Proteomics is a rapidly evolving discipline that involves studying whole-cell protein content used to identify biomarkers, drug-targets, and drugs for diseases. In this research, Proteomics is combined with a computer-based simulations technique called Molecular Docking to get an insight into the binding modes of a small-molecule, phospho-Cyclic Dipeptide Dibenzyl (pCDP-DB) to pharmacologically important proteins identified in its interactome. Human _-enolase (ENO1) and Nucleoporin 98 (NUP98) are two such pharmacologically important proteins that were identified in the interactome of pCDP-DB. The proteins ENO1 and NUP98 play a crucial role in the pathogenesis of Alzheimer's Disease (AD) and COVID-19, respectively. The glycolytic enzyme ENO1 and its upregulation cascades into the downregulation of the amyloidogenic proteolysis of the Amyloid Precursor Protein APP responsible for the onset of AD. The complex of NUP98 with mRNA export factor RAE1 was seen in the interactome of the Sars-Cov-2 protein Orf6. Orf6's cytoplasmic domain is known to sequester the mRNA export complex NUP98-RAE1 to the membrane of cellular Endoplasmic Reticulum and thereby perturbing the type-1 interferon signaling response to a viral infection. To investigate the possible effect pCDP-DB would have on the biochemical activity of these proteins, Molecular Docking simulations were conducted. Two docking servers, namely, SwissDock and HPEPDOCK, were used to perform these simulations. The simulation results indicate that pCDP-DB preferentially docks at a binding pocket at the interface of the ENO1 dimer in a binding mode that would enhance the stability of the dimer and thus upregulate its catalytic activity. Hence, pCDP-DB is predicted to be an ENO1 agonist. The Molecular Docking results with NUP98-RAE1 indicates that pCDP-DB competes with the cytoplasmic domain of Orf6 in binding to its preferred binding site at the NUP98-RAE1 interface. This competitive inhibition of Orf6's cytoplasmic domain is predicted to be useful for COVID-19 therapeutics as the sequestering of NUP98-RAE1 is likely to be prevented.