Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

Iman, Maryam; Saadabadi, Atefeh; Davood, Asghar

doi:10.3906/kim-1402-37

Cited by 23 publications

(15 citation statements)

References 13 publications

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“…The binding energy was indicative of the ligand's contribution and flexibility for the targeted protein. In terms of binding energy, the more negative the value of the standard free energy charge, the better the binding affinity of the ligand with the receptor, hence, the more stable the complex 20 . Therefore, the lowest binding energy scores represent the best protein-ligand binding stability compared to the highest energy score.…”

Section: Resultsmentioning

confidence: 99%

Inhibitory evaluation ofCurculigo latifoliaon α-glucosidase, DPP (IV) andin vitrostudies in antidiabetic with molecular docking relevance to type 2 diabetes mellitus

Zabidi

Ishak

Hamid

et al. 2020

Journal of Enzyme Inhibition and Medicinal Chemistry

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The inhibition of a-glucosidase and DPP enzymes capable of effectively reducing blood glucose level in the management of type 2 diabetes. The purpose of the present study is to evaluate the inhibitory potential of a-glucosidase and DPP (IV) activity including with the 2-NBDG uptake assay and insulin secretion activities through in vitro studies. The selected of active compounds obtained from the screening of compounds by LC-MS were docked with the targeted enzyme that involved in the mechanism of T2DM. From the results, root extracts displayed a better promising outcome in a-glucosidase (IC 50 2.72 ± 0.32) as compared with the fruit extracts (IC 50 3.87 ± 0.32). Besides, root extracts also displayed a better activity in the inhibition of DPP (IV), enhance insulin secretion and glucose uptake activity. Molecular docking results revealing that phlorizin binds strongly with a-glucosidase, DPP (IV) and Insulin receptor (IR) enzymes with achieving the lowest binding energy value. The present work suggests several of the compounds have the potential that contribute towards inhibiting a-glucosidase and DPP (IV) and thus effective in lowering post-prandial hyperglycaemia.

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Section: Resultsmentioning

confidence: 99%

Inhibitory evaluation ofCurculigo latifoliaon α-glucosidase, DPP (IV) andin vitrostudies in antidiabetic with molecular docking relevance to type 2 diabetes mellitus

Zabidi

Ishak

Hamid

et al. 2020

Journal of Enzyme Inhibition and Medicinal Chemistry

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“…Where ΔG is the docking energy, Rcal is 1.987 TK is 298.15 Docking energy is the summation of the ligand's internal energy and the intermolecular energy (30).…”

Section: Resultsmentioning

confidence: 99%

The Natural Ligand for Metalloproteinase-A Multifaceted Drug Target

Shivashankar

Sangeetha

2022

Appl Biochem Biotechnol

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Metalloproteinases are a group of proteinases that extensively depend on metals for their biological activity, i.e., digesting proteins. Their role in developmental stages is indispensable. However, the same enzyme is also found to be a crucial mediator of several diseases like cancer, atheroma, arthritis, atherosclerosis, aneurysms, nephritis, tissue ulcers, brosis, etc. Exogenous metalloproteinases cause severe pathological effects which may even lead to mortality in humans and other higher animals. The major source of exogenous metalloproteinases is through venomous snake bites, which causes exposure of normal tissue later blood vessels to the proteinases. Though the structure and function of metalloproteinases are highly conserved, the accidental exposure causes severe irreversible damages of the exposed tissues and blood vessels which otherwise is a highly regulated process with the endogenous metalloproteinases. Hence, nding a suitable metalloproteinases inhibitor is of great biological importance in mitigating pathological effects. Batimastat is an approved drug prescribed for cancer which mediates its action by inhibiting metalloproteinases. Batimastat is a synthetic hydroxamate molecule with a simple structure that prompted the search for the existence of similar phytochemicals in plants. Computational analysis revealed interaction of Andrographis paniculata phytochemicals with the M domain of snake venom metalloproteinase active site amino acid residues namely ASN203, ARG293, PHE203, LEU206, LYS199, and ALA122 similar to that of the reference compound batimastat. 14acetylandrographolide, 14-deoxy-11,12 didehydroandrographolide, Andrograpanin, Isoandrographolide, and 14-deoxy-11-oxoandrographolide found to show maximum effectiveness against the metalloproteinase. Results of the current study show a possibility of developing potent drug targeting metalloproteinases from plants source.According to WHO, India is home to nearly twenty-four medically important snake species. Of which Russell's viper is classi ed under Category 1 (Highest medical importance) "highly venomous snakes that are common or widespread and cause numerous snakebites, resulting in high levels of morbidity, disability or mortality" (6). In India, Russell's viper is one of the 'Big four' snakes causing the maximum number of deaths due to snakebite (7). Snakebite statistics from 2000-2019 reveal Russell's viper is mainly responsible for bite constituting43%, followed by 21% unknown species, 18% Krait, 12% cobra (8).Hence SVMP is seen as a promising target for treatment against adverse effects of snake venom. This would reduce the mortality rate among snake-bitten patients. In traditional medicine practice, the decoction of various plant parts are been used in several parts of Asia, Africa, Central, and South America for treating snake envenomation (9). Andrographis paniculata is a remarkable plant used for treating various human ailments namely anti-cancer, antidiabetic, antibacterial, antimalarial, antiviral, cardiovascular, and hepatic p...

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“…LGA specified as follows: a maximum number of 250,000 energy evaluations and a maximum number of 27,000 generations (Iman et al, 2015). Binding energy native ligand and ligand copy of receptor protein based on RMSD Value result after docking process with PyRx.…”

Section: Molecular Docking Analysismentioning

confidence: 99%

Identification of Phenols and Triterpenoids Compounds in Michelia champaca for Treating Covid 19 Symptom by in Silico

2021

Nusantara Science and Technology Proceedings

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Michelia champaca is used by the community to treat mild diseases in the population. The plant Michelia champaca produces anti-inflammatory compounds. Some anti-inflammatory classes of compounds include Phenols and Triterpenoids. In disease prevention and treatment mechanics, COVID 19 in particular, the ability of anti-inflammatory compounds is very significant. Coronaviruses are viruses that were first described in 2019 attack the human respiratory system. Cough, a runny nose, and shortness of breath for fever are typical signs of viral infection. In defense mechanisms from coronaviruses, ACE2 is one of the inflammatory mediators used by the body. This study aimed to determine the potential of each group of Phenols and Triterpenoids compounds in Michelia champaca in binding ACE2 in Silico. The method used is docking molecule to find out the potential of anti-inflammatory compound groups. The ligands used in the study were Taraxerol, Taraxeron, Ferulic Acid, and Galic Acid. The protein used in the study was ACE2. The results showed that docking molecules for the Phenols and Triterpenoids groups separately showed that native ligand ACE2 could not bind to ligand copies of the Phenols and Triterpenoids groups. However, there are similar amino acid residues in ligand copy of Gallic acid with NAG. Gallic acid is a compound of phenols. The conclusion of this analysis is the complete ability of treatments and disease prevention in the Michelia Champaca plant as a result of COVID 19. However, the mechanism of interaction of plant compounds with proteins that play a part in the COVID 19 mechanism must still be demonstrated in vitro and in vivo in this research.

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Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

Cited by 23 publications

References 13 publications

Inhibitory evaluation ofCurculigo latifoliaon α-glucosidase, DPP (IV) andin vitrostudies in antidiabetic with molecular docking relevance to type 2 diabetes mellitus

Inhibitory evaluation ofCurculigo latifoliaon α-glucosidase, DPP (IV) andin vitrostudies in antidiabetic with molecular docking relevance to type 2 diabetes mellitus

The Natural Ligand for Metalloproteinase-A Multifaceted Drug Target

Identification of Phenols and Triterpenoids Compounds in Michelia champaca for Treating Covid 19 Symptom by in Silico

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