Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure–activity relationships/tendencies in other 6′-derivatives

References

• Alcolea Palafox, M. (1998). The prediction of vibrational spectra: The use of scale factors. Recent Research Developments in Physical Chemistry India: Transworld Research Network, 2, 213–232.
   Google Scholar
• Alcolea Palafox, M. (2014a). Molecular structure differences between the antiviral nucleoside analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2’-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour. Journal of Biomolecular Structure and Dynamics, 32, 831–851.10.1080/07391102.2013.789402
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M. (2014b). Anticancer drug IUdR and other 5-halogen derivatives of 2′-deoxyuridine: Conformers, hydrates and structure-activity relationships. Structural Chemistry, 25, 53–69.10.1007/s11224-013-0225-1
   Web of Science ®Google Scholar
• Alcolea Palafox, M., & Iza, N. (2010). Tautomerism of the natural thymidine nucleoside and in the antiviral analogue d4T. Structure and influence of an aqueous environment using MP2 and DFT methods. Physical Chemistry Chemical Physics, 12, 881–893.10.1039/b915566j
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., & Iza, N. (2012). Structure of the antiviral Stavudine using quantum chemical methods: Complete conformational space análisis, 3D potential energy surfaces and solid state simulations. Journal of Molecular Structure, 1028, 181–195.10.1016/j.molstruc.2012.06.022
   Web of Science ®Google Scholar
• Alcolea Palafox, M., & Iza, N. (2013). Structure-activity relationships of the antiviral d4T and seven 4′-substituted derivatives using MP2 and DFT methods. Structural Chemistry, 24, 967–980.10.1007/s11224-012-0193-x
   Web of Science ®Google Scholar
• Alcolea Palafox, M., Iza, N., de la Fuente, M., & Navarro, R. (2009). Simulation of the first hydration shell of nucleosides d4T and thymidine: Structures obtained using MP2 and DFT methods. Journal of Physical Chemistry B, 113, 2458–2476.10.1021/jp806684v
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., Iza, N., & Gil, M. (2002). The hydration effect on the uracil frequencies: An experimental and quantum chemical study. Journal of Molecular Structure: THEOCHEM, 585, 69–92.10.1016/S0166-1280(02)00033-7
   Web of Science ®Google Scholar
• Alcolea Palafox, M., Nielsen, O. F., Lang, K., Garg, P., & Rastogi, V. K. (2004). Geometry and vibrational spectra of 5-substituted uracils. Asian Chemistry Letters, 8, 81–93.
   Google Scholar
• Alcolea Palafox, M., Posada-Moreno, P., Villarino-Marín, A. L., Martinez-Rincon, C., Ortuño-Soriano, I., & Zaragoza-García, I. (2011). DFT Calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O. Journal of Computed-Aided Molecular Design, 25, 145–161.10.1007/s10822-010-9406-9
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., & Rastogi, V. K. (2002). Quantum chemical predictions of the vibrational spectra of polyatomic molecules. The uracil molecule and two derivatives. Spectrochimica acta part A: Molecular and biomolecular spectroscopy, 58, 411–440.10.1016/S1386-1425(01)00509-1
   PubMed Web of Science ®Google Scholar
• Alcolea Palafox, M., & Talaya, J. (2010). Hydration analysis of antiviral agent AZT by means of DFT and MP2 calculations. Journal of Physical Chemistry B, 114, 15199–15211.10.1021/jp1048452
   PubMed Web of Science ®Google Scholar
• Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., … Watson, D. G. (1979). The Cambridge crystallographic data centre: Computed-based search, retrieval, analysis and display of information. Acta Crystallographica Section B: Structural Crystallographic Crystal Chemistry, B35, 2331–2339.10.1107/S0567740879009249
   Web of Science ®Google Scholar
• Alvarez-Ros, M. C., & Alcolea Palafox, M. (2013). Molecular structure of the nucleoside analogue inosine using DFT methods: Conformational analysis, crystal simulations and possible behaviour. Journal of Molecular Structure, 1047, 358–371.10.1016/j.molstruc.2013.05.035
   Web of Science ®Google Scholar
• Arissawa, M., Taft, C. A., & Felcman, J. (2003). Investigation of nucleoside analogs with anti-HIV activity. International Journal of Quantum Chemistry, 93, 422–432.10.1002/(ISSN)1097-461X
   Web of Science ®Google Scholar
• Baumgartner, M. T., Motura, M. I., Contreras, R. H., Pierini, A. B., & Briñón, M. C. (2003). Conformational Studies of novel antiretroviral analogs of zidovudine. Nucleosides, Nucleotides & Nucleic Acids, 22, 45–62.
   PubMed Web of Science ®Google Scholar
• Birnbaum, G. I., Giziewicz, J., Gabe, E. J., Lin, T. S., & Prussoff, W. H. (1987). Structure and conformation of 3′-azido-3′-deoxythymidine (AZT), an inhibitor of the HIV (AIDS) virus. Canadian Journal of Chemistry, 65, 2135–2139.10.1139/v87-356
   Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2010). Stability of mutagenic tautomers of uracil and its halogen derivatives: The results of quantum-mechanical investigation. Biopolymers and Cell, 26, 295–298.10.7124/bc
   Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2013). Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantum-chemical analysis. Journal of Biomolecular Structure & Dynamics, 31, 913–936.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., & Hovorun, D. M. (2014). Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis. Journal of Biomolecular Structure & Dynamics, 32, 127–154.
   PubMed Web of Science ®Google Scholar
• Brovarets’, O. O., Yurenko, Y. P., & Hovorun, D. M. (2014). Intermolecular CH…O/N H-bonds in the biologically important pairs of natural nucleobases: A thorough quantum-chemical study. Journal of Biomolecular Structure & Dynamics, 32, 993–1022.
   PubMed Web of Science ®Google Scholar
• Burke, J. D., & Fish, E. N. (2009). Antiviral strategies: The present and beyond. Current Molecular Pharmacology, 2, 32–39.10.2174/1874467210902010032
   PubMedGoogle Scholar
• Carmerman, A., Mastropaolo, D., & Camerman, N. (1987). Azidothymidine: Crystal structure and possible functional role of the azido group. Proceeding of the National Academy of Sciences of the United States of America, 84, 8239–8242.10.1073/pnas.84.23.8239
   PubMed Web of Science ®Google Scholar
• Carpenter, J. E., & Weinhold, F. (1988). Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure. Journal of Molecular Structure: THEOCHEM, 169, 41–62.10.1016/0166-1280(88)80248-3
   Google Scholar
• Choi, Y., George, C., Comin, M. J., Barchi, J. J., Jr, Kim, H. S., Jacobson, K. A., … Marquez, V. E. (2003). A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude. Journal of Medicinal Chemistry, 46, 3292–3299.10.1021/jm030116 g
   PubMed Web of Science ®Google Scholar
• Choi, Y., Moon, H. R., Yoshimura, Y., & Marquez, V. E. (2003). Recent advances in the synthesis of conformationally locked nucleosides and their success in probing the critical question of conformational preferences by their biological targets. Nucleosides, Nucleotides and Nucleic Acids, 22, 547–557.10.1081/NCN-120021954
   PubMed Web of Science ®Google Scholar
• Danilov, V. I., Anisimov, V. M., Kurita, N., & Hovorun, D. M. (2005). MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases. Chemical Physics Letters, 412, 285–293.10.1016/j.cplett.2005.06.123
   Web of Science ®Google Scholar
• Danilov, V. I., van Mourik, T., Kurita, N., Wakabayashi, H., Tsukamoto, T., & Hovorun, D. M. (2009). On the mechanism of the mutagenic action of 5-bromouracil: A DFT study of uracil and 5-bromouracil in a water cluster. Journal of Physical Chemistry A, 113, 2233–2235.10.1021/jp811007j
   PubMed Web of Science ®Google Scholar
• Danilov, V. I., van Mourik, T., & Poltev, V. I. (2006). Modeling of the ‘hydration shell’ of uracil and thymine in small water clusters by DFT and MP2 methods. Chemical Physics Letters, 429, 255–260.10.1016/j.cplett.2006.08.035
   Web of Science ®Google Scholar
• Desiraju, G. R., & Steiner, T. (1999). The weak hydrogen bond. New York, NY: Oxford University Press.
   Google Scholar
• Dyer, I., Low, J. N., Tollin, P., Wilson, H. R., & Howie, R. A. (1988). Structure of 3′-Azido-3′-deoxythymidine, AZT. Acta Crystallographica, C44, 767–769.
   Google Scholar
• Fidanza, N. G., Sosa, G. L., Lobayan, R. M., & Peruchena, N. M. (2005). Topological analysis of the electronic charge density in nucleoside analogues derivatives of the AZT. Effects of X-H···O and X–H···F intramolecular H-bonds. Journal of Molecular Structure: THEOCHEM, 722, 65–78.10.1016/j.theochem.2004.12.039
   Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., G. E.Scuseria, Robb, M. A., Cheeseman, J. R., … Pople, J. A. (2003). Gaussian 03, Revision B.04, Pittsburgh, PA: Gaussian, Inc.
   Google Scholar
• Gorb, L., Shishkin, O., & Leszczynski, J. (2005). Charges of phosphate groups. A role in stabilization of 2′-deoxyribonucleotides. A DFT investigation. Journal of Biomolecular Structure and Dynamics, 22, 441–454.10.1080/07391102.2005.10507015
   PubMed Web of Science ®Google Scholar
• Hao, Z., Cooney, D. A., Farquhar, D., Perno, C. F., Zhang, K., Masood, R., Wilson, Y., Hartman, N. R., Balzarini, J., & Johns, D. G. (1990). Potent DNA chain termination activity and selective inhibition of human immunodeficiency virus reverse transcriptase by 2′,3′-dideoxyuridine-5′-triphosphate. Molecular Pharmacology, 37, 157–163.
   PubMed Web of Science ®Google Scholar
• Hecker, S. J., & Erion, M. D. (2008). Prodrugs of phosphates and phosphonates. Journal of Medicinal Chemistry, 51, 2328–2345.10.1021/jm701260b
   PubMed Web of Science ®Google Scholar
• Hocquet, A., Leulliot, N., & Ghomi, M. (2000). Ground-state properties of nucleic acid constituents studied by density functional calculations. 3. Role of sugar puckering and base orientation on the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides. Journal of Physical Chemistry B, 104, 4560–4568.10.1021/jp994077p
   Web of Science ®Google Scholar
• Hoffmann, M., & Rychlewski, J. (2002). Density functional theory (DFT) and drug design. Reviews of Modern Quantum Chemistry, 2, 1767–1803.
   Google Scholar
• Hovorun, D. M., Gorb, L., & Leszczynski, J. (1999). From the nonplanarity of the amino group to the structural nonrigidity of the molecule: A post-hartree-fock ab initio study of 2-aminoimidazole. International Journal of Quantum Chemistry, 75, 245–253.10.1002/(ISSN)1097-461X
   Web of Science ®Google Scholar
• Hovorun, D. M., Mishchuk, Y. R., & Yurenko, Y. P. (2002). Low-frequency Raman spectra of polycrystalline ribonucleosides. Biopolymer Cell, 18, 219–226.10.7124/bc
   Google Scholar
• Hsu, C.-H., Hu, R., Dutschman, G. E., Yang, G., Krishnan, P., Tanaka, H., … Cheng, Y.-C. (2007). Comparison of the phosphorylation of 4′-Ethynyl 2′,3′-Dihydro-3′-Deoxythymidine with that of other anti-human immunodeficiency virus thymidine analogs. Antimicrobial Agents and Chemotherapy, 51, 1687–1693.10.1128/AAC.01432-06
   PubMed Web of Science ®Google Scholar
• Isayev, O., Furmanchuk, A., Shishkin, O. V., Gorb, L., & Leszczynski, J. (2007). Are isolated nucleic acid bases really planar? A car-parrinello molecular dynamics study. Journal of Physical Chemistry B, 111, 3476–3480.10.1021/jp070857j
   PubMed Web of Science ®Google Scholar
• Ivanova, E. S., Shmagel, N. G., & Vorobyeva, N. N. (2010). Nikavir in chemoprevention regimens for vertical HIV infection transmission. Vorprosy Virusologii, 55, 31–34.
   PubMedGoogle Scholar
• Jalluri, R. K., Yuh, Y. H., & Taylor, E. W. (1993). O–C–N anomeric effect in nucleosides. A major factor underlying the experimentally observed eastern barrier to pseudorotation. In G. R. J. Thatcher (Ed.), The anomeric effect and associated stereo-electronic effects (pp. 277–293). Washington, DC: American Chemical Society.
   Google Scholar
• Jasko, M. V., Shipitsyn, A. V., Khandazhinskaya, A. L., Shirokova, E. A., Sol’yev, P. N., Plyasunova, O. A., & Pokrovskii, A. G. (2006). New derivatives of alkyl- and aminocarbonylphosphonic acids containing 3′-azido-3′-deoxythymidine. Russian Journal of Bioorganic Chemistry, 32, 542–546.10.1134/S1068162006060069
   Web of Science ®Google Scholar
• Jeffrey, G. A., & Saenger, W. (1994). Hydrogen Bonding in Biological Structures. Heidelberg: Springer.
   Google Scholar
• Khandazhinskaya, A. L., Yanvarev, D. V., Jasko, M. V., Shipitsin, A. V., Khalizev, V. A., Shram, S. I., … Kukhanova, M. K. (2009). 5′-Aminocarbonyl phosphonates as new zidovudine depot forms: Antiviral properties, intracellular transformations, and pharmacokinetic parameters. Drug Metabolism and Disposition, 37, 494–501.10.1124/dmd.108.022269
   PubMed Web of Science ®Google Scholar
• Khandazhinskaya, A., Matyugina, E., & Shirokova, E. (2010). Anti-HIV therapy with AZT prodrugs: AZT phosphonate derivatives, current state and prospects. Expert Opinion on Drug Metabolism & Toxicology, 6, 701–714.
   PubMed Web of Science ®Google Scholar
• Krasnokutski, S. A., Ivanov, A. Y., Izvekov, V., Sheina, G. G., & Blagoi, Y. P. (1998). FTIR matrix isolation study of uridine, thymidine, ribose, and glucose. Journal of Molecular Structure, 482, 249–252.
   Web of Science ®Google Scholar
• Kukhanova, M. -K., & Shirokova, E. A. (2005). Frontiers in nucleic acids, Tucker, GA: IHL Press, p. 339–341.
   Google Scholar
• Kukhanova, M. K. (2012). Anti-HIV nucleoside drugs: A retrospective view into the future. Molecular Biology, 46, 768–779.10.1134/S002689331206012X
   Web of Science ®Google Scholar
• Logansen, A. V. (1981). Hydrogen bond (Russian), p. 112. Moscow: Nauka.
   Google Scholar
• Mackman, R. L., Zhan, L. G., Prasad, V., Boojamra, C. G., Chen, J., Douglas, J., … Cihlar, T. (2007). Synthesis and anti-HIV activity of cyclic pyrimidine phosphonomethoxy nucleosides and their prodrugs: A comparison of phosphonates and corresponding nucleosides. Nucleosides, Nucleotides and Nucleic Acids, 26, 573–577.10.1080/15257770701490126
   PubMed Web of Science ®Google Scholar
• Martel, P., Hennion, B., Durand, D., & Calmettes, P. (1994). Low-frequency vibrations of a nucleoside analog. Journal of Biomolecular Structure & Dynamics, 12, 401–411.
   PubMed Web of Science ®Google Scholar
• Nikolaienko, T. Y., Bulavin, L. A., & Hovorun, D. M. (2011). How flexible are DNA constituents? The quantum-mechanical study. Journal of Biomolecular Structure & Dynamics, 29, 563–575.
   PubMed Web of Science ®Google Scholar
• Nikolaienko, T. Y., Bulavin, L. A., & Hovorun, D. M. (2012a). Structural flexibility of DNA-like conformers of canonica 2′-deoxyribonucleosides. Physical Chemistry Chemical Physics, 14, 15554–15561.10.1039/c2cp43120c
   PubMed Web of Science ®Google Scholar
• Nikolaienko, T. Y., Bulavin, L. A., & Hovorun, D. M. (2012b). Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules. Physical Chemistry Chemical Physics, 14, 7441–7447.10.1039/c2cp40176b
   PubMed Web of Science ®Google Scholar
• Nowak, M. J., Lapinski, L., Kwiatkowski, J. S., & Leszczynski, J. (1997). Molecular structure and infrared spectra of the DNA bases and their derivatives: Theory and experiment. In J. Leszczynski (Ed.), Computational Chemistry, Reviews of Current Trends (pp. 140–216). Singapore: World Scientific.
   Google Scholar
• Ortiz, S., Alcolea Palafox, M., Rastogi, V. K., & Tomer, R. (2012). Solid state simulation in the tetramer form of 5-aminoorotic acid: The vibrational spectra and molecular structure by using MP2 and DFT calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 97, 948–962.10.1016/j.saa.2012.06.048
   PubMed Web of Science ®Google Scholar
• Painter, G. R., Aulabaugh, A. E., & Andrews, C. W. (1993). A comparison of the conformations of the 5′-triphosphates of zidovudine (AZT) and thymidine bound to HIV-1 reverse transcriptase. Biochemical and Biophysical Research Communications, 191, 1166–1171.10.1006/bbrc.1993.1339
   PubMed Web of Science ®Google Scholar
• Painter, G. R., Andrews, C. W., & Furman, P. A. (2000). Conformation and local environment of nucleotides bound to HIV type 1 reverse transcriptase (HIV-1 RT) in the ground state. Nucleosides Nucleotides & Nucleic Acids, 19, 13–29.
   PubMed Web of Science ®Google Scholar
• Palamarchuk, G. V., Shishkin, O. V., Gorb, L., & Leszczynski, J. (2009). Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides on DNA conformations. Journal of Biomolecular Structure & Dynamics, 26, 653–661.
   PubMed Web of Science ®Google Scholar
• Palamarchuk, G. V., Shishkin, O. V., Gorb, L., & Leszczynski, J. (2013). Nucleic acid bases in anionic 2′-deoxyribonucleotides: A DFT/B3LYP study of structures, relative stability, and proton affinities. Journal of Physical Chemistry B, 117, 2841–2849.10.1021/jp311363c
   PubMed Web of Science ®Google Scholar
• Panigrahi, S. K., & Desiraju, G. R. (2007). Strong and weak hydrogen bonds in drug-DNA complexes: A statistical analysis. Journal of Bioscience, 32, 677–691.10.1007/s12038-007-0068-2
   PubMed Web of Science ®Google Scholar
• Parang, K., Wiebe, L. I., & Knaus, E. E. (2000). Novel approaches for designing 5′-O-ester prodrugs of 3′-azido-2′3′-dideoxythymidine (AZT). Current Medicinal Chemistry, 7, 995–1039.10.2174/0929867003374372
   PubMed Web of Science ®Google Scholar
• Parthasara, T. K. (1988). Conformation and sandwiching of bases by azido groups in the crystal structure of 3′-azido-3′-deoxy-thymidine (AZT), an antiviral agent that inhibits HIV reverse transcriptase. Biochemical and Biophysical Research Communications, 152, 351–358.10.1016/S0006-291X(88)80721-6
   PubMed Web of Science ®Google Scholar
• Pelmenschikov, A., Hovorun, D. M., Shishkin, O. V., & Leszczynski, J. (2000). A density functional theory study of vibrational coupling between ribose and base rings of nucleic acids with ribosyl guanosine as a model system. Journal of Chemical Physics, 113, 5986–5990.10.1063/1.1290021
   Web of Science ®Google Scholar
• Piperno, A., Chiacchio, M. A., Iannazzo, D., & Romeo, R. (2006). Synthesis and Biological Activity of Phosphonated Nucleosides: Part 1. Furanose, Carbocyclic and Heterocyclic Analogues. Current Medicinal Chemistry, 13(30), 3675–3695.10.2174/092986706779026110
   PubMed Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Y. P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2012). Complete conformational space of the potential HIV-1 reverse transcriptase inhibitors d4U and d4C. A quantum chemical study. Physical Chemistry Chemical Physics, 14, 6787–6795.10.1039/c2cp40290d
   PubMed Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Y. P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2013). Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G. A comprehensive theoretical investigation. Journal of Biomolecular Structure & Dynamics, 32, 730–740.
   PubMed Web of Science ®Google Scholar
• Ponomareva, A. G., Yurenko, Y. P., Zhurakivsky, R. O., van Mourik, T., & Hovorun, D. M. (2014). Conformational landscape of the nucleoside reverse transcriptase inhibitor d4T: A comprehensive quantum-chemical approach. Current Physical Chemistry, 3, 83–92.10.2174/1877946811303010012
   Google Scholar
• Rastogi, V. K., & Alcolea Palafox, M. (2011). Vibrational spectra, tautomerism and thermodynamics of anticarcinogenic drug: 5-fluorouracil. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 79, 970–977.10.1016/j.saa.2011.04.008
   PubMed Web of Science ®Google Scholar
• Rastogi, V. K., Singh, C., Jain, V., & Alcolea Palafox, M. (2000). FTIR and FT-Raman spectra of 5-methyluracil (thymine). Journal of Raman Spectroscopy, 31, 1005–1012.10.1002/(ISSN)1097-4555
   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, 899–926.
   Web of Science ®Google Scholar
• Sabio, M., & Topiol, S. (1992). A conformational analysis of 3′-azido-3′-deoxythymidine. Journal of Computational Chemistry, 13, 478–491.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Saenger, W. (1984). Principles in nucleic acid structure. New York, NY: Springer Verlag.10.1007/978-1-4612-5190-3
   Google Scholar
• Saran, A., & Ojha, R. P. (1993). Viewpoint 5 – conformational studies on anti-AIDS drugs. Journal of Molecular Structure: THEOCHEM, 284, 223–234.10.1016/0166-1280(93)87006-Y
   Google Scholar
• Schultz, C. (2003). Prodrugs of biologically active phosphate esters. Bioorganic & Medicinal Chemistry, 11, 885–898.
   PubMed Web of Science ®Google Scholar
• Shen, J., Wang, H., & Xia, Y. (2013). A DFT study of hydrogen bond interactions between oxidative 2′-deoxyadenosine nucleotides and RNA nucleotides. Structural Chemistry, 24, 559–571.10.1007/s11224-012-0108-x
   Web of Science ®Google Scholar
• Shirokova, E. A., Jasko, M. V., Khandazhinskaya, A. L., Ivanov, A. V., Yanvarev, D. V., Skoblov, Y. S., … Kukhanova, M. K. (2004). New phosphonoformic acid derivatives of 3′-azido-3′-deoxythymidine. Russian Journal of Bioorganic Chemistry, 30, 242–249.10.1023/B:RUBI.0000030131.37092.0a
   Web of Science ®Google Scholar
• Shishkin, O. V., Gorg, L., & Leszczynski, J. (2000). Conformational flexibility of pyrimidine ring in adenine and related compounds. Chemical Physics Letters, 330, 603–611.10.1016/S0009-2614(00)01127-1
   Web of Science ®Google Scholar
• Shishkin, O. V., Gorg, L., & Leszczynski, J. (2009). Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study. Structural Chemistry, 20, 743–749.10.1007/s11224-009-9477-1
   Web of Science ®Google Scholar
• Shishkin, O. V., Gorg, L., Hobza, P., & Leszczynski, J. (2000). Structural nonrigidity of nucleic acid bases. Post-Hartree-Fock ab initio study. International Journal of Quantum Chemistry, 80, 1116–1124.10.1002/(ISSN)1097-461X
   Web of Science ®Google Scholar
• Shishkin, O. V., Gorb, L., Luzanov, A. V., Elstner, M., Suhai, S., & Leszczynski, J. (2003). Structure and conformational flexibility of uracil: A comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods. Journal of Molecular Structure (Theochem), 625, 295–303.10.1016/S0166-1280(03)00032-0
   Web of Science ®Google Scholar
• Shishkin, O. V., Gorg, L., Zhikol, O. A., & Leszczynski, J. (2004a). Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides. Journal of Biomolecular Structure and Dynamics, 21(4), 537–553.10.1080/07391102.2004.10506947
   PubMed Web of Science ®Google Scholar
• Shishkin, O. V., Gorg, L., Zhikol, O. A., & Leszczynski, J. (2004b). Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides. Journal of Biomolecular Structure and Dynamics, 22, 227–243.10.1080/07391102.2004.10506998
   PubMed Web of Science ®Google Scholar
• Shishkin, O. V., Palamarchuk, G. V., Gorb, L., & Leszczynski, J. (2008). Opposite charges assisted extra strong C-H···O hydrogen bond in protonated 2′-deoxyadenosine monophosphate. Chemical Physics Letters, 452, 198–205.10.1016/j.cplett.2007.12.052
   Web of Science ®Google Scholar
• Shishkin, O. V., Pelmenschikov, A., Hovorun, D. M., & Leszczynski, J. (2000a). Molecular structure of free canonical 2′-deoxyribonucleosides: A density functional study. Journal of Molecular Structure, 526, 329–341.10.1016/S0022-2860(00)00497-X
   Web of Science ®Google Scholar
• Shishkin, O. V., Pelmenschikov, A., Hovorun, D. M., & Leszczynski, J. (2000b). Theoretical analysis of low-lying vibrational modes of free canonical 2-deoxyribonucleosides. Chemical Physics, 260, 317–325.10.1016/S0301-0104(00)00251-2
   Web of Science ®Google Scholar
• Taft, C. A., & Paula da Silva, C. H. T. (2006). Cancer and AIDS: New trends in drug design and chemotherapy. Current Computer-Aided Drug Design, 2, 307–324.10.2174/157340906778226382
   Web of Science ®Google Scholar
• Tamara, A., & Alcolea Palafox, M. (2011). Structure and conformational analysis of the anti-HIV AZT 5′-aminocarbonylphosphate prodrug using DFT methods. Chemical Physics, 387, 11–24.10.1016/j.chemphys.2011.06.022
   Web of Science ®Google Scholar
• Troev, K. D., Mitova, V. A., & Ivanov, I. G. (2010). On the design of polymeric 5′-O-ester prodrugs of 3′-azido-2′,3′-dideoxythymidine (AZT). Tetrahedron Letters, 51, 6123–6125.10.1016/j.tetlet.2010.09.076
   Web of Science ®Google Scholar
• Wagner, C. R., Iyer, V. V., & McIntee, E. J. (2000). Pronucleotides: Toward the in vivo delivery of antiviral and anticancer nucleotides. Medicinal Research Reviews, 20, 417–451.10.1002/(ISSN)1098-1128
   PubMed Web of Science ®Google Scholar
• Yates, P. C., & Kirby, S. V. (1993). Molecular mechanics analysis of the conformations of thymidine and implications for the design of anti-AIDS drugs. Structural Chemistry, 4, 299–302.10.1007/BF00681203
   Web of Science ®Google Scholar
• Yekeler, H. (2004). Preferred conformations of some pyrimidine nucleoside reverse transcriptase inhibitors (NRTIs). Journal of Molecular Structure: THEOCHEM, 684, 223–230.10.1016/j.theochem.2004.06.036
   Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2007a). Comprehensive conformational analysis of the nucleoside analogue 2′-β-deoxy-6-azacytidine by DFT and MP2 calculations. Journal of Physical Chemistry B, 111, 6263–6271.10.1021/jp066742 h
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2007b). How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. Journal of Physical Chemistry B, 111, 9655–9663.10.1021/jp073203j
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Ghomi, M., Samijlenko, S. P., & Hovorun, D. M. (2008). Ab initio comprehensive conformational analysis of 2′-deoxyuridine, the Biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum. Journal of Physical Chemistry B, 112, 1240–1250.10.1021/jp074747o
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Samijlenko, S. P., & Hovorun, D. M. (2011). Intramolecular CH…O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their watson-crick pairs. Quantum chemical and AIM analysis. Journal of Biomolecular Structure & Dynamics, 29, 51–65.
   PubMed Web of Science ®Google Scholar
• Yurenko, Y. P., Zhurakivsky, R. O., Samijlenko, S. P., Ghomi, M., & Hovorun, D. M. (2007). The whole of intramolecular H-bonding in the isolated DNA nucleoside thymidine. AIM electron density topological study. Chemical Physics Letters, 447, 140–146.10.1016/j.cplett.2007.09.008
   Web of Science ®Google Scholar
• Zhbankov, R. G., Prihodchenko, L. K., Kolosova, T. E., Andrianov, V. M., Korolevich, M. V., Ratajczak, H., & Marchevka, M. (1998). Investigation of selectively substituted monosaccharides by the method of vibrational spectroscopy and X-ray analysis. Journal of Molecular Structure, 450, 29–40.10.1016/S0022-2860(98)00410-4
   Web of Science ®Google Scholar