Identification of drug candidates against SARS-CoV-2' 3 CLpro, RdRp, PLpro ve spike proteins by virtual screeningapproaches: molecular docking and moleculardynamics studies

Although global human mobility has normalized after the COVID-19 pandemic, the disease remains a major threat due to the emergence of new variants, keeping it a key target for drug development. Considerable efforts have been made to understand the disease, develop treatment options, and ultimately eradicate it. It has been shown that these viruses possess the largest genome size among all known RNA viruses, with their genome consisting of an RNA strand enclosed in a protein coat. In our study, four protein-based enzymes were targeted for the identification of new potential inhibitors. The main protease (3CLpro) is one of the most pivotal targets of SARS-CoV-2, as it is required for the cleavage of viral polyproteins into nonstructural proteins (NSPs), which are essential for viral replication and thus critical to the virus's life cycle. PLpro is another enzymatic protein necessary for the replication process of SARS-CoV-2, and during viral infection, it plays a key role in helping the virus evade the host's innate immune defense. The Spike (S) protein, located on the surface of the SARS-CoV-2 virus, is a large and complex structure that plays a critical role in the virus's attachment to host cells and its subsequent entry. Due to this function, it has been selected as a target for the investigation of novel inhibitors. The RNA-dependent RNA polymerase (RdRp) enzyme also plays a central role in the viral replication cycle. Since RdRp is responsible for replicating the viral genome, its function is vital for the virus's survival and proliferation. This clearly demonstrates the indispensable role of RdRp in the treatment of SARS-CoV-2. This study utilizes a combination of various computational tools including virtual screening, molecular docking, and molecular dynamics (MD) simulations for the development of novel inhibitor candidates targeting the aforementioned biological macromolecules, namely the 3CLpro (PDB: 6LU7) and RdRp (PDB: 6NUR) enzymes. A total of 756,958 and 193,314 molecules from the ZINC15 database were screened against 3CLpro and RdRp, respectively, through structure-based virtual screening, followed by 100-nanosecond MD simulations, and binding free energy calculations. Additionally, new potential inhibitor candidates for PLpro (PDB: 7LOS) and the Spike protein (PDB: 6M0J) were subjected to virtual screening. Over 2 million molecules for PLpro and 717,652 molecules for the Spike protein from the ZINC15 database were screened using structure-based virtual screening approach, followed by molecular docking analyses based on the scores of the co-crystallized ligand.