References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25.
- Afrin, S., Rahman, Y., Sarwar, T., Husain, M. A., Ali, A., & Tabish, M. (2017). Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 186, 66–75. https://doi.org/https://doi.org/10.1016/j.saa.2017.05.073
- Ahmadi, F., Valadbeigi, S., Sajjadi, S. E., Shokoohinia, Y., Azizian, H., & Taheripak, G. (2016). Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis. Chemico-Biological Interactions, 258, 89–101. https://doi.org/https://doi.org/10.1016/j.cbi.2016.08.020
- Ameen, F., Siddiqui, S., Jahan, I., Nayeem, S. M., Ur Rehman, S., & Tabish, M. (2020). A detailed insight into the interaction of memantine with bovine serum albumin: A spectroscopic and computational approach. Journal of Molecular Liquids, 303, 112671.
- Arunadevi, A., Porkodi, J., Ramgeetha, L., & Raman, N. (2019). Biological evaluation, molecular docking and DNA interaction studies of coordination compounds gleaned from a pyrazolone incorporated ligand. Nucleosides, Nucleotides & Nucleic Acids, 38(9), 656–679. https://doi.org/https://doi.org/10.1080/15257770.2019.1597975
- Cao, Y., & He, X. W. (1998). Studies of interaction between safranine T and double helix DNA by spectral methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 54(6), 883–892.
- Chen, A. Y., & Liu, L. F. (1994). DNA topoisomerases: Essential enzymes and lethal targets. Annual Review of Pharmacology and Toxicology, 34, 191–218. https://doi.org/https://doi.org/10.1146/annurev.pa.34.040194.001203
- Chen, H., Liu, Z., Zhou, Z., Jiang, M., Qian, L., & Wu, S. (2003). The regulatory effect of memantine on expression and synthesis of heat shock protein 70 gene in neonatal rat models with cerebral hypoxic ischemia. CHINESE MEDICAL Journal-Beijing-English Edition, 116, 558–564.
- da Silva, A. W. S., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE . BMC Research Notes, 5, 367https://doi.org/https://doi.org/10.1186/1756-0500-5-367
- Danysz, W., & Parsons, C. G. (2003). The NMDA receptor antagonist memantine as a symptomatological and neuroprotective treatment for Alzheimer's disease: Preclinical evidence. Int J Geriatr Psychiatry, 18(Suppl 1), S23–S32. https://doi.org/https://doi.org/10.1002/gps.938
- Darden, T., York, D., & Pedersen, L. (1993). The effect of long-range electrostatic interactions in simulations of macromolecular crystals–a comparison of the ewald and truncated list methods. Journal of Chemical Physics., 98(12), 10089–10092. https://doi.org/https://doi.org/10.1063/1.464397
- Devlin, F. J., Finley, J. W., Stephens, P. J., & Frisch, M. J. (1995). Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields: A comparison of local, nonlocal, and hybrid density functionals. The Journal of Physical Chemistry, 99(46), 16883–16902.
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593.
- Froehlich, E., Mandeville, J. S., Weinert, C. M., Kreplak, L., & Tajmir-Riahi, H. A. (2011). Bundling and aggregation of DNA by cationic dendrimers. Biomacromolecules, 12(2), 511–517. https://doi.org/https://doi.org/10.1021/bm1013102
- Gill, P. M., Johnson, B. G., Pople, J. A., & Frisch, M. J. (1992). The performance of the Becke—Lee—Yang—Parr (B—LYP) density functional theory with various basis sets. Chemical Physics Letters, 197(4-5), 499–505.
- Gills, J. J., LoPiccolo, J., & Dennis, P. A. (2008). Nelfinavir, a new anti-cancer drug with pleiotropic effects and many paths to autophagy. Autophagy, 4(1), 107–109. https://doi.org/https://doi.org/10.4161/auto.5224
- Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). An open-source molecular builder and visualization tool. Version 1.1. 1. Journal of Cheminformatics, 4, 17.
- Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472.
- Husain, M. A., Rehman, S. U., Ishqi, H. M., Sarwar, T., & Tabish, M. (2015a). Spectroscopic and molecular docking evidence of aspirin and diflunisal binding to DNA: A comparative study. RSC Advances, 5(79), 64335–64345.
- Husain, M. A., Sarwar, T., Rehman, S. U., Ishqi, H. M., & Tabish, M. (2015b1). Ibuprofen causes photocleavage through ROS generation and intercalates with DNA: A combined biophysical and molecular docking approach. Physical Chemistry Chemical Physics : Pccp, 17(21), 13837–13850. https://doi.org/https://doi.org/10.1039/c5cp00272a
- Husain, M. A., Yaseen, Z., Rehman, S. U., Sarwar, T., & Tabish, M. (2013). Naproxen intercalates with DNA and causes photocleavage through ROS generation. The FEBS Journal, 280(24), 6569–6580. https://doi.org/https://doi.org/10.1111/febs.12558
- Jameel, M., Jamal, K., Alam, M. F., Ameen, F., Younus, H., & Siddique, H. R. (2020). Interaction of thiamethoxam with DNA: Hazardous effect on biochemical and biological parameters of the exposed organism. Chemosphere, 254, 126875.
- Kausar, T., & Nayeem, S. M. (2018). Identification of small molecule inhibitors of ALK2: A virtual screening, density functional theory, and molecular dynamics simulations study. Journal of Molecular Modeling, 24(9), 262https://doi.org/https://doi.org/10.1007/s00894-018-3789-2
- Khan, N. M., Ahmad, I., Ansari, M. Y., & Haqqi, T. M. (2017). Wogonin, a natural flavonoid, intercalates with genomic DNA and exhibits protective effects in IL-1β stimulated osteoarthritis chondrocytes. Chem. Biol. Interact, 274, 13–23. https://doi.org/https://doi.org/10.1016/j.cbi.2017.06.025
- Kumari, R., Kumar, R., Open Source Drug Discovery Consortium (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962., & Lynn, A. https://doi.org/https://doi.org/10.1021/ci500020m
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: multiple ligand–protein interaction diagrams for drug discovery.
- Li, X. L., Hu, Y. J., Wang, H., Yu, B. Q., & Yue, H. L. (2012). Molecular spectroscopy evidence of berberine binding to DNA: Comparative binding and thermodynamic profile of intercalation. Biomacromolecules, 13(3), 873–880. https://doi.org/https://doi.org/10.1021/bm2017959
- Lindorff‐Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field . Proteins, 78(8), 1950–1958. https://doi.org/https://doi.org/10.1002/prot.22711
- Ling, X., Zhong, W., Huang, Q., & Ni, K. (2008). Spectroscopic studies on the interaction of pazufloxacin with calf thymus DNA. Journal of Photochemistry and Photobiology. B, Biology, 93(3), 172–176. https://doi.org/https://doi.org/10.1016/j.jphotobiol.2008.07.008
- Mandal, A., Ghosh, S., Bothra, A. K., Nanda, A. K., & Ghosh, P. (2012). Synthesis of friedelan triterpenoid analogs with DNA topoisomerase IIα inhibitory activity and their molecular docking studies. European Journal of Medicinal Chemistry, 54, 137–143. https://doi.org/https://doi.org/10.1016/j.ejmech.2012.04.037
- Mansouri-Torshizi, H., Zareian-Jahromi, S., Abdi, K., & Saeidifar, M. (2019). Nonionic but water soluble, [Glycine-Pd-Alanine] and [Glycine-Pd-Valine] complexes. Their synthesis, characterization, antitumor activities and rich DNA/HSA interaction studies. Journal of Biomolecular Structure & Dynamics, 37(13), 3566–3582. https://doi.org/https://doi.org/10.1080/07391102.2018.1520647
- Marvanová, M., Lakso, M., & Wong, G. (2004). Identification of genes regulated by memantine and MK-801 in adult rat brain by cDNA microarray analysis. Neuropsychopharmacology, 29(6), 1070–1079.
- Mati, S. S., Roy, S. S., Chall, S., Bhattacharya, S., & Bhattacharya, S. C. (2013). Unveiling the groove binding mechanism of a biocompatible naphthalimide-based organoselenocyanate with calf thymus DNA: An "ex vivo" fluorescence imaging application appended by biophysical experiments and molecular docking simulations. The Journal of Physical Chemistry. B, 117(47), 14655–14665. https://doi.org/https://doi.org/10.1021/jp4090553
- Monnot, M., Mauffret, O., Lescot, E., & Fermandjian, S. (1992). Probing intercalation and conformational effects of the anticancer drug 2-methyl-9-hydroxyellipticinium acetate in DNA fragments with circular dichroism. European Journal of Biochemistry, 204(3), 1035–1039. https://doi.org/https://doi.org/10.1111/j.1432-1033.1992.tb16725.x
- Mostafavinia, S. E., & Hoshyar, R. (2016). Spectroscopic studies on the interaction of anti cancer rosemary with ctDNA. Gene, Cell and Tissue, 3(2), 35368–35372.
- Nafees, S., Mehdi, S. H., Zafaryab, M., Zeya, B., Sarwar, T., & Rizvi, M. A. (2018). Synergistic interaction of rutin and silibinin on human colon Cancer Cell Line. Archives of Medical Research, 49(4), 226–234. https://doi.org/https://doi.org/10.1016/j.arcmed.2018.09.008
- Neese, F. (2012). The ORCA program system. WIREs Computational Molecular Science, 2(1), 73–78.
- Pagano, B., Mattia, C. A., & Giancola, C. (2009). Applications of isothermal titration calorimetry in biophysical studies of G-quadruplexes. International Journal of Molecular Sciences, 10(7), 2935–2957. https://doi.org/https://doi.org/10.3390/ijms10072935
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
- Pilch, D. S., Kirolos, M. A., Liu, X., Plum, G. E., & Breslauer, K. J. (1995). Berenil [1,3-bis(4'-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties . Biochemistry, 34(31), 9962–9976. https://doi.org/https://doi.org/10.1021/bi00031a019
- Rahman, Y., Afrin, S., Husain, M. A., Sarwar, T., Ali, A., & Tabish, M. (2017). Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study. Archives of Biochemistry and Biophysics, 625, 1–12.
- Rehman, S. U., Sarwar, T., Husain, M. A., Ishqi, H. M., & Tabish, M. (2015). Studying non-covalent drug-DNA interactions. Archives of Biochemistry and Biophysics, 576, 49–60. https://doi.org/https://doi.org/10.1016/j.abb.2015.03.024
- Richards, A. D., & Rodger, A. (2007). Synthetic metallomolecules as agents for the control of DNA structure. Chemical Society Reviews, 36(3), 471–483. https://doi.org/https://doi.org/10.1039/b609495c
- Sarwar, T., Husain, M. A., Rehman, S. U., Ishqi, H. M., & Tabish, M. (2015a). Multi-spectroscopic and molecular modelling studies on the interaction of esculetin with calf thymus DNA. Molecular Biosystems, 11(2), 522–531. https://doi.org/https://doi.org/10.1039/c4mb00636d
- Sarwar, T., Rehman, S. U., Husain, M. A., Ishqi, H. M., & Tabish, M. (2015b). Interaction of coumarin with calf thymus DNA: Deciphering the mode of binding by in vitro studies. International Journal of Biological Macromolecules, 73, 9–16. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2014.10.017
- Sarwar, T., Zafaryab, M., Husain, M. A., Ishqi, H. M., Rehman, S. U., Rizvi, M. M. A., & Tabish, M. (2015c). Redox cycling of endogenous copper by ferulic acid leads to cellular DNA breakage and consequent cell death: A putative cancer chemotherapy mechanism. Toxicology and Applied Pharmacology, 289(2), 251–261. https://doi.org/https://doi.org/10.1016/j.taap.2015.09.018
- Schäfer, A., Horn, H., & Ahlrichs, R. (1992). Fully optimized contracted Gaussian basis sets for atoms Li to Kr. The Journal of Chemical Physics, 97(4), 2571–2577.
- Sharma, S., Yadav, M., Gupta, S. P., Pandav, K., & Kumar, S. (2016). Spectroscopic and structural studies on the interaction of an anticancer β-carboline alkaloid, harmine with GC and AT specific DNA oligonucleotides. Chemico-Biological Interactions, 260, 256–262. https://doi.org/https://doi.org/10.1016/j.cbi.2016.08.025
- Sheng, J., Gan, J., & Huang, Z. (2013). Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Medicinal Research Reviews, 33(5), 1119–1173. https://doi.org/https://doi.org/10.1002/med.21278
- Shujha, S., Shah, A., Muhammad, N., Ali, S., Qureshi, R., Khalid, N., & Meetsma, A. (2010). Diorganotin (IV) derivatives of ONO tridentate Schiff base: Synthesis, crystal structure, in vitro antimicrobial, anti-leishmanial and DNA binding studies. European Journal of Medicinal Chemistry, 45, 2902–2911. https://doi.org/https://doi.org/10.1016/j.ejmech.2010.03.015
- Siddiqui, S., Ameen, F., Jahan, I., Nayeem, S. M., & Tabish, M. (2019). A comprehensive spectroscopic and computational investigation on the binding of the anti-asthmatic drug triamcinolone with serum albumin. New Journal of Chemistry, 43(10), 4137–4151.
- Siddiqui, S., Mujeeb, A., Ameen, F., Ishqi, H. M., Rehman, S. U., & Tabish, M. (2020). Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: A biophysical and molecular docking approaches. Journal of Biomolecular Structure and Dynamics, 38, 1–28.
- Sirajuddin, M., Ali, S., & Badshah, A. (2013). Drug-DNA interactions and their study by UV-Visible, fluorescence spectroscopies and cyclic voltametry. Journal of Photochemistry and Photobiology. B, Biology, 124, 1–19. https://doi.org/https://doi.org/10.1016/j.jphotobiol.2013.03.013
- Temerk, Y., & Ibrahim, H. (2014). Binding mode and thermodynamic studies on the interaction of the anticancer drug dacarbazine and dacarbazine-Cu(II) complex with single and double stranded DNA . Journal of Pharmaceutical and Biomedical Analysis, 95, 26–33. https://doi.org/https://doi.org/10.1016/j.jpba.2014.02.010
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/https://doi.org/10.1002/jcc.20291
- Yuan, J. L., Liu, H., Kang, X., Lv, Z., & Zou, G. L. (2008). Characteristics of the isomeric flavonoids apigenin and genistein binding to hemoglobin by spectroscopic methods. Journal of Molecular Structure, 891(1-3), 333–339.
- Zheng, Y., Zheng, M., Ling, X., Liu, Y., Xue, Y., An, L., Gu, N., Ji, M., & Jin, M. (2013). Design, synthesis, quantum chemical studies and biological activity evaluation of pyrazole-benzimidazole derivatives as potent Aurora A/B kinase inhibitors . Bioorganic & Medicinal Chemistry Letters, 23(12), 3523–3530. https://doi.org/https://doi.org/10.1016/j.bmcl.2013.04.039