Multiple Ligand Simultaneous Docking of Antiviral Drugs and Cyanine Dyes with Proteins

Protein nanoparticles are currently regarded as promising biocompatible and biodegradable systems for targeted delivery of different types of pharmacological agents. Prior to fabricating such kind of drug nanocarriers it is reasonable to evaluate the drug-protein binding affinity and possible interaction modes using the computational tools, particularly, the molecular docking technique. The present study was undertaken to evaluate the possibility of creating the protein nanoparticles carrying the antiviral drugs and cyanine dyes as visualizing agents. The components of the examined systems included endogenous functional proteins cytochrome c, serum albumin, lysozyme and insulin, antiviral drugs favipiravir, molnupiravir, nirmatrelvir and ritonavir, mono- and heptamethinecyanine dyes. Using the multiple ligand simultaneous docking technique, it was demonstrated that: i) the drugs and the dyes occupy different binding sites on the protein molecule and do not interfere with each other; ii) the heptamethines AK7-5 and AK7-6 possess the highest affinity for the proteins; iii) among the examined systems the strongest complexes are formed between the heptamethine dyes and serum albumin. Taken together, the results obtained indicate that albumin-based nanoparticles functionalized by the heptamethine cyanine dyes can be used for targeted delivery of the explored antiviral agents.