Molecular Docking and Interactions of Pueraria Tuberosa with Vascular Endothelial Growth Factor Receptors.
01 Jul 2015-Indian Journal of Pharmaceutical Sciences (Indian J Pharm Sci)-Vol. 77, Iss: 4, pp 439-445
TL;DR: The interaction pattern of the puerarone and tuberostan may provide a hint for a novel drug design for vascular endothelial growth factor tyrosine kinase receptors with better specificity to treat angiogenic disorders.
Abstract: Pueraria tuberosa is known for its therapeutic potentials in cardiovascular disorders, but its effect in angiogenesis has not been studied so far. In this study, a computational approach has been applied to elucidate the role of the phytochemicals in inhibition of angiogenesis through modulation of vascular endothelial growth factor receptors: Vascular endothelial growth factor receptor-1 and vascular endothelial growth factor receptor-2, major factors responsible for angiogenesis. Metabolite structures retrieved from PubChem and KNApSAcK - 3D databases, were docked using AutoDock4.2 tool. Hydrogen bond and molecular docking, absorption, distribution, metabolism and excretion and toxicity predictions were carried out using UCSF Chimera, LigPlot(+) and PreADMET server, respectively. From the docking analysis, it was observed that puerarone and tuberostan had significant binding affinity for the intracellular kinase domain of vascular endothelial growth factor receptors-1 and vascular endothelial growth factor receptor-2 respectively. It is important to mention that both the phytochemicals shared similar interaction profile as that of standard inhibitors of vascular endothelial growth factor receptors. Also, both puerarone and tuberostan interacted with Lys861/Lys868 (adenosine 5'-triphosphate binding site of vascular endothelial growth factor receptors-1/vascular endothelial growth factor receptors-2), thus providing a clue that they may enforce their inhibitory effect by blocking the adenosine 5'-triphosphate binding domain of vascular endothelial growth factor receptors. Moreover, these molecules exhibited good drug-likeness, absorption, distribution, metabolism and excretion properties without any carcinogenic and toxic effects. The interaction pattern of the puerarone and tuberostan may provide a hint for a novel drug design for vascular endothelial growth factor tyrosine kinase receptors with better specificity to treat angiogenic disorders.
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TL;DR: Through molecular docking, this study found Puerarone and Robinin to be the most potential phytochemicals of PTWE for DPP-IV inhibition, and provides the novel active components that contribute to the D PP-IV inhibitory property ofPTWE.
Abstract: We had earlier reported that the extract of Pueraria tuberosa significantly inhibits DPP-IV enzyme, resulting in glucose tolerance response in rats. In this study, we have explored the active phytochemicals responsible for this potential. The results have been validated in both fasting and postprandial states in the plasma of normal rats and also in fasting blood and intestinal homogenates of diabetic models. Pueraria tuberosa water extract (PTWE) was administered to normal Charles Foster rats for 35 days and to diabetic model (65 mg/kg bw) for 10 days. After treatments, oral glucose tolerance test (OGTT) and insulin was done for 90 min, and the changes in the levels of GLP-1, GIP, and DPP-IV activities were monitored in fasting and postprandial states. In the case of the diabetic model, DPP-IV activity was measured in intestinal homogenate and basal insulin in plasma. The components of PTWE were analyzed via HPLC-MS based on their chemical formula, molecular mass, and retention time. Using the molecular docking study, we have selected the top five components having strong binding energy with DPP-IV. The increase in secretion of GLP-1 and GIP was significantly higher in the postprandial state when compared to fasting condition. GLP-1 plasma concentration increased by 5.8 and 2.9 folds and GIP increased by 8.7 and 2.4 folds in PTWE and control rats, respectively. In contrast, the postprandial decrease in DPP-IV specific activities was recorded at 2.3 and 1.4 folds. The response in OGTT and insulin was also consistent with these changes. In comparison to diabetic controls, PTWE-administered rats showed decreased DPP-IV activity in the intestine, leading to enhanced basal insulin concentration. Through molecular docking, we found Puerarone and Robinin to be the most potential phytochemicals of PTWE for DPP-IV inhibition. Binding energy (kcal/mol) and dissociation constant (pM) of Robinin with DPP-IV protein were found to be 7.543 and 2,957,383.75, respectively. For Puerarone, it was 7.376 and 3,920,309, respectively. Thus, this study provides the novel active components that contribute to the DPP-IV inhibitory property of PTWE.
28 citations
Cites background from "Molecular Docking and Interactions ..."
...PT tubers possess many components such as daidzin, puerarin, puerarone, genistein, puetuberosanol, tuberostan, tuberosin, and puerarin 4′,6′-diacetate [32]....
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TL;DR: The MD simulation results suggest that compound-17 binds strongly with RdRp of SARS-CoV-2 and has the potential to develop as a new antiviral against COVID-19 and can be one of the potential candidates for the treatment of CO VID-19.
Abstract: Antiviral drug therapy against SARS-CoV-2 is not yet established and posing a serious global health issue. Remdesivir is the first antiviral compound approved by the US FDA for the SARS-CoV-2 treatment for emergency use, targeting RNA-dependent RNA polymerase (RdRp) enzyme. In this work, we have examined the action of remdesivir and other two ligands screened from the library of nucleotide analogues using docking and molecular dynamics (MD) simulation studies. The MD simulations have been performed for all the ligand-bound RdRp complexes for the 30 ns time scale. This is one of the earlier reports to perform the MD simulations studies using the SARS-CoV-2 RdRp crystal structure (PDB ID 7BTF). The MD trajectories were analyzed and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations were performed to calculate the binding free energy. The binding energy data reveal that compound-17 (-59.6 kcal/mol) binds more strongly as compared to compound-8 (-46.3 kcal/mol) and remdesivir (-29.7 kcal/mol) with RdRp. The detailed analysis of trajectories shows that the remdesivir binds in the catalytic site and forms a hydrogen bond with the catalytic residues from 0 to 0.46 ns. Compound-8 binds in the catalytic site but does not form direct hydrogen bonds with catalytic residues. Compound-17 showed the formation of hydrogen bonds with catalytic residues throughout the simulation process. The MD simulation results such as hydrogen bonding, the center of mass distance analysis, snapshots at a different time interval, and binding energy suggest that compound-17 binds strongly with RdRp of SARS-CoV-2 and has the potential to develop as a new antiviral against COVID-19. Further, the frontier molecular orbital analysis and molecular electrostatic potential (MESP) iso-surface analysis using DFT calculations shed light on the superior binding of compound-17 with RdRp compared to remdesivir and compound-8. The computed as well as the experimentally reported pharmacokinetics and toxicity parameters of compound-17 is encouraging and therefore can be one of the potential candidates for the treatment of COVID-19.
27 citations
TL;DR: In addition to previously studied DPPIV inhibitor, PTY-2 also acts as incretin receptors agonist and protects against STZ-induced diabetes by down regulating β cells apoptosis.
21 citations
Cites background from "Molecular Docking and Interactions ..."
...tuberosa tubers are rich in steroid, triterpenoid, glycoside, carbohydrate, alkaloids, flavanoid, tannin, protein, and amino acids [2,9] such as daidzin, puerarin, puerarone, genistein, puetuberosanol, tuberostan, tuberosin, and puerarin 4′,6′-diacetate [10]....
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Journal Article•
TL;DR: It has been found that 8-c-ascorbyl-(-)-epigallocatechin, rutin and orientin could be the putative molecules for amelioration of post-prandial hyperglycaemia whereas 8- c-asc or byl epigallocatedchin 3-o-gallate and schaftoside could be used to reduce fat absorption in obese persons.
Abstract: Black tea is one of the most widely consumed beverages in the world and traditionally known for its antidiabetic and antiobese property. However, the underlying mechanisms of these properties are not studied widely. In this work, we hypothesize that the reason could be because of the inhibition of gut enzymes by the tea derived phytochemicals. Molecular docking was used to explore the efficacy of tea components to inhibit the key enzymes related with Type II diabetes and obesity; α-glucosidase, α-amylase and lipase. Autodock4.2 molecular docking software that applies Lamarckian Genetic Algorithm was used. The ligand structures were retrieved from PubChem and KNApSAcK-3D database. PreADMET web server was used for Toxicity and ADME predictions. Based on this analysis, it has been found that 8-c-ascorbyl-(-)-epigallocatechin, rutin and orientin could be the putative molecules for amelioration of post-prandial hyperglycaemia whereas 8-c-ascorbyl-(-)-epigallocatechin, 8-c-ascorbyl epigallocatechin 3-o-gallate and schaftoside could be used to reduce fat absorption in obese persons. It can be concluded that these phytochemicals or their derivatives can be used for further in-vitro and in-vivo studies to design valuable drugs.
18 citations
Cites result from "Molecular Docking and Interactions ..."
...The softwares and methodology used in the study is similar to our earlier published works (Asthana et al., 2014; Asthana et al., 2015)....
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TL;DR: The results showed that PTY-2 favorably changed all the expressions via anti-oxidant, anti-apoptotic,Anti-hypoxic and anti-inflammatory pathways, making itself as a protective agent against streptozotocin induced islet stress in rats.
Abstract: The earlier assessment of Pueraria tuberosa (PT) has shown anti-diabetic effects through enhancing incretin action and DPP-IV (Dipeptidyl peptidase-IV) inhibition. The aim of this work was to further explore the protective role of aqueous extract of Pueraria tuberosa tuber (PTY-2) against streptozotocin (STZ) induced islet stress in rats. Diabetes was induced by STZ (65 mg/kg body weight) in charles foster male rats. After 60 days of STZ administration, animals with blood glucose levels > 200 g/dL were considered as diabetic. All the rats were later divided into three groups: Group-1 (STZ untreated normal rats), Group-2 (Diabetic control), and Group-3 (PTY-2 [50 mg/100 g bw treatment for next 10 days to diabetic rats). The rats were then sacrificed after the 10th day of treatment accordingly. STZ treatment led to an increase in expression of Matrix metalloproteinases-9 (MMP-9), Tumour necrosis factor-α (Tnf-α), Hypoxia inducible factor-α (HIF-1α), Vascular endothelial growth factor (VEGF), Interleukin-6 (IL-6), Protein kinase C-e (PKC-e), Nuclear factor kappa-light-chain-enhancer of activated B-cells (NFkB), and Caspase-3. Reverse Transcriptase-PCR (RT-PCR), Immunohistochemistry and Western-Blot analysis showed an increase in the expressions of Superoxide Dismutase (SOD) and Nephrin, and a decrease in the expressions of NFkB, PKC-e, TNF-α, MMP-9, HIF-1α, VEGF, Caspase-3 and IL-6 after 10 days of PTY-2 treatment. The results showed that PTY-2 favorably changed all the expressions via anti-oxidant, anti-apoptotic, anti-hypoxic and anti-inflammatory pathways, making itself as a protective agent against STZ induced islet stress. Further evaluation of PTY-2 might be helpful in establishing its role in the management of diabetes mellitus.
8 citations
References
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TL;DR: Puerarone was synthesized using chalcone oxidation with thallium trinitrate and chromenation of the resulting isoflavone using 3-hydroxyisovaleraldehyde dimethylacetal.
Abstract: Puerarone was synthesized using chalcone oxidation with thallium (III) trinitrate and chromenation of the resulting isoflavone using 3-hydroxyisovaleraldehyde dimethylacetal. The key demethylation step was achieved with boron tribromide.
1 citations