2022
DOI: 10.1007/s11164-022-04831-5
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One-pot synthesis, molecular docking, ADMET, and DFT studies of novel pyrazolines as promising SARS-CoV-2 main protease inhibitors

Abstract: Pyrazoline and its derivatives have numerous prominent pharmacological effects. Focusing on its anti-viral property, we have designed and synthesized three novel pyrazoline derivatives ( A1–A3 ) through one-pot three components and characterized them using different spectroscopic techniques (FT-IR, 1 H NMR, 13 C NMR, and UV). These compounds were evaluated against SARS-CoV-2 main protease utilizing in-silico molecular docking studies. The doc… Show more

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Cited by 23 publications
(11 citation statements)
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“…The generated trajectories recovered from the production step were utilized for analysis of the whole system residues by using tools implemented in the GROMACS and VMD package. , A distance cutoff of the short-range neighbor list 1.0 nm was applied to short-range nonbonded interactions with a pair list distance of 1.2 nm, and Lennard-Jones interactions were smoothly truncated at 1.2 nm (rvdm, rcoulomb = 1.2 nm). Long-range electrostatic interactions were treated using the particle mesh Ewald (PME) method, where a grid spacing of 1.0 Å was used for all simulation cells. For consistency, we applied the same protocol for all MD simulations.…”
Section: Methodsmentioning
confidence: 99%
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“…The generated trajectories recovered from the production step were utilized for analysis of the whole system residues by using tools implemented in the GROMACS and VMD package. , A distance cutoff of the short-range neighbor list 1.0 nm was applied to short-range nonbonded interactions with a pair list distance of 1.2 nm, and Lennard-Jones interactions were smoothly truncated at 1.2 nm (rvdm, rcoulomb = 1.2 nm). Long-range electrostatic interactions were treated using the particle mesh Ewald (PME) method, where a grid spacing of 1.0 Å was used for all simulation cells. For consistency, we applied the same protocol for all MD simulations.…”
Section: Methodsmentioning
confidence: 99%
“…The binding free energy of the simulated complexes (Hem and Neu) were computed based on molecular dynamics (MD) simulation results by GROMACS using snapshots taken from the system’s trajectories (100 ns) followed by gmx_MM-PBSA tool based on AMBER tools MM-PBSA.py module with GROMACS files in which the ligand (L) binds to the protein receptor (R) to form the complex (RL). We are only interested in relative binding energy calculations, where the Gibbs relative binding energy is given by normalΔ G normalb normali normaln normald = Δ G b i n d , v a c u u m + Δ G R L , S o l v a t i o n ( Δ G normalR Δ G normalL ) …”
Section: Methodsmentioning
confidence: 99%
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“…Lamarck genetic algorithm was used to perform 200 molecular docking studies. The intermolecular interaction between CHL and pepsin was studied using AutoDock 4.2.6 [30,31] …”
Section: Methodsmentioning
confidence: 99%
“…Each atom's molecule stability, reactivity, and charge distribution can all be carefully assessed via DFT computing. Based on the energy difference between the lowest unoccupied and highest occupied orbitals, the chemical reactivity and structural stability were identified, and the frontier molecular orbital of the molecule was evaluated [22,23]. Based on the electropositive and electronegative areas, through the mapped surface the molecular electrostatic potential (MEP) was determined, which confirms the molecule's nature of reactivity [24,25].…”
mentioning
confidence: 99%