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Singh S, Gupta A, Singh N, Sengupta PS, Panda SK, Sharma S. Genotyping, in silico screening and molecular dynamics simulation of SNPs of MGMT and ERCC1 gene in lung cancer patients treated with platinum-based doublet chemotherapy. J Biomol Struct Dyn 2023:1-20. [PMID: 37771161 DOI: 10.1080/07391102.2023.2261052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/02/2023] [Indexed: 09/30/2023]
Abstract
Lung cancer, the leading cause of death worldwide, arises from an intricate combination of genetic and environmental factors. Genetic variations can influence the chemotherapeutic response of lung cancer patients in DNA repair genes. This study examines the response to platinum-based drugs among lung cancer patients of North Indian descent who possess genetic variations in the MGMT and ERCC1 genes. P CR-RFLP method was used for genotypic analysis. MedCalc statistical software was used to calculate odds ratios and Median Survival Time (MST). GROMACS software was used to perform Molecular dynamic simulation. ADCC Patients revealed a significant association with MGMT in the heterozygous genotype (HR= 1.56, p=0.02) and also with ERCC1 in both mutant and combined variants (HR= 1.25, p=0.01; HR=0.78, p=0.03). SQCC subjects harbouring ERCC1 polymorphism also reported a 2-fold increase in hazard ratio and a corresponding decrease in survival time for heterozygous and combined variants (HR= 2.55, p=0.02; HR 2.33, p=0.01, respectively). MD simulation results demonstrate a lower RMSD, stable radius of gyration, and lower RMSF, indicating the mutated MGMT protein is more stable than the wild. Further, the docking score for DNA-Wild and DNA-L84F mutants are -201.6 and -131.8, respectively. MD Simulation of the complexes further validated the results. Our study concludes that MGMT and ERCC1 polymorphisms are associated with decreased overall survival. Further, computational analysis of MGMT (rs12917) polymorphism revealed that mutated MGMT cannot bind properly to the DNA and hence cannot properly repair DNA, resulting in lower overall survival.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sidhartha Singh
- Department of Biosciences and Bioengineering, DY Patil International University, Akurdi, Maharashtra, India
| | - Anu Gupta
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Parth Sarthi Sengupta
- Department of Biosciences and Bioengineering, DY Patil International University, Akurdi, Maharashtra, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Shaik TB, Malik MS, Routhu SR, Seddigi ZS, Althagafi II, Kamal A. Evaluation of Anticancer and Anti-Mitotic Properties of Quinazoline and Quinazolino-Benzothiadiazine Derivatives. Anticancer Agents Med Chem 2021; 20:599-611. [PMID: 31884931 DOI: 10.2174/1871520620666191224122204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/12/2019] [Accepted: 09/23/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Cancer is one of the major health and social-economic problems despite considerable progress in its early diagnosis and treatment. Owing to the emergence and increase of multidrug resistance to various conventional drugs, and the continuing importance of health-care expenditure, many researchers have focused on developing novel and effective anticancer compounds. OBJECTIVE Chemical repositories provide a good platform to evaluate and exploit known chemical entities for the identification of other biological activities. In the present study, we have selected an in-house library of synthesized compounds based on two different pharmacophoric scaffolds to evaluate their cytotoxic potency on various cancer cell lines and mechanisms of action. METHODS A series of in-house synthesized quinazoline and quinazolino-benzothiadiazine derivatives were investigated for their anticancer efficacy against a panel of five cancer (DU145, MCF7, HepG2, SKOV3 and MDA-MB-231) and one normal (MRC5) cell lines. Furthermore, the active compound of the study was investigated to elucidate the mechanism of cytotoxicity by performing series of experiments such as cell cycle analysis, inhibition of tubulin polymerization, alteration of mitochondrial membrane potential, determination of endocytic pathway for drug uptake pathway and combination drug treatment. RESULTS Among all the tested compounds, fifteen of them exhibited promising growth-inhibitory effect (0.15- 5.0μM) and induced cell cycle arrest in the G2/M phase. In addition, the selected compounds inhibited the microtubule assembly; altered mitochondrial membrane potential and enhanced the levels of caspase-9 in MCF-7 cells. Furthermore, the active compound with a combination of drugs showed a synergistic effect at lower concentrations, and the drug uptake was mediated through clathrin-mediated endocytic pathway. CONCLUSION Our results indicated that quinazoline and quinazolino-benzothiadiazine conjugates could serve as potential leads in the development of new anticancer agents.
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Affiliation(s)
- Thoukhir B Shaik
- Department of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India.,Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur, A.P, India
| | - M Shaheer Malik
- Department of Chemistry and Central Research Laboratories, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Sunitha R Routhu
- Department of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Zaki S Seddigi
- Department of Environmental Health, College of Public Health and Health Informatics, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Ismail I Althagafi
- Department of Chemistry and Central Research Laboratories, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Ahmed Kamal
- Department of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
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Yar MS, Haider K, Gohel V, Siddiqui NA, Kamal A. Synthetic lethality on drug discovery: an update on cancer therapy. Expert Opin Drug Discov 2020; 15:823-832. [PMID: 32228106 DOI: 10.1080/17460441.2020.1744560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION A novel anticancer therapy is the need of the hour due to growing incidences of resistance to first line cancer chemotherapy. Synthetic lethality (SL) is one of the new age treatment methods being explored for combating the resistance to anticancer agents. In this method, cell mutations are exploited for the development of new therapeutic agents, where, if there is loss of function of one gene, the cell mutations can still be fixed by alternative machinery but if two genes involved in DNA repair undergo loss of function, it causes lethality to the cell. AREAS COVERED The authors condense findings of SL-based novel anticancer regimen. The review emphasizes some of the SL based clinical and preclinical studies of novel targets and therapy. EXPERT OPINION SL conceptualizes a resolution against treatment resistance to anticancer regimen by recognition of therapeutic vulnerabilities in particular cancer cells. A multitude of clinical trials associated with SL and DNA repair are being conducted that will be useful in obtaining a clearer picture pertaining to the use of cancer biomarkers and effectiveness of drugs acting via target-based molecular changes. Furthermore, new anticancer regimen focused on personalized medicines will emerge basing their development upon SL.
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Affiliation(s)
- M Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard , New Delhi, India
| | - Kashif Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard , New Delhi, India
| | - Vivek Gohel
- Department of Pharmacology and Toxicology, NIPER SAS Nagar , Mohali, India
| | | | - Ahmed Kamal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard , New Delhi, India
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Identification and quantification of DNA repair protein poly(ADP ribose) polymerase 1 (PARP1) in human tissues and cultured cells by liquid chromatography/isotope-dilution tandem mass spectrometry. DNA Repair (Amst) 2019; 75:48-59. [PMID: 30743082 DOI: 10.1016/j.dnarep.2019.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Abstract
Poly(ADP ribose) polymerase 1 (PARP1) is a multifunctional DNA repair protein of the base excision repair pathway and plays a major role in the repair of DNA strand breaks and in replication and transcriptional regulation among other functions. Mounting evidence points to the predictive and prognostic value of PARP1 expression in human cancers. Thus, PARP1 has become an important target in cancer therapy, leading to the development of inhibitors as anticancer drugs. In the past, PARP1 expression levels in tissue samples have generally been estimated by indirect and semi-quantitative immunohistochemical methods. Accurate measurement of PARP1 in normal tissues and malignant tumors of patients will be essential for evaluating PARP1 as a predictive and prognostic biomarker in cancer and other diseases, and for the development and use of its inhibitors in cancer therapy. In this work, we present an approach involving liquid chromatography-isotope-dilution tandem mass spectrometry to positively identify and accurately quantify PARP1 in human tissues and cultured cells. We identified and quantified PARP1 in human normal ovarian tissues and malignant ovarian tumors, and in three pairs of human cell lines, each pair consisting of a normal cell line and its cancerous counterpart. Significantly greater expression of PARP1 was observed in malignant ovarian tissues than in normal ovarian tissues. In the case of one pair of cell lines, the cancerous cell line also exhibited greater expression of PARP1 than in normal cell line. We also show the simultaneous measurement of PARP1 and apurinic/apyrimidinic endonuclease 1 (APE1) in a given protein extract. The approach presented in this work is expected to contribute to the accurate quantitative assessment of PARP1 levels in basic research and clinical studies.
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Kim Y, Kim A, Sharip A, Sharip A, Jiang J, Yang Q, Xie Y. Reverse the Resistance to PARP Inhibitors. Int J Biol Sci 2017; 13:198-208. [PMID: 28255272 PMCID: PMC5332874 DOI: 10.7150/ijbs.17240] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/09/2016] [Indexed: 12/24/2022] Open
Abstract
One of the DNA repair machineries is activated by Poly (ADP-ribose) Polymerase (PARP) enzyme. Particularly, this enzyme is involved in repair of damages to single-strand DNA, thus decreasing the chances of generating double-strand breaks in the genome. Therefore, the concept to block PARP enzymes by PARP inhibitor (PARPi) was appreciated in cancer treatment. PARPi has been designed and tested for many years and became a potential supplement for the conventional chemotherapy. However, increasing evidence indicates the appearance of the resistance to this treatment. Specifically, cancer cells may acquire new mutations or events that overcome the positive effect of these drugs. This paper describes several molecular mechanisms of PARPi resistance which were reported most recently, and summarizes some strategies to reverse this type of drug resistance.
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Affiliation(s)
- Yevgeniy Kim
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
| | - Aleksei Kim
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
| | - Ainur Sharip
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
| | - Aigul Sharip
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
| | - Juhong Jiang
- Department of Pathology, the First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qing Yang
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
| | - Yingqiu Xie
- Department of Biology, Nazarbayev University, School of Science and Technology, Astana, 010000, Republic of Kazakhstan
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Ronco C, Martin AR, Demange L, Benhida R. ATM, ATR, CHK1, CHK2 and WEE1 inhibitors in cancer and cancer stem cells. MEDCHEMCOMM 2016; 8:295-319. [PMID: 30108746 DOI: 10.1039/c6md00439c] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/25/2016] [Indexed: 12/15/2022]
Abstract
DNA inevitably undergoes a high number of damages throughout the cell cycle. To preserve the integrity of the genome, cells have developed a complex enzymatic machinery aimed at sensing and repairing DNA lesions, pausing the cell cycle to provide more time to repair, or induce apoptosis if damages are too severe. This so-called DNA-damage response (DDR) is yet considered as a major source of resistance to DNA-damaging treatments in oncology. Recently, it has been hypothesized that cancer stem cells (CSC), a sub-population of cancer cells particularly resistant and with tumour-initiating ability, allow tumour re-growth and cancer relapse. Therefore, DDR appears as a relevant target to sensitize cancer cells and cancer stem cells to classical radio- and chemotherapies as well as to overcome resistances. Moreover, the concept of synthetic lethality could be particularly efficiently exploited in DDR. Five kinases play pivotal roles in the DDR: ATM, ATR, CHK1, CHK2 and WEE1. Herein, we review the drugs targeting these proteins and the inhibitors used in the specific case of CSC. We also suggest molecules that may be of interest for preclinical and clinical researchers studying checkpoint inhibition to sensitize cancer and cancer stem cells to DNA-damaging treatments.
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Affiliation(s)
- Cyril Ronco
- Université Côte d'Azur , CNRS , Institut de Chimie de Nice , UMR7272 - Parc Valrose , 06108 Nice Cedex 2 , France . ; ; Tel: +33 4 92076143
| | - Anthony R Martin
- Université Côte d'Azur , CNRS , Institut de Chimie de Nice , UMR7272 - Parc Valrose , 06108 Nice Cedex 2 , France . ; ; Tel: +33 4 92076143
| | - Luc Demange
- Université Côte d'Azur , CNRS , Institut de Chimie de Nice , UMR7272 - Parc Valrose , 06108 Nice Cedex 2 , France . ; ; Tel: +33 4 92076143.,Université Paris Descartes , Sorbonne Paris Cité , UFR des Sciences Pharmaceutiques , 4 avenue de l'Observatoire , Paris Fr-75006 , France.,Université Paris Descartes , Sorbonne Paris Cité , UFR Biomédicale des Saints Pères , 45 rue des Saints Pères , France
| | - Rachid Benhida
- Université Côte d'Azur , CNRS , Institut de Chimie de Nice , UMR7272 - Parc Valrose , 06108 Nice Cedex 2 , France . ; ; Tel: +33 4 92076143
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