Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking

Kandagalla, Shivananda; Novak, Jurica; Shekarappa, Sharath Belenahalli; Grishina, Maria; Потемкин, В. А.; Kumbar, Bhimanagoud

doi:10.1080/07391102.2021.1990131

Cited by 9 publications

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“…We identified key residues with dominant contributions to the protein–ligand binding, applying the MM/GBSA binding free energy decomposition. In our previous research on the SARS-CoV-2 virus main protease [ 27 ], Kyasanur forest disease virus NS3 protease [ 28 ], and in the development of potent pyrimidine–sulfonamide hybrids as selective BRAFV600E inhibitors [ 29 ], a threshold of −1.5 kcal mol −1 was set for a single residue binding free energy to classify it as a residue with a dominant contribution, and the same criteria were applied in the present study. Only three residues satisfied the criteria, namely Leu126 (−2.2 kcal mol −1 ), Leu217 (−1.7 kcal mol −1 ), and Leu171 (−1.6 kcal mol −1 ) ( Figure 8 ).…”

Section: Resultsmentioning

confidence: 99%

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

et al. 2023

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The enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD-1) is an NADPH-dependent reductase, responsible for the activation of cortisol by reducing cortisone. Resveratrol (RES), a type of natural polyphenol, is reported to be able to slow the progression of cancer and cardiovascular disease and improve the health of mice on a high-calorie diet. In this article, we applied molecular docking and molecular dynamics simulations to investigate the possibility of binding RES to 11β-HSD-1. The 11β-HSD-1:RES complex is stable on the μs time scale, and backbone RMSD-based clustering identified three conformations. Special attention was paid to the interaction pattern between the ligand and the target molecule, revealing hydrogen bonds between the hydroxyl group of RES and Thr124, as well as hydrophobic interactions responsible for the binding. In vivo studies demonstrated the ability of resveratrol at a dose of 40 mg/kg to reduce 11β-HSD-1 activity in the liver of rats under conditions of experimental post-traumatic stress disorder (PTSD), as well as in non-stressed animals. In both cases, the resveratrol-induced reduction in 11β-HSD-1 activity was accompanied by an increase in plasma corticosterone levels and a decrease in anxiety levels in the plus maze test.

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Section: Resultsmentioning

confidence: 99%

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

et al. 2023

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“…Key residues with dominant contributions to protein‐ligand binding were identified by the MM/GBSA binding free energy decomposition. An analogous approach was used in our previous studies of protein‐ligand interactions [60–62] . For the GEN : MMP9 complex, only four residues contribute −1.0 kcal mol −1 or less to the total binding free energy.…”

Section: Resultsmentioning

confidence: 99%

“…An analogous approach was used in our previous studies of protein-ligand interactions. [60][61][62] For the GEN : MMP9 complex, only four residues contribute À 1.0 kcal mol À 1 or less to the total binding free energy. These residues are Leu39, Leu44, Leu187, and Gly186, all of which are nonpolar and hydrophobic.…”

Section: Docking and Molecular Dynamics Simulation Studiesmentioning

confidence: 99%

Green Synthesis of Genistein‐Fortified Zinc Ferrite Nanoparticles as a Potent Hepatic Cancer Inhibitor: Validation through Experimental and Computational Studies

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Adewuyi

et al. 2023

Chemistry & Biodiversity

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In hepatic cancer, precancerous nodules account for damage and inflammation in liver cells. Studies have proved that phyto‐compounds based on biosynthetic metallic nanoparticles display superior action against hepatic tumors. This study targeted the synthesis of genistein‐fortified zinc ferrite nanoparticles (GENP) trailed by anticancer activity assessment against diethylnitrosamine and N‐acetyl‐2‐aminofluorene induced hepatic cancer. The process of nucleation was confirmed by UV/VIS spectrophotometry, X‐ray beam diffraction, field‐emission scanning electron microscopy, and FT‐IR. An in vitro antioxidant assay illustrated that the leaves of Pterocarpus mildbraedii have strong tendency as a reductant and, in the nanoformulation synthesis, as a natural capping agent. A MTT assay confirmed that GENP have a strong selective cytotoxic potential against HepG2 cancer cells. In silico studies of genistein exemplified the binding tendency towards human matrix metalloproteinase comparative to the standard drug marimastat. An in vivo anticancer evaluation showed that GENP effectively inhibit the growth of hepatic cancer by interfering with hepatic and non‐hepatic biochemical markers.

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“…The MM/GBSA binding free energy decomposition was used to identify key residues with dominant contribution to protein–ligand binding. In the study of the SARS-CoV-2 virus, its main protease 84 and the NS3 protease of Kyasanur forest disease virus, 85 a threshold of −1.5 kcal mol −1 was set for the free energy of binding of a single residue to classify it as a residue with dominant contribution, and the same criteria was applied in the present study. Table 4 lists the residues with dominant contributions for T109, T126, T160, and T183 and dabrafenib.…”

Section: Resultsmentioning

confidence: 99%

Gaussian field-based 3D-QSAR and molecular simulation studies to design potent pyrimidine–sulfonamide hybrids as selective BRAF^V600Einhibitors

et al. 2022

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Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking

Cited by 9 publications

References 89 publications

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

Green Synthesis of Genistein‐Fortified Zinc Ferrite Nanoparticles as a Potent Hepatic Cancer Inhibitor: Validation through Experimental and Computational Studies

Gaussian field-based 3D-QSAR and molecular simulation studies to design potent pyrimidine–sulfonamide hybrids as selective BRAF^V600Einhibitors

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Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking

Cited by 9 publications

References 89 publications

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

Can Resveratrol Influence the Activity of 11β-Hydroxysteroid Dehydrogenase Type 1? A Combined In Silico and In Vivo Study

Green Synthesis of Genistein‐Fortified Zinc Ferrite Nanoparticles as a Potent Hepatic Cancer Inhibitor: Validation through Experimental and Computational Studies

Gaussian field-based 3D-QSAR and molecular simulation studies to design potent pyrimidine–sulfonamide hybrids as selective BRAFV600Einhibitors

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Product

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Gaussian field-based 3D-QSAR and molecular simulation studies to design potent pyrimidine–sulfonamide hybrids as selective BRAF^V600Einhibitors