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Alzain AA, Elbadwi FA, Mohamed SGA, Kushk KSA, Bafarhan RI, Alswiri SA, Khushaim SN, Hussein HGA, Abuhajras MYA, Mohamed GA, Ibrahim SRM. Exploring marine-derived compounds for MET signalling pathway inhibition in cancer: integrating virtual screening, ADME profiling and molecular dynamics investigations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:1003-1021. [PMID: 38014514 DOI: 10.1080/1062936x.2023.2284917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
The MET signalling pathway regulates fundamental cellular processes such as growth, division, and survival. While essential for normal cell function, dysregulation of this pathway can contribute to cancer by triggering uncontrolled proliferation and metastasis. Targeting MET activity holds promise as an effective strategy for cancer therapy. Among potential sources of anti-cancer agents, marine organisms have gained attention. In this study, we screened 47,450 natural compounds derived from marine sources within the CMNPD database against the Met crystal structure. By employing HTVS, SP, and XP docking modes, we identified three compounds (CMNPD17595, CMNPD14026, and CMNPD19696) that outperformed a reference molecule in binding affinity to the Met structure. These compounds demonstrated desirable ADME properties. Molecular Dynamics (MD) simulations for 200 ns confirmed the stability of their interactions with Met. Our findings highlight CMNPD17595, CMNPD14026, and CMNPD19696 as potential inhibitors against Met-dependent cancers. Additionally, these compounds offer new avenues for drug development, leveraging their inhibitory effects on Met to combat carcinogenesis.
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Affiliation(s)
- A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - F A Elbadwi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - S G A Mohamed
- Faculty of Dentistry, British University, El Sherouk City, Egypt
| | - K S A Kushk
- Operations Sales Department, United Pharmaceuticals & Medical Supply Co. Ltd, Al Madinah Al-Munawwarah, Saudi Arabia
| | - R I Bafarhan
- Pharmaceutical Care Services, Medical Department, Private Sector, Tabuk, Saudi Arabia
| | - S A Alswiri
- Pharmaceutical Company, Medical Department, Private Sector, Al Madinah Al-Munawwarah, Saudi Arabia
| | - S N Khushaim
- College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - H G A Hussein
- Preparatory Year Program, Batterjee Medical College, Jeddah, Saudi Arabia
| | - M Y A Abuhajras
- Medical Claims Department, Bupa Arabia, Prince Saud AlFaisal, Jeddah, Saudi Arabia
| | - G A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S R M Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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2
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Dai J, Zhang J, Fu D, Liu M, Zhang H, Tang S, Wang L, Xu S, Zhu W, Tang Q, Zheng P, Chen T. Design, synthesis and biological evaluation of 4-(4-aminophenoxy)picolinamide derivatives as potential antitumor agents. Eur J Med Chem 2023; 257:115499. [PMID: 37229832 DOI: 10.1016/j.ejmech.2023.115499] [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: 03/14/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Cancer is a leading cause of death in humans. Molecular targeted therapy for cancer has become a research hotspot as it is associated with low toxicity and high efficiency. In this study, a total of 36 derivatives of 4-(4-aminophenoxy)pyridinamide were designed and synthesized, based on the analysis of the binding patterns of cabozantinib and BMS-777607 to MET protein. Most target compounds exhibited moderate to excellent antiproliferative activity against three different cell lines (A549, HeLa and MCF-7). A total of 7 compounds had stronger inhibitory activities than cabozantinib, and the IC50 value of the most promising compound 46 was 0.26 μM against the A549 cells, which was 2.4 times more active than that of cabozantinib. The structure-activity relationship of the target compounds was analyzed and summarized, and the action mechanism was discussed. The acridine orange (AO) staining assay and cell cycle apoptosis revealed that compound 46 dose-dependently induced apoptosis of A549 cells, and blocked the cells mainly in G0/G1 phase. The IC50 value of compound 46 on c-Met kinase was 46.5 nM. Further docking studies and molecular dynamics simulations signaled that compound 46 formed four key hydrogen bonds to c-Met kinase, and these key amino acids played a major role in binding free energy. In addition, compound 46 also showed good pharmacokinetic characteristics in rats. In conclusion, compound 46 is a promising antitumor agent.
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Affiliation(s)
- Jintian Dai
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China; Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China; Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jianqing Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China; Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430000, China
| | - Dongxue Fu
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Meng Liu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Han Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Sheng Tang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Linxiao Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Qidong Tang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China; Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China.
| | - Ting Chen
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China.
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3
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Luyen ND, Huong LM, Ha NTT, Tra NT, Anh LTT, Tuyen NV, Posta K, Son NT, Pham-The H. Chemical Profile and Biological Activities of Fungal Strains Isolated from Piper nigrum Roots: Experimental and Computational Approaches. Chem Biodivers 2023; 20:e202200456. [PMID: 36564341 DOI: 10.1002/cbdv.202200456] [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: 05/09/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
The current report describes the chemical investigation and biological activity of extracts produced by three fungal strains Fusarium oxysporum, Penicillium simplicissimum, and Fusarium proliferatum isolated from the roots of Piper nigrum L. growing in Vietnam. These fungi were namely determined by morphological and DNA analyses. GC/MS identification revealed that the EtOAc extracts of these fungi were associated with the presence of saturated and unsaturated fatty acids. These EtOAc extracts showed cytotoxicity towards cancer cell lines HepG2, inhibited various microbacterial organisms, especially fungus Aspergillus niger and yeast Candida albicans (the MIC values of 50-100 μg/mL). In α-glucosidase inhibitory assay, they induced the IC50 values of 1.00-2.53 μg/mL were better than positive control acarbose (169.80 μg/mL). The EtOAc extract of F. oxysporum also showed strong anti-inflammatory activity against NO production and PGE-2 level. Four major compounds linoleic acid (37.346 %), oleic acid (27.520 %), palmitic acid (25.547 %), and stearic acid (7.030 %) from the EtOAc extract of F. oxysporum were selective in molecular docking study, by which linoleic and oleic acids showed higher binding affinity towards α-glucosidase than palmitic and stearic acids. In subsequent docking assay with inducible nitric oxide synthase (iNOS), palmitic acid, oleic acid and linoleic acid could be moderate inhibitors.
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Affiliation(s)
- Nguyen Dinh Luyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Le Mai Huong
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Nguyen Thi Thu Ha
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Nguyen Thanh Tra
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Le Thi Tu Anh
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Nguyen Van Tuyen
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Katalin Posta
- Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Pater str 1., Godollo, H-2103, Hungary
| | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, 10000, Vietnam
| | - Hai Pham-The
- Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hanoi, 10000, Vietnam. or
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El-Wakil MH, Teleb M. Transforming Type II to Type I c-Met kinase inhibitors via combined scaffold hopping and structure-guided synthesis of new series of 1,3,4-thiadiazolo[2,3-c]-1,2,4-triazin-4-one derivatives. Bioorg Chem 2021; 116:105304. [PMID: 34534756 DOI: 10.1016/j.bioorg.2021.105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/21/2022]
Abstract
Novel 1,3,4-thiadiazolo[2,3-c]-1,2,4-triazin-4-one derivatives 3a-e, 4a-f and 5a-f were designed as Type I c-Met kinase inhibitors based on scaffold hopping of our previous Type II c-Met kinase lead. Target compounds were then synthesized under the guidance of molecular docking analysis to identify the potential inhibitors that fit the binding pocket of c-Met kinase in the characteristic manner as the reported Type I c-Met kinase inhibitors. All synthesized derivatives were evaluated for their c-Met kinase inhibitory activity at 10 µM concentration, where 3d, 5d and 5f displayed >80% inhibition. Further IC50 investigation of these compounds identified 5d as the most potent c-Met kinase inhibitor with IC50 value of 1.95 µM. Moreover, 5d showed selective antitumor activity against c-Met over-expressing colon HCT-116 and lung A549 adenocarcinoma cells with IC50 values of 6.18 and 10.6 µg/ml, respectively. More significantly, 5d effectively inhibited c-Met phosphorylation in the Western blot experiment. Also, 5d induced cellular apoptosis in HCT-116 cancer cells as well as cell cycle arrest with accumulation of cells in G2/M phase. Finally, kinase selectivity profiling of 5d against nine oncogenic kinases revealed its selectivity to only Tyro3 kinase (% inhibition = 80%, IC50 = 3 µM). All these experimental findings clearly demonstrate that 5d is a potential dual acting inhibitor against c-Met and Tyro3 kinases, standing out as a viable lead that deserves further investigation and development to new generation of antitumor agents.
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Affiliation(s)
- Marwa H El-Wakil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt.
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
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Imana SN, Ningsih EG, Tambunan USF. <i>In silico </i>Identification of Peptide as Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Lung Cancer Treatment. Pak J Biol Sci 2021; 23:567-574. [PMID: 32363843 DOI: 10.3923/pjbs.2020.567.574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Epidermal growth factor receptor (EGFR) is the biomarker for lung cancer in which the protein has the most active mutated genes in lung cancer patients. Peptides have pharmacological potential as drugs because of their bioactivity and accessibility. The research objective was to obtain peptide compounds drug candidates with good interaction and pharmacological properties that can act as an inhibitor for EGFR for lung cancer treatment by using in silico method. MATERIALS AND METHODS EGFR protein structure was obtained from Protein Data Bank and the peptide compounds were retrieved from PubChem. Optimization and energy minimization process were done to prepare the peptides for the simulation. Protein-Ligand Interaction Fingerprint (PLIF) was used to determine the pharmacophore features in the EGFR binding site. Both proteins and ligands underwent a virtual screening through rigid and flexible molecular docking simulation and the best ligands were subjected to a computational ADME-Tox properties prediction. RESULTS After screening through molecular docking simulation, nine best compounds were identified to have a good interaction with EGFR protein according to its binding energy and RMSD value. The compounds were identified to form hydrogen bond interactions with the macromolecule. CONCLUSION Two peptide compounds (PubChem ID: 20832941 and 9805315) have been predicted as the best ligands with desired pharmacological properties for the inhibition of EGFR tyrosine kinase.
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Zhang J, Chen P, Duan Y, Xiong H, Li H, Zeng Y, Liang G, Tang Q, Wu D. Design, synthesis and biological evaluation of 7H-pyrrolo[2,3-d]pyrimidine derivatives containing 1,8-naphthyridine-4-one fragment. Eur J Med Chem 2021; 215:113273. [PMID: 33601310 DOI: 10.1016/j.ejmech.2021.113273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 01/22/2023]
Abstract
In this study, a series of pyrrolo [2,3-d]pyrimidine derivatives containing 1,8-naphthyridine-4-one fragment were synthesized and their biological activity were tested. Most of the target compounds displayed moderate to excellent activity against one or more cancer cell lines and low activity against human normal cell LO2 in vitro. The most promising compound 51, of which the IC50 values were 0.66 μM, 0.38 μM and 0.44 μM against cell lines A549, Hela and MCF-7, shown more remarkable activity and better apoptosis effect than the positive control Cabozantinib. The structure-activity relationships (SARs) indicated that double-EWGs (such as R3 = 2-Cl-4-CF3) on the terminal phenyl rings was a key factor in improving the biological activity. In addition, the further research on compound 51 mainly included c-Met kinase activity and selectivity, concentration dependence, and molecular docking.
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Affiliation(s)
- Jianqing Zhang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China; Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, PR China
| | - Pengqin Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Yongli Duan
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China (UESTC), Chengdu, 610054, PR China
| | - Hehua Xiong
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Quality Control and Pharmacovigilance, Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Hongmin Li
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, PR China
| | - Yao Zeng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, PR China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Qidong Tang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China; Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, PR China.
| | - Di Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
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7
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Wu G, Yu G, Yu Y, Yang S, Duan Z, Wang W, Liu Y, Yu R, Li J, Zhu T, Gu Q, Li D. Chemoreactive-Inspired Discovery of Influenza A Virus Dual Inhibitor to Block Hemagglutinin-Mediated Adsorption and Membrane Fusion. J Med Chem 2020; 63:6924-6940. [PMID: 32520560 DOI: 10.1021/acs.jmedchem.0c00312] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Owing to the emergence of drug resistance and high morbidity and mortality, the need for novel anti-influenza A virus (IAV) drugs with divergent targets is highly sought after. Herein, we reveal the discovery of an anti-IAV agent as a dual inhibitor to block hemagglutinin-mediated adsorption and membrane fusion using a chemoreactive ortho-quinone methide (o-QM) equivalent. Based on the o-QM equivalent nonenzymatically multipotent behavior, we created a series of clavatol-derived pseudo-natural products and found that penindolone (PND), a new diclavatol indole adduct, exhibited potent and broad-spectrum anti-IAV activities with low risk of inducing drug resistance. Distinct from current anti-IAV drugs, PND possesses a novel scaffold and is the first IAV inhibitor targeting both HA1 and HA2 subunits of virus hemagglutinin to dually block the IAV adsorption and membrane fusion process. More importantly, intranasal and oral administration of PND can protect mice against IAV-induced death and weight loss, superior to the effects of the clinical drug oseltamivir. Thus, the use of chemoreactive intermediates could expand our understanding of chemical diversity and aid in the development of anti-IAV drugs with novel targets.
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Affiliation(s)
- Guangwei Wu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Guihong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Yunjia Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Shuang Yang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Zhongwei Duan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, People's Republic of China
| | - Yankai Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 26003, Shandong, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, People's Republic of China
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8
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Large-Scale Virtual Screening Against the MET Kinase Domain Identifies a New Putative Inhibitor Type. Molecules 2020; 25:molecules25040938. [PMID: 32093126 PMCID: PMC7070486 DOI: 10.3390/molecules25040938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
By using an ensemble-docking strategy, we undertook a large-scale virtual screening campaign in order to identify new putative hits against the MET kinase target. Following a large molecular dynamics sampling of its conformational space, a set of 45 conformers of the kinase was retained as docking targets to take into account the flexibility of the binding site moieties. Our screening funnel started from about 80,000 chemical compounds to be tested in silico for their potential affinities towards the kinase binding site. The top 100 molecules selected—thanks to the molecular docking results—were further analyzed for their interactions, and 25 of the most promising ligands were tested for their ability to inhibit MET activity in cells. F0514-4011 compound was the most efficient and impaired this scattering response to HGF (Hepatocyte Growth Factor) with an IC50 of 7.2 μM. Interestingly, careful docking analysis of this molecule with MET suggests a possible conformation halfway between classical type-I and type-II MET inhibitors, with an additional region of interaction. This compound could therefore be an innovative seed to be repositioned from its initial antiviral purpose towards the field of MET inhibitors. Altogether, these results validate our ensemble docking strategy as a cost-effective functional method for drug development.
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9
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Xiong H, Cheng J, Zhang J, Zhang Q, Xiao Z, Zhang H, Tang Q, Zheng P. Design, Synthesis, and Biological Evaluation of Pyridineamide Derivatives Containing a 1,2,3-Triazole Fragment as Type II c-Met Inhibitors. Molecules 2019; 25:molecules25010010. [PMID: 31861448 PMCID: PMC6983042 DOI: 10.3390/molecules25010010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022] Open
Abstract
A series of 4-(pyridin-4-yloxy)benzamide derivatives containing a 1,2,3-triazole fragment were designed, synthesized, and their inhibitory activity against A549, HeLa, and MCF-7 cancer cell lines was evaluated. Most compounds exhibited moderate to potent antitumor activity against the three cell lines. Among them, the promising compound B26 showed stronger inhibitory activity than Golvatinib, with IC50 values of 3.22, 4.33, and 5.82 μM against A549, HeLa, and MCF-7 cell lines, respectively. The structure–activity relationships (SARs) demonstrated that the modification of the terminal benzene ring with a single electron-withdrawing substituent (fluorine atom) and the introduction of a pyridine amide chain with a strong hydrophilic group (morpholine) to the hinge region greatly improved the antitumor activity. Meanwhile, the optimal compound B26 showed potent biological activity in some pharmacological experiments in vitro, such as cell morphology study, dose-dependent test, kinase activity assay, and cell cycle experiment. Finally, the molecular docking simulation was performed to further explore the binding mode of compound B26 with c-Met.
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Affiliation(s)
| | | | | | | | | | | | - Qidong Tang
- Correspondence: (Q.T.); (P.Z.); Tel.: +86-791-8380-2393 (P.Z.)
| | - Pengwu Zheng
- Correspondence: (Q.T.); (P.Z.); Tel.: +86-791-8380-2393 (P.Z.)
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10
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Zhang S, Song Q, Wang X, Wei Z, Yu R, Wang X, Jiang T. Virtual Screening Guided Design, Synthesis and Bioactivity Study of Benzisoselenazolones (BISAs) on Inhibition of c-Met and Its Downstream Signalling Pathways. Int J Mol Sci 2019; 20:E2489. [PMID: 31137515 PMCID: PMC6566228 DOI: 10.3390/ijms20102489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022] Open
Abstract
c-Met is a transmembrane receptor tyrosine kinase and an important therapeutic target for anticancer drugs. In this study, we designed a small library containing 300 BISAs molecules that consisted of carbohydrates, amino acids, isothiourea, tetramethylthiourea, guanidine and heterocyclic groups and screened c-Met targeting compounds using docking and MM/GBSA. Guided by virtual screening, we synthesised a series of novel compounds and their activity on inhibition of the autophosphorylation of c-Met and its downstream signalling pathway proteins were evaluated. We found a panel of benzisoselenazolones (BISAs) obtained by introducing isothiourea, tetramethylthiourea and heterocyclic groups into the C-ring of Ebselen, including 7a, 7b, 8a, 8b and 12c (with IC50 values of less than 20 μM in MET gene amplified lung cancer cell line EBC-1), exhibited more potent antitumour activity than Ebselen by cell growth assay combined with in vitro biochemical assays. In addition, we also tested the antitumour activity of three cancer cell lines without MET gene amplification/activation, including DLD1, MDA-MB-231 and A549. The neuroblastoma SK-N-SH cells with HGF overexpression which activates MET signalling are sensitive to MET inhibitors. The results reveal that our compounds may be nonspecific multitarget kinase inhibitors, just like type-II small molecule inhibitors. Western blot analysis showed that these inhibitors inhibited autophosphorylation of c-MET, and its downstream signalling pathways, such as PI3K/AKT and MARK/ERK. Results suggest that bensoisoselenones can be used as a scaffold for the design of c-Met inhibiting drug leads, and this study opens up new possibilities for future antitumour drug design.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Qiaoling Song
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Xueting Wang
- Center for High Performance Computing & System simulation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Zhiqiang Wei
- Center for High Performance Computing & System simulation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
| | - Xin Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
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11
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Kang J, Chen HJ, Wang Z, Liu J, Li B, Zhang T, Yang Z, Wu YL, Yang JJ. Osimertinib and Cabozantinib Combinatorial Therapy in an EGFR-Mutant Lung Adenocarcinoma Patient with Multiple MET Secondary-Site Mutations after Resistance to Crizotinib. J Thorac Oncol 2017; 13:e49-e53. [PMID: 29128427 DOI: 10.1016/j.jtho.2017.10.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Jin Kang
- Guangdong Cardiovascular Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Zheng Wang
- Asia Innovative Medicines, AstraZeneca, Shanghai, People's Republic of China
| | - Jing Liu
- Burning Rock Biotech, Guangzhou, People's Republic of China
| | - Bing Li
- Burning Rock Biotech, Guangzhou, People's Republic of China
| | - Tengfei Zhang
- Burning Rock Biotech, Guangzhou, People's Republic of China
| | - Zhenfan Yang
- Asia Innovative Medicines, AstraZeneca, Shanghai, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China; Medical Research Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Jin-Ji Yang
- Guangdong Cardiovascular Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China; Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China.
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