Exploration of interaction behavior between spiro[indene-2,2'-[1,3,5]oxathiazine]-1,3-diones and DNA with the help of DFT, molecular docking, and MD simulations

References

• Abdelatef, S. A., El-Saadi, M. T., Amin, N. H., Abdelazeem, A. H., & Abdellatif, K. R. (2018). Synthesis and anticancer screening of novel spiro [chromaffin-2, 4′-piperidin]-4-one derivatives with apoptosis-inducing activity, Journal of Applied Pharmaceutical Science. 8(1) 009–016.
   Google Scholar
• Ali, I., Lone, M. N., Alothman, Z. A., & Alwarthan, A. (2017). Insights into the pharmacology of new heterocycles embedded with oxopyrrolidine rings: DNA binding, molecular docking, and anticancer studies. Journal of Molecular Liquids, 234, 391–402. https://doi.org/10.1016/j.molliq.2017.03.112
   Web of Science ®Google Scholar
• Ali, I., Mukhtar, S. D., Hsieh, M. F., Alothman, Z. A., & Alwarthan, A. (2018). Facile synthesis of indole heterocyclic compounds based micellar nano anti-cancer drugs. RSC Advances, 8(66), 37905–37914. https://doi.org/10.1039/C8RA07060A
   PubMed Web of Science ®Google Scholar
• Badalkhani-Khamseh, F., Bahrami, A., Ebrahim-Habibi, A., & Hadipour, N. L. (2017). Complexation of nicotinic acid with first generation poly (amidoamine) dendrimers: A microscopic view from density functional theory. Chemical Physics Letters, 684, 103–112. https://doi.org/10.1016/j.cplett.2017.06.042
   Web of Science ®Google Scholar
• Badalkhani-Khamseh, F., Ebrahim-Habibi, A., & Hadipour, N. L. (2017). Atomistic computer simulations on multi-loaded PAMAM dendrimers: A comparison of amine-and hydroxyl-terminated dendrimers. Journal of Computer-Aided Molecular Design, 31(12), 1097–1111. https://doi.org/10.1007/s10822-017-0091-9
   PubMed Web of Science ®Google Scholar
• Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A, 38(6), 3098–3100. https://doi.org/10.1103/PhysRevA.38.3098
   PubMed Web of Science ®Google Scholar
• Brouwer, W. G., Bell, A. R., Blem, A. R., & Davis, R. A. (1987). 3-aryl-5, 6-dihydro-1, 4, 2-oxathiazines and their oxides. Google Patents.
   Google Scholar
• Canet, D. (1998). On the calculation of spectral density functions for spin interactions without axial symmetry. Concepts in Magnetic Resonance, 10(5), 291–297. https://doi.org/10.1002/(SICI)1099-0534(1998)10:5<291::AID-CMR2>3.0.CO;2-S
   Google Scholar
• Carreira, E. M., & Fessard, T. C. (2014). Four-membered ring-containing spirocycles: Synthetic strategies and opportunities. Chemical Reviews, 114(16), 8257–8322. https://doi.org/10.1021/cr500127b
   PubMed Web of Science ®Google Scholar
• Chee, G.-L., Bhattarai, B., Gietz, R. D., Alrushaid, S., Nitiss, J. L., & Hasinoff, B. B. (2012). Chemical reactivity and microbicidal action of bethoxazin. Bioorganic & Medicinal Chemistry, 20(4), 1494–1501. https://doi.org/10.1016/j.bmc.2011.12.051
   PubMed Web of Science ®Google Scholar
• Da Silva, A. W. S., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Delano, W. L. (2002). The PyMOL molecular graphics system. Version 1.8, Schrödinger LLC 10,
   Google Scholar
• Esfandiarpour, R., Hosseini, M. R., Hadipour, N. L., & Bahrami, A. (2019). Density functional theory evaluation of pristine and BN-doped biphenylene nanosheets to detect HCN. Journal of Molecular Modeling, 25(6), 163. https://doi.org/10.1007/s00894-019-4048-x
   PubMed Web of Science ®Google Scholar
• Fringuelli, R., Milanese, L., & Schiaffella, F. (2005). Role of 1, 4-benzothiazine derivatives in medicinal chemistry. Mini-Reviews in Medicinal Chemistry, 5(12), 1061–1073. https://doi.org/10.2174/138955705774933365
   PubMed Web of Science ®Google Scholar
• Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. (2009). Gaussian 09, Revision A. 02. Gaussian, Inc. There is no corresponding record for this reference.[Google Scholar] (2015).
   Google Scholar
• Geary, G. C., Nortcliffe, A., Pearce, C. A., Hamza, D., Jones, G., & Moody, C. J. (2018). Densely functionalised spirocyclic oxetane-piperidine scaffolds for drug discovery. Bioorganic & Medicinal Chemistry, 26(4), 791–797. https://doi.org/10.1016/j.bmc.2017.12.012
   PubMed Web of Science ®Google Scholar
• Gomtsyan, A. (2012). Heterocycles in drugs and drug discovery. Chemistry of Heterocyclic Compounds, 48(1), 7–10. https://doi.org/10.1007/s10593-012-0960-z
   Web of Science ®Google Scholar
• Günther, H., Zolotoyabko, E., Hermann, K., Berova, N., Woody, R., Polavarapu, P., & Nakanishi, K. (2015). Molecular Orbitals and organic chemical reactions-reference edition. Wiley‐VCH Verlag GmbH & Co. KGaA.
   Google Scholar
• Hoff, S., & Zwanenburg, E. (1972). 6-acetamido-5, 6-dihydro-1, 4, 2-oxathiazines a novel class of compounds. Tetrahedron Letters, 13(52), 5267–5268. https://doi.org/10.1016/S0040-4039(01)85226-6
   Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Hwang, G.-S., Jones, G. B., & Goldberg, I. H. (2004). Stereochemical control of small molecule binding to bulged DNA: Comparison of structures of spirocyclic enantiomer-bulged DNA complexes. Biochemistry, 43(3), 641–650. https://doi.org/10.1021/bi035824i
   PubMed Web of Science ®Google Scholar
• Jayaram, B., Singh, T., Mukherjee, G., Mathur, A., Shekhar, S., & Shekhar, V. (2012). Sanjeevini: A freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics, 13(S17), S7. https://doi.org/10.1186/1471-2105-13-S17-S7
   PubMed Web of Science ®Google Scholar
• Kirichok, A. A., Shton, I. O., Pishel, I. M., Zozulya, S. A., Borysko, P. O., Kubyshkin, V., Zaporozhets, O. A., Tolmachev, A. A., & Mykhailiuk, P. K. (2018). Synthesis of multifunctional spirocyclic azetidines and their application in drug discovery. Chemistry - A European Journal, 24(21), 5444–5449. https://doi.org/10.1002/chem.201800193
   PubMed Web of Science ®Google Scholar
• Lee, C., Yang, W., & Parr, R. (1988). Development of the Colle-Salvetti conelation energy formula into a functional of the electron density. Physical Review B, 37(2), 785–789. https://doi.org/10.1103/PhysRevB.37.785
   PubMed Web of Science ®Google Scholar
• Li, H., & Dryhurst, G. (1997). Irreversible inhibition of mitochondrial complex I by 7‐(2‐aminoethyl)‐3, 4‐dihydro‐5‐hydroxy‐2H‐1, 4‐benzothiazine‐3‐carboxylic acid (DHBT‐1): A putative nigral endotoxin of relevance to Parkinson's disease. Journal of Neurochemistry, 69(4), 1530–1541. https://doi.org/10.1046/j.1471-4159.1997.69041530.x
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead-and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Livendahl, M., Jamroskovic, J., Hedenström, M., Görlich, T., Sabouri, N., & Chorell, E. (2017). Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA. Organic & Biomolecular Chemistry, 15(15), 3265–3275. https://doi.org/10.1039/c7ob00300e
   PubMed Web of Science ®Google Scholar
• McWeeny, R. (1962). Perturbation theory for the Fock-Dirac density matrix. Physical Review, 126(3), 1028–1034. https://doi.org/10.1103/PhysRev.126.1028
   Web of Science ®Google Scholar
• Miteva, M. A., Violas, S., Montes, M., Gomez, D., Tuffery, P., & Villoutreix, B. O. (2006). FAF-Drugs: Free ADME/tox filtering of compound collections. Nucleic Acids Research, 34(suppl_2), W738–W744. https://doi.org/10.1093/nar/gkl065
   PubMedGoogle Scholar
• Mohamed, M. F., Abdelmoniem, A. M., Elwahy, A. H., & Abdelhamid, I. A. (2018). DNA fragmentation, cell cycle arrest, and docking study of novel bis spiro-cyclic 2-oxindole of pyrimido [4, 5-b] quinoline-4, 6-dione derivatives against breast carcinoma. Current Cancer Drug Targets, 18(4), 372–381. https://doi.org/10.2174/1568009617666170630143311
   PubMed Web of Science ®Google Scholar
• Mondal, S., Mukherjee, S., Yetra, S. R., Gonnade, R. G., & Biju, A. T. (2017). Organocatalytic enantioselective vinylogous michael-aldol cascade for the synthesis of spirocyclic compounds. Organic Letters, 19(16), 4367–4370. https://doi.org/10.1021/acs.orglett.7b02085
   PubMed Web of Science ®Google Scholar
• Noji, S., Hara, Y., Miura, T., Yamanaka, H., Maeda, K., Hori, A., Yamamoto, H., Obika, S., Inoue, M., & Hase, Y. (2020). Discovery of a Janus kinase inhibitor bearing a highly three-dimensional spiro scaffold: JTE-052 (delgocitinib) as a new dermatological agent to treat inflammatory skin disorders. Journal of Medicinal Chemistry, 63(13), 7163–7185. https://doi.org/10.1021/acs.jmedchem.0c00450
   PubMed Web of Science ®Google Scholar
• O'boyle, N. M., Tenderholt, A. L., & Langner, K. M. (2008). Cclib: A library for package‐independent computational chemistry algorithms. Journal of Computational Chemistry, 29(5), 839–845. https://doi.org/10.1002/jcc.20823
   PubMed Web of Science ®Google Scholar
• Parr, R. G., Szentpály, Lv., Liu, S., & Electrophilicity, i. (1999). Electrophilicity Index. Journal of the American Chemical Society, 121(9), 1922–1924. ) https://doi.org/10.1021/ja983494x
   Web of Science ®Google Scholar
• Pektaş, S., Koçak, S. B., Başterzi, N. S., Kılıç, Z., Zeyrek, C. T., Coban, B., Yildiz, U., & Çelik, Ö. (2018). spiro-Cyclotriphosphazenes containing 4-hydroxyphenylethyl pendant arm: Syntheses, structural characterization and DNA interaction study. Inorganica Chimica Acta, 474, 51–65. https://doi.org/10.1016/j.ica.2018.01.016
   Web of Science ®Google Scholar
• Raju, R., Panicker, C. Y., Nayak, P. S., Narayana, B., Sarojini, B., Van Alsenoy, C., & Al-Saadi, A. A. (2015). FT-IR, molecular structure, first order hyperpolarizability, MEP, HOMO and LUMO analysis and NBO analysis of 4-[(3-acetylphenyl) amino]-2-methylidene-4-oxobutanoic acid. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 134, 63–72. https://doi.org/10.1016/j.saa.2014.06.051
   PubMed Web of Science ®Google Scholar
• Reed, A. E., Curtiss, L. A., & Weinhold, F. (1988). Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chemical Reviews, 88(6), 899–926. https://doi.org/10.1021/cr00088a005
   Web of Science ®Google Scholar
• Salehpour, M., Azizian, J., & Kefayati, H. (2017). Clean synthesis of novel spiro [indene-2, 2’-[1, 3, 5]-oxathiazine]-1, 3-diones in water. Chinese Chemical Letters, 28(5), 1079–1082. https://doi.org/10.1016/j.cclet.2016.12.036
   Web of Science ®Google Scholar
• Schurko, R. W., Wasylishen, R. E., & Phillips, A. D. (1998). A definitive example of aluminum-27 chemical shielding anisotropy. Academic Press.
   Google Scholar
• Shi, C., Zhang, Y., Wang, T., Lu, W., Zhang, S., Guo, B., Chen, Q., Luo, C., Zhou, X., & Yang, Y. (2019). Design, synthesis, and biological evaluation of novel DNA gyrase-inhibiting spiropyrimidinetriones as potent antibiotics for treatment of infections caused by multidrug-resistant gram-positive bacteria. Journal of Medicinal Chemistry, 62(6), 2950–2973. https://doi.org/10.1021/acs.jmedchem.8b01750
   PubMed Web of Science ®Google Scholar
• Škopić, M. K., Willems, S., Wagner, B., Schieven, J., Krause, N., & Brunschweiger, A. (2017). Exploration of a Au (I)-mediated three-component reaction for the synthesis of DNA-tagged highly substituted spiroheterocycles. Organic & Biomolecular Chemistry, 15(40), 8648–8654. https://doi.org/10.1039/c7ob02347b
   PubMed Web of Science ®Google Scholar
• Taylor, A. P., Robinson, R. P., Fobian, Y. M., Blakemore, D. C., Jones, L. H., & Fadeyi, O. (2016). Modern advances in heterocyclic chemistry in drug discovery. Organic & Biomolecular Chemistry, 14(28), 6611–6637. https://doi.org/10.1039/C6OB00936K
   PubMed Web of Science ®Google Scholar
• Trost, B. M., & Zuo, Z. (2021). Regiodivergent synthesis of spirocyclic compounds through pd‐catalyzed regio‐and enantioselective [3 + 2] spiroannulation. Angewandte Chemie, 133(11), 5870–5874. https://doi.org/10.1002/ange.202016439
   Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• 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/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   Web of Science ®Google Scholar
• Wang, R., Fang, X., Lu, Y., & Wang, S. (2004). The PDBbind database: Collection of binding affinities for protein − ligand complexes with known three-dimensional structures. Journal of Medicinal Chemistry, 47(12), 2977–2980. https://doi.org/10.1021/jm030580l
   PubMed Web of Science ®Google Scholar
• Wang, R., Fang, X., Lu, Y., Yang, C.-Y., & Wang, S. (2005). The PDBbind database: Methodologies and updates. Journal of Medicinal Chemistry, 48(12), 4111–4119. https://doi.org/10.1021/jm048957q
   PubMed Web of Science ®Google Scholar
• Wang, R., Lai, L., & Wang, S. (2002). Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-Aided Molecular Design, 16(1), 11–26. https://doi.org/10.1023/A:1016357811882
   PubMed Web of Science ®Google Scholar
• Wei, W., Cherukupalli, S., Jing, L., Liu, X., & Zhan, P. (2020). Fsp3: A new parameter for drug-likeness. Drug Discovery Today. , 25(10), 1839–1845. https://doi.org/10.1016/j.drudis.2020.07.017
   PubMed Web of Science ®Google Scholar
• Woliński, K., & Sadlej, A. J. (1980). Self-consistent perturbation theory: Open-shell states in perturbation-dependent non-orthogonal basis sets. Molecular Physics, 41(6), 1419–1430. https://doi.org/10.1080/00268978000103631
   Web of Science ®Google Scholar
• Wolinski, K., Hinton, J. F., & Pulay, P. (1990). Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. Journal of the American Chemical Society, 112(23), 8251–8260. https://doi.org/10.1021/ja00179a005
   Web of Science ®Google Scholar
• Zhang, T. Y. (2017). The evolving landscape of heterocycles in drugs and drug candidates. Advances in Heterocyclic Chemistry, Elsevier, 121, 1–12.
   Web of Science ®Google Scholar
• Zheng, Y.-J., & Tice, C. M. (2016). The utilization of spirocyclic scaffolds in novel drug discovery. Expert Opinion on Drug Discovery, 11(9), 831–834. https://doi.org/10.1080/17460441.2016.1195367
   PubMed Web of Science ®Google Scholar