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Cavalcante BRR, Freitas RD, Siquara da Rocha LO, Santos RSB, Souza BSDF, Ramos PIP, Rocha GV, Gurgel Rocha CA. In silico approaches for drug repurposing in oncology: a scoping review. Front Pharmacol 2024; 15:1400029. [PMID: 38919258 PMCID: PMC11196849 DOI: 10.3389/fphar.2024.1400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction: Cancer refers to a group of diseases characterized by the uncontrolled growth and spread of abnormal cells in the body. Due to its complexity, it has been hard to find an ideal medicine to treat all cancer types, although there is an urgent need for it. However, the cost of developing a new drug is high and time-consuming. In this sense, drug repurposing (DR) can hasten drug discovery by giving existing drugs new disease indications. Many computational methods have been applied to achieve DR, but just a few have succeeded. Therefore, this review aims to show in silico DR approaches and the gap between these strategies and their ultimate application in oncology. Methods: The scoping review was conducted according to the Arksey and O'Malley framework and the Joanna Briggs Institute recommendations. Relevant studies were identified through electronic searching of PubMed/MEDLINE, Embase, Scopus, and Web of Science databases, as well as the grey literature. We included peer-reviewed research articles involving in silico strategies applied to drug repurposing in oncology, published between 1 January 2003, and 31 December 2021. Results: We identified 238 studies for inclusion in the review. Most studies revealed that the United States, India, China, South Korea, and Italy are top publishers. Regarding cancer types, breast cancer, lymphomas and leukemias, lung, colorectal, and prostate cancer are the top investigated. Additionally, most studies solely used computational methods, and just a few assessed more complex scientific models. Lastly, molecular modeling, which includes molecular docking and molecular dynamics simulations, was the most frequently used method, followed by signature-, Machine Learning-, and network-based strategies. Discussion: DR is a trending opportunity but still demands extensive testing to ensure its safety and efficacy for the new indications. Finally, implementing DR can be challenging due to various factors, including lack of quality data, patient populations, cost, intellectual property issues, market considerations, and regulatory requirements. Despite all the hurdles, DR remains an exciting strategy for identifying new treatments for numerous diseases, including cancer types, and giving patients faster access to new medications.
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Affiliation(s)
- Bruno Raphael Ribeiro Cavalcante
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Raíza Dias Freitas
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Social and Pediatric Dentistry of the School of Dentistry, Federal University of Bahia, Salvador, Brazil
| | - Leonardo de Oliveira Siquara da Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
| | | | - Bruno Solano de Freitas Souza
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
| | - Pablo Ivan Pereira Ramos
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Center of Data and Knowledge Integration for Health (CIDACS), Salvador, Brazil
| | - Gisele Vieira Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
| | - Clarissa Araújo Gurgel Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
- Department of Propaedeutics, School of Dentistry of the Federal University of Bahia, Salvador, Brazil
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Kuang Y, Ma X, Shen W, Rao Q, Yang S. Discovery of 3CLpro inhibitor of SARS-CoV-2 main protease. Future Sci OA 2023; 9:FSO853. [PMID: 37090493 PMCID: PMC10116374 DOI: 10.2144/fsoa-2023-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Coronavirus main protease (3CLpro), a special cysteine protease in coronavirus family, is highly desirable in the life cycle of coronavirus. Here, molecular docking, ADMET pharmacokinetic profiles and molecular dynamics (MD) simulation were performed to develop specific 3CLpro inhibitor. The results showed that the 137 compounds originated from Chinese herbal have good binding affinity to 3CLpro. Among these, Cleomiscosin C, (+)-Norchelidonine, Protopine, Turkiyenine, Isochelidonine and Mallotucin A possessed prominent drug-likeness properties. Cleomiscosin C and Turkiyenine exhibited excellent pharmacokinetic profiles. Furthermore, the complex of Cleomiscosin C with SARS-CoV-2 main protease presented high stability. The findings in this work indicated that Cleomiscosin C is highly promising as a potential 3CLpro inhibitor, thus facilitating the development of effective drugs for COVID-19.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, Zhejiang, 311300, PR China
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Mozibullah M, Junaid M. Biological Role of the PAK4 Signaling Pathway: A Prospective Therapeutic Target for Multivarious Cancers. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Li Y, Lu Q, Xie C, Yu Y, Zhang A. Recent advances on development of p21-activated kinase 4 inhibitors as anti-tumor agents. Front Pharmacol 2022; 13:956220. [PMID: 36105226 PMCID: PMC9465411 DOI: 10.3389/fphar.2022.956220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022] Open
Abstract
The p21-activated kinase 4 (PAK4) is a member of the PAKs family. It is overexpressed in multiple tumor tissues. Pharmacological inhibition of PAK4 attenuates proliferation, migration, and invasion of cancer cells. Recent studies revealed that inhibition of PAK4 sensitizes immunotherapy which has been extensively exploited as a new strategy to treat cancer. In the past few years, a large number of PAK4 inhibitors have been reported. Of note, the allosteric inhibitor KPT-9274 has been tested in phase Ⅰ clinic trials. Herein, we provide an update on recent research progress on the PAK4 mediated signaling pathway and highlight the development of the PAK4 small molecular inhibitors in recent 5 years. Meanwhile, challenges, limitations, and future developmental directions will be discussed as well.
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Affiliation(s)
- Yang Li
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghu Xie
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yiming Yu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ao Zhang
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Ao Zhang,
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5
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Yao H, Ren Y, Yan J, Liu J, Hu J, Yan M, Li X. Design, Synthesis, and Evaluation of New Mesenchymal–Epithelial Transition Factor (c-Met) Kinase Inhibitors with Dual Chiral Centers. Molecules 2022; 27:molecules27175359. [PMID: 36080127 PMCID: PMC9457593 DOI: 10.3390/molecules27175359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
A series of tepotinib derivatives with two chiral centers was designed, synthesized, and evaluated as anticancer agents. The optimal compound (R, S)-12a strongly exhibited antiproliferative activity against MHCC97H cell lines with an IC50 value of 0.002 μM, compared to tepotinib (IC50 = 0.013 μM). Mechanistic studies revealed that compound (R, S)-12a significantly inhibited c-Met activation, as well as the downstream AKT signaling pathway, and suppressed wound closure. Moreover, compound (R, S)-12a induced cellular apoptosis and cell cycle arrest at the G1 phase in a dose-dependent fashion.
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Affiliation(s)
- Han Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyuan Ren
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Yan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiadai Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jinhui Hu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
- Correspondence: (J.H.); (M.Y.)
| | - Ming Yan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Correspondence: (J.H.); (M.Y.)
| | - Xingshu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Differential roles and regulation of the protein kinases PAK4, PAK5 and PAK6 in melanoma cells. Biochem J 2022; 479:1709-1725. [PMID: 35969127 PMCID: PMC9444074 DOI: 10.1042/bcj20220184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/30/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022]
Abstract
The protein kinases PAK4, PAK5 and PAK6 comprise a family of ohnologues. In multiple cancers including melanomas PAK5 most frequently carries non-synonymous mutations; PAK6 and PAK4 have fewer; and PAK4 is often amplified. To help interpret these genomic data, initially we compared the cellular regulation of the sister kinases and their roles in melanoma cells. In common with many ohnologue protein kinases, PAK4, PAK5 and PAK6 each have two 14-3-3-binding phosphosites of which phosphoSer99 is conserved. PAK4 localises to the leading edge of cells in response to phorbol ester-stimulated binding of 14-3-3 to phosphoSer99 and phosphoSer181, which are phosphorylated by two different PKCs or PKDs. These phosphorylations of PAK4 are essential for its phorbol ester-stimulated phosphorylation of downstream substrates. In contrast, 14-3-3 interacts with PAK5 in response to phorbol ester-stimulated phosphorylation of Ser99 and epidermal growth factor-stimulated phosphorylation of Ser288; whereas PAK6 docks onto 14-3-3 and is prevented from localising to cell–cell junctions when Ser133 is phosphorylated in response to cAMP-elevating agents via PKA and insulin-like growth factor 1 via PKB/Akt. Silencing of PAK4 impairs viability, migration and invasive behaviour of melanoma cells carrying BRAFV600E or NRASQ61K mutations. These defects are rescued by ectopic expression of PAK4, more so by a 14-3-3-binding deficient PAK4, and barely by PAK5 or PAK6. Together these genomic, biochemical and cellular data suggest that the oncogenic properties of PAK4 are regulated by PKC–PKD signalling in melanoma, while PAK5 and PAK6 are dispensable in this cancer.
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Yuan Y, Zhang H, Li D, Li Y, Lin F, Wang Y, Song H, Liu X, Li F, Zhang J. PAK4 in cancer development: Emerging player and therapeutic opportunities. Cancer Lett 2022; 545:215813. [DOI: 10.1016/j.canlet.2022.215813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
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Wang Y, Hu B, Zhang Y, Wang D, Luo Z, Wang J, Zhang F. Perspective of structural flexibility on selective inhibition towards CYP1B1 over CYP1A1 by α-naphthoflavone analogs. Phys Chem Chem Phys 2021; 23:20230-20246. [PMID: 34474468 DOI: 10.1039/d1cp02541d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Research on action selectivity between CYP1A1 and CYP1B1 is particularly valuable for cancer chemoprevention and chemotherapy. However, they share a very close similarity in their ligand-binding pockets that α-naphthoflavone (ANF) is the co-crystal ligand for both isoforms, which poses a major challenge in revealing their selectivity mechanism. Therefore, three selective CYP1B1 inhibitors derived from ANF were selected to illustrate the structural basis for the selectivity between the two isoforms via a comprehensive computational strategy. It was found that the sustainability of the π-π stacking interactions with the phenylalanine residues of the two isoforms, namely, Phe123, Phe224, and Phe258 for CYP1A1, and Phe134, Phe231, and Phe268 for CYP1B1, played a crucial role in determining the selectivity of ligands with a classic aromatic conjugation system like ANF and its derivatives for CYP1B1 versus CYP1A1. Of note, the structural flexibility of the corresponding protein domains mainly orchestrated the sustainability of the corresponding π-π stacking interactions, thereby determining the binding selectivity. Therefore, the structure modification of naphthoflavone lead compounds into preferable binding configurations to satisfy the π-π stacking interactions of the key phenylalanine residues within CYP1B1 would be an inspiring strategy devised to improve the inhibitory selectivity towards CYP1B1. Collectively, this study revealed valuable insight into understanding the selective mechanism between CYP1A1 and CYP1B1 from the perspective of structural flexibility, which sheds light on the future rational design of CYP1B1 selective inhibitors.
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Affiliation(s)
- Ying Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yupeng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Dong Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Zhaohu Luo
- 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, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Fengjiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
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Shi S, Wang H, Wang J, Wang Y, Xue X, Hou Z, Yao GD, Huang XX, Zhao H, Liu Q, Song SJ. Semi-synthesis and biological evaluation of flavone hybrids as multifunctional agents for the potential treatment of Alzheimer's disease. Bioorg Chem 2020; 100:103917. [PMID: 32442817 DOI: 10.1016/j.bioorg.2020.103917] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
7-O-galloyltricetiflavan (GTF), a natural flavonoid, is known to exert anti-oxidation and neuroprotective activity, which are related to the prevention of Alzheimer's disease (AD). In this study, three series of GTF hybrids have been designed, synthesized and evaluated as multifunctional agents for treatment AD. The biological assays indicated that most of them showed strong inhibitory effect on self-induced β-amyloid (Aβ) aggregation, and a significant ability to inhibit ChEs. Among them, compound A15 exhibited best inhibition of Aβ aggregation (78.81% at 20 μM), potent AChE inhibitory potencies (IC50, 0.56 μM), and compound C4 presented the highest ability to inhibit BuChE (IC50, 5.77 μM). Furthermore, kinetic, molecular modeling and molecular dynamics studies revealed that A15 and C4 could interact with the catalytic active site of AChE and BuChE, respectively. In addition, compounds A15 and C4 could cross the blood-brain barrier in vitro. More importantly, A15 and C4 also showed excellent neuroprotective activities against H2O2-induced human neuroblastoma SH-SY5Y cells damage and nearly no toxicity on SH-SY5Y cells. All of these outstanding in vitro results indicated A15 and C4 as the leading structure worthy of further investigation.
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Affiliation(s)
- Shaochun Shi
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Huibin Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, PR China
| | - Yvxi Wang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiaobian Xue
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zilin Hou
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Hongwei Zhao
- Jilin Yizheng Pharmaceutical Group Co., Ltd., Jilin Province, Siping 136001, People's Republic of China
| | - Qingbo Liu
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China; Jilin Yizheng Pharmaceutical Group Co., Ltd., Jilin Province, Siping 136001, People's Republic of China.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
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Pourshojaei Y, Abiri A, Eskandari K, Haghighijoo Z, Edraki N, Asadipour A. Phenoxyethyl Piperidine/Morpholine Derivatives as PAS and CAS Inhibitors of Cholinesterases: Insights for Future Drug Design. Sci Rep 2019; 9:19855. [PMID: 31882733 PMCID: PMC6934599 DOI: 10.1038/s41598-019-56463-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylcholinesterase (AChE) catalyzes the conversion of Aβ peptide to its aggregated form and the peripheral anionic site (PAS) of AChE is mainly involved in this phenomenon. Also catalytic active site (CAS) of donepezil stimulates the break-down of acetylcholine (ACh) and depletion of ACh in cholinergic synapses are well established in brains of patients with AD. In this study, a set of compounds bearing phenoxyethyl amines were synthesized and their inhibitory activity toward electric eel AChE (eeAChE) and equine butyrylcholinesterase (eqBuChE) were evaluated. Molecular dynamics (MD) was employed to record the binding interactions of best compounds against human cholinesterases (hAChE and hBuChE) as well as donepezil as reference drug. In vitro results revealed that compound 5c is capable of inhibiting eeAChE activity at IC50 of 0.50 µM while no inhibitory activity was found for eqBuChE for up to 100 µM concentrations. Compound 5c, also due to its facile synthesis, small structure and high selectivity for eeAChE would be very interesting candidate in forthcoming studies. The main interacting parts of compound 5c and compound 7c (most potent eeAChE and eqBuChE inhibitors respectively) with receptors which confer selectivity for AChE and BuChE inhibition were identified, discussed, and compared with donepezil’s interactions. Also during MD simulation it was discovered for the first time that binding of substrates like donepezil to dual CAS and PAS or solely CAS region might have a suppressive impact on 4-α-helical bundles near the tryptophan amphiphilic tetramerization (WAT) domain of AChE and residues which are far away from AChE active site. The results proposed that residues involved in donepezil interactions (Trp86 and Phe295) which are located in CAS and mid-gorge are the mediator of conformational changes in whole protein structure.
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Affiliation(s)
- Yaghoub Pourshojaei
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Khalil Eskandari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Zahra Haghighijoo
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Asadipour
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
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Gao Y, Wang H, Wang J, Cheng M. In silico studies on p21-activated kinase 4 inhibitors: comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations, and MM-GBSA calculation. J Biomol Struct Dyn 2019; 38:4119-4133. [PMID: 31556340 DOI: 10.1080/07391102.2019.1673823] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
P21-activated kinase 4 (PAK4) is a serine/threonine protein kinase, which is associated with many cancer diseases, and thus being considered as a potential drug target. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations were performed to explore the structure-activity relationship of a series of pyrropyrazole PAK4 inhibitors. The statistical parameters of comparative molecular field analysis (CoMFA, Q 2 = 0.837, R 2 = 0.990, and R 2 pred = 0.967) and comparative molecular similarity indices analysis (CoMSIA, Q 2 = 0.720, R 2 = 0.972, and R 2 pred = 0.946) were obtained from 3D-QSAR model, which exhibited good predictive ability and significant statistical reliability. The binding mode of PAK4 with its inhibitors was obtained through molecular docking study, which indicated that the residues of GLU396, LEU398, LYS350, and ASP458 were important for activity. Molecular mechanics generalized born surface area (MM-GBSA) method was performed to calculate the binding free energy, which indicated that the coulomb, lipophilic and van der Waals (vdW) interactions made major contributions to the binding affinity. Furthermore, through 100 ns MD simulations, we obtained the key amino acid residues and the types of interactions they participated in. Based on the constructed 3D-QSAR model, some novel pyrropyrazole derivatives targeting PAK4 were designed with improved predicted activities. Pharmacokinetic and toxicity predictions of the designed PAK4 inhibitors were obtained by the pkCSM, indicating these compounds had better absorption, distribution, metabolism, excretion and toxicity (ADMET) properties. Above research provided a valuable insight for developing novel and effective pyrropyrazole compounds targeting PAK4.
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Affiliation(s)
- Yinli Gao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
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