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Huo D, Wang S, Kong Y, Qin Z, Yan A. Discovery of Novel Epidermal Growth Factor Receptor (EGFR) Inhibitors Using Computational Approaches. J Chem Inf Model 2021; 62:5149-5164. [PMID: 34931847 DOI: 10.1021/acs.jcim.1c00884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The epidermal growth factor receptor (EGFR) signaling pathway plays an important role in cell growth, proliferation, differentiation, and other physiological processes, which makes the EGFR a promising target for anticancer therapies. The discovery of novel EGFR inhibitors may provide a solution to the problem of drug resistance. In this work, we performed a ligand-based virtual screening (LBVS) protocol for finding novel EGFR inhibitors from a 5.3 million compound library. First, the 3D shape-based similarity was used to obtain structurally novel EGFR inhibitors. In this study, we tried three queries; two were crystal structures and one was generated from deep generative models of graphs (DGMG). Next, we have built four structure-activity relationship (SAR) models and three quantitative structure-activity relationship (QSAR) models based on an SVM method for further screening of highly active EGFR inhibitors. Experimental validations led to the identification of nine hits out of 18 tested compounds. Among them, hit 1, hit 5, and hit 6 had IC50 values around 80 nM against EGFR whose interactions with EGFR were further investigated by molecular dynamics simulations.
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Affiliation(s)
- Donghui Huo
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shiyu Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Kong
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zijian Qin
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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Ligand-Based Pharmacophore Modeling, Molecular Docking, and Molecular Dynamic Studies of Dual Tyrosine Kinase Inhibitor of EGFR and VEGFR2. Int J Mol Sci 2020; 21:ijms21207779. [PMID: 33096664 PMCID: PMC7590020 DOI: 10.3390/ijms21207779] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor 2 (VEGFR2) play an important role in cancer growth. Both of them have close relationships. Expression of EGFR will induce an angiogenic factor (VEGF) release for binding with VEGFR2. However, the existence of VEGF up-regulation independent of EGFR leads to cancer cell resistance to anti-EGFR. Therefore, a therapeutic approach targeting EGFR and VEGFR2 simultaneously may improve the outcome of cancer treatment. The present study was designed to identify potential compounds as a dual inhibitor of EGFR and VEGFR2 by the computational method. Firstly, the ligand-based pharmacophore model for each target was setup to screen of ZINC database of purchasable compounds. The hit compounds obtained by pharmacophore screening were then further screened by molecular docking studies. Taking erlotinib (EGFR inhibitor) and axitinib (VEGFR2 inhibitor) as reference drugs, six potential compounds (ZINC08398597, ZINC12047553, ZINC16525481, ZINC17418102, ZINC21942954, and ZINC38484632) were selected based on their docking scores and binding interaction. However, molecular dynamics simulations demonstrated that only ZINC16525481 and ZINC38484632 which have good binding free energy and stable hydrogen bonding interactions with EGFR and VEGFR2. The result represents a promising starting point for developing potent dual tyrosine kinases inhibitor of EGFR and VEGFR2.
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Ornnork N, Kiriwan D, Lirdprapamongkol K, Choowongkomon K, Svasti J, Eurtivong C. Molecular dynamics, MM/PBSA and in vitro validation of a novel quinazoline-based EGFR tyrosine kinase inhibitor identified using structure-based in silico screening. J Mol Graph Model 2020; 99:107639. [PMID: 32534372 DOI: 10.1016/j.jmgm.2020.107639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/27/2022]
Abstract
EGFR-TK has been a target strongly associated with the development of NSCLCs. A structure-based virtual screening campaign was launched against EGFR-TK by virtual screening a 3D library of 167 commercially available small molecules downloaded from ChemBridge Corporation. The virtual screen identified 12 virtual hit molecules, which were biologically evaluated against an EGFR-TK inhibitor-sensitive NSCLC cell line, A549. A quinazoline-based molecule 1, was most active and displayed ∼58% cytotoxicity at 20 μM single dose. The mode of cell death suggests molecule 1 induced apoptosis, which is characteristic of EGFR-TK pathway inhibition. A 50 ns MD simulation was conducted on three different systems: free EGFR-TK, molecule 1 complexed to EGFR-TK, and the positive control, lapatinib, complexed to EGFR-TK. The MD simulations showed increase in stabilisation of the EGFR-TK structure for the complexed systems, i.e., lower RMSDs and RMSFs for complexed EGFR-TK structures compared to the free EGFR-TK system. The binding affinities were estimated using MM/PBSA in the last 10 ns of the MD simulation that revealed comparable binding free energies between molecule 1 and lapatinib, ΔGbind = -25.0 and -23.9 kcal/mol, respectively. Per residue binding free energy decomposition studies revealed non-polar interactions contributed mostly to the binding free energies. Residues Leu718, Arg841 and Phe856 were predicted to contribute most to the binding free energies for molecule 1.
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Affiliation(s)
- Narittira Ornnork
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Duangnapa Kiriwan
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Chatchakorn Eurtivong
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand.
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Zhang J, Song Y, Liang Y, Zou H, Zuo P, Yan M, Jing S, Li T, Wang Y, Li D, Zhang T, Wei Z. Cucurbitacin IIa interferes with EGFR-MAPK signaling pathway leads to proliferation inhibition in A549 cells. Food Chem Toxicol 2019; 132:110654. [DOI: 10.1016/j.fct.2019.110654] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/25/2019] [Accepted: 06/29/2019] [Indexed: 12/20/2022]
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Inhibiting two cellular mutant epidermal growth factor receptor tyrosine kinases by addressing computationally assessed crystal ligand pockets. Future Med Chem 2019; 11:833-846. [PMID: 30724109 DOI: 10.4155/fmc-2018-0525] [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] [Indexed: 01/13/2023] Open
Abstract
Aim: Blocking receptor tyrosine kinases is a useful strategy for inhibiting the overexpression of EGFR. However, the quality of crystal pocket is an essential issue for virtually identifying new leads for surviving resistance cancer cells. Results: With the examinating crystal pocket quality by the self-docking root-mean-square deviation (RMSD) calculation, we used the two best kinase pockets of mutant EGFR kinases, T790M/L858R and G719S, for virtual screening. After sorting all the docking poses of the 57,177 library compounds by consensus scores, three evidently blocked cellular EGFR phosphorylation in the H1975 and SW48 cell lines. Conclusion: The computationally assessed qualities of crystal pockets of crystal EGFR kinases can help identify new cellular active and target-specific ligands rapidly and at low cost.
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Tang H, Liu Y, Wang C, Zheng H, Chen Y, Liu W, Chen X, Zhang J, Chen H, Yang Y, Yang J. Inhibition of COX-2 and EGFR by Melafolone Improves Anti-PD-1 Therapy through Vascular Normalization and PD-L1 Downregulation in Lung Cancer. J Pharmacol Exp Ther 2018; 368:401-413. [PMID: 30591531 DOI: 10.1124/jpet.118.254359] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
Checkpoint blockade therapy has been proven efficacious in lung cancer patients. However, primary/acquired resistance hampers its efficacy. Therefore, there is an urgent need to develop novel strategies to improve checkpoint blockade therapy. Here we tested whether dual inhibition of cyclooxygenase-2 (COX-2) and epidermal growth factor receptor (EGFR) by flavonoid melafolone improves program death 1 (PD-1) checkpoint blockade therapy through normalizing tumor vasculature and PD-1 ligand (PD-L1) downregulation. Virtual screening assay, cellular thermal shift assay, and enzyme inhibition assay identified melafolone as a potential inhibitor of COX-2 and EGFR. In Lewis lung carcinoma (LLC) and CMT167 models, dual inhibition of COX-2 and EGFR by melafolone promoted survival, tumor growth inhibition, and vascular normalization, and ameliorated CD8+ T-cell suppression, accompanied by the downregulation of transforming growth factor-β (TGF-β), vascular endothelial growth factor (VEGF), and PD-L1 in the tumor cells. Mechanistically, dual inhibition of COX-2 and EGFR in lung cancer cells by melafolone increased the migration of pericyte, decreased the proliferation and migration of endothelial cells, and enhanced the proliferation and effector function of CD8+ T cells through VEGF, TGF-β, or PD-L1 downregulation and PI3K/AKT inactivation. Notably, melafolone improved PD-1 immunotherapy against LLC and CMT167 tumors. Together, dual inhibition of COX-2 and EGFR by melafolone improves checkpoint blockade therapy through vascular normalization and PD-L1 downregulation and, by affecting vessels and immune cells, may be a promising combination strategy for the treatment of human lung cancer.
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Affiliation(s)
- Honglin Tang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Yanzhuo Liu
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Chenlong Wang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Hao Zheng
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Yaxin Chen
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Wen Liu
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Xuewei Chen
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Jing Zhang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Honglei Chen
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Yuqing Yang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Jing Yang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-Related Diseases (H.T., Y.L., C.W., H.Z., Y.C., W.L., X.C., J.Z., J.Y.) and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
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Zhi Y, Wu X, Shen W, Wang Y, Zhou X, He P, Pan J, Chen Z, Li W, Zhou Z. Synthesis and pharmacological evaluation of novel epidermal growth factor receptor inhibitors against prostate tumor cells. Oncol Lett 2018; 16:6522-6530. [PMID: 30405791 PMCID: PMC6202546 DOI: 10.3892/ol.2018.9438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/15/2017] [Indexed: 01/27/2023] Open
Abstract
The aim of the present study was to investigate the activities of novel synthetic epidermal growth factor receptor (EGFR) inhibitors (ZINC05463076, ZINC2102846 and ZINC19901103) against prostate tumors, in vitro models and investigate the potential underlying mechanisms. A panel of prostate tumor cell lines (LNCaP, DU-145, PC-3 and LNCaP-AI cells) were used to evaluate antitumor activity of ZINC05463076, ZINC2102846, and ZINC19901103 in vitro. Cell growth and clonal formation were determined by MTT assay and Soft agar colony formation assay, respectively. An EGFR kinase assay following treatment of the compounds was performed by ELISA. Cell cycle-regulating proteins, including cyclin-dependent kinase (CDK)1, CKD2, CKD4 and inhibitory effects of these compounds on downstream signaling were analyzed by western blotting. Flow cytometry was performed to investigate apoptosis and cell cycle phases of the treated cells. It was revealed that all compounds synthesized in the present study demonstrated significant EGFR inhibition abilities, compared with approved EGFR inhibitor drug gefitinib. Treatment of LNCaP, DU-145, PC3 and LNCaP-AI cells with these compounds revealed cell proliferation inhibition and colony formation suppression dose-dependently in vitro. The agents impaired phosphorylation of EGFR and extracellular signal-regulated kinase 1/2 and suppressed their downstream signaling. In addition, these novel synthetic agents decreased the expression level of survivin, which may induce G1 cell cycle phase arrest and cell apoptosis in PCa cells subsequently. Collectively, ZINC05463076, ZINC2102846 and ZINC19901103 exhibited significant antitumor activity in human prostate tumors in vitro, by inhibiting EGFR and promoting apoptosis, which suggested a rationale for clinical development in prostate tumor therapy.
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Affiliation(s)
- Yi Zhi
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China.,Department of Urology, Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, P.R. China
| | - Xiaojun Wu
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Wenhao Shen
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Yongquan Wang
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Xiaozhou Zhou
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Peng He
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jinhong Pan
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Zhiwen Chen
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Weibing Li
- Department of Urology, Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, P.R. China
| | - Zhansong Zhou
- Urology Institute of People Liberation Army, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
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D'Souza W, Saranath D. OMICS, Oral Cancer Molecular Landscapes, and Clinical Practice. ACTA ACUST UNITED AC 2017; 21:689-703. [DOI: 10.1089/omi.2017.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wendy D'Souza
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai, India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai, India
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10
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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Kumar V, Krishna S, Siddiqi MI. Virtual screening strategies: recent advances in the identification and design of anti-cancer agents. Methods 2014; 71:64-70. [PMID: 25171960 DOI: 10.1016/j.ymeth.2014.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/31/2014] [Accepted: 08/19/2014] [Indexed: 01/29/2023] Open
Abstract
Virtual screening (VS) is a well-established technique, which is now routinely employed in computer aided drug designing process. VS can be broadly classified into two categories, i.e., ligand-based and structure-based approach. In recent years, VS has emerged as a time saving and cost effective technique, capable of screening millions of compounds in a user friendly manner. In the area of cancer drug design, VS methods have been widely used and helped in identifying novel molecules as potential anti-cancer agents. Both ligand-based VS (LBVS) structure-based VS (SBVS) methods have been highly useful in the identification of a number of potential anti-cancer agents exhibiting activities in nanomolar range. In tune with the rapid progress in the enhancement of computational power, VS has witnessed significant change in terms of speed and hit rate and in future it is expected that VS will be a preferential alternative to high throughput screening (HTS). This review, discusses recent trends and contribution of VS in the area of anti-cancer drug discovery.
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Affiliation(s)
- Vikash Kumar
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India; Academy of Scientific and Innovative Research, New Delhi, India.
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Shi Z, An N, Lu BM, Zhou N, Yang SL, Zhang B, Li CY, Wang ZJ, Wang F, Wu CF, Bao JK. Identification of novel kinase inhibitors by targeting a kinase-related apoptotic protein-protein interaction network in HeLa cells. Cell Prolif 2014; 47:219-30. [PMID: 24645986 PMCID: PMC6496802 DOI: 10.1111/cpr.12098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 12/28/2013] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Protein kinases orchestrate activation of signalling cascades in response to extra- and intracellular stimuli for regulation of cell proliferation. They are directly involved in a variety of diseases, particularly cancers. Systems biology approaches have become increasingly important in understanding regulatory frameworks in cancer, and thus may facilitate future anti-cancer discoveries. Moreover, it has been suggested and confirmed that high-throughput virtual screening provides a novel, effective way to reveal small molecule protein kinase inhibitors. Accordingly, we aimed to identify kinase targets and novel kinase inhibitors. MATERIALS AND METHODS A series of bioinformatics methods, such as network construction, molecular docking and microarray analyses were performed. RESULTS In this study, we computationally constructed the appropriate global human protein-protein interaction network with data from online databases, and then modified it into a kinase-related apoptotic protein-protein interaction network. Subsequently, we identified several kinases as potential drug targets according to their differential expression observed by microarray analyses. Then, we predicted relevant microRNAs, which could target the above-mentioned kinases. Ultimately, we virtually screened a number of small molecule natural products from Traditional Chinese Medicine (TCM)@Taiwan database and identified a number of compounds that are able to target polo-like kinase 1, cyclin-dependent kinase 1 and cyclin-dependent kinase 2 in HeLa cervical carcinoma cells. CONCLUSIONS Taken together, all these findings might hopefully facilitate discovery of new kinase inhibitors that could be promising candidates for anti-cancer drug development.
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Affiliation(s)
- Z. Shi
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
- School of Life SciencesGuizhou Normal UniversityGuiyang550001China
| | - N. An
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - B. M. Lu
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - N. Zhou
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - S. L. Yang
- School of Life SciencesGuizhou Normal UniversityGuiyang550001China
| | - B. Zhang
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - C. Y. Li
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - Z. J. Wang
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - F. Wang
- China National Biotec Group Company LimitedBeijing100029China
| | - C. F. Wu
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
| | - J. K. Bao
- School of Life Sciences & Key Laboratory of Bio‐resourcesMinistry of EducationSichuan UniversityChengdu610064China
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A novel inhibitor of Mammalian triosephosphate isomerase found by an in silico approach. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2014; 2014:469125. [PMID: 25383217 PMCID: PMC4207401 DOI: 10.1155/2014/469125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/18/2013] [Accepted: 01/07/2014] [Indexed: 12/20/2022]
Abstract
Triosephosphate isomerase (TIM) is an essential, highly conserved component of glycolysis. Tumors are often dependent on glycolysis for energy and metabolite production (the Warburg effect). Glycolysis inhibitors thus show promise as cancer treatments. TIM inhibition, unlike inhibition of other glycolysis enzymes, also produces toxic methylglyoxal targeted to regions of high glycolysis, an effect that might also be therapeutically useful. Thus TIM is an attractive drug target. A total of 338,562 lead-like molecules were analyzed computationally to find TIM inhibitors by an efficient “double screen” approach. The first fragment-sized compounds were studied using structure-based virtual screening to identify binding motifs for mammalian TIM. Subsequently, larger compounds, filtered to meet the binding criteria developed in the first analysis, were ranked using a second round of structure-based virtual screening. A compound was found that inhibited mammalian TIM in vitro in the micromolar range. Docking and molecular dynamics (MD) suggested that the inhibitor made hydrogen bond contacts with TIM catalytic residues. In addition, hydrophobic contacts were made throughout the binding site. All predicted inhibitor-TIM interactions involved TIM residues that were highly conserved. The discovered compound may provide a scaffold for elaboration of other inhibitors.
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Sun XQ, Chen L, Li YZ, Li WH, Liu GX, Tu YQ, Tang Y. Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors. Acta Pharmacol Sin 2014; 35:301-10. [PMID: 24335842 PMCID: PMC4076596 DOI: 10.1038/aps.2013.148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/10/2013] [Indexed: 01/25/2023] Open
Abstract
AIM To develop a novel 3D-QSAR approach for study of the epidermal growth factor receptor tyrosine kinase (EGFR TK) and its inhibitors. METHODS One hundred thirty nine EGFR TK inhibitors were classified into 3 clusters. Ensemble docking of these inhibitors with 19 EGFR TK crystal structures was performed. Three protein structures that showed the best recognition of each cluster were selected based on the docking results. Then, a novel QSAR (ensemble-QSAR) building method was developed based on the ligand conformations determined by the corresponding protein structures. RESULTS Compared with the 3D-QSAR model, in which the ligand conformations were determined by a single protein structure, ensemble-QSAR exhibited higher R2 (0.87) and Q2 (0.78) values and thus appeared to be a more reliable and better predictive model. Ensemble-QSAR was also able to more accurately describe the interactions between the target and the ligands. CONCLUSION The novel ensemble-QSAR model built in this study outperforms the traditional 3D-QSAR model in rationality, and provides a good example of selecting suitable protein structures for docking prediction and for building structure-based QSAR using available protein structures.
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Affiliation(s)
- Xian-qiang Sun
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Lei Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yao-zong Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Department of Chemistry, Umeå University, S-90187 Umeå, Sweden
| | - Wei-hua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Gui-xia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yao-quan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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Synthesis of annulated heterocyclic systems based on 4-CF3- or 4-CHF2-3-cyano-(1H)-pyridine-2-thiones. Russ Chem Bull 2013. [DOI: 10.1007/s11172-013-0321-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Ngoei KRW, Ng DCH, Gooley PR, Fairlie DP, Stoermer MJ, Bogoyevitch MA. Identification and characterization of bi-thiazole-2,2'-diamines as kinase inhibitory scaffolds. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1077-88. [PMID: 23410953 DOI: 10.1016/j.bbapap.2013.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 01/30/2013] [Accepted: 02/03/2013] [Indexed: 11/18/2022]
Abstract
Based on bioinformatics interrogation of the genome, >500 mammalian protein kinases can be clustered within seven different groups. Of these kinases, the mitogen-activated protein kinase (MAPK) family forms part of the CMGC group of serine/threonine kinases that includes extracellular signal regulated kinases (ERKs), cJun N-terminal kinases (JNKs), and p38 MAPKs. With the JNKs considered attractive targets in the treatment of pathologies including diabetes and stroke, efforts have been directed to the discovery of new JNK inhibitory molecules that can be further developed as new therapeutics. Capitalizing on our biochemical understanding of JNK, we performed in silico screens of commercially available chemical databases to identify JNK1-interacting compounds and tested their in vitro JNK inhibitory activity. With in vitro and cell culture studies, we showed that the compound, 4'-methyl-N(2)-3-pyridinyl-4,5'-bi-1,3-thiazole-2,2'-diamine (JNK Docking (JD) compound 123, but not the related compound (4'-methyl-N~2~-(6-methyl-2-pyridinyl)-4,5'-bi-1,3-thiazole-2,2'-diamine (JD124), inhibited JNK1 activity towards a range of substrates. Molecular docking, saturation transfer difference NMR experiments and enzyme kinetic analyses revealed both ATP- and substrate-competitive inhibition of JNK by JD123. In characterizing JD123 further, we noted its ATP-competitive inhibition of the related p38-γ MAPK, but not ERK1, ERK2, or p38-α, p38-β or p38-δ. Further screening of a broad panel of kinases using 10μM JD123, identified inhibition of kinases including protein kinase Bβ (PKBβ/Aktβ). Appropriately modified thiazole diamines, as typified by JD123, thus provide a new chemical scaffold for development of inhibitors for the JNK and p38-γ MAPKs as well as other kinases that are also potential therapeutic targets such as PKBβ/Aktβ.
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Affiliation(s)
- Kevin R W Ngoei
- Department of Biochemistry and Molecular Biology, University of Melbourne, Victoria, Australia
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