Ayoung Baek


2 Discovery of Human HMG-Coa Reductase Inhibitors Using Structure-Based Pharmacophore Modeling Combined with Molecular Dynamics Simulation Methodologies

Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek, Shalini John


3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we performed structure-based pharmacophore modeling combined with molecular dynamics (MD) simulation. Four HMGR inhibitors were used for MD simulation and representative structure of each simulation were selected by clustering analysis. Four structure-based pharmacophore models were generated using the representative structure. The generated models were validated used in virtual screening to find novel scaffolds for inhibiting HMGR. The screened compounds were filtered by applying drug-like properties and used in molecular docking. Finally, four hit compounds were obtained and these complexes were refined using energy minimization. These compounds might be potential leads to design novel HMGR inhibitor.

Keywords: molecular dynamics simulation, Anti-hypercholesterolemia drug, HMGR inhibitor, Structure-based pharmacophore modeling

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1 Molecular Mechanism of Amino Acid Discrimination for the Editing Reaction of E.coli Leucyl-tRNA Synthetase

Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek


Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.

Keywords: Molecular Dynamics, Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase

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1 Understanding Inhibitory Mechanism of the Selective Inhibitors of Cdk5/p25 Complex by Molecular Modeling Studies

Authors: Minky Son, Ayoung Baek, Amir Zeb, Shailima Rampogu, Sang H. Yoon, Keun W. Lee


Neurotoxic insults activate calpain, which in turn produces truncated p25 from p35. p25 forms hyperactivated Cdk5/p25 complex, and thereby induces severe neuropathological aberrations including hyperphosphorylated tau, neuroinflammation, apoptosis, and neuronal death. Inhibition of Cdk5/p25 complex alleviates aberrant phosphorylation of tau to mitigate AD pathology. PHA-793887 and Roscovitine have been investigated as selective inhibitors of Cdk5/p25 with IC50 values 5nM and 160nM, respectively, but their mechanistic studies remain unknown. Herein, computational simulations have explored the binding mode and interaction mechanism of PHA-793887 and Roscovitine with Cdk5/p25. Docking results suggested that PHA-793887 and Rsocovitine have occupied the ATP-binding site of Cdk5 and obtained highest docking (GOLD) score of 66.54 and 84.03, respectively. Furthermore, molecular dynamics (MD) simulation demonstrated that PHA-793887 and Roscovitine established stable RMSD of 1.09 Å and 1.48 Å with Cdk5/p25, respectively. Profiling of polar interactions suggested that each inhibitor formed hydrogen bonds (H-bond) with catalytic residues of Cdk5 and could remain stable throughout the molecular dynamics simulation. Additionally, binding free energy calculation by molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) suggested that PHA-793887 and Roscovitine had lowest binding free energies of -150.05 kJ/mol and -113.14 kJ/mol, respectively with Cdk5/p25. Free energy decomposition demonstrated that polar energy by H-bond between the Glu81 of Cdk5 and PHA-793887 is the essential factor to make PHA-793887 highly selective towards Cdk5/p25. Overall, this study provided substantial evidences to explore mechanistic interactions of the selective inhibitors of Cdk5/p25 and could be used as fundamental considerations in the development of structure-based selective inhibitors of Cdk5/p25.

Keywords: Cdk5/p25 inhibition, molecular modeling of Cdk5/p25, PHA-793887 and roscovitine, selective inhibition of Cdk5/p25

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