Investigation of papain-like protease (PLpro) inhibitors for the treatment of COVİD-19 using in silico methods

The new coronavirus pandemic, which started in December 2019 in Wuhan, China, affects the world. This disease, caused by the SARS-CoV-2 virus, was named COVID-19. While 647 million people were caught worldwide; 6.6 million people lost their lives. While there are more than 17 million cases in Turkey, the number of deaths is over 100 thousand. There are a total of 7 drugs, including 6 vaccines approved for treatment, 3 drugs that interact with different targets of the virus, and 4 drugs that have been approved for different diseases and received their second approval for COVID-19. There are three structural proteins on the membrane of coronaviruses: S, membrane and envelope proteins. Virus RNA contains four functional proteins: 3-chymotrypsin-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and helicase. Important drug targets for new inhibitor research for the treatment of COVID-19; PLpro is 3CLpro, RdRp and S protein. There is no inhibitor that interacts with the PLpro enzyme, which is the drug target selected within the scope of the thesis. The PLpro enzyme is an enzyme that enables the replication of the virus and can impair host immunity. The PLpro enzyme is a very important drug target with these functions. The PLpro enzyme consists of two main parts, the ubiquitin-like (UbI) part and the active part, which includes the areas of the fingers, thumb and palm. Inhibitors that bind to the active site of the PLpro enzyme are covalently bound. The enzyme has a newly discovered BL2 region in the palm area. PLpro enzyme substrates do not bind to this site. Inhibitors that bind to the BL2 region by non-covalent interactions can indirectly disrupt the active site and prevent substrate binding to the active site, thereby providing enzyme inhibition. This thesis includes four calculations: validation, molecular docking, virtual ligand scanning and ADMEt. In the first step, validation study was performed using Autodock Vina program for 7LBS PDB encoded protein-ligand complex with low IC50 (0.56 µM) that can interact with the newly discovered BL2 region of SARS-CoV-2 PLpro enzyme and XR8-24 ligand belonging to this complex. As a result of redoking calculations, the experimental (x-ray) and computational results were matched, the RMSD value was found to be 1.723Å, and the value being less than 2Å indicates the suitability of the chosen method. The calculated Ki value of the ligand was found to be 108 nM. In the second stage, molecular docking calculations for a total of 43 ligands, 8 drugs approved for different diseases, and 35 plant phytochemicals belonging to 10 different plants such as red sage and birch, determined by experimental studies that are thought to interact with the PLpro enzyme in the literature, were determined by experimental studies Autodock Vina program. As a result of docking calculations with 7LBS protein-ligand complex, binding energy and computational Ki values were found. It was determined that the molecule with the highest binding energy and calculated Ki value was Tanshinone IIA. In the third step, 98 molecules with similar properties to Tanshinone IIA were downloaded as a data set with the ZINC15 database by scanning virtual ligands. Second docking calculations were made to these molecules with the same parameters as the molecular docking calculations, and 21 molecules with the highest binding energy were determined; ADME and toxicology (absorption-distribution-metabolism-excretion-toxicity) calculations were made. The study was completed by identifying 14 molecules that obtained appropriate results from the determined ADMEt tests. These obtained molecules may be effective in terms of antiviral drug design as PLpro enzyme inhibitor for the COVID-19 pandemic, and may contribute significantly to finding a precursor molecule.