Binding Pattern Elucidation of NNK and NNAL Cigarette Smoke Carcinogens with NER Pathway Enzymes: an Onco-Informatics Study |
Jamal, Qazi Mohammad Sajid
(Department of Health Information Management, College of Applied Medical Sciences, Buraydah Colleges, Al-Qassim-Buraydah King Abdulaziz Road, East Qassim University)
Dhasmana, Anupam (Environmental Carcinogenesis & Toxico-informatics Laboratory, Department of Biosciences and Bioengineering, Integral University) Lohani, Mohtashim (Environmental Carcinogenesis & Toxico-informatics Laboratory, Department of Biosciences and Bioengineering, Integral University) Firdaus, Sumbul (Environmental Carcinogenesis & Toxico-informatics Laboratory, Department of Biosciences and Bioengineering, Integral University) Ansari, Md Yousuf (Pharmaco-informatics Department, National Institute of Pharmaceutical Education and Research (NIPER)) Sahoo, Ganesh Chandra (Pharmaco-informatics Department, National Institute of Pharmaceutical Education and Research (NIPER)) Haque, Shafiul (Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University) |
1 | Accelrys Software Inc., Discovery Studio Modeling Environment, Release 4.0, San Diego: Accelrys Software Inc, 2013. |
2 | Araki M, Masutani C, Takemura M, et al (2001). Centrosome protein centrin 2/caltractin 1 is part of the xeroderma pigmentosum group C complex that initiates global genome nucleotide excision repair. J Biol Chem, 276, 18665-72. DOI |
3 | Berman HM, Westbrook J, Feng Z, et al (2000). The protein data bank. Nucl Acids Res, 28, 235-42. DOI |
4 | Brooks BR, Bruccoleri RE, Olafson BD, et al (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem, 4, 187-217. DOI |
5 | Brooks BR, Brooks CL, Mackerell AD Jr, et al (2009). M. CHARMM: the biomolecular simulation program. J Comput Chem, 30, 1545-614. DOI |
6 | Ceccaldi R, WO'Connor K, et al (2015). A unique subset of epithelial ovarian cancers with platinum sensitivity and PARP inhibitor. Cancer Res, 75, 628-34. DOI |
7 | Chen R, Li L, Weng Z (2003). ZDOCK: An initial-stage proteindocking algorithm. Proteins, 52, 80-7. DOI ScienceOn |
8 | Goodsell DS, Morris GM, Olson AJ, (1996). Automated docking of flexible ligands: applications of AutoDock. J Mol Recognition, 9, 1-5. DOI |
9 | Jamal QMS, M Lohani, M H Siddiqui, et al (2012). Molecular interaction analysis of cigarette smoke carcinogens NNK and NNAL with enzymes involved in DNA repair pathways: An in silico approach. Bioinformation, 8, 795-800. DOI |
10 | Lv X, Wang J, Dong Z Lv, Qin Y (2009). DNA-Bound peptides control the mRNA transcription through CDK7. Peptides, 30, 681-8. DOI |
11 | Mirijanian DT, Mannige RV, Zuckermann RN, et al (2014). Development and use of an atomistic CHARMM-based forcefield for peptoid simulation. J Comput Chem, 35, 360-70. DOI |
12 | Morris GM, Goodsell DS, Halliday RS, et al (1998). Automated docking using Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem, 19, 1639-62. DOI |
13 | Mou F-F, Wang L-W (2013). Predictive role of computer simulation in assessing signaling pathways of crizotinibtreated A549 lung cancer cells. Asian Pac J Cancer Prev, 13, 3119-21. |
14 | Morris GM, Huey R, Lindstrom W, et al (2009). Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J Comp Chem, 16, 2785-91. |
15 | Nouspikel T (2009). DNA repair in mammalian cells: Nucleotide excision repair: variations on versatility. Cell Mol Life Sci, 66, 994-1009. DOI |
16 | Pence HE, Williams A (2010). Chemspider: an online chemical information resource. J Chemical Education, 87, 1123-4. DOI |
17 | Pierce BG, Wiehe K, Hwang H, et al (2014). ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics, 30, 1771-3. DOI |
18 | Rouillon C, White MF (2011). The evolution and mechanisms of nucleotide excision repair proteins. Res Microbiol, 162, 19-26. DOI |
19 | Sugasawa K, Ng JM, Masutani C, et al (1997). Two human homologs of Rad23 are functionally interchangeable in complex formation and stimulation of XPC repair activity. JH Mol Cell Biol, 17, 6924-31. DOI |
20 | Syota Matsumoto, Eric S Fischer, Takeshi Yasuda, et al (2015). Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein. Nucl Acids Res. |
21 | Szklarczyk D, Franceschini A, Kuhn M, et al (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucl Acids Res, 39, 561-8. DOI |
22 | Tsai CW, Chen JL, Yang CS (2012). An improved LGA for protein ligand docking prediction. Proceedings of IEEE congress on evolutionary computation, pp. 1-6. |
23 | Xue J, Yang S, Seng S (2014). Mechanisms of cancer induction by tobacco-specific NNK and NNN. Cancer, 6, 1138-56. DOI |
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