Quantum chemical and molecular modeling studies of twenty therapeutic nucleosides and nucleoside analogues

Naturally occurring and synthetic, chemically modified nucleosides and nucleoside analogues are suggested to be effective therapeutic agents against different diseases, especially viral diseases, and cancer. Theoretical studies including molecular dynamics simulations are often necessary for the determination of the stability, conformational characteristics, binding efficiency, etc. of such residues. Here, we report AMBER force field parameters and topologies, including glycosidic torsion parameters and partial atomic charges for a set of twenty therapeutically important nucleosides/nucleoside analogues most of which are known/potential antiviral and antitumor agents. These parameter sets would be useful for future simulation studies involving these residues and for further improvements. We also report molecular properties observed from quantum mechanical calculations and conformational characteristics extracted from molecular dynamics simulations of these residues using the newly derived parameter sets. Our results would enrich the understanding of their functional characteristics, activity, and efficacy as therapeutic agents and possibly for their repurposing against other similar diseases.