Structural and Molecular Packing study of Three New Amidophosphoric Acid Esters and Assessment of Their Inhibiting Activity Against SARS-CoV-2 by Molecular Docking

Three new compounds of amidophosphoric acid esters with a [OCH2C(CH3)(2)CH2O]P(O)[X] segment (where X=cyclopentylamido (1), 2-aminopyridinyl (2) and pyrrolidinyl (3)) were synthesized and studied using FT-IR and P-31/C-13/H-1 NMR spectroscopies and single-crystal X-ray diffraction analysis. The compounds crystallize in the triclinic space groups P1? for 1 and 3 and in the orthorhombic space group Pca2(1) for 2, where the asymmetric unit consists of three symmetrically-independent molecules for 1 and one molecule for 2 and 3. The intermolecular interactions and supramolecular assemblies are assessed by Hirshfeld surface analysis and enrichment ratios. The results reveal that the substituent effect plays an important role in directing the supramolecular structures. The presence of the aromatic substituent aminopyridine in 2 providing the C-H horizontal ellipsis pi interactions leads to a larger variety in interactions including H horizontal ellipsis H, H horizontal ellipsis O/O horizontal ellipsis H, H horizontal ellipsis C/C horizontal ellipsis H and H horizontal ellipsis N/N horizontal ellipsis H contacts, whereas the packings of the compounds 1 and 3 bearing aliphatic substituents only include H horizontal ellipsis H and H horizontal ellipsis O/O horizontal ellipsis H contacts. The enrichment ratios affirm the importance of O horizontal ellipsis H/H horizontal ellipsis O contacts reflecting the hydrogen bond N-H horizontal ellipsis O interactions to be the enriched contacts. Compounds 1-3 were also investigated along with five similar reported structures with a [OCH2C(CH3)(2)CH2O]P(O) segment for their inhibitory behavior against SARS-CoV-2. The molecular docking results illustrate that the presence of the aromatic amido substituent versus the aliphatic type provides a more favorable condition for their biological activities.