Designing, docking and molecular dynamics simulation studies of novel cloperastine analogues as anti-allergic agents: homology modeling and active site prediction for the human histamine H1 receptor

Abstract

The present study predicts a three-dimensional model for the histamine H1 receptor and the design of antihistamine inhibitors using cloperastine as the core molecule by docking studies.

Molecular Modeling of µ Opioid Receptor Ligands with Various Functional Properties: PZM21, SR-17018, Morphine, and Fentanyl—Simulated Interaction Patterns Confronted with Experimental Data

“…One ligand–receptor complex returned by a docking program captures just one moment of the mutual orientation of a compound and protein. More computationally demanding but also much more informative method is molecular dynamics (MD), which enables simulation of the behavior of the modeled system (e.g., ligand–protein complex) in time [ 19 , 20 ].…”

Molecular mechanism of inhibition of COVID-19 main protease by β-adrenoceptor agonists and adenosine deaminase inhibitors using in silico methods

“…MD simulation is an important tool to understand the structural and dynamical behavior of biological system (Daddam et al, 2020 ; Das et al, 2019 ; Venugopal et al, 2020 ). The stability of complex formed between covid-19 main protease (6LU7) and the top-scored ligands was analyzed by 100 ns simulations by Gromacs 2018.4 (Abraham et al, 2015 ) using SPC/E water model (Mark & Nilsson, 2001 ).…”

Molecular Modeling of Histamine Receptors—Recent Advances in Drug Discovery

“…Methyl (MMA), propyl (PMA) and isopropyl (IMA) N-methylanthranilate, originally found in the leaf essential oil of Choisya ternata , were reported to establish interactions with D 3.32 , Y 3.33 , S 3.36 , I 3.40 , W 4.56 , N 5.46 , F 5.47 , F 6.44 , W 6.48 , Y 6.51 , F 6.52 , F 6.55 and I 7.39 [ 76 ]. In 2020, a set of 35 antihistamines was designed using cloperastine as the core molecule in docking and molecular dynamics studies, however, no experimental binding studies were performed [ 107 ]. Another study involving in silico design, synthesis, ADME profiling and evaluation of antagonistic effects of 1,8-naphthyridine-3-carboxylic acid analogues was carried out using chlorpheniramine as the standard drug.…”