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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.
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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
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Alles SRA, Smith PA. Peripheral Voltage-Gated Cation Channels in Neuropathic Pain and Their Potential as Therapeutic Targets. FRONTIERS IN PAIN RESEARCH 2022; 2:750583. [PMID: 35295464 PMCID: PMC8915663 DOI: 10.3389/fpain.2021.750583] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
The persistence of increased excitability and spontaneous activity in injured peripheral neurons is imperative for the development and persistence of many forms of neuropathic pain. This aberrant activity involves increased activity and/or expression of voltage-gated Na+ and Ca2+ channels and hyperpolarization activated cyclic nucleotide gated (HCN) channels as well as decreased function of K+ channels. Because they display limited central side effects, peripherally restricted Na+ and Ca2+ channel blockers and K+ channel activators offer potential therapeutic approaches to pain management. This review outlines the current status and future therapeutic promise of peripherally acting channel modulators. Selective blockers of Nav1.3, Nav1.7, Nav1.8, Cav3.2, and HCN2 and activators of Kv7.2 abrogate signs of neuropathic pain in animal models. Unfortunately, their performance in the clinic has been disappointing; some substances fail to meet therapeutic end points whereas others produce dose-limiting side effects. Despite this, peripheral voltage-gated cation channels retain their promise as therapeutic targets. The way forward may include (i) further structural refinement of K+ channel activators such as retigabine and ASP0819 to improve selectivity and limit toxicity; use or modification of Na+ channel blockers such as vixotrigine, PF-05089771, A803467, PF-01247324, VX-150 or arachnid toxins such as Tap1a; the use of Ca2+ channel blockers such as TTA-P2, TTA-A2, Z 944, ACT709478, and CNCB-2; (ii) improving methods for assessing “pain” as opposed to nociception in rodent models; (iii) recognizing sex differences in pain etiology; (iv) tailoring of therapeutic approaches to meet the symptoms and etiology of pain in individual patients via quantitative sensory testing and other personalized medicine approaches; (v) targeting genetic and biochemical mechanisms controlling channel expression using anti-NGF antibodies such as tanezumab or re-purposed drugs such as vorinostat, a histone methyltransferase inhibitor used in the management of T-cell lymphoma, or cercosporamide a MNK 1/2 inhibitor used in treatment of rheumatoid arthritis; (vi) combination therapy using drugs that are selective for different channel types or regulatory processes; (vii) directing preclinical validation work toward the use of human or human-derived tissue samples; and (viii) application of molecular biological approaches such as clustered regularly interspaced short palindromic repeats (CRISPR) technology.
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Affiliation(s)
- Sascha R A Alles
- Department of Anesthesiology and Critical Care Medicine, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Peter A Smith
- Department of Pharmacology, Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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Li B, Liu R, Yang J, Luo J, Yao L, Li M, Zheng X, Jiang R, Nie H, Zhang S. Iridium-Catalyzed Asymmetric Hydrogenation of Sterically Hindered Cyclic Imines for Enantioselective Synthesis of Tetrahydroisoquinolines. Org Lett 2020; 23:140-144. [PMID: 33351639 DOI: 10.1021/acs.orglett.0c03858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An efficient enantioselective hydrogenation of sterically hindered cyclic imines catalyzed by the Ir-tBu-ax-Josiphos complex has been described, producing a series of useful chiral bulky tetrahydroisoquinoline analogs in high isolated yields (85-96%) with good to excellent enantioselectivities (74-99% ee). This transformation provided highly straightforward access to the useful derivatives of tetrahydroisoquinolines, which are of great potential value in drug molecule and natural product research.
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Affiliation(s)
- Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, The College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Ruixia Liu
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Jing Yang
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Jingyuan Luo
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Lin Yao
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Muqiong Li
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, The College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Ru Jiang
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Huifang Nie
- School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Shengyong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, The College of Life Sciences, Northwest University, Xi'an 710069, P. R. China.,School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
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Kolade SO, Izunobi JU, Hosten EC, Olasupo IA, Ogunlaja AS, Familoni OB. Synthesis, crystal structure and docking studies of tetracyclic 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide and its precursors. Acta Crystallogr C Struct Chem 2020; 76:810-820. [PMID: 32756044 DOI: 10.1107/s2053229620009626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
The title compound, 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide, C15H11IN2O2S (8), was synthesized via the metal-free intramolecular N-iodosuccinimide (NIS)-mediated radical oxidative sp3-C-H aminative cyclization of 2-(2'-aminobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H16N2O2S (7). The amino adduct 7 was prepared via a two-step reaction, starting from the condensation of 2-nitrobenzenesulfonyl chloride (4) with 1,2,3,4-tetrahydroisoquinoline (5), to afford 2-(2'-nitrobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H14N2O4S (6), in 82% yield. The catalytic hydrogenation of 6 with hydrogen gas, in the presence of 10% palladium-on-charcoal catalyst, furnished 7. Products 6-8 were characterized by their melting points, IR and NMR (1H and 13C) spectroscopy, and single-crystal X-ray diffraction. The three compounds crystallized in the monoclinic space group, with 7 exhibiting classical intramolecular hydrogen bonds of 2.16 and 2.26 Å. All three crystal structures exhibit centrosymmetric pairs of intermolecular C-H...π(ring) and/or π-π stacking interactions. The docking studies of molecules 6, 7 and 8 with deoxyribonucleic acid (PDB id: 1ZEW) revealed minor-groove binding behaviours without intercalation, with 7 presenting the most favourable global energy of the three molecules. Nonetheless, molecule 8 interacted strongly with the DNA macromolecule, with an attractive van der Waals energy of -15.53 kcal mol-1.
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Affiliation(s)
- Sherif O Kolade
- Chemistry, University of Lagos, Akoka-Yaba, Lagos 100001, Nigeria
| | | | - Eric C Hosten
- Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth 6031, South Africa
| | - Idris A Olasupo
- Chemistry, University of Lagos, Akoka-Yaba, Lagos 100001, Nigeria
| | - Adeniyi S Ogunlaja
- Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth 6031, South Africa
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Punirun T, Soorukram D, Kuhakarn C, Reutrakul V, Pohmakotr M. Oxidative Difluoromethylation of Tetrahydroisoquinolines Using TMSCF 2SPh: Synthesis of Fluorinated Pyrrolo[2,1-a]isoquinolines and Benzo[a]quinolizidines. J Org Chem 2018; 83:765-782. [PMID: 29271203 DOI: 10.1021/acs.joc.7b02783] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An efficient C1-difluoromethylation of tetrahydroisoquinolenes was achieved using TMSCF2SPh as a difluoromethylating agent and 2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (TEMPO+BF4-) as an oxidant. The process provides an access to a variety of C1-difluoro(phenylsulfanyl)methylated tetrahydroisoquinoline adducts in good yields. These adducts were employed as key precursors for preparing fluorinated pyrrolo[2,1-a]isoquinoline and benzo[a]quinolizidines.
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Affiliation(s)
- Teerachai Punirun
- Center of Excellence for Innovation in Chemistry (PERCH-CIC) and Department of Chemistry, Faculty of Science, Mahidol University , Rama VI Road, Bangkok 10400, Thailand
| | - Darunee Soorukram
- Center of Excellence for Innovation in Chemistry (PERCH-CIC) and Department of Chemistry, Faculty of Science, Mahidol University , Rama VI Road, Bangkok 10400, Thailand
| | - Chutima Kuhakarn
- Center of Excellence for Innovation in Chemistry (PERCH-CIC) and Department of Chemistry, Faculty of Science, Mahidol University , Rama VI Road, Bangkok 10400, Thailand
| | - Vichai Reutrakul
- Center of Excellence for Innovation in Chemistry (PERCH-CIC) and Department of Chemistry, Faculty of Science, Mahidol University , Rama VI Road, Bangkok 10400, Thailand
| | - Manat Pohmakotr
- Center of Excellence for Innovation in Chemistry (PERCH-CIC) and Department of Chemistry, Faculty of Science, Mahidol University , Rama VI Road, Bangkok 10400, Thailand
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Botz B, Bölcskei K, Helyes Z. Challenges to develop novel anti-inflammatory and analgesic drugs. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27576790 DOI: 10.1002/wnan.1427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 07/30/2016] [Indexed: 12/11/2022]
Abstract
Chronic inflammatory diseases and persistent pain of different origin represent common medical, social, and economic burden, and their pharmacotherapy is still an unresolved issue. Therefore, there is a great and urgent need to develop anti-inflammatory and analgesic agents with novel mechanisms of action, but it is a very challenging task. The main problem is the relatively large translational gap between the preclinical experimental data and the clinical results due to characteristics of the models, difficulties with the investigational techniques particularly for pain, as well as species differences in the mechanisms. We summarize here the current state-of-the-art medication and related ongoing strategies, and the novel targets with lead molecules under clinical development. The first members of the gold-standard categories, such as nonsteroidal anti-inflammatory drugs, glucocorticoids, and opioids, were introduced decades ago, and since then very few drugs with novel mechanisms of action have been successfully taken to the clinics despite considerable development efforts. Several biologics targeting different key molecules have provided breakthrough in some autoimmune/inflammatory diseases, but they are expensive, only parenterally available, their long-term side effects often limit their administration, and they do not effectively reduce pain. Some kinase inhibitors and phosphodiesterase-4 blockers have recently been introduced as new directions. There are in fact some promising novel approaches at different clinical stages of drug development focusing on transient receptor potential vanilloid 1/ankyrin 1 channel antagonism, inhibition of voltage-gated sodium/calcium channels, several enzymes (kinases, semicarbazide-sensitive amine oxidases, and matrix metalloproteinases), cytokines/chemokines, transcription factors, nerve growth factor, and modulation of several G protein-coupled receptors (cannabinoids, purinoceptors, and neuropeptides). WIREs Nanomed Nanobiotechnol 2017, 9:e1427. doi: 10.1002/wnan.1427 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bálint Botz
- Department of Radiology, Faculty of Medicine, University of Pécs, Pécs, Hungary.,János Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Kata Bölcskei
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Pécs, Pécs, Hungary
| | - Zsuzsanna Helyes
- János Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Pécs, Pécs, Hungary.,MTA-PTE NAP B Chronic Pain Research Group, Faculty of Medicine, University of Pécs, Pécs, Hungary
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Tibbs GR, Posson DJ, Goldstein PA. Voltage-Gated Ion Channels in the PNS: Novel Therapies for Neuropathic Pain? Trends Pharmacol Sci 2016; 37:522-542. [DOI: 10.1016/j.tips.2016.05.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/24/2016] [Accepted: 05/03/2016] [Indexed: 12/19/2022]
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