Investigation of inhibition and activation of some enzymes and proteins by allosteric effect using molecular modeling methods

Molecular dynamic simulation (MDS) methods are widely used in the field of health, as in many other fields. MDS methods are preferred by scientists considering the consumables used in experimental analyzes and the time spent in the examination of polyatomic systems. It is possible to investigate the catalysis functions of enzymes in the field of drug design with MDS methods. In this thesis, it was investigated whether Covid Basic Protease (MPro) and Carbonic Anhydrase II (CA II) enzymes can be inhibited by allosteric mechanism or not by MDS calculations. In the study, simulations of 200 ns were performed using the Amber-18 Molecular Dynamics Simulation Package for both ligand-free and ligand-based structures of each enzyme. One of the enzymes subject to the study is MPro secreted by the SARS-CoV-2 virus with the access code 6M03 PDB. This enzyme is a critical cysteine enzyme required for viral replication and transcription. Its inhibition can stop the production of infectious viral particles and thus alleviate the disease symptoms of COVID-19 infection. Therefore, since the beginning of the epidemic, MPro has been at the center of drug development research for the treatment of Sars-CoV-2 infection. For this purpose, FDA-approved drugs in the DrugBank database were subjected to a virtual screening experiment with Molecular Docking (MK) technique in this study. Drugs that bind strongly away from the catalytic site of MPro were identified using the MK technique. The drug Dihydroergotamine (DHE) with the strongest binding score was selected for the MDS study. The other enzyme that is the subject of this thesis is the CA II metallo-enzyme with access code 4QY3 in the PDB database. There are many drugs based on the inhibition of CA II, which are currently used in the treatment of many diseases, especially glaucoma. In the inhibition mechanism of all these drugs, the inhibitor makes a semi-covalent bond with Zinc (Zn) in the active site of CA II. It has been shown in the literature that the CA II inhibitor 2-[(S)-benzylsulfinyl]benzoic acid (3G1) ligand, which is the subject of this study, performs inhibition by binding to a point outside the active site without interacting directly with the Zn atom in the active site. In this study, the inhibition mechanism of 3G1 ligand, which inhibits CA II with allosteric effect, was investigated. Hydrogen bonding analysis, dynamic cross-correlation, communication bias, dynamic interaction amino acid network analysis using trajectory files obtained from MDSs of DHE-MPro complex, Apo-MPro, 3G1-CA II and Apo-CA II systems to reveal the allosteric inhibition effect. and computational tools such as transfer entropy were used. The obtained results support that the hydrogen bonding interactions of DHE with GLU278 and THR280 located between Protomer A and Protomer B affect the structure of the side chain of CYS145 in the catalytic site of MPro. Given the role of CYS145 in the catalytic cycle, this conformational change is likely to be a mechanism for inhibiting MPro. In CA II enzyme, it was observed that the 3G1 ligand bound by hydrogen bonding with amino acids TYR7 and ASN11 caused significant changes in the dihedral angles of amino acids GLN92, GLY102, GLN103, GLN104, ASP110, LYS113 and THR198 in the active site of the enzyme. It can be considered that this structural change occurring in the active site is highly likely to affect the H2O, CO2, CO3-2 and OH cycles. It can be thought that inhibition occurs with the interruption of this cycle. The findings have important information about the allosteric effect and inhibition mechanisms of MPro and CA II enzymes, and which amino acids should be manipulated. It is thought that this information will be useful in the design of new allosteric inhibitors of the mentioned enzymes.