Molecular Docking, 3D Structure-Based Pharmacophore Modeling, and ADME Prediction of Alpha Mangostin and Its Derivatives against Estrogen Receptor Alpha

Muchtaridi, Muchtaridi; Dermawan, Doni; Yusuf, Muhammad

doi:10.5530/jyp.2018.10.58

Cited by 44 publications

(30 citation statements)

References 14 publications

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“…The conformation results from the docking simulation were clustered using a root mean square deviation (RMSD) with tolerance of 2.0 Å. 17 The guest-host conformation with the lowest Gibbs free binding energy (∆G) was chosen from the most favored cluster. The guest-host complexes from docking simulation were visualized using Jmol Molecular Viewer 14.29 and BIOVIA Discovery Studio Visualizer 2017.…”

Section: Molecular Docking Simulationmentioning

confidence: 99%

Host-Guest Interactions of α−Mangostin with (α,β,γ)−Cyclodextrins: Semi-Empirical Quantum Mechanical Methods of PM6 and PM7

Dermawan¹,

Wathoni²,

Muchtaridi³

2018

JYP

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Objective: This study aimed to investigate the molecular interactions, geometrical properties, encapsulation process and calculated energy of the inclusion complexes system between α−mangostin (guest) with α−cyclodextrin, β−cyclodextrin and γ-cyclodextrin (hosts) in an aqueous environment using the semi-empirical quantum mechanical methods of PM6 and PM7. Materials and Methods: Molecular docking simulation and semi-empirical quantum mechanical calculations of PM6 and PM7 were employed to identify the molecular interactions between α−mangostin and three types of cyclodextrin. Results: The inclusion complex formation energy values of all α−mangostin/cyclodextrin that obtained by the semiempirical PM7 method were significantly lower than complexation energy obtained by the semi-empirical PM6 method. Conclusion: The inclusion complex of α−mangostin/γ−cyclodextrin is the most favorable pathway of inclusion complex formation of α−mangostin with cyclodextrin because it has the highest negative value of free binding energy (∆G) and complexation energy (∆E) compared to α−mangostin/α−cyclodextrin and α−mangostin/β−cyclodextrin.

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Section: Molecular Docking Simulationmentioning

confidence: 99%

Host-Guest Interactions of α−Mangostin with (α,β,γ)−Cyclodextrins: Semi-Empirical Quantum Mechanical Methods of PM6 and PM7

Dermawan¹,

Wathoni²,

Muchtaridi³

2018

JYP

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“…Molecular modelling performed on estrogen-related receptors is not an exception. As the studies are performed mostly to search for new agonists or antagonists, the ligands re-docked into the ERs or SHBG are mainly E2 [ 52 , 53 , 54 , 55 , 56 , 57 ] and 4-hydroxytamoxifen [ 52 , 58 , 59 ]. RMSD value in most of the studies varies from 0.26 to 1.4Å, which proves the correctness of the docking methods in finding the proper orientation of the ligand in the active site.…”

Section: Application Of Molecular Modelling Methods In the Study Omentioning

confidence: 99%

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

Mazurek

Szeleszczuk

Simonson

et al. 2020

IJMS

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In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure–activity relationship (QSAR) analyses to examine estrogen’s structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations. Apart from molecular mechanics and statistical methods, quantum mechanics calculations are also employed in the studies of estrogens and xenoestrogens. Their applications include computation of spectroscopic properties, both vibrational and Nuclear Magnetic Resonance (NMR), and also in quantum molecular dynamics simulations and crystal structure prediction. The main aim of this review is to present the great potential and versatility of various molecular modelling methods in the studies on estrogens and xenoestrogens.

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“…XP module docked the compounds with better precision and accuracy. The XP parameters like docking score glide energy and glide model value were calculated within the Schrodinger v11.5 (Additional file 1) [17, 31–33].…”

Section: Methodsmentioning

confidence: 99%

“…Structure based drug designing (SBDD) and ligand based drug designing (LBDD) techniques are employed as important drug discovery tools in rational drug designing process [16]. Molecular docking is the advanced computational used techniques in SBDD to obtain optimized conformation of ligand–receptor interaction and to study their relative orientation through the minimized energy free system [17]. Computer aided drug designing (CADD) is fast, economical modernized technique that gives valuable, accurate and deep understandings of experimental findings and new suggestions for molecular structures to be synthesized [18].…”

Section: Introductionmentioning

confidence: 99%

4-(4-Bromophenyl)-thiazol-2-amine derivatives: synthesis, biological activity and molecular docking study with ADME profile

et al. 2019

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In order to overcome the challenges of microbial resistance as well as to improve the effectiveness and selectivity of chemotherapeutic agents against cancer, a novel series of 4-(4-bromophenyl)-thiazol-2-amine derivatives was synthesized and its molecular structures were confirmed by physicochemical and spectral characteristics. The synthesized compounds were further evaluated for their in vitro antimicrobial activity using turbidimetric method and anticancer activity against oestrogen receptor positive human breast adenocarcinoma cancer cell line (MCF7) by Sulforhodamine B (SRB) assay. The antimicrobial activity results revealed that compound p2 , p3 , p4 and p6 exhibited promising antimicrobial activity that are comparable to standard norfloxacin (antibacterial) and fluconazole (antifungal). Anticancer screening results demonstrated that compound p2 was found to be the most active one against cancer cell line when compared to the rest of the compounds and comparable to the standard drug (5-fluorouracil). The molecular docking study demonstrated that compounds, p2 , p3 , p4 and p6 displayed good docking score within binding pocket of the selected PDB ID (1JIJ, 4WMZ and 3ERT) and showed promising ADME properties. Electronic supplementary material The online version of this article (10.1186/s13065-019-0575-x) contains supplementary material, which is available to authorized users.

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Molecular Docking, 3D Structure-Based Pharmacophore Modeling, and ADME Prediction of Alpha Mangostin and Its Derivatives against Estrogen Receptor Alpha

Cited by 44 publications

References 14 publications

Host-Guest Interactions of α−Mangostin with (α,β,γ)−Cyclodextrins: Semi-Empirical Quantum Mechanical Methods of PM6 and PM7

Host-Guest Interactions of α−Mangostin with (α,β,γ)−Cyclodextrins: Semi-Empirical Quantum Mechanical Methods of PM6 and PM7

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

4-(4-Bromophenyl)-thiazol-2-amine derivatives: synthesis, biological activity and molecular docking study with ADME profile

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