1
|
Xu M, Lu Z, Wu Z, Gui M, Liu G, Tang Y, Li W. Development of In Silico Models for Predicting Potential Time-Dependent Inhibitors of Cytochrome P450 3A4. Mol Pharm 2023; 20:194-205. [PMID: 36458739 DOI: 10.1021/acs.molpharmaceut.2c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the major drug metabolizing enzymes in the human body and metabolizes ∼30-50% of clinically used drugs. Inhibition of CYP3A4 must always be considered in the development of new drugs. Time-dependent inhibition (TDI) is an important P450 inhibition type that could cause undesired drug-drug interactions. Therefore, identification of CYP3A4 TDI by a rapid convenient way is of great importance to any new drug discovery effort. Here, we report the development of in silico classification models for prediction of potential CYP3A4 time-dependent inhibitors. On the basis of the CYP3A4 TDI data set that we manually collected from literature and databases, both conventional machine learning and deep learning models were constructed. The comparisons of different sampling strategies, molecular representations, and machine-learning algorithms showed the benefits of a balanced data set and the deep-learning model featured by GraphConv. The generalization ability of the best model was tested by screening an external data set, and the prediction results were validated by biological experiments. In addition, several structural alerts that are relevant to CYP3A4 time-dependent inhibitors were identified via information gain and frequency analysis. We anticipate that our effort would be useful for identification of potential CYP3A4 time-dependent inhibitors in drug discovery and design.
Collapse
Affiliation(s)
- Minjie Xu
- 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, Shanghai200237, China
| | - Zhou Lu
- 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, Shanghai200237, China
| | - Zengrui Wu
- 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, Shanghai200237, China
| | - Minyan Gui
- 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, Shanghai200237, 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, Shanghai200237, 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, Shanghai200237, 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, Shanghai200237, China
| |
Collapse
|
2
|
McKittrick BA, Caldwell JP, Bara T, Boykow G, Chintala M, Clader J, Czarniecki M, Courneya B, Duffy R, Fleming L, Giessert R, Greenlee WJ, Heap C, Hong L, Huang Y, Iserloh U, Josien H, Khan T, Korfmacher W, Liang X, Mazzola R, Mitra S, Moore K, Orth P, Rajagopalan M, Roy S, Sakwa S, Strickland C, Vaccaro H, Voigt J, Wang H, Wong J, Zhang R, Zych A. Iminopyrimidinones: A novel pharmacophore for the development of orally active renin inhibitors. Bioorg Med Chem Lett 2015; 25:1592-6. [DOI: 10.1016/j.bmcl.2015.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
|
3
|
Yokokawa F. Recent progress on the discovery of non-peptidic direct renin inhibitors for the clinical management of hypertension. Expert Opin Drug Discov 2013; 8:673-90. [DOI: 10.1517/17460441.2013.791279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
4
|
Lorthiois E, Breitenstein W, Cumin F, Ehrhardt C, Francotte E, Jacoby E, Ostermann N, Sellner H, Kosaka T, Webb RL, Rigel DF, Hassiepen U, Richert P, Wagner T, Maibaum J. The discovery of novel potent trans-3,4-disubstituted pyrrolidine inhibitors of the human aspartic protease renin from in silico three-dimensional (3D) pharmacophore searches. J Med Chem 2013; 56:2207-17. [PMID: 23425156 DOI: 10.1021/jm3017078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The small-molecule trans-3,4-disubstituted pyrrolidine 6 was identified from in silico three-dimensional (3D) pharmacophore searches based on known X-ray structures of renin-inhibitor complexes and demonstrated to be a weakly active inhibitor of the human enzyme. The unexpected binding mode of the more potent enantiomer (3S,4S)-6a in an extended conformation spanning the nonprime and S1' pockets of the recombinant human (rh)-renin active site was elucidated by X-ray crystallography. Initial structure-activity relationship work focused on modifications of the hydrophobic diphenylamine portion positioned in S1 and extending toward the S2 pocket. Replacement with an optimized P3-P1 pharmacophore interacting to the nonsubstrate S3(sp) cavity eventually resulted in significantly improved in vitro potency and selectivity. The prototype analogue (3S,4S)-12a of this new class of direct renin inhibitors exerted blood pressure lowering effects in a hypertensive double-transgenic rat model after oral administration.
Collapse
Affiliation(s)
- Edwige Lorthiois
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Subramanian G. Computational modeling and design of renin inhibitors. Bioorg Med Chem Lett 2013; 23:460-5. [DOI: 10.1016/j.bmcl.2012.11.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/11/2012] [Accepted: 11/14/2012] [Indexed: 11/25/2022]
|
6
|
Nakamura Y, Fujimoto T, Ogawa Y, Sugita C, Miyazaki S, Tamaki K, Takahashi M, Matsui Y, Nagayama T, Manabe K, Mizuno M, Masubuchi N, Chiba K, Nishi T. Discovery of DS-8108b, a Novel Orally Bioavailable Renin Inhibitor. ACS Med Chem Lett 2012; 3:754-8. [PMID: 24900544 DOI: 10.1021/ml300168e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/18/2012] [Indexed: 11/28/2022] Open
Abstract
A novel orally bioavailable renin inhibitor, DS-8108b (5), showing potent renin inhibitory activity and excellent in vivo efficacy is described. We report herein the synthesis and pharmacological effects of 5 including renin inhibitory activity in vitro, suppressive effects of ex vivo plasma renin activity (PRA) in cynomolgus monkey, pharmacokinetic data, and blood pressure-lowering effects in an animal model. Compound 5 demonstrated inhibitory activities toward human renin (IC50 = 0.9 nM) and human and monkey PRA (IC50 = 1.9 and 6.3 nM, respectively). Oral administration of single doses of 3 and 10 mg/kg of 5 in cynomolgus monkey on pretreatment with furosemide led to dose-dependent significant reductions in ex vivo PRA and sustained lowering of mean arterial blood pressure for more than 12 h.
Collapse
Affiliation(s)
- Yuji Nakamura
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Teppei Fujimoto
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yasuyuki Ogawa
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chie Sugita
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Shojiro Miyazaki
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Kazuhiko Tamaki
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Mizuki Takahashi
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yumi Matsui
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takahiro Nagayama
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Kenichi Manabe
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Makoto Mizuno
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Noriko Masubuchi
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Katsuyoshi Chiba
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takahide Nishi
- Lead Discovery & Optimization Research Laboratories I, ‡Lead Discovery & Optimization Research Laboratories II, §Cardiovascular-Metabolics Research Laboratories, ∥Biological Research Laboratories, ⊥Drug Metabolism & Pharmacokinetics Research Laboratories, and #Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| |
Collapse
|
7
|
Fournier PA, Arbour M, Cauchon E, Chen A, Chefson A, Ducharme Y, Falgueyret JP, Gagné S, Grimm E, Han Y, Houle R, Lacombe P, Lévesque JF, MacDonald D, Mackay B, McKay D, Percival MD, Ramtohul Y, St-Jacques R, Toulmond S. Design and synthesis of potent, isoxazole-containing renin inhibitors. Bioorg Med Chem Lett 2012; 22:2670-4. [DOI: 10.1016/j.bmcl.2012.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/02/2012] [Accepted: 03/05/2012] [Indexed: 11/27/2022]
|
8
|
3,4-Diarylpiperidines as potent renin inhibitors. Bioorg Med Chem Lett 2012; 22:1953-7. [DOI: 10.1016/j.bmcl.2012.01.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/12/2012] [Accepted: 01/13/2012] [Indexed: 01/21/2023]
|
9
|
An integrated computational workflow for efficient and quantitative modeling of renin inhibitors. Bioorg Med Chem 2012; 20:851-8. [DOI: 10.1016/j.bmc.2011.11.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/22/2011] [Accepted: 11/28/2011] [Indexed: 12/19/2022]
|
10
|
Chen A, Aspiotis R, Campeau LC, Cauchon E, Chefson A, Ducharme Y, Falgueyret JP, Gagné S, Han Y, Houle R, Laliberté S, Larouche G, Lévesque JF, McKay D, Percival D. Renin inhibitors for the treatment of hypertension: Design and optimization of a novel series of spirocyclic piperidines. Bioorg Med Chem Lett 2011; 21:7399-404. [DOI: 10.1016/j.bmcl.2011.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/30/2011] [Accepted: 10/04/2011] [Indexed: 11/29/2022]
|
11
|
Renin inhibitors for the treatment of hypertension: Design and optimization of a novel series of tertiary alcohol-bearing piperidines. Bioorg Med Chem Lett 2011; 21:3976-81. [DOI: 10.1016/j.bmcl.2011.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 11/17/2022]
|
12
|
Lévesque JF, Bleasby K, Chefson A, Chen A, Dubé D, Ducharme Y, Fournier PA, Gagné S, Gallant M, Grimm E, Hafey M, Han Y, Houle R, Lacombe P, Laliberté S, MacDonald D, Mackay B, Papp R, Tschirret-Guth R. Impact of passive permeability and gut efflux transport on the oral bioavailability of novel series of piperidine-based renin inhibitors in rodents. Bioorg Med Chem Lett 2011; 21:5547-51. [PMID: 21784634 DOI: 10.1016/j.bmcl.2011.06.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 12/31/2022]
Abstract
An oral bioavailability issue encountered during the course of lead optimization in the renin program is described herein. The low F(po) of pyridone analogs was shown to be caused by a combination of poor passive permeability and gut efflux transport. Substitution of pyridone ring for a more lipophilic moiety (logD>1.7) had minimal effect on rMdr1a transport but led to increased passive permeability (P(app)>10 × 10(-6) cm/s), which contributed to overwhelm gut transporters and increase rat F(po). LogD and in vitro passive permeability determination were found to be key in guiding SAR and improve oral exposure of renin inhibitors.
Collapse
Affiliation(s)
- Jean-François Lévesque
- Merck Frosst Centre for Therapeutic Research, 16711 Trans Canada Highway, Kirkland, Québec, Canada H9H 3L1.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Campeau LC, Dolman SJ, Gauvreau D, Corley E, Liu J, Guidry EN, Ouellet SG, Steinhuebel D, Weisel M, O’Shea PD. Convergent Kilo-Scale Synthesis of a Potent Renin Inhibitor for the Treatment of Hypertension. Org Process Res Dev 2011. [DOI: 10.1021/op2001063] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Louis-Charles Campeau
- Global Process Chemistry, Merck-Frosst, 16711 Trans Canada Highway, Kirkland, Québec H9H 3L1, Canada
| | - Sarah J. Dolman
- Global Process Chemistry, Merck-Frosst, 16711 Trans Canada Highway, Kirkland, Québec H9H 3L1, Canada
| | - Danny Gauvreau
- Global Process Chemistry, Merck-Frosst, 16711 Trans Canada Highway, Kirkland, Québec H9H 3L1, Canada
| | - Ed Corley
- Global Process Chemistry, Merck, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Jinchu Liu
- Global Process Chemistry, Merck, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Erin N. Guidry
- Global Process Chemistry, Merck, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Stéphane G. Ouellet
- Global Process Chemistry, Merck-Frosst, 16711 Trans Canada Highway, Kirkland, Québec H9H 3L1, Canada
| | - Dietrich Steinhuebel
- Global Process Chemistry, Merck, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Mark Weisel
- Global Process Chemistry, Merck, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Paul D. O’Shea
- Global Process Chemistry, Merck-Frosst, 16711 Trans Canada Highway, Kirkland, Québec H9H 3L1, Canada
| |
Collapse
|