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Wang Z, Wang S, Wang H, Hu B, Qi Z, Zhang Y, Song P, Cai Q, Yang H, Wang J. Uncovering the selectivity mechanism of phosphodiesterase 7A/8A inhibitors through computational studies. Phys Chem Chem Phys 2024; 26:11770-11781. [PMID: 38566586 DOI: 10.1039/d3cp03913g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The expression of phosphodiesterase 7A (PDE7A) and phosphodiesterase 8A (PDE8) genes is integral to human signaling pathways, and the inhibition of PDE7A has been associated with the onset of various diseases, including effects on the immune system and nervous system. The development of PDE7 selective inhibitors can promote research on immune and nervous system diseases, such as multiple sclerosis, chronic inflammation, and autoimmune responses. PDE8A is expressed alongside PDE8B, and its inhibitory mechanism is still unclear. Studying the mechanisms of selective inhibitors against different PDE subtypes is crucial to prevent potential side effects, such as nausea and cardiac toxicity, and the sequence similarity of the two protein subtypes was 55.9%. Therefore, it is necessary to investigate the differences of both subtypes' ligand binding sites. Selective inhibitors of two proteins were chosen to summarize the reason for their selectivity through molecular docking, molecular dynamics simulation, alanine scanning mutagenesis, and MM-GBSA calculation. We found that Phe384PDE7A, Leu401PDE7A, Gln413PDE7A, Tyr419PDE7A, and Phe416PDE7A in the active site positively contribute to the selectivity towards PDE7A. Additionally, Asn729PDE8A, Phe767PDE8A, Gln778PDE8A, and Phe781PDE8A positively contribute to the selectivity towards PDE8A.
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Affiliation(s)
- Zhijian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Shizun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Hanxun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Baichun Hu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zhuo Qi
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yaming Zhang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Pengfei Song
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Qingkui Cai
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Huali Yang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
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Liu Y, Chen Y, Zhang J, Ran G, Cheng Z, Wang X, Liao Y, Mao X, Peng Y, Li W, Zheng J. Dihydrotanshinone I-Induced CYP1 Enzyme Inhibition and Alteration of Estradiol Metabolism. Drug Metab Dispos 2024; 52:188-197. [PMID: 38123940 DOI: 10.1124/dmd.123.001490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Dihydrotanshinone I (DHTI) is a pharmacologically active component occurring in the roots of the herbal medicine Salvia miltiorrhiza Bunge. This study investigated DHTI-induced inhibition of CYP1A1, CYP1A2, and CYP1B1 with the aim to determine the potential effects of DHTI on the bioactivation of estradiol (E2), possibly related to preventive/therapeutic strategy for E2-associated breast cancer. Ethoxyresorufin as a specific substrate for CYP1s was incubated with human recombinant CYP1A1, CYP1A2, or CYP1B1 in the presence of DHTI at various concentrations. Enzymatic inhibition and kinetic behaviors were examined by monitoring the formation of the corresponding product. Molecular docking was further conducted to define the interactions between DHTI and the three CYP1s. The same method and procedure were employed to examine the DHTI-induced alteration of E2 metabolism. DHTI showed significant inhibition of ethoxyresorufin O-deethylation activity catalyzed by CYP1A1, CYP1A2 and CYP1B1 in a concentration-dependent manner (IC50 = 0.56, 0.44, and 0.11 μM, respectively). Kinetic analysis showed that DHTI acted as a competitive type of inhibitor of CYP1A1 and CYP1B1, whereas it noncompetitively inhibited CYP1A2. The observed enzyme inhibition was independent of NADPH and time. Molecular docking analysis revealed hydrogen bonding interactions between DHTI and Asp-326 of CYP1B1. Moreover, DHTI displayed preferential activity to inhibit 4-hydroxylation of E2 (a genotoxic pathway) mediated by CYP1B1. Exposure to DHTI could reduce the risk of genotoxicity induced by E2. SIGNIFICANCE STATEMENT: CYP1A1, CYP1A2, and CYP1B1 enzymes are involved in the conversion of estradiol (E2) into 2-hydroxyestradiol (2-OHE2) and 4-hydroxyestradiol (4-OHE2) through oxidation. 2-OHE2 is negatively correlated with breast cancer risk, and 4-OHE2 may be a significant initiator and promoter of breast cancer. The present study revealed that dihydrotanshinone I (DHTI) competitively inhibits CYP1A1/CYP1B1 and noncompetitively inhibits CYP1A2. DHTI exhibits a preference for inhibiting the genotoxicity associated with E2 4-hydroxylation pathway mediated by CYP1B1, potentially reducing the risk of 4-OHE2-induced genotoxicity.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Jingyu Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Guangyun Ran
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Zihao Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Xin Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Yufen Liao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Xu Mao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics (Y.L., Y.C., J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education (J.Zhe.), School of Basic Medical Sciences (Y.L., Y.C., J.Zhe.), and School of Pharmacy (J.Zha., G.R., Z.C., X.W., Y.L., W.L., J.Zhe.), Guizhou Medical University, Guiyang, Guizhou, China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, China (Y.P., J.Zhe.); and Department of Pharmaceutical Analysis, College of Pharmacy, Mudanjiang Medical University, Mudanjiang, China (X.M.)
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5
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Zhang H, Xu P, Wang T, Wang S, Li W, Mao J, Wang J, Zhang F, Cheng M. Design, synthesis and biological evaluation of highly potent and selective CYP1B1 inhibitors. NEW J CHEM 2023. [DOI: 10.1039/d2nj05691g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
A series of highly potent and selective CYP1B1 inhibitors based on N-phenyl-[2,4′-bithiazol]-2′-amine were obtained and their structure–activity-relationships were analyzed.
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Affiliation(s)
- Haoyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ping Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ting Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shiyu Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jianping Mao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Fengjiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China
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6
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Raju B, Narendra G, Verma H, Kumar M, Sapra B, Kaur G, jain SK, Silakari O. Machine Learning Enabled Structure-Based Drug Repurposing Approach to Identify Potential CYP1B1 Inhibitors. ACS OMEGA 2022; 7:31999-32013. [PMID: 36120033 PMCID: PMC9476183 DOI: 10.1021/acsomega.2c02983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Drug-metabolizing enzyme (DME)-mediated pharmacokinetic resistance of some clinically approved anticancer agents is one of the main reasons for cancer treatment failure. In particular, some commonly used anticancer medicines, including docetaxel, tamoxifen, imatinib, cisplatin, and paclitaxel, are inactivated by CYP1B1. Currently, no approved drugs are available to treat this CYP1B1-mediated inactivation, making the pharmaceutical industries strive to discover new anticancer agents. Because of the extreme complexity and high risk in drug discovery and development, it is worthwhile to come up with a drug repurposing strategy that may solve the resistance problem of existing chemotherapeutics. Therefore, in the current study, a drug repurposing strategy was implemented to find the possible CYP1B1 inhibitors using machine learning (ML) and structure-based virtual screening (SB-VS) approaches. Initially, three different ML models were developed such as support vector machines (SVMs), random forest (RF), and artificial neural network (ANN); subsequently, the best-selected ML model was employed for virtual screening of the selleckchem database to identify potential CYP1B1 inhibitors. The inhibition potency of the obtained hits was judged by analyzing the crucial active site amino acid interactions against CYP1B1. After a thorough assessment of docking scores, binding affinities, as well as binding modes, four compounds were selected and further subjected to in vitro analysis. From the in vitro analysis, it was observed that chlorprothixene, nadifloxacin, and ticagrelor showed promising inhibitory activity toward CYP1B1 in the IC50 range of 0.07-3.00 μM. These new chemical scaffolds can be explored as adjuvant therapies to address CYP1B1-mediated drug-resistance problems.
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Affiliation(s)
- Baddipadige Raju
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gera Narendra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Himanshu Verma
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Manoj Kumar
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Bharti Sapra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gurleen Kaur
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Subheet Kumar jain
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Om Silakari
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
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