Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: a comprehensive theoretical investigation

Abstract

A comprehensive quantum-chemical investigation of the conformational landscapes of two nucleoside HIV-1 reverse transcriptase inhibitors, 2′,3′-didehydro-2′,3′-dideoxyadenosine (d4A), and 2′,3′-didehydro-2′,3′-dideoxyguanosine (d4G), has been performed at the MP2/6-311++G(d,p)//B3LYP/6-31G(d,p) level of theory. It was found that d4A can adopt 21 conformers within a 5.17 kcal/mol Gibbs free energy range, whereas d4G has 20 conformers within 6.23 kcal/mol at T = 298.15 K. Both nucleosides are shaped by a sophisticated network of specific noncovalent interactions, including conventional (OHO, NHO) and weak (CHO, CHN) hydrogen bonds, as well as dihydrogen (CHHC) contacts. For the OHO, NHO, and CHO hydrogen bonds, natural bond orbital analysis revealed hyperconjugative interactions between the oxygen lone pairs and the antibonding orbital of the donor group. For the CHHC contacts, the electron density migrates from the antibonding orbital, corresponding to the CH group of the sugar residue, to the bonding orbital relative to the same group in the nucleobase. The results confirm the current belief that the biological activity of d4A and d4G is connected with the termination of the DNA chain synthesis in the 5′–3′ direction. Thus, these nucleosides act as competitive HIV-1 reverse transcriptase inhibitors.

Keywords:

• 2′,3′-didehydro-2′,3′-dideoxyadenosine
• 2′,3′-didehydro-2′,3′-dideoxyguanosine
• d4A
• d4G
• conformational analysis
• hydrogen bonds
• H-bonds
• biological activity
• nucleoside reverse transcriptase inhibitors
• density functional theory
• electron density topological analysis
• NBO analysis
• compliance constants

Acknowledgements

The authors greatly appreciate useful discussion of the results with Prof. M. Ghomi and Dr B. Hernandez (Université Paris 13). Y.P.Y. is deeply grateful to Gaussian Inc. for granting a G03 molecular modeling package for the Win32 platform. This work was partly supported by the State Fund for Fundamental Research of Ukraine within Ukrainian-Slovenian bilateral research project (No М/451-2011).