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Ren F, Zhu W, Yang S, Zhang C, Hou Y, Li R, Wen J, Zou LH, Gao M, Wang WL, Wu Z, Shao A. Coumarin-Based Fluorescent Inhibitors for Photocontrollable Bioactivation. Mol Pharm 2023. [PMID: 37104703 DOI: 10.1021/acs.molpharmaceut.3c00279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Activation of the IRE-1/XBP-1 pathway is related to many human diseases. Coumarin-based derivatives acting as both IRE-1 inhibitors and bright fluorophores are highly desirable to establish an integrated fluorescent inhibitor system. Here, we take insights into the aqueous stability of a photocaged IRE-1 inhibitor PC-D-F07 through a structure activity relationship. The substituent effects indicate that the electron-withdrawing -NO2 moiety in the photocage combined with the tricyclic coumarin fluorophore contribute to the structural stability of PC-D-F07. To optimize the photocage of PC-D-F07, we incorporate a 1-ethyl-2-nitrobenzyl or 2-nitrobenzyl photolabile moiety on the hydroxyl group of the IRE-1 inhibitor to generate RF-7 and RF-8. Upon photoactivation, both RF-7 and RF-8 present an increased fluorescence response, sequentially enabling the unlocking of the ortho-1,3-dioxane acetal for the release of active IRE-1 inhibitors. Moreover, RF-7 exhibits a high repolarization ratio of converting M2-type tumor-associated macrophages (M2-TAMs) to M1-type immune-responsive macrophages. This provides a novel prodrug strategy of modulating druggable fluorophore backbones to achieve spatiotemporally controllable drug release for precise cancer treatment.
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Affiliation(s)
- Fei Ren
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wendi Zhu
- Department of Clinical Medicine, PUMC & CAMS, Beijing 100730, China
| | - Shuke Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingchao Hou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Runqi Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liang-Hua Zou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Min Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhihong Wu
- Department of Clinical Medicine, PUMC & CAMS, Beijing 100730, China
| | - Andong Shao
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
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2
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Fayyazi N, Mostashari-Rad T, Ghasemi JB, Ardakani MM, Kobarfard F. Molecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19. J Biomol Struct Dyn 2022; 40:11787-11808. [PMID: 34405765 DOI: 10.1080/07391102.2021.1965914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has posed serious threat to the health and has inflicted huge costs in the world. Discovering potent compounds is a critical step to inhibit coronavirus. 3CLpro and RdRp are the most conserved targets associated with COVID-19. In this study, three-dimensional pharmacophore modeling, scaffold hopping, molecular docking, structure-based virtual screening, QSAR-based ADMET predictions and molecular dynamics analysis were used to identify inhibitors for these targets. Binding free energies estimated by molecular docking for each ligand in different binding sites of RdRp were used to predict the active site. Previously reported active 3CLpro and RdRp inhibitors were used to build a pharmacophore model to develop different scaffolds. Structure-based simulations and pharmacophore modeling based on Hip Hop algorithm converged in a state that suggest hydrogen bond acceptor and donor features have a critical role in the two binding sites. Further validations indicated that the best pharmacophore model has fairly good correlation values compared with approved inhibitors. Structure-based simulation results approved that GLu166 and Gln189 in 3CLpro and Lys551 and Glu811 in RdRp, are critical residues for dual activities. Ten compounds were extracted from pharmacophore-based virtual screening in six databases. The results, gained by repurposing approach, suggest the effectiveness of these ten compounds with different scaffolds as possible inhibitors of the two targets. Some quinoline-based hybrid derivatives also were designed. QSAR descriptors plot predicted that the scaffolds have had accepted pharmacokinetic profiles. Multiple molecular dynamics simulations in 100 ns and MM/PBSA studies of some reference inhibitors and the novel compounds in complex with both targets demonstrated stable complexes and confirmed the interaction modes. Based on different computational methods, COVID-19 multi-target inhibitors are proposed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tahereh Mostashari-Rad
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jahan B Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Mehran Mirabzadeh Ardakani
- Department of Traditional Pharmacy, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Farzad Kobarfard
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3
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Akella M, Malla R. Molecular modeling and in vitro study on pyrocatechol as potential pharmacophore of CD151 inhibitor. J Mol Graph Model 2020; 100:107681. [PMID: 32738620 DOI: 10.1016/j.jmgm.2020.107681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/25/2020] [Accepted: 06/24/2020] [Indexed: 11/24/2022]
Abstract
CD151 has been recognized as a prognostic marker, the therapeutic target of breast cancers, but less explored for small molecule inhibitors due to lack of a validated model. The 3-D structure of CD151 large extracellular loop (LEL) was modeled using the LOMETS server and validated by the Ramachandran plot. The validated structure was employed for molecular docking and structure-based pharmacophore analysis. Druglikeness was evaluated by the ADMET description protocol. Antiproliferative activity was evaluated by MTT, BrdU incorporation, flow cytometry, and cell death ELISAPLUS assay. This study predicted the best model for CD151-LEL with 94.1% residues in favored regions and Z score -2.79 kcal/mol using the threading method. The web-based receptor cavity method identified one functional target site, which was suitable for the binding of aromatic and heterocyclic compounds. Molecular docking study identified pyrocatechol (PCL) and 5-fluorouracil (FU) as potential leads of CD151-LEL. The pharmacophore model identified interaction points of modeled CD151-LEL with PCL and FU. Also, the analysis of ADMET properties revealed the drug-likeness of PCL and FU. The viability of MDA-MB 231 cells was significantly reduced with PCL and FU but less affected MCF-12A, normal healthy breast epithelial cell line. With 50% toxic concentration, both PCL and FU significantly inhibited 82.46 and 87.12% proliferation, respectively, of MDA-MB 231 cells by altering morphology and inducing G1 cell cycle arrest and apoptosis. In addition, PCL and FU inhibited the CD151 expression by 4.5-and 4.8-folds, respectively. This study suggests the further assessment of pyrocatechol as a potential lead of CD151 in breast cancer at the molecular level.
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Affiliation(s)
- Manasa Akella
- Cancer Biology Lab, Dept. of Biochemistry and Bioinformatics, Institute of Science, GITAM (Deemed to Be University), Visakhapatnam, 530045, Andhra Pradesh, India
| | - RamaRao Malla
- Cancer Biology Lab, Dept. of Biochemistry and Bioinformatics, Institute of Science, GITAM (Deemed to Be University), Visakhapatnam, 530045, Andhra Pradesh, India.
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4
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Potent arylamide derivatives as dual-target antifungal agents: Design, synthesis, biological evaluation, and molecular docking studies. Bioorg Chem 2020; 99:103749. [DOI: 10.1016/j.bioorg.2020.103749] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/01/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
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5
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Zhang X, Yan J, Wang H, Wang Y, Wang J, Zhao D. Molecular docking, 3D-QSAR, and molecular dynamics simulations of thieno[3,2-b]pyrrole derivatives against anticancer targets of KDM1A/LSD1. J Biomol Struct Dyn 2020; 39:1189-1202. [PMID: 32036765 DOI: 10.1080/07391102.2020.1726819] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a histone-modifying enzyme, which has been proposed as a promising target for anticancer drug development. Extensive research on LSD1 inhibitors has been performed since its discovery. In order to get more information for lead identification and optimization, we carried out a molecular modeling study on a set of 43 thieno[3,2-b]pyrrole competitive inhibitors of LSD1 using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations. Based on the co-crystallized conformer-based alignment (CCBA) method, 3D-QSAR model of thieno[3,2-b]pyrrole derivatives as LSD1 inhibitors was established. The significant statistics (q2 = 0.595, r2 = 0.959, r2pred = 0.846) of the 3D-QSAR indicated the good predictive power and statistical reliability of this model. Based on the corresponding contour maps six LSD1 inhibitors were designed and their activities were predicted by 3D-QSAR model. Meanwhile, molecular docking was performed to simulate the probable binding modes between ligands and LSD1 protein. The molecular interactions mainly contributions to the binding affinity for LSD1 inhibitions were further supplemented by 100 ns MD simulations and binding free energy calculation.
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Affiliation(s)
- Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Jiangkun Yan
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Ying Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P.R. China
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6
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Fayyazi N, Esmaeili S, Taheri S, Ribeiro FF, Scotti MT, Scotti L, Ghasemi JB, Saghaei L, Fassihi A. Pharmacophore Modeling, Synthesis, Scaffold Hopping and Biological β- Hematin Inhibition Interaction Studies for Anti-malaria Compounds. Curr Top Med Chem 2020; 19:2743-2765. [DOI: 10.2174/1568026619666191116160326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/02/2019] [Accepted: 10/01/2019] [Indexed: 01/23/2023]
Abstract
Backgound:Exploring potent compounds is critical to generating multi-target drug discovery. Hematin crystallization is an important mechanism of malaria.Methods:A series of chloroquine analogues were designed using a repositioning approach to develop new anticancer compounds. Protein-ligand interaction fingerprints and ADMET descriptors were used to assess docking performance in virtual screenings to design chloroquine hybrid β-hematin inhibitors. A PLS algorithm was applied to correlate the molecular descriptors to IC50 values. The modeling presented excellent predictive power with correlation coefficients for calibration and cross-validation of r2 = 0.93 and q2 = 0.72. Using the model, a series of 4-aminoquinlin hybrids were synthesized and evaluated for their biological activity as an external test series. These compounds were evaluated for cytotoxic cell lines and β-hematin inhibition.Results:The target compounds exhibited high β-hematin inhibition activity and were 3-9 times more active than the positive control. Furthermore, all the compounds exhibited moderate to high cytotoxic activity. The most potent compound in the dataset was docked with hemoglobin and its pharmacophore features were generated. These features were used as input to the Pharmit server for screening of six databases.Conclusion:The compound with the best score from ChEMBL was 2016904, previously reported as a VEGFR-2 inhibitor. The 11 compounds selected presented the best Gold scores with drug-like properties and can be used for drug development.
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Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
| | - Somayeh Esmaeili
- Traditional Medicine and Medical Material Research Center (TMRC), Shahid beheshti University of Medical Sciences, Tehran, Iran
| | - Salman Taheri
- Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Frederico F. Ribeiro
- Synthesis and Drug Delivery Laboratory, Biological Sciences Department, Paraíba State University, João Pessoa, Brazil
| | | | | | - Jahan B. Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Lotfollah Saghaei
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran
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7
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Molecular dynamics simulation and 3D-pharmacophore analysis of new quinoline-based analogues with dual potential against EGFR and VEGFR-2. Int J Biol Macromol 2020; 142:94-113. [DOI: 10.1016/j.ijbiomac.2019.09.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/03/2019] [Accepted: 09/10/2019] [Indexed: 11/20/2022]
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8
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Li R, Wang H, Wang J, Cheng M. PB-10, a thiazolo[4,5-d] pyrimidine derivative, targets p21-activated kinase 4 in human colorectal cancer cells. Bioorg Med Chem Lett 2019; 30:126807. [PMID: 31740249 DOI: 10.1016/j.bmcl.2019.126807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/08/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Targeting p21-activated kinase 4 (PAK4) is a potential therapeutic strategy against human colorectal cancer (CRC). In this study, we synthesized a series of novel thiazolo[4,5-d]pyrimidine derivatives (PB-1-12) and identified PB-10 (PAK4 IC50 = 15.12 μM) as a potential and potent PAK4 inhibitor. Our results showed that PB-10 significantly suppressed the proliferation and colony formation of human CRC cells. PB-10 also arrested HCT-116 CRC cells at sub G0/G1 phase while promoting the expression of proapoptotic proteins. In addition, PB-10 inhibited migration, invasion, and adhesion as well as the PAK4 downstream signaling pathway in HCT-116 cells. Molecular docking analysis showed possible binding modes between PB-10 and PAK4. Our study provides a novel compound that may block the PAK4 signaling in CRC cells.
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Affiliation(s)
- Ruijuan Li
- College of Pharmacy, Inner Mongolia Medical University, Huhhot 010110, PR China; Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, PR China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, PR China.
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9
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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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10
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Song PL, Wang G, Su Y, Wang HX, Wang J, Li F, Cheng MS. Strategy and validation of a structure-based method for the discovery of selective inhibitors of PAK isoforms and the evaluation of their anti-cancer activity. Bioorg Chem 2019; 91:103168. [DOI: 10.1016/j.bioorg.2019.103168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023]
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11
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Su Y, Song P, Wang H, Hu B, Wang J, Cheng MS. Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation. J Biomol Struct Dyn 2019; 38:3825-3837. [DOI: 10.1080/07391102.2019.1664330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuan Su
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Peilu Song
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Mao-Sheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
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12
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Li D, Zhao C, Ding H, Wu Q, Ren T, Wang J, Chen C, Zhao Q. A novel inhibitor of ADAM17 sensitizes colorectal cancer cells to 5-Fluorouracil by reversing Notch and epithelial-mesenchymal transition in vitro and in vivo. Cell Prolif 2018; 51:e12480. [PMID: 30069943 PMCID: PMC6528951 DOI: 10.1111/cpr.12480] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/04/2018] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Colorectal cancer is one of the most common malignancies both in men and women. Owing to metastasis and resistance, the prognosis of colorectal cancerCRC patients remains extremely poor with chemotherapy. A disintegrin and metalloproteinase 17 (ADAM17) induces the activation of Notch pathway and contributes to the chemoresistance. This study aimed to discover a novel ADAM17 inhibitor and investigate the chemosensitization effect. MATERIALS AND METHODS Pharmacophore model, western blot and enzymatic assay were used to discover ZLDI-8. Cell proliferation was determined by MTT and colony formation assay. Cell migratory and invasive ability were determined by wound healing scratch and transwell assay. Immunofluorescence images and western blot analysed the expression of Notch or epithelial-mesenchymal transition (EMT) pathway markers. Xenografts were employed to evaluate the chemosensitization effect of ZLDI-8 in vivo. RESULTS We found that ZLDI-8 cell-specifically inhibited the proliferation of CRC, and this effect was due to abrogation of ADAM17 and Notch pathway. Meanwhile, we reported for the first time that ZLDI-8 synergistically improved the anti-tumour and anti-metastasis activity of 5-fluorouracil or irinotecan by reversing Notch and EMT pathways. Interestingly, in vivo studies further demonstrated that ZLDI-8 promoted the anti-tumour effect of 5-fluorouracil through Notch and EMT reversal. CONCLUSIONS A novel ADAM17 inhibitor ZLDI-8 may be a potential chemosensitizer which sensitized CRC cells to 5-fluorouracil or irinotecan by reversing Notch and EMT pathways.
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Affiliation(s)
- Dan‐Dan Li
- Department of PharmacyGeneral Hospital of Shenyang Military Area CommandShenyangChina
- Department of Traditional Chinese MedicineShenyang Pharmaceutical UniversityShenyangChina
| | - Chang‐Hao Zhao
- College of PharmacyThe Heilongjiang University of Traditional Chinese MedicineHeilongjiangChina
| | - Huai‐Wei Ding
- Key Laboratory of Structure‐Based Drug Design and Discovery of Ministry of EducationShenyang Pharmaceutical UniversityShenyangChina
| | - Qiong Wu
- Department of PharmacyGeneral Hospital of Shenyang Military Area CommandShenyangChina
| | - Tian‐Shu Ren
- Department of PharmacyGeneral Hospital of Shenyang Military Area CommandShenyangChina
| | - Jian Wang
- Key Laboratory of Structure‐Based Drug Design and Discovery of Ministry of EducationShenyang Pharmaceutical UniversityShenyangChina
| | - Cong‐Qin Chen
- Department of PharmacyGeneral Hospital of Shenyang Military Area CommandShenyangChina
- Department of PharmacyLongyan First HospitalFujian Medical UniversityLongyanChina
| | - Qing‐Chun Zhao
- Department of PharmacyGeneral Hospital of Shenyang Military Area CommandShenyangChina
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13
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Sun B, Zhang H, Liu M, Hou Z, Liu X. Structure-based virtual screening and ADME/T-based prediction analysis for the discovery of novel antifungal CYP51 inhibitors. MEDCHEMCOMM 2018; 9:1178-1187. [PMID: 30109006 DOI: 10.1039/c8md00230d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/02/2018] [Indexed: 12/24/2022]
Abstract
With the increasing incidence of pathogenic fungi and drug-resistant fungi in clinic, it has become very important to develop the novel rate-limiting enzyme 14α-demethylase (CYP51) as an antifungal inhibitor. In this study, a method involving structure-based virtual screening was employed. First, a publicly available database was obtained from the Dow Chemical Company, and the database was screened by the designed pharmacophore model of CYP51 inhibitors. Then, the pharmacophore search hits were docked into the CYP51 crystal structure. Finally, sixteen compounds were selected for in vitro antifungal inhibition assay, and most of the compounds showed a certain degree of antifungal activity. In particular, compounds 3, 4, and 9 exhibited significant antifungal and anti-drug resistance activities by blocking the synthesis of ergosterol. The molecular docking and ADME/T properties of the compounds 3, 4, and 9 were further predicted, and the results indicated that they can form hydrophobic and coordination interactions with the active sites of CYP51. At the same time, compounds 4 and 9 showed promising drug-like properties. This study reveals that the compounds can be further optimized and developed as lead compounds.
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Affiliation(s)
- Bin Sun
- Department of Medicinal Chemistry , School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , PR China . .,Institute of BioPharmaceutical Research , Liaocheng University , 1 Hunan Road , Liaocheng 252000 , PR China
| | - Hong Zhang
- Liaocheng People's Hospital , 67 Dongchang Road , Liaocheng 252000 , PR China
| | - Min Liu
- Institute of BioPharmaceutical Research , Liaocheng University , 1 Hunan Road , Liaocheng 252000 , PR China
| | - Zhuang Hou
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , School of Pharmaceutical Engineering , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenhe District , Shenyang 110016 , PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry , School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , Jinan 250012 , PR China .
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14
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Huang H, Jiang H, Zhang X, Li W, Wang P, Liu F, Wang J, Bai M, Cheng M. Computer-aided drug design, synthesis and identification of disulfide compounds as novel and potential allosteric PAK1 inhibitors. RSC Adv 2018; 8:11894-11901. [PMID: 35539390 PMCID: PMC9079282 DOI: 10.1039/c8ra00621k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/08/2018] [Indexed: 11/21/2022] Open
Abstract
p21-activated kinase 1 (PAK1) is an evolutionarily conserved serine/threonine protein kinase, which has been considered as one of the key regulatory factors in signaling network of tumor cells. Therefore, inhibition of PAK1 may be a potential approach to treat many types of solid tumors. Several allosteric inhibitors of PAK1 have been identified, and the most well known one is IPA-3. But its biological activity is not satisfied, and the structure activity relationship (SAR) of PAK1 allosteric inhibitors is unclear. In this study, we designed and synthesized 13 potential allosteric inhibitors by using computer-aided drug design based on the structure of the existing PAK1 allosteric inhibitors. All the compounds were characterized by 1H-NMR and 13C-NMR, among which six were not reported previously. SAR was investigated by pharmacological studies and In03 and In06 showed increased PAK1 inhibition than previously reported IPA-3. These findings could guide further structure optimization of PAK1 inhibitors. p21-activated kinase 1 (PAK1) is an evolutionarily conserved serine/threonine protein kinase, which has been considered as one of the key regulatory factors in signaling network of tumor cells.![]()
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Affiliation(s)
- Hanwei Huang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University 155 Nanjing North Street, Heping District Shenyang China 110001
| | - Hailun Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University China
| | - Wei Li
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology Shenyang China
| | - Pengliang Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University 155 Nanjing North Street, Heping District Shenyang China 110001
| | - Funan Liu
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University 155 Nanjing North Street, Heping District Shenyang China 110001
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University China
| | - Mingfeng Bai
- Vanderbilt University Institute of Imaging Science (VUIIS), Vanderbilt University Medical Center Nashville Tennessee 37232 USA.,Center for Molecular Probes, Vanderbilt University Medical Center Nashville Tennessee 37232 USA.,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center Nashville Tennessee 37232 USA.,Vanderbilt-Ingram Cancer Center (VICC), Vanderbilt University Medical Center Nashville Tennessee 37232 USA
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University China
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15
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Krishna S, Shukla S, Lakra AD, Meeran SM, Siddiqi MI. Identification of potent inhibitors of DNA methyltransferase 1 (DNMT1) through a pharmacophore-based virtual screening approach. J Mol Graph Model 2017; 75:174-188. [PMID: 28582695 DOI: 10.1016/j.jmgm.2017.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1. We have derived a pharmacophore model with the help of available DNMT1 inhibitors. Utilising this model, we performed the virtual screening of Maybridge chemical library and the identified hits were then subsequently filtered based on the Naïve Bayesian classification model. The molecules that have returned from this classification model were subjected to ensemble based docking. We have selected 10 molecules for the biological assay by inspecting the interactions portrayed by these molecules. Three out of the ten tested compounds have shown DNMT1 inhibitory activity. These compounds were also found to demonstrate potential inhibition of cellular proliferation in human breast cancer MDA-MB-231 cells. In the present study, we have utilized a multi-step virtual screening protocol to identify inhibitors of DNMT1, which offers a starting point to develop more potent DNMT1 inhibitors as anti-cancer agents.
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Affiliation(s)
- Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Samriddhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Amar Deep Lakra
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Syed Musthapa Meeran
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India.
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16
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Mandalapu D, Singh DK, Gupta S, Balaramnavar VM, Shafiq M, Banerjee D, Sharma VL. Discovery of monocarbonyl curcumin hybrids as a novel class of human DNA ligase I inhibitors: in silico design, synthesis and biology. RSC Adv 2016. [DOI: 10.1039/c5ra25853g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A pharmacophore model identified a novel class of hLigI inhibitors to treat cancer. 36 compounds were synthesized and the identified inhibitor, compound 23 shown antiligase activity at IC50 24.9 μM by abolishing the interaction between hLigI and DNA.
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Affiliation(s)
- Dhanaraju Mandalapu
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Deependra Kumar Singh
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Sonal Gupta
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishal M. Balaramnavar
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Mohammad Shafiq
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Dibyendu Banerjee
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishnu Lal Sharma
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
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