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Approaches for Identification and Validation of Antimicrobial Compounds of Plant Origin: A Long Way from the Field to the Market
Published in Mahendra Rai, Chistiane M. Feitosa, Eco-Friendly Biobased Products Used in Microbial Diseases, 2022
Lívia Maria Batista Vilela, Carlos André dos Santos-Silva, Ricardo Salas Roldan-Filho, Pollyanna Michelle da Silva, Marx de Oliveira Lima, José Rafael da Silva Araújo, Wilson Dias de Oliveira, Suyane de Deus e Melo, Madson Allan de Luna Aragão, Thiago Henrique Napoleão, Patrícia Maria Guedes Paiva, Ana Christina Brasileiro-Vidal, Ana Maria Benko-Iseppon
Biomolecular compounds are dynamic bodies with molecular rearrangements in their structure due to the environment (physiological conditions) and their targets (Reif and Zacharias 2019). Molecular Dynamics (MD) simulations use classical mechanics to describe these motions in biomolecules. This in silico technique is commonly used to assess structural dynamics and stability of biological compounds (Dror et al. 2012; Reif and Zacharias 2019).
Computational Biology and Bioinformatics in Anti-SARS-CoV-2 Drug Development
Published in Debmalya Barh, Kenneth Lundstrom, COVID-19, 2022
Traditional structure-based drug discovery applies the computational ligand-receptor–binding modeling and virtual screening, whereas the stability of the resulting ligand-protein complexes is confirmed by molecular dynamics simulation. All potentially druggable SARS-CoV-2 proteins were subjected to these analyses, and the number of computational studies dedicated to finding potential drugs targeting these proteins is mounting. For example, Hosseini et al. conducted molecular docking and virtual screening of 1,615 FDA-approved drugs on the binding pocket of SARS-CoV-2 Mpro, PLpro, and RdRp proteins [127]. The authors used AutoDock Vina, Glide, and rDock followed by MD simulation using GROMACS on the top inhibitors and identified six novel ligands as potential inhibitors against SARS-CoV-2, such as antiemetics rolapitant and ondansetron for Mpro; labetalol and levomefolic acid for PLpro; and leucal and antifungal natamycin for RdRp [127]. Chourasia et al. investigated in silico binding of epigallocatechin gallate (EGCG), and other catechins to SARS-CoV-2 proteins and identified papain-like protease protein (PLPro) as a binding partner [128].
Science and Mathematics: Newtonian Dynamics and Molecular Dynamics
Published in John R. Helliwell, The Whats of a Scientific Life, 2019
I trace the thematic origin of one equation in physics, Newton’s force equals mass times acceleration equation of dynamics, familiar to anyone driving a car or moving an object. As an application in chemistry and molecular biology it is known as molecular dynamics.
Inhibition by components of Glycyrrhiza uralensis of 3CLpro and HCoV-OC43 proliferation
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2023
Jang Hoon Kim, Yea-In Park, Mok Hur, Woo Tae Park, Youn-Ho Moon, Yun-Chan Huh, Tae IL Kim, Min Hye Kang, Jong Seong Kang, Chong Woon Cho, Junsoo Park
Molecular dynamics analysis was performed as described previously.17 The Gromacs 4.6.5 package was used to simulate the complex of 3CLpro with polyphenols. The complex was charged by a Gromos96 54a6 force field. Ligand topology was generated by The GlycoBioChem PRODRG Server. The charged complex was dissolved in water in a cubic box using the simple point charge water model and ionised with sodium. mdp files were generated following the instructions for GROMACS.19 The mdp files were minimised to a maximal force of 10 kJ/mol using the steepest-descent method. The product was further equilibrated by 300 K NVT in 1 bar NPT for 100 ps. Finally, a molecular dynamics simulation was conducted for 30 ns. The results were analysed using g_utility. The data were visualised using SigmaPlot (San Jose, CA, USA) and Chimaera (San Francisco, CA, USA).16,17,19
Screening of rosmarinic acid from Salvia miltiorrhizae acting on the novel target TRPC1 based on the ‘homology modelling–virtual screening–molecular docking–affinity assay–activity evaluation’ method
Published in Pharmaceutical Biology, 2023
Wei Quan, Yuan Wang, Yu-han Chen, Qing Shao, Yang-ze Gong, Jie-wen Hu, Wei-hai Liu, Zi-jun Wu, Jie Wang, Shan-bo Ma, Xiao-qiang Li
Molecular dynamics simulations were performed using Gromacs 2020.1, in which the charm36-jul2020 force field was chosen. The protein and molecule complex were solved with TIP3P water and immersed in a dodecahedron box extending to at least 1 nm of the solvent on all sides. Also, the system was neutralized by Na+ and Cl–, and then 0.15 M NaCl was added. The energy was minimized by the steepest descent algorithm for 5000 steps, and it generated a maximum force of less than 1000 kJ/mol/nm. After energy minimization, the system was equilibrated in a constrained NVT (number of particles, volume, temperature) and NPT (number of particles, pressure, temperature) and ran for 100 ps. NVT equilibration ensured the desired temperature (300 K), under which we sought to establish the proper orientation of the protein. After NVT equilibration, we stabilized the pressure of the system under an NPT ensemble. Through NVT and NPT equilibration, it was well-equilibrated at 300 K and 1 bar. Finally, MD simulations of the TRPC1 were carried out for 100 ns. Trajectories were saved every 10 ps for analysis. The Verlet cut-off scheme and a Leap-frog integrator with a step size of 2 fs were applied. For temperature coupling, the modified Berendsen thermostat and the Parrinello-Rahman barostat for pressure coupling were used. For long-range electrostatic interaction, the particle mesh Ewald method was used. The root-mean-square displacement (RMSD) was calculated by GROMACS 2020.1.
Carbonic anhydrase inhibitory activity of phthalimide-capped benzene sulphonamide derivatives
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2023
Deepak Shilkar, Mohd Usman Mohd Siddique, Silvia Bua, Sabina Yasmin, Mrunali Patil, Ajay Kumar Timiri, Claudiu T. Supuran, Venkatesan Jayaprakash
For molecular dynamics simulations, the GROMACS package (version 2023.2, single precision)39 was used with the CHARMM36 force field40. The protein structure was prepared by removing water molecules and adding hydrogen atoms, followed by energy minimisation using the steepest descent algorithm. The system was solvated in a cubic box of TIP3P water molecules, with a minimum distance of 10 Å between the protein and box edges. The system was neutralised by the addition of counterions (Na+ or Cl−) using the GROMACS Genion module. The simulation was performed using an NPT ensemble with periodic boundary conditions, temperature of 300 K, and pressure of 1 atm. The equations of motion were integrated using the leapfrog algorithm, with a time step of 2 fs. Long-range electrostatic interactions were calculated using the particle mesh Ewald method, with a cut-off distance of 12 Å. The simulations were run for 300 ns, and the coordinates and velocities were saved every 10 ps for analysis.