Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer

Abstract Background Ovarian cancer is the world’s dreaded disease and its prevalence is expanding globally. The study of integrated molecular networks is crucial for the basic mechanism of cancer cells and their progression. During the present investigation, we have examined different flavonoids tha...

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Autores principales:	Suchitra Maheswari Ajjarapu, Apoorv Tiwari, Gohar Taj, Dev Bukhsh Singh, Sakshi Singh, Sundip Kumar
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	AKT1 Point mutation ADME QSAR Virtual docking Dynamic simulations Therapeutics. Pharmacology RM1-950 Toxicology. Poisons RA1190-1270
Acceso en línea:	https://doaj.org/article/ab676c28deb344d19d67adb2976dc443
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spelling	oai:doaj.org-article:ab676c28deb344d19d67adb2976dc4432021-11-08T10:45:48ZSimulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer10.1186/s40360-021-00512-y2050-6511https://doaj.org/article/ab676c28deb344d19d67adb2976dc4432021-11-01T00:00:00Zhttps://doi.org/10.1186/s40360-021-00512-yhttps://doaj.org/toc/2050-6511Abstract Background Ovarian cancer is the world’s dreaded disease and its prevalence is expanding globally. The study of integrated molecular networks is crucial for the basic mechanism of cancer cells and their progression. During the present investigation, we have examined different flavonoids that target protein kinases B (AKT1) protein which exerts their anticancer efficiency intriguing the role in cross-talk cell signalling, by metabolic processes through in-silico approaches. Method Molecular dynamics simulation (MDS) was performed to analyze and evaluate the stability of the complexes under physiological conditions and the results were congruent with molecular docking. This investigation revealed the effect of a point mutation (W80R), considered based on their frequency of occurrence, with AKT1 protein. Results The ligand with high docking scores and favourable behaviour on dynamic simulations are proposed as potential W80R inhibitors. A virtual screening analysis was performed with 12,000 flavonoids satisfying Lipinski’s rule of five according to which drug-likeness is predicted based on its pharmacological and biological properties to be active and taken orally. The pharmacokinetic ADME (adsorption, digestion, metabolism, and excretion) studies featured drug-likeness. Subsequently, a statistically significant 3D-QSAR model of high correlation coefficient (R2) with 0.822 and cross-validation coefficient (Q2) with 0.6132 at 4 component PLS (partial least square) were used to verify the accuracy of the models. Taxifolin holds good interactions with the binding domain of W80R, highest Glide score of − 9.63 kcal/mol with OH of GLU234 and H bond ASP274 and LEU156 amino acid residues and one pi-cation interaction and one hydrophobic bond with LYS276. Conclusion Natural compounds have always been a richest source of active compounds with a wide variety of structures, therefore, these compounds showed a special inspiration for medical chemists. The present study has aimed molecular docking and molecular dynamics simulation studies on taxifolin targeting W80R mutant protein of protein kinase B/serine- threonine kinase/AKT1 (EC:2.7.11.1) protein of ovarian cancer for designing therapeutic intervention. The expected result supported the molecular cause in a mutant form which resulted in a gain of ovarian cancer. Here we discussed validations computationally and yet experimental evaluation or in vivo studies are endorsed for further study. Several of these compounds should become the next marvels for early detection of ovarian cancer.Suchitra Maheswari AjjarapuApoorv TiwariGohar TajDev Bukhsh SinghSakshi SinghSundip KumarBMCarticleAKT1Point mutationADMEQSARVirtual dockingDynamic simulationsTherapeutics. PharmacologyRM1-950Toxicology. PoisonsRA1190-1270ENBMC Pharmacology and Toxicology, Vol 22, Iss 1, Pp 1-23 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	AKT1 Point mutation ADME QSAR Virtual docking Dynamic simulations Therapeutics. Pharmacology RM1-950 Toxicology. Poisons RA1190-1270
spellingShingle	AKT1 Point mutation ADME QSAR Virtual docking Dynamic simulations Therapeutics. Pharmacology RM1-950 Toxicology. Poisons RA1190-1270 Suchitra Maheswari Ajjarapu Apoorv Tiwari Gohar Taj Dev Bukhsh Singh Sakshi Singh Sundip Kumar Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
description	Abstract Background Ovarian cancer is the world’s dreaded disease and its prevalence is expanding globally. The study of integrated molecular networks is crucial for the basic mechanism of cancer cells and their progression. During the present investigation, we have examined different flavonoids that target protein kinases B (AKT1) protein which exerts their anticancer efficiency intriguing the role in cross-talk cell signalling, by metabolic processes through in-silico approaches. Method Molecular dynamics simulation (MDS) was performed to analyze and evaluate the stability of the complexes under physiological conditions and the results were congruent with molecular docking. This investigation revealed the effect of a point mutation (W80R), considered based on their frequency of occurrence, with AKT1 protein. Results The ligand with high docking scores and favourable behaviour on dynamic simulations are proposed as potential W80R inhibitors. A virtual screening analysis was performed with 12,000 flavonoids satisfying Lipinski’s rule of five according to which drug-likeness is predicted based on its pharmacological and biological properties to be active and taken orally. The pharmacokinetic ADME (adsorption, digestion, metabolism, and excretion) studies featured drug-likeness. Subsequently, a statistically significant 3D-QSAR model of high correlation coefficient (R2) with 0.822 and cross-validation coefficient (Q2) with 0.6132 at 4 component PLS (partial least square) were used to verify the accuracy of the models. Taxifolin holds good interactions with the binding domain of W80R, highest Glide score of − 9.63 kcal/mol with OH of GLU234 and H bond ASP274 and LEU156 amino acid residues and one pi-cation interaction and one hydrophobic bond with LYS276. Conclusion Natural compounds have always been a richest source of active compounds with a wide variety of structures, therefore, these compounds showed a special inspiration for medical chemists. The present study has aimed molecular docking and molecular dynamics simulation studies on taxifolin targeting W80R mutant protein of protein kinase B/serine- threonine kinase/AKT1 (EC:2.7.11.1) protein of ovarian cancer for designing therapeutic intervention. The expected result supported the molecular cause in a mutant form which resulted in a gain of ovarian cancer. Here we discussed validations computationally and yet experimental evaluation or in vivo studies are endorsed for further study. Several of these compounds should become the next marvels for early detection of ovarian cancer.
format	article
author	Suchitra Maheswari Ajjarapu Apoorv Tiwari Gohar Taj Dev Bukhsh Singh Sakshi Singh Sundip Kumar
author_facet	Suchitra Maheswari Ajjarapu Apoorv Tiwari Gohar Taj Dev Bukhsh Singh Sakshi Singh Sundip Kumar
author_sort	Suchitra Maheswari Ajjarapu
title	Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
title_short	Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
title_full	Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
title_fullStr	Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
title_full_unstemmed	Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer
title_sort	simulation studies, 3d qsar and molecular docking on a point mutation of protein kinase b with flavonoids targeting ovarian cancer
publisher	BMC
publishDate	2021
url	https://doaj.org/article/ab676c28deb344d19d67adb2976dc443
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Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer

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