Molecular dynamic simulation of hydroxymethylglutaryl-coa reductase inhibitors from gnetum gnemon l. Seed extract

Yuditya Artha, Arif Arrahman, Azminah, Arry Yanuar

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Objective: Gnetum gnemon L. (melinjo) seed extract contained trans-resveratrol which has been shown to inhibit hydroxymethylglutaryl-CoA (HMG-CoA) reductase. Therefore it has a potent activity for lowering blood cholesterol. This study was carried out to determine the molecular dynamics simulation of HMG-CoA reductase inhibitors from Gnetum gnemon L. seed extract. Methods: Molecular dynamics simulation using AMBER was used. The simulation was set at 300 K as default temperature and 310 K, average human body temperature. The main parameters of this study were ligand-residue interaction, binding affinity, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonds analysis, molecular mechanics Poisson Boltzmann surface area (MMPBSA), and molecular mechanics generalized born surface area (MMGBSA). Results: In the simulation study, trans-resveratrol, trans-piceid, gnemonol M, gnemonoside B, viniferin and gnetin C had shown lower energy than HMG (PDB ID: MAH), the substrate of HMG-CoA Reductase. Free energy binding obtained from simulation was between 11.1 to -31.38 kcal/mol. Conclusion: The simulation at 310 K was preferable than 300 K as more interactions were performed and higher affinity was obtained.

Original languageEnglish
Pages (from-to)793-797
Number of pages5
JournalPharmacognosy Journal
Volume10
Issue number4
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

Gnetum
Hydroxymethylglutaryl CoA Reductases
Molecular Dynamics Simulation
Mechanics
Seeds
Oxidoreductases
Hydroxymethylglutaryl-CoA Reductase Inhibitors
Body Temperature
Human Body
Hydrogen
Cholesterol
Ligands
Temperature
resveratrol

Keywords

  • Gnetum gnemon L
  • Hydroxymethylglutaryl-CoA reductase inhibitor
  • Molecular dynamics
  • Trans-resveratrol

Cite this

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title = "Molecular dynamic simulation of hydroxymethylglutaryl-coa reductase inhibitors from gnetum gnemon l. Seed extract",
abstract = "Objective: Gnetum gnemon L. (melinjo) seed extract contained trans-resveratrol which has been shown to inhibit hydroxymethylglutaryl-CoA (HMG-CoA) reductase. Therefore it has a potent activity for lowering blood cholesterol. This study was carried out to determine the molecular dynamics simulation of HMG-CoA reductase inhibitors from Gnetum gnemon L. seed extract. Methods: Molecular dynamics simulation using AMBER was used. The simulation was set at 300 K as default temperature and 310 K, average human body temperature. The main parameters of this study were ligand-residue interaction, binding affinity, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonds analysis, molecular mechanics Poisson Boltzmann surface area (MMPBSA), and molecular mechanics generalized born surface area (MMGBSA). Results: In the simulation study, trans-resveratrol, trans-piceid, gnemonol M, gnemonoside B, viniferin and gnetin C had shown lower energy than HMG (PDB ID: MAH), the substrate of HMG-CoA Reductase. Free energy binding obtained from simulation was between 11.1 to -31.38 kcal/mol. Conclusion: The simulation at 310 K was preferable than 300 K as more interactions were performed and higher affinity was obtained.",
keywords = "Gnetum gnemon L, Hydroxymethylglutaryl-CoA reductase inhibitor, Molecular dynamics, Trans-resveratrol",
author = "Yuditya Artha and Arif Arrahman and Azminah and Arry Yanuar",
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Molecular dynamic simulation of hydroxymethylglutaryl-coa reductase inhibitors from gnetum gnemon l. Seed extract. / Artha, Yuditya; Arrahman, Arif; Azminah; Yanuar, Arry.

In: Pharmacognosy Journal, Vol. 10, No. 4, 01.01.2018, p. 793-797.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

T1 - Molecular dynamic simulation of hydroxymethylglutaryl-coa reductase inhibitors from gnetum gnemon l. Seed extract

AU - Artha, Yuditya

AU - Arrahman, Arif

AU - Azminah,

AU - Yanuar, Arry

PY - 2018/1/1

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N2 - Objective: Gnetum gnemon L. (melinjo) seed extract contained trans-resveratrol which has been shown to inhibit hydroxymethylglutaryl-CoA (HMG-CoA) reductase. Therefore it has a potent activity for lowering blood cholesterol. This study was carried out to determine the molecular dynamics simulation of HMG-CoA reductase inhibitors from Gnetum gnemon L. seed extract. Methods: Molecular dynamics simulation using AMBER was used. The simulation was set at 300 K as default temperature and 310 K, average human body temperature. The main parameters of this study were ligand-residue interaction, binding affinity, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonds analysis, molecular mechanics Poisson Boltzmann surface area (MMPBSA), and molecular mechanics generalized born surface area (MMGBSA). Results: In the simulation study, trans-resveratrol, trans-piceid, gnemonol M, gnemonoside B, viniferin and gnetin C had shown lower energy than HMG (PDB ID: MAH), the substrate of HMG-CoA Reductase. Free energy binding obtained from simulation was between 11.1 to -31.38 kcal/mol. Conclusion: The simulation at 310 K was preferable than 300 K as more interactions were performed and higher affinity was obtained.

AB - Objective: Gnetum gnemon L. (melinjo) seed extract contained trans-resveratrol which has been shown to inhibit hydroxymethylglutaryl-CoA (HMG-CoA) reductase. Therefore it has a potent activity for lowering blood cholesterol. This study was carried out to determine the molecular dynamics simulation of HMG-CoA reductase inhibitors from Gnetum gnemon L. seed extract. Methods: Molecular dynamics simulation using AMBER was used. The simulation was set at 300 K as default temperature and 310 K, average human body temperature. The main parameters of this study were ligand-residue interaction, binding affinity, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonds analysis, molecular mechanics Poisson Boltzmann surface area (MMPBSA), and molecular mechanics generalized born surface area (MMGBSA). Results: In the simulation study, trans-resveratrol, trans-piceid, gnemonol M, gnemonoside B, viniferin and gnetin C had shown lower energy than HMG (PDB ID: MAH), the substrate of HMG-CoA Reductase. Free energy binding obtained from simulation was between 11.1 to -31.38 kcal/mol. Conclusion: The simulation at 310 K was preferable than 300 K as more interactions were performed and higher affinity was obtained.

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