Computational Analyses of Cytidine and Aza-Cytidine Molecular Structures
Keywords:Cytidine, Aza-cytidine, In silico, Density functional theory
Structural features of cytidine and aza-cytidine were analyzed in this work by means of in silico approach of computational methodologies. The structures were optimized and their corresponding molecular and atomic scales properties were evaluated. The results indicated that nitrogen substitution of cytidine could lead to new properties for aza-cytidine in comparison with the original form. The trend was approved by the obtained orbital energy levels and representations. Moreover, the pyrimidine ring was the site of detection of significant changes versus the almost unchanged sugar group of the structure. Finally, the structural modification could yield meaningful changes for the structures of derivatives, which are comparable with the original structures for expected specific properties and activities. Computer-based works could reveal insightful information for such purposes.
Watson JD, Crick FH. A structure for deoxyribose nucleic acid. Nature. 1953;171:737-738.
Šponer J, Hobza P. Nonempirical ab initio calculations on DNA base pairs. Chem Phys. 1996;204:365-372.
Partovi T, Mirzaei M, Hadipour NL. The C–H…O hydrogen bonding effects on the 17O electric field gradient and chemical shielding tensors in crystalline 1-methyluracil: A DFT study. Z Naturforsch A. 2006;61:383-388.
Mohammadi-Manesh E, Mir-Mahdevar M. Adsorption behavior of guanine, adenine, thymine, and cytosine of DNA on zinc oxide-graphene nanosensor: A DFT study. Synth Metal. 2020;267:116486.
Lankaš F, Šponer J, Hobza P, Langowski J. Sequence-dependent elastic properties of DNA. J Mol Biol. 2000;299:695-709.
Mirzaei M, Meskinfam M, Yousefi M. A cytosine-assisted carbon nanotubes junction: DFT studies. Superlat Microstruct. 2012;52:158-164.
Sherafati M, Rad AS, Ardjmand M, Heydarinasab A, Peyravi M, Mirzaei M. Beryllium oxide (BeO) nanotube provides excellent surface towards adenine adsorption: a dispersion-corrected DFT study in gas and water phases. Cur Appl Phys. 2018;18:1059-1065.
Vetter IR, Wittinghofer A. The guanine nucleotide-binding switch in three dimensions. Science. 2001;294:1299-1304.
Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. J Mol Model. 2011;17:695-699.
Mirzaei M. Uracil-functionalized ultra-small (n, 0) boron nitride nanotubes (n= 3–6): Computational studies. Superlat Microstruct. 2013;57:44-50.
Cochrane G, Karsch-Mizrachi I, Takagi T, Sequence Database Collaboration IN. The international nucleotide sequence database collaboration. Nucl Acids Res. 2016;44:48-50.
Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. Int J Nano Dimens. 2013;3:175-179.
Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlat Microstruct. 2012;52:612-617.
Mirzaei M, Kalhor HR, Hadipour NL. Investigating purine-functionalised carbon nanotubes and their properties: a computational approach. IET Nanobiotechnol. 2011;5:32-35.
Ghamsari PA, Samadizadeh M, Mirzaei M. Cytidine derivatives as inhibitors of methyltransferase enzyme. Eurasian Chem Commun. 2020;2:433-439.
De Simone J, Heller P, Hall L, Zwiers D. 5-Azacytidine stimulates fetal hemoglobin synthesis in anemic baboons. Proc Nat Acad Sci. 1982;79:4428-4431.
Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Adv J Sci Eng. 2020;1:62-66.
Ozkendir OM. Electronic structure study of Sn-substituted InP semiconductor. Adv J Sci Eng. 2020;1:7-11.
Mirzaei M. Science and engineering in silico. Adv J Sci Eng. 2020;1:1-2.
Mirzaei M, Harismah K, Da'i M, Salarrezaei E, Roshandel Z. Screening efficacy of available HIV protease inhibitors on COVID-19 protease. J Mil Med. 2020;22:100-107.
Mirzaei M. The NMR parameters of the SiC-doped BN nanotubes: a DFT study. Physica E. 2010;42:1954-1957.
Wechter WJ, Johnson MA, Hall CM, Warner DT, Berger AE, Wenzel AH, Gish DT, Neil GL. Nucleic acids. 14. ara-cytidine acylates. Use of drug design predictors in structure-activity relation correlation. J Med Chem. 1975;18:339-344.
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 09 A.01. Gaussian Inc., Wallingford; 2013.
Mirzaei M, Gülseren O, Hadipour N. DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs. Comput Theorl Chem. 2016;1090:67-73.
Mirzaei M. Lab-in-Silico: An international journal. Lab-in-Silico. 2020;1:1-2.
Harismah K, Mirzaei M. In silico interactions of steviol with monoamine oxidase enzymes. Lab-in-Silico. 2020;1:3-6.
Gunaydin S, Alcan V, Mirzaei M, Ozkendir OM. Electronic structure study of Fe substituted RuO2 semiconductor. Lab-in-Silico. 2020;1:7-10.
Harismah K, Mirzaei M. Steviol and iso-steviol vs. cyclooxygenase enzymes: In silico approach. Lab-in-Silico. 2020;1:11-15.
Tahmasebi E, Shakerzadeh E. Potential application of B40 fullerene as an innovative anode material for Ca-ion batteries: In silico investigation. Lab-in-Silico. 2020;1:16-20.
Mirzaei M, Nouri A, Giahi M, Meskinfam M. Computational NQR study of a boron nitride nanocone. Monatsh Chem. 2010;141:305-307.
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