Computational protocol: Evaluating Andrographolide as a Potent Inhibitor of NS3-4A Protease and Its Drug-Resistant Mutants Using In Silico Approaches

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Protocol publication

[…] The investigated compounds Andrographolide and Asunaprevir were drawn using Marvin sketch []. Ligand optimization was carried out using Chemistry at Harvard Molecular Mechanics (CHARMm) and macro molecular force field (MMF) followed by energy minimization protocol []. Several ligand conformations were generated based on bond energy, CHARM energy, dihedral energy, electrostatic energy, initial potential energy, and initial RMS gradient values. The drug likeliness was evaluated using the Lipinski rule of 5 via Lipinski drug filter protocol []. The studies on the ADME of aqueous solubility, blood brain barrier level, hepatotoxicity, plasma protein binding levels, and CYP2D6 were carried out []. Toxicity profile of the ligand molecules was predicted by using TOPKAT which applies a range of robust, cross validated, and Quantitative Structure-Toxicity Relationship (QSTR) models for assessing specific toxicological endpoints. The toxicity profile also included NTP carcinogenicity, mutagenicity, and developmental toxicity and skin irritation assessment []. The studies were performed using Discovery studio 3.5 (Accelrys). [...] For molecular docking studies, a flexible docking approach was employed using the LeadIT [] software in which wild NS3 protease and mutants R155K and D168A were considered as receptor proteins. The docking results for receptor-ligand complex comprised intermolecular interaction energies, namely, hydrogen bonding and hydrophobic and electrostatic interaction. Receptor-ligand complex with least binding energy was used to infer the best binding compound. Molecular dynamics (MD) simulations for both proteins and ligands were performed in a flexible manner that allowed binding site to be relaxed around the ligand and directly estimate the effect of explicit water molecules. MD-based computational techniques are available for estimating the binding free energy which includes thermodynamic integration (TI), free energy perturbation (FEP), linear interaction energy (LIE), and molecular mechanics/Poisson-Boltzmann and surface area (MM/PB-SA) methods. Three best receptor-ligand complexes were subjected to molecular dynamics studies based on steepest decent minimization protocol. For dynamics study, the following parameters, heating steps and time steps set as 2000 and 0.001, respectively, equilibration steps and time steps set as 1000 and 0.001, respectively, for the overall production period of 20 ns with time steps as 0.001 and temperature factor of 300 K, were considered. The best conformations were selected based on the least potential energy value []. […]

Pipeline specifications

Software tools TOPKAT, LeadIt
Application Drug design
Organisms Andrographis paniculata
Diseases Hepatitis C, Infection, Neural Tube Defects
Chemicals Ribavirin