SAR models for predicting inhibitors and inducers of these CYPs using GUSAR and PASS software. The developed (Q)SAR models could be applied for assessment of the interaction of novel drug-like substances with the major human CYPs. The created (Q)SAR models demonstrated reasonable accuracy of prediction. They have been implemented in the web application P450-Analyzer that is freely available via the Internet.
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Korotkevich EI, Rudik AV, Dmitriev AV, Lagunin AA, Filimonov DA. [Predict of metabolic stability of xenobiotics by the PASS and GUSAR programs]. Biomed Khim 2021; 67:295-299. [PMID: 34142537 DOI: 10.18097/pbmc20216703295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Metabolic stability refers to the susceptibility of compounds to the biotransformation; it is characterized by such pharmacokinetic parameters as half-life (T1/2) and clearance (CL). Generally, these parameters are estimated by in vitro assays, which are based on cells or subcellular fractions (mainly liver microsomal enzymes) and serve as models of the processes occurring in living organisms. Data obtained from the experiments are used to build QSAR (Quantitative Structure-Activity Relationship) models. More than 8000 compounds with known CL and/or T1/2 values obtained in vitro using human liver microsomes were selected from the freely available ChEMBL v.27 database. GUSAR (General Unrestricted Structure-Activity Relationships) and PASS (Prediction of Activity Spectra for Substances) softwares were used to make quantitative and classification models. The quality of the models was evaluated using 5-fold cross-validation. Compounds were subdivided into "stable" and "unstable" by means of the following threshold parameters: T1/2 = 30 minutes, CL = 20 ml/min/kg. The accuracy of the models ranged from 0.5 (calculated in 5-fold CV on the test set for the half-life prediction quantitative model) to 0.96 (calculated in 5-fold CV on the test set for the clearance prediction classification model).
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Affiliation(s)
- E I Korotkevich
- Institute of Biomedical Chemistry, Moscow, Russia; Medico-biological Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - A V Rudik
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Dmitriev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Lagunin
- Institute of Biomedical Chemistry, Moscow, Russia; Medico-biological Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
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Amiranashvili L, Nadaraia N, Merlani M, Kamoutsis C, Petrou A, Geronikaki A, Pogodin P, Druzhilovskiy D, Poroikov V, Ciric A, Glamočlija J, Sokovic M. Antimicrobial Activity of Nitrogen-Containing 5-Alpha-androstane Derivatives: In Silico and Experimental Studies. Antibiotics (Basel) 2020; 9:antibiotics9050224. [PMID: 32365907 PMCID: PMC7277561 DOI: 10.3390/antibiotics9050224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
We evaluated the antimicrobial activity of thirty-one nitrogen-containing 5-α-androstane derivatives in silico using computer program PASS (Prediction of Activity Spectra for Substances) and freely available PASS-based web applications (such as Way2Drug). Antibacterial activity was predicted for 27 out of 31 molecules; antifungal activity was predicted for 25 out of 31 compounds. The results of experiments, which we conducted to study the antimicrobial activity, are in agreement with the predictions. All compounds were found to be active with MIC (Minimum Inhibitory Concentration) and MBC (Minimum Bactericidal Concentration) values in the range of 0.0005–0.6 mg/mL. The activity of all studied 5-α-androstane derivatives exceeded or was equal to those of Streptomycin and, except for the 3β-hydroxy-17α-aza-d-homo-5α-androstane-17-one, all molecules were more active than Ampicillin. Activity against the resistant strains of E. coli, P. aeruginosa, and methicillin-resistant Staphylococcus aureus was also shown in experiments. Antifungal activity was determined with MIC and MFC (Minimum Fungicidal Concentration) values varying from 0.007 to 0.6 mg/mL. Most of the compounds were found to be more potent than the reference drugs Bifonazole and Ketoconazole. According to the results of docking studies, the putative targets for antibacterial and antifungal activity are UDP-N-acetylenolpyruvoylglucosamine reductase and 14-α-demethylase, respectively. In silico assessments of the acute rodent toxicity and cytotoxicity obtained using GUSAR (General Unrestricted Structure-Activity Relationships) and CLC-Pred (Cell Line Cytotoxicity Predictor) web-services were low for the majority of compounds under study, which contributes to the chances for those compounds to advance in the development.
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Affiliation(s)
- Lela Amiranashvili
- TSMU I. Kutateladze Institute of Pharmacochemistry, P. Sarajishvili str. 36, Tbilisi 0159, Georgia; (L.A.); (N.N.); (M.M.)
| | - Nanuli Nadaraia
- TSMU I. Kutateladze Institute of Pharmacochemistry, P. Sarajishvili str. 36, Tbilisi 0159, Georgia; (L.A.); (N.N.); (M.M.)
| | - Maia Merlani
- TSMU I. Kutateladze Institute of Pharmacochemistry, P. Sarajishvili str. 36, Tbilisi 0159, Georgia; (L.A.); (N.N.); (M.M.)
| | | | - Anthi Petrou
- School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Athina Geronikaki
- School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Correspondence: ; Tel.: +302301997616
| | - Pavel Pogodin
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (P.P.); (D.D.); (V.P.)
| | - Dmitry Druzhilovskiy
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (P.P.); (D.D.); (V.P.)
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (P.P.); (D.D.); (V.P.)
| | - Ana Ciric
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, 11060 Beograd, Serbia; (A.C.); (J.G.); (M.S.)
| | - Jasmina Glamočlija
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, 11060 Beograd, Serbia; (A.C.); (J.G.); (M.S.)
| | - Marina Sokovic
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, 11060 Beograd, Serbia; (A.C.); (J.G.); (M.S.)
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Rudik A, Bezhentsev V, Dmitriev A, Lagunin A, Filimonov D, Poroikov V. Metatox - Web application for generation of metabolic pathways and toxicity estimation. J Bioinform Comput Biol 2020; 17:1940001. [PMID: 30866738 DOI: 10.1142/s0219720019400018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Xenobiotics biotransformation in humans is a process of the chemical modifications, which may lead to the formation of toxic metabolites. The prediction of such metabolites is very important for drug development and ecotoxicology studies. We created the web-application MetaTox ( http://way2drug.com/mg ) for the generation of xenobiotics metabolic pathways in the human organism. For each generated metabolite, the estimations of the acute toxicity (based on GUSAR software prediction), organ-specific carcinogenicity and adverse effects (based on PASS software prediction) are performed. Generation of metabolites by MetaTox is based on the fragments datasets, which describe transformations of substrates structures to a metabolites structure. We added three new classes of biotransformation reactions: Dehydrogenation, Glutathionation, and Hydrolysis, and now metabolite generation for 15 most frequent classes of xenobiotic's biotransformation reactions are available. MetaTox calculates the probability of formation of generated metabolite - it is the integrated assessment of the biotransformation reactions probabilities and their sites using the algorithm of PASS ( http://way2drug.com/passonline ). The prediction accuracy estimated by the leave-one-out cross-validation (LOO-CV) procedure calculated separately for the probabilities of biotransformation reactions and their sites is about 0.9 on the average for all reactions.
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Affiliation(s)
- Anastasiya Rudik
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Vladislav Bezhentsev
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Alexander Dmitriev
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Alexey Lagunin
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia.,† Medico-Biological Faculty, Pirogov Russian National Research Medical University, 1 Ostrovitianov Street, Moscow 117997, Russia
| | - Dmitry Filimonov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
| | - Vladimir Poroikov
- * Department of Bioinformatics, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, Moscow 119121, Russia
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Stolbov LA, Druzhilovskiy DS, Filimonov DA, Nicklaus MC, Poroikov VV. (Q)SAR Models of HIV-1 Protein Inhibition by Drug-Like Compounds. Molecules 2019; 25:molecules25010087. [PMID: 31881687 PMCID: PMC6983201 DOI: 10.3390/molecules25010087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
Despite the achievements of antiretroviral therapy, discovery of new anti-HIV medicines remains an essential task because the existing drugs do not provide a complete cure for the infected patients, exhibit severe adverse effects, and lead to the appearance of resistant strains. To predict the interaction of drug-like compounds with multiple targets for HIV treatment, ligand-based drug design approach is widely applied. In this study, we evaluated the possibilities and limitations of (Q)SAR analysis aimed at the discovery of novel antiretroviral agents inhibiting the vital HIV enzymes. Local (Q)SAR models are based on the analysis of structure–activity relationships for molecules from the same chemical class, which significantly restrict their applicability domain. In contrast, global (Q)SAR models exploit data from heterogeneous sets of drug-like compounds, which allows their application to databases containing diverse structures. We compared the information for HIV-1 integrase, protease and reverse transcriptase inhibitors available in the EBI ChEMBL, NIAID HIV/OI/TB Therapeutics, and Clarivate Analytics Integrity databases as the sources for (Q)SAR training sets. Using the PASS and GUSAR software, we developed and validated a variety of (Q)SAR models, which can be further used for virtual screening of new antiretrovirals in the SAVI library. The developed models are implemented in the freely available web resource AntiHIV-Pred.
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Affiliation(s)
- Leonid A. Stolbov
- Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry, 10 bldg. 8, Pogodinskaya str., 119121 Moscow, Russia; (L.A.S.); (D.S.D.); (D.A.F.)
| | - Dmitry S. Druzhilovskiy
- Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry, 10 bldg. 8, Pogodinskaya str., 119121 Moscow, Russia; (L.A.S.); (D.S.D.); (D.A.F.)
| | - Dmitry A. Filimonov
- Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry, 10 bldg. 8, Pogodinskaya str., 119121 Moscow, Russia; (L.A.S.); (D.S.D.); (D.A.F.)
| | - Marc C. Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Vladimir V. Poroikov
- Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry, 10 bldg. 8, Pogodinskaya str., 119121 Moscow, Russia; (L.A.S.); (D.S.D.); (D.A.F.)
- Correspondence:
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Butina YV, Kudayarova TV, Danilova EA, Islyaikin MK. [The prediction of the spectrum of biological activity and antimicrobial properties of diaminoazoles]. Biomed Khim 2019; 65:99-102. [PMID: 30950814 DOI: 10.18097/pbmc20196502099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The work is devoted to predicting and studying biological properties of N-substituted analogs of 3,5-diamino-1,2,4-thiadiazole, which, in their turn, include in the composition of many drugs that exhibit a wide range of pharmacological actions. For searching of new alternative drugs with an antibacterial activity, but lacking resistance of microorganism strains to them, a computer screening of 2N-alkyl-substituted 5-amino-3-imino-1,2,4-thiadiazolines previously synthesized by us was carried out. The prediction of the spectrum of biological activity, as well as the determination of the probable toxicity of these compounds, was performed using the freely available computer programs PASS, Anti-Bac-Pred, and GUSAR. The study of the antibacterial activity in vitro against gram-positive (Staphylococcus aureus, Staphylococcus saprophyticus, Staphylococcus epidermidis) and gram-negative (Escherichia coli, Pseudomonas aeruginosae) bacterial strains was performed by the disco-diffusion method. Experimental data roughly correspond to the predictions.
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Affiliation(s)
- Yu V Butina
- Ivanovo State Medical Academy, Ivanovo, Russia
| | - T V Kudayarova
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russia
| | - E A Danilova
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russia
| | - M K Islyaikin
- Ivanovo State University of Chemistry and Technology, Ivanovo, Russia
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Lagunin AA, Romanova MA, Zadorozhny AD, Kurilenko NS, Shilov BV, Pogodin PV, Ivanov SM, Filimonov DA, Poroikov VV. Comparison of Quantitative and Qualitative (Q)SAR Models Created for the Prediction of K i and IC 50 Values of Antitarget Inhibitors. Front Pharmacol 2018; 9:1136. [PMID: 30364128 PMCID: PMC6192375 DOI: 10.3389/fphar.2018.01136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Abstract
Estimation of interaction of drug-like compounds with antitargets is important for the assessment of possible toxic effects during drug development. Publicly available online databases provide data on the experimental results of chemical interactions with antitargets, which can be used for the creation of (Q)SAR models. The structures and experimental Ki and IC50 values for compounds tested on the inhibition of 30 antitargets from the ChEMBL 20 database were used. Data sets with Ki and IC50 values including more than 100 compounds were created for each antitarget. The (Q)SAR models were created by GUSAR software using quantitative neighborhoods of atoms (QNA), multilevel neighborhoods of atoms (MNA) descriptors, and self-consistent regression. The accuracy of (Q)SAR models was validated by the fivefold cross-validation procedure. The balanced accuracy was higher for qualitative SAR models (0.80 and 0.81 for Ki and IC50 values, respectively) than for quantitative QSAR models (0.73 and 0.76 for Ki and IC50 values, respectively). In most cases, sensitivity was higher for SAR models than for QSAR models, but specificity was higher for QSAR models. The mean R 2 and RMSE were 0.64 and 0.77 for Ki values and 0.59 and 0.73 for IC50 values, respectively. The number of compounds falling within the applicability domain was higher for SAR models than for the test sets.
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Affiliation(s)
- Alexey A. Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria A. Romanova
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anton D. Zadorozhny
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia S. Kurilenko
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris V. Shilov
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel V. Pogodin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Sergey M. Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A. Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Zakharov AV, Varlamova EV, Lagunin AA, Dmitriev AV, Muratov EN, Fourches D, Kuz'min VE, Poroikov VV, Tropsha A, Nicklaus MC. QSAR Modeling and Prediction of Drug-Drug Interactions. Mol Pharm 2016; 13:545-56. [PMID: 26669717 DOI: 10.1021/acs.molpharmaceut.5b00762] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Severe adverse drug reactions (ADRs) are the fourth leading cause of fatality in the U.S. with more than 100,000 deaths per year. As up to 30% of all ADRs are believed to be caused by drug-drug interactions (DDIs), typically mediated by cytochrome P450s, possibilities to predict DDIs from existing knowledge are important. We collected data from public sources on 1485, 2628, 4371, and 27,966 possible DDIs mediated by four cytochrome P450 isoforms 1A2, 2C9, 2D6, and 3A4 for 55, 73, 94, and 237 drugs, respectively. For each of these data sets, we developed and validated QSAR models for the prediction of DDIs. As a unique feature of our approach, the interacting drug pairs were represented as binary chemical mixtures in a 1:1 ratio. We used two types of chemical descriptors: quantitative neighborhoods of atoms (QNA) and simplex descriptors. Radial basis functions with self-consistent regression (RBF-SCR) and random forest (RF) were utilized to build QSAR models predicting the likelihood of DDIs for any pair of drug molecules. Our models showed balanced accuracy of 72-79% for the external test sets with a coverage of 81.36-100% when a conservative threshold for the model's applicability domain was applied. We generated virtually all possible binary combinations of marketed drugs and employed our models to identify drug pairs predicted to be instances of DDI. More than 4500 of these predicted DDIs that were not found in our training sets were confirmed by data from the DrugBank database.
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Affiliation(s)
- Alexey V Zakharov
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick , 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Ekaterina V Varlamova
- Department of Molecular Structure and Cheminformatics, A.V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine , Lustdorfskaya Doroga 86, Odessa 65080, Ukraine.,Chemical-Technological Department, Odessa National Polytechnic University , 1 Shevchenko Ave, Odessa 65000, Ukraine
| | - Alexey A Lagunin
- Institute of Biochemical Chemistry , 10/8, Pogodinskaya street, 119121 Moscow, Russia.,Medico-Biological Department, Pirogov Russian National Research Medical University , Ostrovitianov str. 1, Moscow 117997, Russia
| | - Alexander V Dmitriev
- Institute of Biochemical Chemistry , 10/8, Pogodinskaya street, 119121 Moscow, Russia
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina , Beard Hall 301, CB#7568, Chapel Hill, North Carolina 27599, United States
| | - Denis Fourches
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Victor E Kuz'min
- Department of Molecular Structure and Cheminformatics, A.V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine , Lustdorfskaya Doroga 86, Odessa 65080, Ukraine
| | - Vladimir V Poroikov
- Institute of Biochemical Chemistry , 10/8, Pogodinskaya street, 119121 Moscow, Russia
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina , Beard Hall 301, CB#7568, Chapel Hill, North Carolina 27599, United States
| | - Marc C Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick , 376 Boyles Street, Frederick, Maryland 21702, United States
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