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Lin IL, Lin YT, Chang YC, Kondapuram SK, Lin KH, Chen PC, Kuo CY, Coumar MS, Cheung CHA. The SMAC mimetic GDC-0152 is a direct ABCB1-ATPase activity modulator and BIRC5 expression suppressor in cancer cells. Toxicol Appl Pharmacol 2024; 485:116888. [PMID: 38452945 DOI: 10.1016/j.taap.2024.116888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Upregulation of the multidrug efflux pump ABCB1/MDR1 (P-gp) and the anti-apoptotic protein BIRC5/Survivin promotes multidrug resistance in various human cancers. GDC-0152 is a DIABLO/SMAC mimetic currently being tested in patients with solid tumors. However, it is still unclear whether GDC-0152 is therapeutically applicable for patients with ABCB1-overexpressing multidrug-resistant tumors, and the molecular mechanism of action of GDC-0152 in cancer cells is still incompletely understood. In this study, we found that the potency of GDC-0152 is unaffected by the expression of ABCB1 in cancer cells. Interestingly, through in silico and in vitro analysis, we discovered that GDC-0152 directly modulates the ABCB1-ATPase activity and inhibits ABCB1 multidrug efflux activity at sub-cytotoxic concentrations (i.e., 0.25×IC50 or less). Further investigation revealed that GDC-0152 also decreases BIRC5 expression, induces mitophagy, and lowers intracellular ATP levels in cancer cells at low cytotoxic concentrations (i.e., 0.5×IC50). Co-treatment with GDC-0152 restored the sensitivity to the known ABCB1 substrates, including paclitaxel, vincristine, and YM155 in ABCB1-expressing multidrug-resistant cancer cells, and it also restored the sensitivity to tamoxifen in BIRC5-overexpressing tamoxifen-resistant breast cancer cells in vitro. Moreover, co-treatment with GDC-0152 restored and potentiated the anticancer effects of paclitaxel in ABCB1 and BIRC5 co-expressing xenograft tumors in vivo. In conclusion, GDC-0152 has the potential for use in the management of cancer patients with ABCB1 and BIRC5-related drug resistance. The findings of our study provide essential information to physicians for designing a more patient-specific GDC-0152 clinical trial program in the future.
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Affiliation(s)
- I-Li Lin
- Department of Radiology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600566, Taiwan
| | - Yu-Ting Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Yung-Chieh Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University 701, Tainan, Taiwan
| | - Sree Karani Kondapuram
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Kai-Hsuan Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University 701, Tainan, Taiwan
| | - Pin-Chen Chen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chung-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Chun Hei Antonio Cheung
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University 701, Tainan, Taiwan.
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Kalita B, Coumar MS. Deciphering Breast Cancer Metastasis Cascade: A Systems Biology Approach Integrating Transcriptome and Interactome Insights for Target Discovery. OMICS 2024; 28:148-161. [PMID: 38484298 DOI: 10.1089/omi.2023.0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Breast cancer is the lead cause of cancer-related deaths among women globally. Breast cancer metastasis is a complex and still inadequately understood process and a key dimension of mortality attendant to breast cancer. This study reports dysregulated genes across metastatic stages and tissues, shedding light on their molecular interplay in disease pathogenesis and new possibilities for drug discovery. Comprehensive analyses of gene expression data from primary breast tumor, circulating tumor cells, and distant metastatic sites in the brain, lung, liver, and bone were conducted. Genes dysregulated across multiple stages and tissues were identified as metastatic cascade genes, and are further classified based on functional associations with metastasis-related mechanisms. Their interactions with HUB genes in interactome networks were scrutinized, followed by pathway enrichment analysis. Validation for their potential as targets included assessments for survival, druggability, prognostic marker status, secretome annotation, protein expression, and cell type marker association. Results displayed critical genes in the metastatic cascade and those specific to metastatic sites, revealing the involvement of the collagen degradation and assembly of collagen fibrils and other multimeric structure pathways in driving metastasis. Notably, pivotal cascade genes FABP4, CXCL12, APOD, and IGF1 emerged with high metastatic potential, linked to significant druggability and survival scores, establishing them as potential molecular targets. The significance of this research lies in its potential to uncover novel biomarkers for early detection, therapeutic targets, and a deeper understanding of the molecular mechanisms underpinning the metastatic cascade in breast cancer, and with an eye to precision/personalized medicine.
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Affiliation(s)
- Bikashita Kalita
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Kondapuram SK, Ramachandran HK, Arya H, Coumar MS. Targeting survivin for cancer therapy: Strategies, small molecule inhibitors and vaccine based therapeutics in development. Life Sci 2023; 335:122260. [PMID: 37963509 DOI: 10.1016/j.lfs.2023.122260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Survivin is a member of the family of inhibitors of apoptosis proteins (IAPs). It is involved in the normal mitotic process and acts as an anti-apoptotic molecule. While terminally differentiated normal tissues lack survivin, several human malignancies have significant protein levels. Resistance to chemotherapy and radiation in tumor cells is associated with survivin expression. Decreased tumor development, apoptosis, and increased sensitivity to chemotherapy and radiation are all effects of downregulating survivin expression or activity. As a prospective cancer treatment, small molecules targeting the transcription and translation of survivin and molecules that can directly bind with the survivin are being explored both in pre-clinical and clinics. Pre-clinical investigations have found and demonstrated the effectiveness of several small-molecule survivin inhibitors. Unfortunately, these inhibitors have also been shown to have off-target effects, which could limit their clinical utility. In addition to small molecules, several survivin peptide vaccines are currently under development. These vaccines are designed to elicit a cytotoxic T-cell response against survivin, which could lead to the destruction of tumor cells expressing survivin. Some survivin-based vaccines are advancing through Phase II clinical studies. Overall, survivin is a promising cancer drug target. However, challenges still need to be addressed before the survivin targeted therapies can be widely used in the clinics.
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Affiliation(s)
- Sree Karani Kondapuram
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Hema Kasthuri Ramachandran
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Hemant Arya
- Institute for Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India.
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Brindangnanam P, Ashokkumar K, Kamaraj S, Coumar MS. Exploring imidazo[4,5- g]quinoline-4,9-dione derivatives as Acinetobacter baumannii efflux pump inhibitor: an in silico approach. J Biomol Struct Dyn 2023:1-20. [PMID: 37937796 DOI: 10.1080/07391102.2023.2279287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. World Health Organization (WHO) statistics show that globally 0.7 million people are dying yearly due to the emergence of AMR. By 2050, the expected number of lives lost will be 10 million per year. Acinetobacter baumannii is a dreadful nosocomial pathogen that has developed multidrug resistance (MDR) to several currently prescribed antibiotics worldwide. Overexpression of drug efflux transporters (DETs) is one of the mechanisms of multidrug resistance (MDR) in Acinetobacter baumannii. Therefore, blocking the DET can raise the efficacy of the existing antibiotics by increasing their residence time inside the bacteria. In silico screening of five synthetic compounds against three drug efflux pump from A. baumannii has identified KSA5, a novel imidazo[4,5-g]quinoline-4,9-dione derivative, to block the efflux of antibiotics. Molecular docking and simulation results showed that KSA5 could bind to adeB, adeG, and adeJ by consistently interacting with ligand-binding site residues. KSA5 has a higher binding free energy and a lower HOMO-LUMO energy gap than PAβN, suggesting a better ability to interact and inhibit DETs. Further analysis showed that KSA5 is a drug-like molecule with optimal physicochemical and ADME properties. Hence, KSA5 could be combined with antibiotics to overcome antimicrobial resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
| | - Krishnan Ashokkumar
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Velllore, India
| | - Sriraghavan Kamaraj
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Velllore, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
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Boopathi S, Meenatchi R, Brindangnanam P, Sudhakaran G, Coumar MS, Arockiaraj J. Microbiome analysis of Litopenaeus vannamei reveals Vibrio as main risk factor of white faeces syndrome. Aquaculture 2023; 576:739829. [DOI: 10.1016/j.aquaculture.2023.739829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
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Li MC, Coumar MS, Lin SY, Lin YS, Huang GL, Chen CH, Lien TW, Wu YW, Chen YT, Chen CP, Huang YC, Yeh KC, Yang CM, Kalita B, Pan SL, Hsu TA, Yeh TK, Chen CT, Hsieh HP. Development of Furanopyrimidine-Based Orally Active Third-Generation EGFR Inhibitors for the Treatment of Non-Small Cell Lung Cancer. J Med Chem 2023; 66:2566-2588. [PMID: 36749735 PMCID: PMC9969398 DOI: 10.1021/acs.jmedchem.2c01434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The development of orally bioavailable, furanopyrimidine-based double-mutant (L858R/T790M) EGFR inhibitors is described. First, selectivity for mutant EGFR was accomplished by replacing the (S)-2-phenylglycinol moiety of 12 with either an ethanol or an alkyl substituent. Then, the cellular potency and physicochemical properties were optimized through insights from molecular modeling studies by implanting various solubilizing groups in phenyl rings A and B. Optimized lead 52 shows 8-fold selective inhibition of H1975 (EGFRL858R/T790M overexpressing) cancer cells over A431 (EGFRWT overexpressing) cancer cells; western blot analysis further confirmed EGFR mutant-selective target modulation inside the cancer cells by 52. Notably, 52 displayed in vivo antitumor effects in two different mouse xenograft models (BaF3 transfected with mutant EGFR and H1975 tumors) with TGI = 74.9 and 97.5% after oral administration (F = 27%), respectively. With an extraordinary kinome selectivity (S(10) score of 0.017), 52 undergoes detailed preclinical development.
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Affiliation(s)
- Mu-Chun Li
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
- Biomedical
Translation Research Center, Academia Sinica, Taipei City 115202, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Department
of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet 605014, Pondicherry, India
| | - Shu-Yu Lin
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Yih-Shyan Lin
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Guan-Lin Huang
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Tzu-Wen Lien
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Yi-Wen Wu
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei City 110301, Taiwan, ROC
| | - Yen-Ting Chen
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Ching-Ping Chen
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Yu-Chen Huang
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Kai-Chia Yeh
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Chen-Ming Yang
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Bikashita Kalita
- Department
of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet 605014, Pondicherry, India
| | - Shiow-Lin Pan
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei City 110301, Taiwan, ROC
- Ph.D.
Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei City 110301, Taiwan, ROC
| | - Tsu-An Hsu
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350401, Taiwan, ROC
- Biomedical
Translation Research Center, Academia Sinica, Taipei City 115202, Taiwan, ROC
- Department
of Chemistry, National Tsing Hua University, Hsinchu City 300044, Taiwan, ROC
- , . Phone: +886-37-206-166
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Bhavani GV, Kondapuram SK, Shamsudeen AF, Coumar MS, Selvin J, Kannan T. Synthesis, antitubercular evaluation, and molecular docking studies of hybrid pyridinium salts derived from isoniazid. Drug Dev Res 2023; 84:470-483. [PMID: 36744647 DOI: 10.1002/ddr.22039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/08/2023] [Accepted: 01/15/2023] [Indexed: 02/07/2023]
Abstract
In the quest to develop potent inhibitors for Mycobacterium tuberculosis, novel isoniazid-based pyridinium salts were designed, synthesized, and tested for their antimycobacterial activities against the H37 Rv strain of Mycobacterium tuberculosis using rifampicin as a standard. The pyridinium salts 4k, 4l, and 7d showed exceptional antimycobacterial activities with MIC90 at 1 µg/mL. The in vitro cytotoxicity and pharmacokinetics profiles of these compounds were established for the identification of a lead molecule using in vivo efficacy proof-of-concept studies and found that the lead compound 4k possesses LC50 value at 25 µg/mL. The in vitro antimycobacterial activity results were further supported by in silico studies with good binding affinities ranging from -9.8 to -11.6 kcal/mol for 4k, 4l, and 7d with the target oxidoreductase DprE1 enzyme. These results demonstrate that pyridinium salts derived from isoniazid can be a potentially promising pharmacophore for the development of novel antitubercular candidates.
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Affiliation(s)
| | | | | | | | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, India
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Kondapuram SK, Coumar MS. Pan-cancer gene expression analysis: Identification of deregulated autophagy genes and drugs to target them. Gene X 2022; 844:146821. [PMID: 35985410 DOI: 10.1016/j.gene.2022.146821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Identifying suitable deregulated targets in autophagy pathway is essential for developing autophagy modulating cancer therapies. With this aim, we systematically analyzed the expression levels of genes that contribute to the execution of autophagy in 21 cancers. Deregulated genes for 21 cancers were analyzed using the level 3 mRNA data from TCGAbiolinks. A total of 574 autophagy genes were mapped to the deregulated genes across 21 cancers. PPI network, cluster analysis, gene enrichment, gene ontology, KEGG pathway, patient survival, protein expression and cMap analysis were performed. Among the autophagy genes, 260 were upregulated, and 43 were downregulated across pan-cancer. The upregulated autophagy genes - CDKN2A and BIRC5 - were the most frequent signatures in cancers and could be universal cancer biomarkers. Significant involvement of autophagy process was found in 8 cancers (CHOL, HNSC, GBM, KICH, KIRC, KIRP, LIHC and SARC). Fifteen autophagy hub genes (ATP6V0C, BIRC5, HDAC1, IL4, ITGB1, ITGB4, MAPK3, mTOR, cMYC, PTK2, SRC, TCIRG1, TP63, TP73 and ULK1) were found to be linked with patients survival and also expressed in cancer patients tissue samples, making them as potential drug targets for these cancers. The deregulated autophagy genes were further used to identify drugs Losartan, BMS-345541, Embelin, Abexinostat, Panobinostat, Vorinostat, PD-184352, PP-1, XMD-1150, Triplotide, Doxorubicin and Ouabain, which could target one or more autophagy hub genes. Overall, our findings shed light on the most frequent cancer-associated autophagy genes, potential autophagy targets and molecules for cancer treatment. These findings can accelerate autophagy modulation in cancer therapy.
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Affiliation(s)
- Sree Karani Kondapuram
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry- 605014, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry- 605014, India.
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Singh A, Kumar P, Sarvagalla S, Bharadwaj T, Nayak N, Coumar MS, Giri R, Garg N. Functional inhibition of c-Myc using novel inhibitors identified through “hot spot” targeting. J Biol Chem 2022; 298:101898. [PMID: 35378126 PMCID: PMC9065629 DOI: 10.1016/j.jbc.2022.101898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 12/14/2022] Open
Abstract
Protein–protein interactions drive various biological processes in healthy as well as disease states. The transcription factor c-Myc plays a crucial role in maintaining cellular homeostasis, and its deregulated expression is linked to various human cancers; therefore, it can be considered a viable target for cancer therapeutics. However, the structural heterogeneity of c-Myc due to its disordered nature poses a major challenge to drug discovery. In the present study, we used an in silico alanine scanning mutagenesis approach to identify “hot spot” residues within the c-Myc/Myc-associated factor X interface, which is highly disordered and has not yet been systematically analyzed for potential small molecule binding sites. We then used the information gained from this analysis to screen potential inhibitors using a conformation ensemble approach. The fluorescence-based biophysical experiments showed that the identified hit molecules displayed noncovalent interactions with these hot spot residues, and further cell-based experiments showed substantial in vitro potency against diverse c-Myc-expressing cancer/stem cells by deregulating c-Myc activity. These biophysical and computational studies demonstrated stable binding of the hit compounds with the disordered c-Myc protein. Collectively, our data indicated effective drug targeting of the disordered c-Myc protein via the determination of hot spot residues in the c-Myc/Myc-associated factor X heterodimer.
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Brindangnanam P, Sawant AR, Prashanth K, Coumar MS. Bacterial effluxome as a barrier against antimicrobial agents: structural biology aspects and drug targeting. Tissue Barriers 2021; 10:2013695. [PMID: 34957912 DOI: 10.1080/21688370.2021.2013695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. The bacterial membrane is the first layer of defense for the bacteria against antimicrobial agents (AMA), specifically transporters in the membrane efflux these AMA out of the bacteria and plays a significant role in the AMR development. Understanding the structure and the functions of these efflux transporters is essential to overcome AMR. This review discusses efflux transporters (primary, secondary, and tripartite), their domain architectures, substrate specificities, and efflux pump inhibitors (EPI). Special emphasis on nosocomial ESKAPEE (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli) pathogens, their multidrug efflux targets and inhibitors are discussed. Deep knowledge about the functioning of efflux pumps and their structural aspects will open up opportunities for developing new EPI, which could be used along with AMA as combination therapy to overcome the emerging AMR crisis.
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Affiliation(s)
- Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Khan MIK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S, Dhayalan A. The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels. Biochim Biophys Acta Mol Cell Res 2021; 1868:119079. [PMID: 34147559 DOI: 10.1016/j.bbamcr.2021.119079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/13/2021] [Indexed: 01/23/2023]
Abstract
The protein lysine methyltransferase, SMYD2 is involved in diverse cellular events by regulating protein functions through lysine methylation. Though several substrate proteins of SMYD2 are well-studied, only a limited number of its interaction partners have been identified and characterized. Here, we performed a yeast two-hybrid screening of SMYD2 and found that the ribosomal protein, eL21 could interact with SMYD2. SMYD2-eL21 interaction in the human cells was confirmed by immunoprecipitation methods. In vitro pull-down assays revealed that SMYD2 interacts with eL21 directly through its SET and MYND domain. Computational mapping, followed by experimental studies identified that Lys81 and Lys83 residues of eL21 are important for the SMYD2-eL21 interaction. Evolutionary analysis showed that these residues might have co-evolved with the emergence of SMYD2. We found that eL21 regulates the steady state levels of SMYD2 by promoting its transcription and inhibiting its proteasomal degradation. Importantly, SMYD2-eL21 interaction plays an important role in regulating cell proliferation and its dysregulation might lead to tumorigenesis. Our findings highlight a novel extra-ribosomal function of eL21 on regulating SMYD2 levels and imply that ribosomal proteins might regulate wide range of cellular functions through protein-protein interactions in addition to their core function in translation.
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Affiliation(s)
- Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | | | - Reshma Ramachandran
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India
| | - Somlee Gupta
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Rashmi Mishra
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India.
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Kalita B, Coumar MS. Deciphering molecular mechanisms of metastasis: novel insights into targets and therapeutics. Cell Oncol (Dordr) 2021; 44:751-775. [PMID: 33914273 DOI: 10.1007/s13402-021-00611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The transition of a primary tumour to metastatic progression is driven by dynamic molecular changes, including genetic and epigenetic alterations. The metastatic cascade involves bidirectional interactions among extracellular and intracellular components leading to disintegration of cellular junctions, cytoskeleton reorganization and epithelial to mesenchymal transition. These events promote metastasis by reprogramming the primary cancer cell's molecular framework, enabling them to cause local invasion, anchorage-independent survival, cell death and immune resistance, extravasation and colonization of distant organs. Metastasis follows a site-specific pattern that is still poorly understood at the molecular level. Although various drugs have been tested clinically across different metastatic cancer types, it has remained difficult to develop efficacious therapeutics due to complex molecular layers involved in metastasis as well as experimental limitations. CONCLUSIONS In this review, a systemic evaluation of the molecular mechanisms of metastasis is outlined and the potential molecular components and their status as therapeutic targets and the associated pre-clinical and clinical agents available or under investigations are discussed. Integrative methods like pan-cancer data analysis, which can provide clinical insights into both targets and treatment decisions and help in the identification of crucial components driving metastasis such as mutational profiles, gene signatures, associated pathways, site specificities and disease-gene phenotypes, are discussed. A multi-level data integration of the metastasis signatures across multiple primary and metastatic cancer types may facilitate the development of precision medicine and open up new opportunities for future therapies.
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Affiliation(s)
- Bikashita Kalita
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014, India.
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Sarvagalla S, Lin TY, Kondapuram SK, Cheung CHA, Coumar MS. Survivin - caspase protein-protein interaction: Experimental evidence and computational investigations to decipher the hotspot residues for drug targeting. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Chandar Charles MR, Li MC, Hsieh HP, Coumar MS. Mimicking H3 Substrate Arginine in the Design of G9a Lysine Methyltransferase Inhibitors for Cancer Therapy: A Computational Study for Structure-Based Drug Design. ACS Omega 2021; 6:6100-6111. [PMID: 33718701 PMCID: PMC7948220 DOI: 10.1021/acsomega.0c04710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/09/2021] [Indexed: 05/30/2023]
Abstract
G9a protein methyltransferase is a potential epigenetic drug target in different cancers and other disease conditions overexpressing the enzyme. G9a is responsible for the H3K9 dimethylation mark, which epigenetically regulates gene expression. Arg8 and Lys9 of the H3 substrate peptide are the two crucial residues for substrate-specific recognition and methylation. Several substrate competitive inhibitors are reported for the potent inhibition of G9a by incorporating lysine mimic groups in the inhibitor design. In this study, we explored the concept of arginine mimic strategy. The hydrophobic segment of the reported inhibitors BIX-01294 and UNC0638 was replaced by a guanidine moiety (side-chain moiety of arginine). The newly substituted guanidine moieties of the inhibitors were positioned similar to the Arg8 of the substrate peptide in molecular docking. Additionally, improved reactivity of the guanidine-substituted inhibitors was observed in density functional theory studies. Molecular dynamics, molecular mechanics Poisson-Boltzmann surface area binding free energy, linear interaction energy, and potential mean force calculated from steered molecular dynamics simulations of the newly designed analogues show enhanced conformational stability and improved H-bond potential and binding affinity toward the target G9a. Moreover, the presence of both lysine and arginine mimics together shows a drastic increase in the binding affinity of the inhibitor towards G9a. Hence, we propose incorporating a guanidine group to imitate the substrate arginine's side chain in the inhibitor design to improve the potency of G9a inhibitors.
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Affiliation(s)
- M. Ramya Chandar Charles
- Centre
for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Mu-Chun Li
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli
County, Taiwan 350, ROC
- Department
of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300, Taiwan
| | - Hsing-Pang Hsieh
- Institute
of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli
County, Taiwan 350, ROC
- Department
of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300, Taiwan
- Biomedical
Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mohane Selvaraj Coumar
- Centre
for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
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15
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Reddy JS, Chen CM, Coumar MS, Sun HY, Sun N, Hsieh HP. Development of a Robust Scale-Up Synthetic Route for BPR1K871: A Clinical Candidate for the Treatment of Acute Myeloid Leukemia and Solid Tumors. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Julakanti Satyanarayana Reddy
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chih-Ming Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Hsu-Yi Sun
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Na Sun
- China Gateway Pharmaceutical Development Co, Shanghai 201417, China
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- Biomedical Translation Research Centre, Academia Sinica, Taipei 11520, Taiwan, ROC
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16
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Erusappan T, Kondapuram SK, Ekambaram SP, Coumar MS. Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach. J Mol Model 2021; 27:14. [PMID: 33403456 DOI: 10.1007/s00894-020-04651-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/16/2020] [Indexed: 11/30/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disorder that commonly affects multiple joints of the body. Currently, there is no permanent cure to the disease, but it can be managed with several potent drugs that cause serious side effects on prolonged use. Traditional remedies are considered promising for the treatment of several diseases, particularly chronic conditions, because they have lower side effects compared to synthetic drugs. In folklore, the rhizome of Alpinia calcarata Roscoe (Zingiberaceae) is used as a major ingredient of herbal formulations to treat RA. Phytoconstituents reported in A. calcarata rhizomes are diterpenoids, sesquiterpenoid, flavonoids, phytosterol, and volatile oils. The present study is intended to understand the molecular-level interaction of phytoconstituents present in A. calcarata rhizomes with RA molecular targets using computational approaches. A total of 30 phytoconstituents reported from the plant were used to carry out docking with 36 known targets of RA. Based on the docking results, 4 flavonoids were found to be strongly interacting with the RA targets. Further, molecular dynamics simulation confirmed stable interaction of quercetin with 6 targets (JAK3, SYK, MMP2, TLR8, IRAK1, and JAK1), galangin with 2 targets (IRAK1 and JAK1), and kaempferol (IRAK1) with one target of RA. Moreover, the presence of these three flavonoids was confirmed in the A. calcarata rhizome extract using LC-MS analysis. The computational study suggests that flavonoids present in A. calcarata rhizome may be responsible for RA modulatory activity. Particularly, quercetin and galangin could be potential development candidates for the treatment of RA. Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach.
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Affiliation(s)
- Thamizharasi Erusappan
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Sree Karani Kondapuram
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Sanmuga Priya Ekambaram
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India.
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.
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17
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Parcha PK, Sarvagalla S, Ashok C, Sudharshan SJ, Dyavaiah M, Coumar MS, Rajasekaran B. Repositioning antispasmodic drug Papaverine for the treatment of chronic myeloid leukemia. Pharmacol Rep 2021; 73:615-628. [PMID: 33389727 DOI: 10.1007/s43440-020-00196-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Papaverine is a benzylisoquinoline alkaloid from the plant Papaver somniferum (Opium poppy). It is approved as an antispasmodic drug by the US FDA and is also reported to have anti-cancer properties. Here, Papaverine's activity in chronic myeloid leukemia (CML) is explored using Saccharomyces cerevisiae, mammalian cancer cell lines, and in silico studies. METHODS The sensitivity of wild-type and mutant (anti-oxidant defense, apoptosis) strains of S. cerevisiae to the drug Papaverine was tested by colony formation, spot assays, and AO/EB staining. In vitro cytotoxic effect was investigated on HCT15 (colon), A549 (lung), HeLa (cervical), and K562 (Bcr-Abl positive CML), and RAW 264.7 cell lines; cell cycle, mitochondrial membrane potential, ROS detection analyzed in K562 cells using flow cytometry and apoptotic markers, Bcr-Abl signaling pathways examined by western blotting. Molecular docking and molecular dynamics simulation of Papaverine against the target Bcr-Abl were also carried out. RESULTS Investigation in S. cerevisiae evidenced Papaverine induces ROS-mediated apoptosis. Subsequent in vitro examination showed that CML cell line K562 was more sensitive to the drug Papaverine. Papaverine induces ROS generation, promotes apoptosis, and inhibits Bcr-Abl downstream signaling. Papaverine acts synergistically with the drug Imatinib. Furthermore, the docking and molecular dynamic simulation studies supported that Papaverine binds to the allosteric site of Bcr-Abl. CONCLUSION The data presented here have added support to the concept of polypharmacology of existing drugs and natural compounds to interact with more than one target. This study provides a proof-of-concept for repositioning Papaverine as an anti-CML drug.
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Affiliation(s)
- Phani Krishna Parcha
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sailu Sarvagalla
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - S J Sudharshan
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| | - Baskaran Rajasekaran
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
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18
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Arya H, Coumar MS. Design of novel ROCK inhibitors using fragment-based de novo drug design approach. J Mol Model 2020; 26:249. [PMID: 32829478 DOI: 10.1007/s00894-020-04493-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/30/2020] [Indexed: 12/01/2022]
Abstract
Rho-associated coiled-coil protein kinase (ROCK) is playing a vital role in the regulation of key cellular events and also responsible for causing several pathological conditions such as cancer, hypertension, Alzheimer's, cerebral vasospasm, and cardiac stroke. Therefore, it has attracted us to target ROCK protein as a potential therapeutic target for combating various diseases. Consequently, we investigated the active site of ROCK I protein and designed novel leads against the target using the de novo evolution drug design approach. Caffeic acid (an aglycone of acteoside) as a scaffold and fragments from 336 reported ROCK inhibitors were used for the design of novel leads. Multiple copy simultaneous search docking was used to identify the suitable fragments to be linked with the scaffold. Basic medicinal chemistry rules, coupled with structural insights generated by docking, led to the design of 7a, 8a, 9a, and 10a as potential ROCK I inhibitors. The designed leads showed better binding than the approved drug fasudil and also interacted with the key hinge region residue Met156 of ROCK I. Further, molecular dynamics (MD) simulation revealed that the protein-ligand complexes were stable and maintained the hydrogen bond with Met156 throughout the MD run. The promising in silico outcomes suggest that the designed compounds could be suitable anti-cancer leads that need to be synthesized and tested in various cancer cell lines. Graphical abstract.
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Affiliation(s)
- Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.
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19
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Syed SB, Lin SY, Arya H, Fu IH, Yeh TK, Charles MRC, Periyasamy L, Hsieh HP, Coumar MS. Overcoming vincristine resistance in cancer: Computational design and discovery of piperine-inspired P-glycoprotein inhibitors. Chem Biol Drug Des 2020; 97:51-66. [PMID: 32633857 DOI: 10.1111/cbdd.13758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/05/2020] [Accepted: 06/28/2020] [Indexed: 01/03/2023]
Abstract
P-glycoprotein (P-gp)/MDR-1 plays a major role in the development of multidrug resistance (MDR) by pumping the chemotherapeutic drugs out of the cancer cells and reducing their efficacy. A number of P-gp inhibitors were reported to reverse the MDR when co-administered with chemotherapeutic drugs. Unfortunately, none has approved for clinical use due to toxicity issues. Some of the P-gp inhibitors tested in the clinics are reported to have cross-reactivity with CYP450 drug-metabolizing enzymes, resulting in unpredictable pharmacokinetics and toxicity of co-administered chemotherapeutic drugs. In this study, two piperine analogs (3 and 4) having lower cross-reactivity with CYP3A4 drug-metabolizing enzyme are identified as P-glycoprotein (P-gp) inhibitors through computational design, followed by synthesis and testing in MDR cancer cell lines over-expressing P-gp (KB ChR 8-5, SW480-VCR, and HCT-15). Both the analogs significantly increased the vincristine efficacy in MDR cancer cell lines at low micromole concentrations. Specifically, 3 caused complete reversal of vincristine resistance in KB ChR 8-5 cells and found to act as competitive inhibitor of P-gp as well as potentiated the vincristine-induced NF-KB-mediated apoptosis. Therefore, 3 ((2E,4E)-1-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-5-(4-hydroxy-3-methoxyphenyl)penta-2,4-dien-1-one) can serve as a potential P-gp inhibitor for in vivo investigations, to reverse multidrug resistance in cancer.
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Affiliation(s)
- Safiulla Basha Syed
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India.,DBT-Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, India
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
| | - I-Hsuan Fu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | | | - Latha Periyasamy
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Kalapet, India
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
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20
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Lin TY, Chan HH, Chen SH, Sarvagalla S, Chen PS, Coumar MS, Cheng SM, Chang YC, Lin CH, Leung E, Cheung CHA. BIRC5/Survivin is a novel ATG12-ATG5 conjugate interactor and an autophagy-induced DNA damage suppressor in human cancer and mouse embryonic fibroblast cells. Autophagy 2019; 16:1296-1313. [PMID: 31612776 PMCID: PMC7469615 DOI: 10.1080/15548627.2019.1671643] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BIRC5/Survivin is known as a dual cellular functions protein that directly regulates both apoptosis and mitosis in embryonic cells during embryogenesis and in cancer cells during tumorigenesis and tumor metastasis. However, BIRC5 has seldom been demonstrated as a direct macroautophagy/autophagy regulator in cells. ATG7 expression and ATG12-ATG5-ATG16L1 complex formation are crucial for the phagophore elongation during autophagy in mammalian cells. In this study, we observed that the protein expression levels of BIRC5 and ATG7 were inversely correlated, whereas the expression levels of BIRC5 and SQSTM1/p62 were positively correlated in normal breast tissues and tumor tissues. Mechanistically, we found that BIRC5 negatively modulates the protein stability of ATG7 and physically binds to the ATG12-ATG5 conjugate, preventing the formation of the ATG12-ATG5-ATG16L1 protein complex in human cancer (MDA-MB-231, MCF7, and A549) and mouse embryonic fibroblast (MEF) cells. We also observed a concurrent physical dissociation between BIRC5 and ATG12-ATG5 (but not CASP3/caspase-3) and upregulation of autophagy in MDA-MB-231 and A549 cells under serum-deprived conditions. Importantly, despite the fact that upregulation of autophagy is widely thought to promote DNA repair in cells under genotoxic stress, we found that BIRC5 maintains DNA integrity through autophagy negative-modulations in both human cancer and MEF cells under non-stressed conditions. In conclusion, our study reveals a novel role of BIRC5 in cancer cells as a direct regulator of autophagy. BIRC5 may act as a "bridging molecule", which regulates the interplay between mitosis, apoptosis, and autophagy in embryonic and cancer cells. ABBREVIATIONS ACTA1: actin; ATG: autophagy related; BIRC: baculoviral inhibitor of apoptosis repeat-containing; BAF: bafilomycin A1; CQ: chloroquine; CASP3: caspase 3; HSPB1/Hsp27: heat shock protein family B (small) member 1/heat shock protein 27; IAPs: inhibitors of apoptosis proteins; IP: immunoprecipitation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PLA: proximity ligation assay; SQSTM1/p62: sequestosome 1; siRNA: small interfering RNA.
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Affiliation(s)
- Tzu-Yu Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Hsiu-Han Chan
- Department of Pharmacology, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Shang-Hung Chen
- National Institute of Cancer Research, National Health Research Institutes , Tainan, Taiwan.,Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Sailu Sarvagalla
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Pai-Sheng Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Siao Muk Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Yung-Chieh Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Chun-Hui Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University , Tainan, Taiwan
| | - Euphemia Leung
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, University of Auckland , Auckland, New Zealand
| | - Chun Hei Antonio Cheung
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan.,Department of Pharmacology, College of Medicine, National Cheng Kung University , Tainan, Taiwan
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21
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Arya H, Yadav CS, Lin SY, Syed SB, Charles MRC, Kannadasan S, Hsieh HP, Singh SS, Gajurel PR, Coumar MS. Design of a potent anticancer lead inspired by natural products from traditional Indian medicine. J Biomol Struct Dyn 2019; 38:3563-3577. [PMID: 31526250 DOI: 10.1080/07391102.2019.1664326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (standard ROCK inhibitor) were used to design hybrid molecules. The designed molecules interact with the key hinge region residue Met156/Met157 of ROCK I/II in a stable manner according to our docking and molecular dynamics simulations. These compounds were synthesized and tested in vitro in SW480, MDA-MB-231, and A-549 cancer cell lines. The most promising compound was chemically optimized to obtain a thiourea analog, 6a (IC50 = 25 µM), which has >3-fold higher antiproliferative activity than fasudil (IC50 = 87 µM) in SW480 cells. Treatment with this molecule also inhibits the migration of colon cancer cells and induces cell apoptosis. Further, SPR experiments suggests that the binding affinity of 6a with ROCK I protein is better than that of fasudil. Hence, the drug-like natural product analog 6a constitutes a highly promising new anticancer lead.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - C Suresh Yadav
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shu-Yu Lin
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C
| | - Safiulla Basha Syed
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India.,DBT- Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | | | - Sathananthan Kannadasan
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hsing-Pang Hsieh
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C
| | - Sorokhaibam Sureshkumar Singh
- Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed University), Nirjuli, India
| | - Padma Raj Gajurel
- Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed University), Nirjuli, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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22
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Tsai SL, Chang YC, Sarvagalla S, Wang S, Coumar MS, Cheung CHA. Cloning, expression, and purification of the recombinant pro-apoptotic dominant-negative survivin T34A-C84A protein in Escherichia coli. Protein Expr Purif 2019; 160:73-83. [DOI: 10.1016/j.pep.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/14/2019] [Accepted: 04/12/2019] [Indexed: 01/07/2023]
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23
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24
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Singh VK, Coumar MS. Chronic Myeloid Leukemia: Existing Therapeutic Options and Strategies to Overcome Drug Resistance. Mini Rev Med Chem 2019; 19:333-345. [PMID: 30332954 DOI: 10.2174/1389557518666181017124854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/26/2018] [Accepted: 08/30/2018] [Indexed: 01/13/2023]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease caused due to translocation between chromosome 9 and 22 leading to a chimeric gene product known as Bcr-Abl. Bcr-Abl fusion protein has constitutively activated Abl tyrosine kinase activity which is responsible for the uncontrolled proliferation in CML The tyrosine kinase inhibitors (TKIs) such as Imatinib, Dasatinib, and Nilotinib are the current first-line treatments approved by the United States Food and Drug Administration (US FDA) for the treatment of the disease. Despite the spectacular progress made over the decade with the TKIs, patients develop resistance to these TKIs. In such cases, stem cell transplant therapy, which is limited by donor availability, is the only proven cure for the patients. This highlights the need for the development of new strategies for CML treatment. The Bcr-Abl point mutations, including the gatekeeper T315I mutations, are the principal cause for the development of resistance to TKIs. However, other mechanisms are also involved in the failure of TKI therapy. This review outlines the Bcr-Abl dependent and independent mechanism of TKIs resistance development and the strategies used to overcome drug resistance, such as the development of ATP site and allosteric site inhibitors. Binding mode and structural elements of Bcr-Abl inhibition are discussed with emphasis on pathways involved in this complex disease to determine alternative strategies and combination therapies.
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Affiliation(s)
- Vivek Kumar Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
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25
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Ramya Chandar Charles M, Hsieh HP, Selvaraj Coumar M. Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study. J Biomol Struct Dyn 2018; 37:2581-2592. [PMID: 30047835 DOI: 10.1080/07391102.2018.1491422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mono- and di-methylation of the H3K9 residue in the histone tail by G9a lysine methyltransferase is associated with transcriptional suppression of genes. Here, we use molecular dynamics simulation and free energy calculations of five different modified/mutated G9a substrate peptides to elucidate the rationale behind the substrate binding to G9a. We also investigated the binding energy contribution based architecture of the active site of G9a to understand substrate and inhibitor binding. Wild-type peptide (H3K9) shows better binding affinity than mono- and di-methylated lysine (K9) and other modified peptides (K9A and R8A). Arg8 of the substrate peptide is crucial for determining the degree of conformational freedom/stability of the wild-type substrate peptide, as well as binding to G9a. Our results also suggest that the G9a active site is segregated into energy rich and low regions, and the energy rich region alone is used by the inhibitors for binding. These insights into the active site architecture should be taken into consideration in virtual screening experiments designed to discover novel inhibitors for G9a. In particular, compounds that could interact with the six residues of G9a - Asp1074, Asp1083, Leu1086, Asp1088, Tyr1154 and Phe1158 - should be preferentially tested in G9a inhibition biological assays. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hsing-Pang Hsieh
- b Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan , Taiwan , ROC
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26
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Hsu YC, Coumar MS, Wang WC, Shiao HY, Ke YY, Lin WH, Kuo CC, Chang CW, Kuo FM, Chen PY, Wang SY, Li AS, Chen CH, Kuo PC, Chen CP, Wu MH, Huang CL, Yen KJ, Chang YI, Hsu JTA, Chen CT, Yeh TK, Song JS, Shih C, Hsieh HP. Discovery of BPR1K871, a quinazoline based, multi-kinase inhibitor for the treatment of AML and solid tumors: Rational design, synthesis, in vitro and in vivo evaluation. Oncotarget 2018; 7:86239-86256. [PMID: 27863392 PMCID: PMC5349910 DOI: 10.18632/oncotarget.13369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/07/2016] [Indexed: 12/15/2022] Open
Abstract
The design and synthesis of a quinazoline-based, multi-kinase inhibitor for the treatment of acute myeloid leukemia (AML) and other malignancies is reported. Based on the previously reported furanopyrimidine 3, quinazoline core containing lead 4 was synthesized and found to impart dual FLT3/AURKA inhibition (IC50 = 127/5 nM), as well as improved physicochemical properties. A detailed structure-activity relationship study of the lead 4 allowed FLT3 and AURKA inhibition to be finely tuned, resulting in AURKA selective (5 and 7; 100-fold selective over FLT3), FLT3 selective (13; 30-fold selective over AURKA) and dual FLT3/AURKA selective (BPR1K871; IC50 = 19/22 nM) agents. BPR1K871 showed potent anti-proliferative activities in MOLM-13 and MV4-11 AML cells (EC50 ∼ 5 nM). Moreover, kinase profiling and cell-line profiling revealed BPR1K871 to be a potential multi-kinase inhibitor. Functional studies using western blot and DNA content analysis in MV4-11 and HCT-116 cell lines revealed FLT3 and AURKA/B target modulation inside the cells. In vivo efficacy in AML xenograft models (MOLM-13 and MV4-11), as well as in solid tumor models (COLO205 and Mia-PaCa2), led to the selection of BPR1K871 as a preclinical development candidate for anti-cancer therapy. Further detailed studies could help to investigate the full potential of BPR1K871 as a multi-kinase inhibitor.
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Affiliation(s)
- Yung Chang Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Chun-Wei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Fu-Ming Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Pei-Yi Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Sing-Yi Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - An-Siou Li
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Po-Chu Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Ching-Ping Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Ming-Hsine Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Chen-Lung Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Kuei-Jung Yen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Yun-I Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - John T-A Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan, ROC.,Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, ROC
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Syed SB, Arya H, Fu IH, Yeh TK, Periyasamy L, Hsieh HP, Coumar MS. Targeting P-glycoprotein: Investigation of piperine analogs for overcoming drug resistance in cancer. Sci Rep 2017; 7:7972. [PMID: 28801675 PMCID: PMC5554262 DOI: 10.1038/s41598-017-08062-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/04/2017] [Indexed: 01/08/2023] Open
Abstract
P-glycoprotein (P-gp) is a drug transporter that effluxes chemotherapeutic drugs and is implicated in the development of resistance of cancer cells to chemotherapeutic drugs. To date, no drug has been approved to inhibit P-gp and restore chemotherapy efficacy. Moreover, majority of the reported inhibitors have high molecular weight and complex structures, making it difficult to understand the basic structural requirement for P-gp inhibition. In this study, two structurally simple, low molecular weight piperine analogs Pip1 and Pip2 were designed and found to better interact with P-gp than piperine in silico. A one step, acid-amine coupling reaction between piperic acid and 6,7-dimethoxytetrahydroisoquinoline or 2-(3,4-dimethoxyphenyl)ethylamine afforded Pip1 and Pip2, respectively. In vitro testing in drug resistant P-gp overexpressing KB (cervical) and SW480 (colon) cancer cells showed that both analogs, when co-administered with vincristine, colchicine or paclitaxel were able to reverse the resistance. Moreover, accumulation of P-gp substrate (rhodamine 123) in the resistant cells, a result of alteration of the P-gp efflux, was also observed. These investigations suggest that the natural product analog - Pip1 ((2E,4E)-5-(benzo[d][1,3]dioxol-5-yl)-1-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1 H)-yl)penta-2,4-dien-1-one) - is superior to piperine and could inhibit P-gp function. Further studies are required to explore the full potential of Pip1 in treating drug resistant cancer.
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Affiliation(s)
- Safiulla Basha Syed
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.,DBT-Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - I-Hsuan Fu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 350, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 350, Taiwan, ROC
| | - Latha Periyasamy
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 350, Taiwan, ROC. .,Department of Chemistry, National Tsing Hua University, Hsinchu, 350, Taiwan, ROC.
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.
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Singh P, Sailu S, Palchamy E, Coumar MS, Baluchamy S. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 2017; 34:145. [PMID: 28730333 DOI: 10.1007/s12032-017-1008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022]
Abstract
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.
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Affiliation(s)
- Prachi Singh
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sarvagalla Sailu
- Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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29
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Abstract
Background: Piperine was widely used in traditional medicine for inducing sterility and abortion. Objective: To evaluate the effect of the piperine on testis of male albino rats Materials and Methods: Adult male rats were divided into four groups (n = 12). Group I (control): Rats were given vehicle p.o. i.e. 0.5% carboxymethyl cellulose in normal saline daily for 60 days, Group II (ED): Rats received piperine at a dose of 10 mg/kg body weight (b.w.) daily, Group III (E4D): Rats received piperine at a dose of 10 mg/kg b.w. on every 4th day, Group IV (E7D): Rats received piperine at a dose of 10 mg/kg b.w. on every 7th day. Half of the animals from each group were sacrificed after the treatment period (60 days), and the remaining were kept for drug-free withdrawal period (60 days) and then sacrificed. Results: Piperine significantly decreased the reproductive organ weights in groups ED and E4D. Piperine induced hormonal imbalance by altering the serum levels of follicle-stimulating hormone, luteinizing hormone, sex hormone binding globulin, serum, and testicular testosterone in groups ED and E4D. Furthermore, piperine decreased the activity of germ cell markers and Leydig cellular steroidogenic enzymes in the groups ED and E4D after 60 days. All the above-altered values returned to normal levels after withdrawal period. Histopathological findings also supported the above findings. Conclusion: From the above data, it can be concluded that piperine could be a good lead molecule for the development of reversible oral male contraceptive. SUMMARY Piperine was employed for the contraceptive purposes in traditional medicine Piperine significantly impaired the spermatogenesis by decreasing the testicular hormone synthesis in groups ED and E4D Piperine disrupted the testicular antioxidant system by promoting the ROS production and hydroxyl radical generation in rat testis in groups ED and E4D Histopathological evidence supported the disruption of spermatogenesis by piperine All the effects of piperine after the treatment period (i.e. 60 days) were back to normal after the withdrawal period (i.e., after 120 days).
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Affiliation(s)
- Gopichand Chinta
- DBT-Interdesciplinary Program in Life sciences, Pondicherry University, Puducherry, India
| | | | - Latha Periyasamy
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry Universty, Kalapet, Puducherry, India
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Chan HH, Coumar MS, Cheng SM, Tsai SL, Lin CH, Chen SH, Leung E, Cheung CHA. Abstract 3303: Survivin negatively-regulates autophagy through interference with the formation of Atg5-Atg12-Atg16L complex in breast cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Survivin, a member of the inhibitors-of-apoptosis proteins family, is highly expressed in different cancers and its expression is correlated with tumorigenesis and tumor metastasis. At the cellular and molecular levels, Survivin is a dual functions protein that promotes mitosis and also inhibits apoptosis. In this study, we found that Survivin is a novel negative-regulator of autophagy. Molecular analysis and computational modeling revealed that Survivin negatively regulates the formation of Atg5-Atg12 conjugates, which plays important roles in the process of autophagosome elongation, in breast cancer cells. It also negatively regulates the expression and activity of cathepsin L in cells. Interestingly, we found that Survivin binds to p62/SQSTM1 and LC3B and is also an autophagic substrate protein, in which its expression is in part directly regulated by autophagy at the protein level. Finally, mechanistic study revealed YM155, a Survivin inhibitor that was originally developed to inhibit Survivin gene transcription, downregulates Survivin expression in part through autophagic protein degradation. Taken together, findings of this study provide new mechanistic insights into both molecular functions and regulations of Survivin and the molecular mechanism of actions of YM155, a drug currently undergoing clinical trials for cancer treatment.
Citation Format: Hsiu-Han Chan, Mohane Selvaraj Coumar, Siao-Muk Cheng, Shing-Ling Tsai, Chun-Hui Lin, Shang-Hung Chen, Euphemia Leung, Chun Hei Antonio Cheung. Survivin negatively-regulates autophagy through interference with the formation of Atg5-Atg12-Atg16L complex in breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3303. doi:10.1158/1538-7445.AM2017-3303
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Affiliation(s)
- Hsiu-Han Chan
- 1National Cheng Kung Univ. College of Medicine, Tainan, Taiwan
| | | | - Siao-Muk Cheng
- 1National Cheng Kung Univ. College of Medicine, Tainan, Taiwan
| | - Shing-Ling Tsai
- 1National Cheng Kung Univ. College of Medicine, Tainan, Taiwan
| | - Chun-Hui Lin
- 1National Cheng Kung Univ. College of Medicine, Tainan, Taiwan
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31
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Parcha P, Sarvagalla S, Madhuri B, Pajaniradje S, Baskaran V, Coumar MS, Rajasekaran B. Identification of natural inhibitors of Bcr-Abl for the treatment of chronic myeloid leukemia. Chem Biol Drug Des 2017; 90:596-608. [PMID: 28338290 DOI: 10.1111/cbdd.12983] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 11/28/2022]
Abstract
Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder of the hematopoietic stem cells, characterized at the molecular level by the bcr/abl gene rearrangement. Even though targeting the fusion gene product Bcr-Abl protein is a successful strategy, development of drug resistance and that of drug intolerance are currently the limitations for Bcr-Abl-targeted CML therapy. With an aim to develop natural Bcr-Abl inhibitors, we performed virtual screening (VS) of ZINC natural compound database by docking with Abl kinase using Glide software. Two natural inhibitors ZINC08764498 (hit1) and ZINC12891610 (hit2) were selected by considering their high Glide docking score and critical interaction with the hinge region residue Met-318 of Abl kinase. The reactivity of the two molecules was assessed computationally by density functional theory calculations. Further, the conformational transition, hydrogen bond interactions, and the binding energies were investigated during 10-ns molecular dynamics simulation of the Abl-hit complex. When tested in vitro, hit1 compared to hit2 showed selective inhibition of cell proliferation and induction of apoptosis in Bcr-Abl-positive K-562 leukemia cells. In summary, our results demonstrate that ZINC08764498, a coumarin derivative identified through VS, is a potential natural inhibitor for the treatment of CML.
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Affiliation(s)
- Phanikrishna Parcha
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India.,DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sailu Sarvagalla
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Bindu Madhuri
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India.,Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sankar Pajaniradje
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Vinitha Baskaran
- Department of Medicine and Health Sciences, SRM University, Kattankulathur, Chennai, India
| | - Mohane Selvaraj Coumar
- DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India.,Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Baskaran Rajasekaran
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India.,DBT-Interdisciplinary Program in Life Sciences, School of Life Sciences, Pondicherry University, Puducherry, India
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32
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Syed SB, Coumar MS. P-Glycoprotein Mediated Multidrug Resistance Reversal by Phytochemicals: A Review of SAR & Future Perspective for Drug Design. Curr Top Med Chem 2017; 16:2484-508. [PMID: 26873188 DOI: 10.2174/1568026616666160212123814] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/15/2015] [Accepted: 11/23/2015] [Indexed: 11/22/2022]
Abstract
A major impediment for cancer chemotherapy is the development of multidrug-resistance (MDR). Continuous use of chemotherapeutic drugs during cancer therapy induces the expression of PGlycoprotein (P-gp, MDR1), an ATP dependant transporter, which in turn reduces the intracellular accumulation of chemotherapeutic drugs leading to MDR. Extensive research over the years has identified several potential P-gp inhibitors, both synthetic as well as natural origin, to overcome the MDR during cancer chemotherapy. In this review, we discuss the cellular pathways involved and transcription factors regulating the expression of P-gp. A number of phytochemicals are reported to inhibit P-gp activity and MDR1 expression; the structure-activity relationship (SAR) among the phytochemicals for P-gp inhibition and the effect of these phytochemicals on cellular signaling pathways regulating P-gp expression are discussed in detail. Moreover, structural biology and mutagenesis studies on P-gp along with docking studies throw light on the structural requirements for P-gp inhibition. Insight provided in the review about the phytochemicals molecular mechanism and SAR could catalyze the design of potent P-gp inhibitors in the future and could help to overcome MDR in cancer chemotherapy.
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Affiliation(s)
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India.
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33
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Sarvagalla S, Coumar MS. Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase. Pharmaceutical Sciences 2017. [DOI: 10.4018/978-1-5225-1762-7.ch043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most of the developed kinase inhibitor drugs are ATP competitive and suffer from drawbacks such as off-target kinase activity, development of resistance due to mutation in the ATP binding pocket and unfavorable intellectual property situations. Besides the ATP binding pocket, protein kinases have binding sites that are involved in Protein-Protein Interactions (PPIs); these PPIs directly or indirectly regulate the protein kinase activity. Of recent, small molecule inhibitors of PPIs are emerging as an alternative to ATP competitive agents. Rational design of inhibitors for kinase PPIs could be carried out using molecular modeling techniques. In silico tools available for the prediction of hot spot residues and cavities at the PPI sites and the means to utilize this information for the identification of inhibitors are discussed. Moreover, in silico studies to target the Aurora B-INCENP PPI sites are discussed in context. Overall, this chapter provides detailed in silico strategies that are available to the researchers for carrying out structure-based drug design of PPI inhibitors.
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Singh VK, Chang HH, Kuo CC, Shiao HY, Hsieh HP, Coumar MS. Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors. J Biomol Struct Dyn 2016; 35:1833-1848. [DOI: 10.1080/07391102.2016.1196462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Vivek Kumar Singh
- School of Life Sciences, Centre for Bioinformatics, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Hsin-Huei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, National Cheng Kung University Medical College, Tainan, Taiwan
- Graduate Program for Aging, China Medical University, Taichung, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- School of Life Sciences, Centre for Bioinformatics, Pondicherry University, Kalapet, Puducherry 605014, India
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35
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Sarvagalla S, Hsieh HP, Coumar MS. Therapeutic polymeric nanoparticles and the methods of making and using thereof: a patent evaluation of WO2015036792. Expert Opin Ther Pat 2016; 26:751-5. [PMID: 27167102 DOI: 10.1080/13543776.2016.1188919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Evaluation of the patent application WO2015036792 claiming therapeutic polymeric nanoparticles loaded with AZD1152-hqpa (aurora kinase inhibitor), and methods of making and using same for the treatment of cancer, is described. The claimed polymeric nano-formulations containing hydrophobic acid significantly improved the pharmacokinetic profiles (slow/sustained drug release profile) of the drug AZD1152-hqpa, as compared to the control agent (AZD1152). Drug efficacy and tolerability were also improved, and toxicity decreased in in vivo animal experiments, resulting in a better therapeutic index for the nano-formulation. Hence, the nano-formulated AZD1152-hqpa could be tested in the clinic at a dose level similar to, or higher than, that used for AZD1152, with lower incidence of toxicity.
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Affiliation(s)
- Sailu Sarvagalla
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Kalapet , Puducherry , India
| | - Hsing Pang Hsieh
- b Institute of Biotechnology and Pharmaceutical Research , National Health Research Institutes , Zhunan , Taiwan , ROC
| | - Mohane Selvaraj Coumar
- a Centre for Bioinformatics, School of Life Sciences , Pondicherry University , Kalapet , Puducherry , India
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36
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Sarvagalla S, Cheung CHA, Tsai JY, Hsieh HP, Coumar MS. Disruption of protein–protein interactions: hot spot detection, structure-based virtual screening and in vitro testing for the anti-cancer drug target – survivin. RSC Adv 2016. [DOI: 10.1039/c5ra22927h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hot spot detection at the protein–protein interaction interface using computational tools helped to identify indinavir as survivin inhibitor.
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Affiliation(s)
- Sailu Sarvagalla
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry 605014
- India
| | - Chun Hei Antonio Cheung
- Department of Pharmacology
- College of Medicine
- National Cheng Kung University
- Tainan
- Republic of China
| | - Ju-Ya Tsai
- Department of Pharmacology
- College of Medicine
- National Cheng Kung University
- Tainan
- Republic of China
| | - Hsing Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research
- National Health Research Institutes
- Miaoli County 350
- Republic of China
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry 605014
- India
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37
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Chinta G, Ramya Chandar Charles M, Klopčič I, Sollner Dolenc M, Periyasamy L, Selvaraj Coumar M. In Silico and In Vitro Investigation of the Piperine's Male Contraceptive Effect: Docking and Molecular Dynamics Simulation Studies in Androgen-Binding Protein and Androgen Receptor. Planta Med 2015; 81:804-812. [PMID: 26039262 DOI: 10.1055/s-0035-1546082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the molecular mechanism of action of traditional medicines is an important step towards developing marketable drugs from them. Piperine, an active constituent present in the Piper species, is used extensively in Ayurvedic medicines (practiced on the Indian subcontinent). Among others, piperine is known to possess a male contraceptive effect; however, the molecular mechanism of action for this effect is not very clear. In this regard, detailed docking and molecular dynamics simulation studies of piperine with the androgen-binding protein and androgen receptors were carried out. Androgen receptors control male sexual behavior and fertility, while the androgen-binding protein binds testosterone and maintains its concentration at optimal levels to stimulate spermatogenesis in the testis. It was found that piperine docks to the androgen-binding protein, similar to dihydrotestosterone, and to androgen receptors, similar to cyproterone acetate (antagonist). Also, the piperine-androgen-binding protein and piperine-androgen receptors interactions were found to be stable throughout 30 ns of molecular dynamics simulation. Further, two independent simulations for 10 ns each also confirmed the stability of these interactions. Detailed analysis of the piperine-androgen-binding protein interactions shows that piperine interacts with Ser42 of the androgen-binding protein and could block the binding with its natural ligands dihydrotestosterone/testosterone. Moreover, piperine interacts with Thr577 of the androgen receptors in a manner similar to the antagonist cyproterone acetate. Based on the in silico results, piperine was tested in the MDA-kb2 cell line using the luciferase reporter gene assay and was found to antagonize the effect of dihydrotestosterone at nanomolar concentrations. Further detailed biochemical experiments could help to develop piperine as an effective male contraceptive agent in the future.
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Affiliation(s)
- Gopichand Chinta
- Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | | | - Ivana Klopčič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Latha Periyasamy
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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Ke YY, Singh VK, Coumar MS, Hsu YC, Wang WC, Song JS, Chen CH, Lin WH, Wu SH, Hsu JTA, Shih C, Hsieh HP. Homology modeling of DFG-in FMS-like tyrosine kinase 3 (FLT3) and structure-based virtual screening for inhibitor identification. Sci Rep 2015; 5:11702. [PMID: 26118648 PMCID: PMC4483777 DOI: 10.1038/srep11702] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/23/2022] Open
Abstract
The inhibition of FMS-like tyrosine kinase 3 (FLT3) activity using small-molecule inhibitors has emerged as a target-based alternative to traditional chemotherapy for the treatment of acute myeloid leukemia (AML). In this study, we report the use of structure-based virtual screening (SBVS), a computer-aided drug design technique for the identification of new chemotypes for FLT3 inhibition. For this purpose, homology modeling (HM) of the DFG-in FLT3 structure was carried using two template structures, including PDB ID: 1RJB (DFG-out FLT3 kinase domain) and PDB ID: 3LCD (DFG-in CSF-1 kinase domain). The modeled structure was able to correctly identify known DFG-in (SU11248, CEP-701, and PKC-412) and DFG-out (sorafenib, ABT-869 and AC220) FLT3 inhibitors, in docking studies. The modeled structure was then used to carry out SBVS of an HTS library of 125,000 compounds. The top scoring 97 compounds were tested for FLT3 kinase inhibition, and two hits (BPR056, IC50 = 2.3 and BPR080, IC50 = 10.7 μM) were identified. Molecular dynamics simulation and density functional theory calculation suggest that BPR056 (MW: 325.32; cLogP: 2.48) interacted with FLT3 in a stable manner and could be chemically optimized to realize a drug-like lead in the future.
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Affiliation(s)
- Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Vivek Kumar Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Yung Chang Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Szu-Huei Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - John T A Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
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Cheung CHA, Sarvagalla S, Lee JYC, Huang YC, Coumar MS. Aurora kinase inhibitor patents and agents in clinical testing: an update (2011 - 2013). Expert Opin Ther Pat 2014; 24:1021-38. [PMID: 24965505 DOI: 10.1517/13543776.2014.931374] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Aurora kinase A, B and C, members of serine/threonine kinase family, are key regulators of mitosis. As Aurora kinases are overexpressed in many of the human cancers, small-molecule inhibitors of Aurora kinase have emerged as a possible treatment option for cancer. AREAS COVERED In 2009 and 2011, the literature pertaining to Aurora kinase inhibitors and their patents was reviewed. Here, the aim is to update the information for Aurora kinase inhibitors in clinical trials and the patents filed between the years 2011 and 2013. Pubmed, Scopus®, Scifinder®, USPTO, EPO and www.clinicaltrials.gov databases were used for searching the literature and patents for Aurora kinase inhibitors. EXPERT OPINION Even though both Aurora sub-type selective as well as pan-selective inhibitors show preclinical and clinical efficacy, so far no Aurora kinase inhibitor has been approved for clinical use. Particularly, dose-limiting toxicity (neutropenia) is a key issue that needs to be addressed. Preliminary evidence suggests that the use of selective Aurora A inhibitors could avoid Aurora B-mediated neutropenia in clinical settings. Also, use of adjunctive agents such as granulocyte stimulating factor to overcome neutropenia associated with Aurora B inhibition could be an answer to overcome the toxicity and bring Aurora inhibitors to market in the future.
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Affiliation(s)
- Chun Hei Antonio Cheung
- National Cheng Kung University, College of Medicine, Department of Pharmacology , Tainan, Taiwan , Republic of China
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Arya H, Coumar MS. Virtual screening of traditional Chinese medicine (TCM) database: identification of fragment-like lead molecules for filariasis target asparaginyl-tRNA synthetase. J Mol Model 2014; 20:2266. [PMID: 24842326 DOI: 10.1007/s00894-014-2266-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/23/2014] [Indexed: 12/28/2022]
Abstract
Lymphatic filariasis (LF) is a vector borne infectious disease caused by the nematode Wuchereria bancrofti, Brugia malayi, and Brugia timori. Over 120 million people are affected by LF in the world, of which two-thirds are in Asia. The infection restricts the normal flow of lymph from the infected area resulting in swelling of the extremities and causing permanent disability. As the available drugs for the treatment of LF are becoming ineffective due to the development of resistance, there is an urgent need to find new leads for drug development. In this study, asparaginyl-tRNA synthetase (AsnRS; PDB ID: 2XGT) essential for the protein bio-synthesis in the filarial nematode was used to carry out virtual screening (VS) of plant constituents from traditional Chinese medicine (TCM) database. Docking as well as E-pharmacophore based VS were carried out to identify the hits. The top scoring hits, Agri 1 (1,3,8-trihydroxy-4,5-dimethoxyxanthen-9-one-3-O-beta-D-glucopyranoside) and Agri 2 (5,7-dihydroxy-2-propylchromone 7-O-beta-D-glucopyranoside), constituents of Agrimonia pilosa, were selected for molecular dynamics (MD) simulation study for 10 ns. MD simulation showed that both the glycosides Agri 1 and Agri 2 were forming stable interactions with the target protein. Moreover, docking and MD simulation of the lead A (1,3,8-trihydroxy-4,5-dimethoxyxanthen-9-one; Mol. Wt.: 304.25; CLogP: 3.07) and lead B (5,7-dihydroxy-2-propylchromone; Mol. Wt.: 220.22; CLogP: 3.02), the aglycones of Agri 1 and Agri 2, respectively, were carried out with the target AsnRS. The in silico investigations of the aglycones suggest that the lead B could be a suitable fragment-like lead molecule for anti-filarial drug discovery.
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Affiliation(s)
- Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
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Mohankumar K, Pajaniradje S, Sridharan S, Singh VK, Ronsard L, Banerjea AC, Benson CS, Coumar MS, Rajagopalan R. Mechanism of apoptotic induction in human breast cancer cell, MCF-7, by an analog of curcumin in comparison with curcumin – An in vitro and in silico approach. Chem Biol Interact 2014; 210:51-63. [DOI: 10.1016/j.cbi.2013.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/20/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
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Shiao HY, Coumar MS, Chang CW, Ke YY, Chi YH, Chu CY, Sun HY, Chen CH, Lin WH, Fung KS, Kuo PC, Huang CT, Chang KY, Lu CT, Hsu JTA, Chen CT, Jiaang WT, Chao YS, Hsieh HP. Optimization of Ligand and Lipophilic Efficiency To Identify an in Vivo Active Furano-Pyrimidine Aurora Kinase Inhibitor. J Med Chem 2013; 56:5247-60. [DOI: 10.1021/jm4006059] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hui-Yi Shiao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School
of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Chun-Wei Chang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Yi-Yu Ke
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Ya-Hui Chi
- Institute of Cellular and System
Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chang-Ying Chu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsu-Yi Sun
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Hwa Chen
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Ka-Shu Fung
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Po-Chu Kuo
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chin-Ting Huang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Kai-Yen Chang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Cheng-Tai Lu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - John T. A. Hsu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Weir-Torn Jiaang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Yu-Sheng Chao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
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Peng YH, Shiao HY, Tu CH, Liu PM, Hsu JTA, Amancha PK, Wu JS, Coumar MS, Chen CH, Wang SY, Lin WH, Sun HY, Chao YS, Lyu PC, Hsieh HP, Wu SY. Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors. J Med Chem 2013; 56:3889-903. [DOI: 10.1021/jm400072p] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi-Hui Peng
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chih-Hsiang Tu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Pang-Min Liu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - John Tsu-An Hsu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Prashanth Kumar Amancha
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School
of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014,
India
| | - Chun-Hwa Chen
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Sing-Yi Wang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hsu-Yi Sun
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Yu-Sheng Chao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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Ke YY, Shiao HY, Hsu YC, Chu CY, Wang WC, Lee YC, Lin WH, Chen CH, Hsu JTA, Chang CW, Lin CW, Yeh TK, Chao YS, Coumar MS, Hsieh HP. 3D-QSAR-assisted drug design: identification of a potent quinazoline-based Aurora kinase inhibitor. ChemMedChem 2012; 8:136-48. [PMID: 23172777 DOI: 10.1002/cmdc.201200464] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Indexed: 02/02/2023]
Abstract
We describe the 3D-QSAR-assisted design of an Aurora kinase A inhibitor with improved physicochemical properties, in vitro activity, and in vivo pharmacokinetic profiles over those of the initial lead. Three different 3D-QSAR models were built and validated by using a set of 66 pyrazole (Model I) and furanopyrimidine (Model II) compounds with IC(50) values toward Aurora kinase A ranging from 33 nM to 10.5 μM. The best 3D-QSAR model, Model III, constructed with 24 training set compounds from both series, showed robustness (r(2) (CV) =0.54 and 0.52 for CoMFA and CoMSIA, respectively) and superior predictive capacity for 42 test set compounds (R(2) (pred) =0.52 and 0.67, CoMFA and CoMSIA). Superimposition of CoMFA and CoMSIA Model III over the crystal structure of Aurora kinase A suggests the potential to improve the activity of the ligands by decreasing the steric clash with Val147 and Leu139 and by increasing hydrophobic contact with Leu139 and Gly216 residues in the solvent-exposed region of the enzyme. Based on these suggestions, the rational redesign of furanopyrimidine 24 (clog P=7.41; Aurora A IC(50) =43 nM; HCT-116 IC(50) =400 nM) led to the identification of quinazoline 67 (clog P=5.28; Aurora A IC(50) =25 nM; HCT-116 IC(50) =23 nM). Rat in vivo pharmacokinetic studies showed that 67 has better systemic exposure after i.v. administration than 24, and holds potential for further development.
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Affiliation(s)
- Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
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Yeh JY, Coumar MS, Shiao HY, Lin TJ, Lee YC, Hung HC, Ko S, Kuo FM, Fang MY, Huang YL, Hsu JTA, Yeh TK, Shih SR, Chao YS, Horng JT, Hsieh HP. Anti-influenza drug discovery: identification of an orally bioavailable quinoline derivative through activity- and property-guided lead optimization. ChemMedChem 2012; 7:1546-50. [PMID: 22821876 DOI: 10.1002/cmdc.201200259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 12/16/2022]
Abstract
From a high-throughput screening (HTS) hit with inhibitory activity against virus-induced cytophathic in the low micromolar range, we have developed a potent anti-influenza lead through careful optimization without compromising the drug-like properties of the compound. An orally bioavailable compound was identified as a lead agent with nanomolar activity against influenza, representing a 140-fold improvement over the initial hit.
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Affiliation(s)
- Jiann-Yih Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli County 350, Taiwan, RoC
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Cheung CHA, Coumar MS, Chang JY, Hsieh HP. Aurora kinase inhibitor patents and agents in clinical testing: an update (2009-10). Expert Opin Ther Pat 2011; 21:857-84. [PMID: 21591849 DOI: 10.1517/13543776.2011.574614] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Mitosis is a key step in the cell cycle and is controlled by several cell cycle regulators, including aurora kinases. Aurora family members A, B and C are essential for spindle assembly, centrosome maturation, chromosomal segregation and cytokinesis. Overexpression/amplification of aurora kinases has been implicated in oncogenic transformation, including the development of chromosomal instability in cancer cells. Hence, the use of aurora kinase small molecule inhibitors as a potential molecular-targeted therapeutic intervention for cancer is being pursued by various researchers. AREA COVERED This review provides an update on aurora kinase inhibitors based on developments from 2009 to 2010. The medicinal chemistry aspects of aurora kinase inhibitors, with a particular emphasis on the patent literature, are reviewed. Databases such as PubMed, SCOPUS®, Scifinder® and www.clinicaltrials.gov database were used to search for literature in the preparation of this review. EXPERT OPINION Around a dozen aurora kinase inhibitors are currently undergoing various Phase I-II evaluations for different human cancers. Instead of being applied as a monotherapy, combinations of aurora kinase inhibitors and existing chemotherapeutic compounds seem to give better therapeutic outcomes and are, therefore, a promising future cancer therapy.
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Affiliation(s)
- Chun Hei Antonio Cheung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan, Republic of China
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Cheung CHA, Lin WH, Hsu JTA, Hour TC, Yeh TK, Ko S, Lien TW, Coumar MS, Liu JF, Lai WY, Shiao HY, Lee TR, Hsieh HP, Chang JY. BPR1K653, a novel Aurora kinase inhibitor, exhibits potent anti-proliferative activity in MDR1 (P-gp170)-mediated multidrug-resistant cancer cells. PLoS One 2011; 6:e23485. [PMID: 21887256 PMCID: PMC3160846 DOI: 10.1371/journal.pone.0023485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 07/18/2011] [Indexed: 12/30/2022] Open
Abstract
Background Over-expression of Aurora kinases promotes the tumorigenesis of cells. The aim of this study was to determine the preclinical profile of a novel pan-Aurora kinase inhibitor, BPR1K653, as a candidate for anti-cancer therapy. Since expression of the drug efflux pump, MDR1, reduces the effectiveness of various chemotherapeutic compounds in human cancers, this study also aimed to determine whether the potency of BPR1K653 could be affected by the expression of MDR1 in cancer cells. Principal Findings BPR1K653 specifically inhibited the activity of Aurora-A and Aurora-B kinase at low nano-molar concentrations in vitro. Anti-proliferative activity of BPR1K653 was evaluated in various human cancer cell lines. Results of the clonogenic assay showed that BPR1K653 was potent in targeting a variety of cancer cell lines regardless of the tissue origin, p53 status, or expression of MDR1. At the cellular level, BPR1K653 induced endo-replication and subsequent apoptosis in both MDR1-negative and MDR1-positive cancer cells. Importantly, it showed potent activity against the growth of xenograft tumors of the human cervical carcinoma KB and KB-derived MDR1-positive KB-VIN10 cells in nude mice. Finally, BPR1K653 also exhibited favorable pharmacokinetic properties in rats. Conclusions and Significance BPR1K653 is a novel potent anti-cancer compound, and its potency is not affected by the expression of the multiple drug resistant protein, MDR1, in cancer cells. Therefore, BPR1K653 is a promising anti-cancer compound that has potential for the management of various malignancies, particularly for patients with MDR1-related drug resistance after prolonged chemotherapeutic treatments.
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Affiliation(s)
- Chun Hei Antonio Cheung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan R.O.C.
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - John Tsu-An Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - Tzyh-Chyuan Hour
- Institute of Biochemistry, Kaohsiung Medical University, Kaohsiung, Taiwan R.O.C.
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - Shengkai Ko
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - Tzu-Wen Lien
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Jin-Fen Liu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan R.O.C.
| | - Wen-Yang Lai
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan R.O.C.
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
| | - Tian-Ren Lee
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan R.O.C.
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C.
- * E-mail: (JYC); (HPH)
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan R.O.C.
- Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan R.O.C.
- * E-mail: (JYC); (HPH)
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49
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Tung YS, Coumar MS, Wu YS, Shiao HY, Chang JY, Liou JP, Shukla P, Chang CW, Chang CY, Kuo CC, Yeh TK, Lin CY, Wu JS, Wu SY, Liao CC, Hsieh HP. Scaffold-Hopping Strategy: Synthesis and Biological Evaluation of 5,6-Fused Bicyclic Heteroaromatics To Identify Orally Bioavailable Anticancer Agents. J Med Chem 2011; 54:3076-80. [DOI: 10.1021/jm101027s] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yen-Shih Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Yu-Shan Wu
- Department of Chemistry, Tunghai University, 181 Taichung Harbor Road Section 3, Taichung 407, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Jing-Ping Liou
- College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - Paritosh Shukla
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Wei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chi-Yen Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Ching-Chuan Kuo
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chin-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Chen Liao
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
- Department of Chemistry, Chung Yuan Christian University, Chungli 320, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
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50
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Wu JS, Peng YH, Wu JM, Hsieh CJ, Wu SH, Coumar MS, Song JS, Lee JC, Tsai CH, Chen CT, Liu YW, Chao YS, Wu SY. Discovery of non-glycoside sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors by ligand-based virtual screening. J Med Chem 2010; 53:8770-4. [PMID: 21090651 DOI: 10.1021/jm101080v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A ligand-based virtual screening strategy (a combination of pharmacophore model generation, shape-based scoring, and structure clustering analysis) was developed to discover novel SGLT2 inhibitors. The best pharmacophore model, generated from eight glycoside inhibitors, was utilized to virtually screen three chemical databases that led to the identification of three non-glycoside SGLT2 inhibitors. This is the first report of the generation of a pharmacophore model from glycosides that has then been used to discover novel non-glycosides hits.
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Affiliation(s)
- Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan Town, Miaoli County 350, Taiwan, Republic of China
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