Treatment of Hydrogen Bonds in Protein Simulations

Gao, Ya; Ye, Mei; Zhang, John Z. H.

doi:10.5772/61049

Cited by 12 publications

(6 citation statements)

References 44 publications

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“…Hydrogen bonds and their relative strength in a water environment are necessary to enhance the protein–ligand binding . According to the study of Gao et al, a hydrogen bond forms when an electronegative atom in a H-bond acceptor nears to a hydrogen atom bonded to another electronegative atom in a H-bond donor . The results obtained could be used to explain the phenomenon in the above sections where the lipase’s catalytic activity was higher in the solvents with high log P .…”

Section: Resultsmentioning

confidence: 99%

Kinetics and Mechanism of Solvent Influence on the Lipase-Catalyzed 1,3-Diolein Synthesis

et al. 2020

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1,3-Diacylglycerol preparation has roused increasing attention in recent years as the 1,3-diacylglycerol-rich oils can suppress the deposition of visceral fat and prevent the body weight increasing. Lipozyme TL IM-mediated esterification of oleic acid with monoolein was effective for 1,3-diacylglycerol production. During the esterification process, the solvent shows obvious influence on the diolein synthesis as well as the 1,3-diolein production. This work investigated the related kinetics and mechanism of the solvent effect on the esterification and Lipozyme TL IM performance. The results indicated that both the esterification rate constant and the acyl migration rate constant positively correlated with the log P of the solvent, while the site specificity of lipase has negative correlation with solvent log P . The acylation toward the 2-position of 1-monoolein was more sensitive to the solvent log P compared to the 1-position of glycerides. Molecular dynamics simulation revealed that solvents with different log P influenced the structure of Lipozyme TL IM including RMSD, hydrogen bond, and radial distribution function to a large extent, which subsequently led to the catalytic activity and selectivity variation of the lipase.

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Section: Resultsmentioning

confidence: 99%

Kinetics and Mechanism of Solvent Influence on the Lipase-Catalyzed 1,3-Diolein Synthesis

et al. 2020

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“…The binding complex of isorhamnetin as observed in uPA involves H-bond interaction with the key residue of Ser190 with a distance of 2.43 Å (strong hydrogen bond). In the formation of a hydrogen bond, the distance between the H and the acceptor (A) atoms must be smaller compared to the sum of their corresponding van der Waals radii [39]. The binding conformations of the final snapshot of rhamnetin, quercetin, kaempferol, and doxorubicin in the MD simulation revealed different H-bond interactions from the docking results (Figure 6).…”

Section: Hydrogen Bond Interactionmentioning

confidence: 92%

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Tjahjono

Sari

Ibrahim

2022

J. Math. Fund. Sci.

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The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin.

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“…They play an indispensable role in the stabilization of the original structure of proteins. Therefore, it is essential to explain the thermodynamic properties of inter/intraprotein hydrogen bonds (Gao, Mei, & Zhang, 2015). Based on the results obtained on RMSD, RMSF, hydrogen bond occupancy, and binding energy of MM/PBSA, we assume that the 3CL-Pro complex is the most stable complex among other complexes.…”

Section: Mm/pbsa (Molecular Mechanics Energies With the Poisson-boltzmann Surface Area Method)mentioning

confidence: 99%

Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates

Awaluddin¹,

Batubara²,

Wahyudi³

2021

Valensi

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.

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Treatment of Hydrogen Bonds in Protein Simulations

Cited by 12 publications

References 44 publications

Kinetics and Mechanism of Solvent Influence on the Lipase-Catalyzed 1,3-Diolein Synthesis

Kinetics and Mechanism of Solvent Influence on the Lipase-Catalyzed 1,3-Diolein Synthesis

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates

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