1
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Hu XM, Hou YY, Teng XR, Liu Y, Li Y, Li W, Li Y, Ai CZ. Prediction of cytochrome P450-mediated bioactivation using machine learning models and in vitro validation. Arch Toxicol 2024; 98:1457-1467. [PMID: 38492097 DOI: 10.1007/s00204-024-03701-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Abstract
Cytochrome P450 (P450)-mediated bioactivation, which can lead to the hepatotoxicity through the formation of reactive metabolites (RMs), has been regarded as the major problem of drug failures. Herein, we purposed to establish machine learning models to predict the bioactivation of P450. On the basis of the literature-derived bioactivation dataset, models for Benzene ring, Nitrogen heterocycle and Sulfur heterocycle were developed with machine learning methods, i.e., Random Forest, Random Subspace, SVM and Naïve Bayes. The models were assessed by metrics like "Precision", "Recall", "F-Measure", "AUC" (Area Under the Curve), etc. Random Forest algorithms illustrated the best predictability, with nice AUC values of 0.949, 0.973 and 0.958 for the test sets of Benzene ring, Nitrogen heterocycle and Sulfur heterocycle models, respectively. 2D descriptors like topological indices, 2D autocorrelations and Burden eigenvalues, etc. contributed most to the models. Furthermore, the models were applied to predict the occurrence of bioactivation of an external verification set. Drugs like selpercatinib, glafenine, encorafenib, etc. were predicted to undergo bioactivation into toxic RMs. In vitro, IC50 shift experiment was performed to assess the potential of bioactivation to validate the prediction. Encorafenib and tirbanibulin were observed of bioactivation potential with shifts of 3-6 folds or so. Overall, this study provided a reliable and robust strategy to predict the P450-mediated bioactivation, which will be helpful to the assessment of adverse drug reactions (ADRs) in clinic and the design of new candidates with lower toxicities.
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Affiliation(s)
- Xin-Man Hu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Yan-Yao Hou
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Xin-Ru Teng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Yong Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, 2 Dagong Road, Panjin, 124221, People's Republic of China
| | - Yu Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Wei Li
- Translational Medicine Research Institute, College of Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, 136 Jiangyangzhong Road, Yangzhou, 225001, People's Republic of China.
| | - Yan Li
- Department of Materials Science and Chemical Engineering, Dalian University of Technology, Dalian, 116023, Liaoning, People's Republic of China
| | - Chun-Zhi Ai
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China.
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2
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Mazzolari A, Perazzoni P, Sabato E, Lunghini F, Beccari AR, Vistoli G, Pedretti A. MetaSpot: A General Approach for Recognizing the Reactive Atoms Undergoing Metabolic Reactions Based on the MetaQSAR Database. Int J Mol Sci 2023; 24:11064. [PMID: 37446241 DOI: 10.3390/ijms241311064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The prediction of drug metabolism is attracting great interest for the possibility of discarding molecules with unfavorable ADME/Tox profile at the early stage of the drug discovery process. In this context, artificial intelligence methods can generate highly performing predictive models if they are trained by accurate metabolic data. MetaQSAR-based datasets were collected to predict the sites of metabolism for most metabolic reactions. The models were based on a set of structural, physicochemical, and stereo-electronic descriptors and were generated by the random forest algorithm. For each considered biotransformation, two types of models were developed: the first type involved all non-reactive atoms and included atom types among the descriptors, while the second type involved only non-reactive centers having the same atom type(s) of the reactive atoms. All the models of the first type revealed very high performances; the models of the second type show on average worst performances while being almost always able to recognize the reactive centers; only conjugations with glucuronic acid are unsatisfactorily predicted by the models of the second type. Feature evaluation confirms the major role of lipophilicity, self-polarizability, and H-bonding for almost all considered reactions. The obtained results emphasize the possibility of recognizing the sites of metabolism by classification models trained on MetaQSAR database. The two types of models can be synergistically combined since the first models identify which atoms can undergo a given metabolic reactions, while the second models detect the truly reactive centers. The generated models are available as scripts for the VEGA program.
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Affiliation(s)
- Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, I-20133 Milano, Italy
| | - Pietro Perazzoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, I-20133 Milano, Italy
| | - Emanuela Sabato
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, I-20133 Milano, Italy
| | - Filippo Lunghini
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy
| | - Andrea R Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, I-80131 Napoli, Italy
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, I-20133 Milano, Italy
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, I-20133 Milano, Italy
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3
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Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features. J Chem Inf Model 2023. [PMID: 37336765 DOI: 10.1021/acs.jcim.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the major drug-metabolizing enzymes in the human body and is responsible for the metabolism of ∼50% of clinically used drugs. Therefore, the identification of the compound's sites of metabolism (SOMs) mediated by CYP3A4 is of utmost importance in the early stage of drug discovery and development. Herein, docking-based approaches incorporating geometric features were used for SOMs prediction of CYP3A4 substrates. The cross-docking poses of a relatively large data set containing 474 substrates were analyzed in depth, and a widely observed geometric pattern called the close proximity of SOMs was derived from the poses. On the basis of the close proximity, several structure-based models have been constructed, which demonstrated better performance than those structure-based models using the criterion of Fe-SOM distance. For further improving the prediction performance, the structure-based models were also combined with the well-known ligand-based model SMARTCyp. One combined model exhibited good performance on the SOMs prediction of an external substrate set containing kinase inhibitors, PROTACs, approved drugs, and some lead compounds.
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Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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4
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Zhu R, Liu Y, Yang Y, Min Q, Li H, Chen L. Cytochrome P450 Monooxygenases Catalyse Steroid Nucleus Hydroxylation with Regio‐ and Stereo‐selectivity. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Zhao Y, Chen X, Ding Z, He C, Gao G, Lyu S, Gao Y, Du J. Identification of Novel CD39 Inhibitors Based on Virtual Screening and Enzymatic Assays. J Chem Inf Model 2021; 62:5289-5304. [PMID: 34648290 DOI: 10.1021/acs.jcim.1c00590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The accumulation of adenosine in the tumor microenvironment mediates immunosuppression and promotes tumor growth and proliferation. Intervention of the adenosine pathway is an important direction of antitumor immunity research. CD39 is an important ecto-nucleotidases for adenosine generation, therefore targeting the CD39-adenosine pathway is an emerging immune checkpoint for anticancer treatment. However, currently no CD39 inhibitor has been approved by the U.S. Food and Drug Administration. The development of CD39 drugs is urgent for clinical application. In this study, we combined homology modeling, virtual screening, and in vitro enzymatic activity to characterize the structural features of the CD39 protein and identify a triazinoindole-based compound as a CD39 inhibitor. The identified inhibitor and one of its analogues could effectively prevent the enzymatic activity of CD39 with IC50 values of 27.42 ± 5.52 and 79.24 ± 12.21 μM, respectively. At the same time, the inhibitor significantly inhibited the adenosine monophosphate production in colorectal cancer cell lines (HT29 and MC38) and thereafter prevented cell proliferation. Molecular docking studies, mutagenesis, and microscale thermophoresis indicated that residues such as R85 could be the main contributor in binding triazinoindole compounds. The binding mode can potentially be utilized for hit-to-lead optimization, and the identified inhibitor can be further tested for its anticancer activity in vivo or may serve as a chemical agent to study CD39-related functions.
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Affiliation(s)
- Yunshuo Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaotong Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhe Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chuanjie He
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guanfei Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Sifan Lyu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanfeng Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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6
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Ngoepe MP, Moeno S. Evaluation of Pipemidic Acid Derivatives for Potential Antimicrobial Activity Application: In silico Studies on Bioactivity. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200730165219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Pipemidic acid is a broad-spectrum quinolone antibacterial agent for the
treatment of chronic urinary tract infections against both gram-positive and gram-negative bacteria.
Both quinolone and fluoroquinolone antibiotics have been useful in combating bacterial infections.
However, patients suffer severe side effects when they stop taking the medication. The piperazinyl
region of pipemidic acid is highly responsible for the side effects.
Objective:
The objective of this study is to design new compounds in which the piperazinyl region is
masked by way of conjugation to benzoic acid derivatives.
Methods:
In silico studies were conducted using AutoDockTools software for ligand-protein
docking. The docking scores were compared to the parent pipemidic acid docked to Bacterial DNA
(deoxyribonucleic acid) gyrase and GABA (gamma-Aminobutyric acid) receptor from the PDB
(Protein Data Bank) database. Sites of metabolism, biological activity, quantum chemical
descriptors, and ADME (absorption, distribution, metabolism, and excretion) property predictions
for each designed ligand were also evaluated.
Results:
The docking studies and biological activity predictions showed good anti-infective properties
(ligand PAR03) whilst also suggesting a reduction in GABA receptor agonist activity. The performance
of PAR03 correlates with its electronic properties showing electrophilic character (can
generate Reactive Electrophilic Species (RES)).
Conclusion:
The results from this study indicate that modification of the piperazinyl region of pipemidic
acid can be an effective way to improve the drug potency whilst also ensuring reduction of
the associated side effects.
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Affiliation(s)
- Mpho Phehello Ngoepe
- Department of Oral Biological Sciences, School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, South Africa
| | - Sharon Moeno
- Department of Oral Biological Sciences, School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, South Africa
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7
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Kreutzer FP, Meinecke A, Schmidt K, Fiedler J, Thum T. Alternative strategies in cardiac preclinical research and new clinical trial formats. Cardiovasc Res 2021; 118:746-762. [PMID: 33693475 PMCID: PMC7989574 DOI: 10.1093/cvr/cvab075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
An efficient and safe drug development process is crucial for the establishment of new drugs on the market aiming to increase quality of life and life-span of our patients. Despite technological advances in the past decade, successful launches of drug candidates per year remain low. We here give an overview about some of these advances and suggest improvements for implementation to boost preclinical and clinical drug development with a focus on the cardiovascular field. We highlight advantages and disadvantages of animal experimentation and thoroughly review alternatives in the field of three-dimensional cell culture as well as preclinical use of spheroids and organoids. Microfluidic devices and their potential as organ-on-a-chip systems, as well as the use of living animal and human cardiac tissues are additionally introduced. In the second part, we examine recent gold standard randomized clinical trials and present possible modifications to increase lead candidate throughput: adaptive designs, master protocols, and drug repurposing. In silico and N-of-1 trials have the potential to redefine clinical drug candidate evaluation. Finally, we briefly discuss clinical trial designs during pandemic times.
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Affiliation(s)
- Fabian Philipp Kreutzer
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Anna Meinecke
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Kevin Schmidt
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.,Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.,Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
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8
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Russell LE, Schleiff MA, Gonzalez E, Bart AG, Broccatelli F, Hartman JH, Humphreys WG, Lauschke VM, Martin I, Nwabufo C, Prasad B, Scott EE, Segall M, Takahashi R, Taub ME, Sodhi JK. Advances in the study of drug metabolism - symposium report of the 12th Meeting of the International Society for the Study of Xenobiotics (ISSX). Drug Metab Rev 2020; 52:395-407. [PMID: 32456484 DOI: 10.1080/03602532.2020.1765793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The 12th International Society for the Study of Xenobiotics (ISSX) meeting, held in Portland, OR, USA from July 28 to 31, 2019, was attended by diverse members of the pharmaceutical sciences community. The ISSX New Investigators Group provides learning and professional growth opportunities for student and early career members of ISSX. To share meeting content with those who were unable to attend, the ISSX New Investigators herein elected to highlight the "Advances in the Study of Drug Metabolism" symposium, as it engaged attendees with diverse backgrounds. This session covered a wide range of current topics in drug metabolism research including predicting sites and routes of metabolism, metabolite identification, ligand docking, and medicinal and natural products chemistry, and highlighted approaches complemented by computational modeling. In silico tools have been increasingly applied in both academic and industrial settings, alongside traditional and evolving in vitro techniques, to strengthen and streamline pharmaceutical research. Approaches such as quantum mechanics simulations facilitate understanding of reaction energetics toward prediction of routes and sites of drug metabolism. Furthermore, in tandem with crystallographic and orthogonal wet lab techniques for structural validation of drug metabolizing enzymes, in silico models can aid understanding of substrate recognition by particular enzymes, identify metabolic soft spots and predict toxic metabolites for improved molecular design. Of note, integration of chemical synthesis and biosynthesis using natural products remains an important approach for identifying new chemical scaffolds in drug discovery. These subjects, compiled by the symposium organizers, presenters, and the ISSX New Investigators Group, are discussed in this review.
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Affiliation(s)
- Laura E Russell
- Department of Physiology and Pharmacology, University of Western Ontario, London, ON, Canada
| | - Mary Alexandra Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eric Gonzalez
- Division of Pre-Clinical Innovation, Therapeutic Development Branch, National Center for Advancing Translational Sciences, Bethesda, MD, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aaron G Bart
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Fabio Broccatelli
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Jessica H Hartman
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Bhagwat Prasad
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Emily E Scott
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.,Department of Medicinal Chemistry and Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Mitchell E Taub
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Jasleen K Sodhi
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, CA, USA
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9
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Preclinical toxicity of innovative molecules: In vitro, in vivo and metabolism prediction. Chem Biol Interact 2020; 315:108896. [DOI: 10.1016/j.cbi.2019.108896] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/19/2019] [Accepted: 11/08/2019] [Indexed: 11/22/2022]
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10
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Nair PC, McKinnon RA, Miners JO. Computational Prediction of the Site(s) of Metabolism and Binding Modes of Protein Kinase Inhibitors Metabolized by CYP3A4. Drug Metab Dispos 2019; 47:616-631. [DOI: 10.1124/dmd.118.085167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023] Open
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11
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Fast Methods for Prediction of Aldehyde Oxidase-Mediated Site-of-Metabolism. Comput Struct Biotechnol J 2019; 17:345-351. [PMID: 30949305 PMCID: PMC6429535 DOI: 10.1016/j.csbj.2019.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022] Open
Abstract
Aldehyde Oxidase (AO) is an enzyme involved in the metabolism of aldehydes and N-containing heterocyclic compounds. Many drug compounds contain heterocyclic moieties, and AO metabolism has lead to failure of several late-stage drug candidates. Therefore, it is important to take AO-mediated metabolism into account early in the drug discovery process, and thus, to have fast and reliable models to predict the site of metabolism (SOM). We have collected a dataset of 78 substrates of human AO with a total of 89 SOMs and 347 non-SOMs and determined atomic descriptors for each compound. The descriptors comprise NMR shielding and ESP charges from density functional theory (DFT), NMR chemical shift from ChemBioDraw, and Gasteiger charges from RDKit. Additionally, atomic accessibility was considered using 2D-SASA and relative span descriptors from SMARTCyp. Finally, stability of the product, the metabolite, was determined with DFT and also used as a descriptor. All descriptors have AUC larger than 0.75. In particular, descriptors related to the chemical shielding and chemical shift (AUC = 0.96) and ESP charges (AUC = 0.96) proved to be good descriptors. We recommend two simple methods to identify the SOM for a given molecule: 1) use ChemBioDraw to calculate the chemical shift or 2) calculate ESP charges or chemical shift using DFT. The first approach is fast but somewhat difficult to automate, while the second is more time-consuming, but can easily be automated. The two methods predict correctly 93% and 91%, respectively, of the 89 experimentally observed SOMs.
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12
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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13
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Lee KSS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys 2016; 613:1-11. [PMID: 27983948 DOI: 10.1016/j.abb.2016.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an important therapeutic target of many diseases, such as chronic obstructive pulmonary disease (COPD) and diabetic neuropathic pain. It acts by hydrolyzing and thus regulating specific bioactive long chain polyunsaturated fatty acid epoxides (lcPUFA), like epoxyeicosatrienoic acids (EETs). To better predict which epoxides could be hydrolyzed by sEH, one needs to dissect the important factors and structural requirements that govern the binding of the substrates to sEH. This knowledge allows further exploration of the physiological role played by sEH. Unfortunately, a crystal structure of sEH with a substrate bound has not yet been reported. In this report, new photoaffinity mimics of a sEH inhibitor and EET regioisomers were prepared and used in combination with peptide sequencing and computational modeling, to identify the binding orientation of different regioisomers and enantiomers of EETs into the catalytic cavity of sEH. Results indicate that the stereochemistry of the epoxide plays a crucial role in dictating the binding orientation of the substrate.
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Affiliation(s)
- Kin Sing Stephen Lee
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Connie J Ng
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Weitao Jia
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Armann Andaya
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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