Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein

Fu, Yi; Zhao, Junming; Chen, Zhiguo

doi:10.1155/2018/3502514

Cited by 141 publications

(77 citation statements)

References 34 publications

(35 reference statements)

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“…The number of hydrogen bonds were calculated because this is another significant element influencing protein stabilization. The higher number of hydrogen bonds represents the higher stability of ligands with the proteins (Fu et al, 2018). In this study, the epitope YGIFAITAL showed maximum number of hydrogen bonds with both HLA proteins, which depicts the better binding ability of YGIFAITAL epitope.…”

Section: Discussionmentioning

confidence: 49%

“…We performed MD simulation calculation RMSD to observe the stability of the epitope-HLA complex. The higher RMSD value represents the higher flexibility of HLA-epitope binding (Dash et al, 2017;Fu, Zhao, & Chen, 2018). In case of bonding with HLA-C*03:03, YGIFAITAL was much more stable compared to KVLYGIFAI-HLA-C*03:03 throughout the simulations.…”

Section: Discussionmentioning

confidence: 97%

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In Silico Epitope-Based Peptide Vaccine Design against Invasive Non Typhoidal <em>Salmonella </em>(iNTS) Through Immunoinformatic Approaches

Ali¹,

Jahan²,

Khatun³

et al. 2020

Preprint

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Salmonella, especially invasive non-typhoidal Salmonella (iNTS) are responsible for developing various invasive diseases, and possess higher mortality rate, due to their higher antibiotic resistance profile than the other bacteria. Therefore, the present study was concerned to develop epitope based peptide vaccine against iNTS species as a successive and substitute protective measures. The study considered comprehensive Immunoinformatic approaches, followed by molecular docking and molecular dynamics simulation to predict the efficient vaccine candidate T cell and B cell epitopes, based on the outer membrane proteins. The study identified two best epitopes YGIFAITAL and KVLYGIFAI from total iNTS outer membrane proteins, which showed higher immunity, non-allergenicity, non-toxicity and also showed higher conservancy and population coverage values. Both epitopes showed higher binding affinity and stability towards HLA-C* 03:03. The MM-PBSA binding free energy showed the YGIFAITAL epitope binds more tightly with both MHC-I and MHC-II molecules. The total contact, H-bond analysis and RMSF results also validate the efficiency of these epitopes as vaccine candidate. The projected B cell epitopes AAPVQVGEAAGS, TGGGDGSNT and TGGGDGSNTGTTTT showed higher antigenicity. Overall, the study concluded that these epitopes can be considered as the potential vaccine candidate to make a successive vaccine against iNTS species. However, this result further needs to be validate by wet lab research to make successive vaccine with these projected epitopes.

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Section: Discussionmentioning

confidence: 49%

Section: Discussionmentioning

confidence: 97%

In Silico Epitope-Based Peptide Vaccine Design against Invasive Non Typhoidal <em>Salmonella </em>(iNTS) Through Immunoinformatic Approaches

Ali¹,

Jahan²,

Khatun³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In immunoinformatics, one crucial use of molecular docking is the simulation of binding between T lymphocyte epitopes and their respective MHC molecules [197][198][199]. The binding affinity between a receptor and its ligand can be defined by the energy released during spontaneous bond formation between the two and the lower the energy, the more tightly bound the receptor is to its ligand [200,201]. Our selected 7 T lymphocyte epitopes had 32 corresponding MHC alleles ( Table 2).…”

Section: Discussionmentioning

confidence: 99%

Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach

Ahammad

Lira

2020

International Journal of Biological Macromolecules

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SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine against the virus is paramount. This study resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. Various immunoinformatics tools were utilized to predict T and B lymphocyte epitopes. The epitopes were channeled through a filtering pipeline comprised of antigenicity, toxicity, allergenicity, and cytokine inducibility evaluation with the goal of selecting epitopes capable of generating both T and B cell-mediated immune responses. Molecular docking simulation between the epitopes and their corresponding MHC molecules was carried out. 13 epitopes, a highly immunogenic adjuvant, elements for proper sub-cellular trafficking, a secretion booster, and appropriate linkers were combined for constructing the vaccine. The vaccine was found to be antigenic, almost neutral at physiological pH, non-toxic, non-allergenic, capable of generating a robust immune response and had a decent worldwide population coverage. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.

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“…The molecular docking simulation is a study that conjures the orientation of ligand in the receptor (enzyme or protein) [18].…”

Section: Molecular Docking Simulations Of Ligandmentioning

confidence: 99%

Discovery of GPX4 inhibitor by molecular docking simulation as a potential ferroptosis inducer

Fatonah

Tambunan²,

Pamungkas

et al. 2020

Biointerface Res Appl Chem

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As one of the most complex diseases in the world, cancer continues as one of the significant public health problems. It was recorded by 2014 that cancer caused 1,551,000 death in Indonesia. One type of programmed cell death (PCD) that played a role in cancer cell treatment is Ferroptosis. Ferroptosis is PCD on iron and characterized by the inactivation of glutathione-dependent peroxidase (GPx4). In this research, a new therapeutic strategy for cancer was developed through the computational approach on synthetic compounds to discover its potential as an inhibitor of GPx4. About 688 compounds derivative from mercaptosuccinic acid acquired from the Zinc15 database. These compounds screened through the Lipinski’s Rule of Three and pharmacological prediction to eliminate ligands with undesired molecular properties. After that, the ligands underwent both rigid and flexible molecular docking simulations to predict their inhibition activity toward GPx4. From molecular docking simulation, (2S)-2-[(Z)-3-phenylprop-2-enyl]sulfanylbutanedioic acid show favorable characteristics as a drug candidate.

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Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein

Cited by 141 publications

References 34 publications

In Silico Epitope-Based Peptide Vaccine Design against Invasive Non Typhoidal <em>Salmonella </em>(iNTS) Through Immunoinformatic Approaches

In Silico Epitope-Based Peptide Vaccine Design against Invasive Non Typhoidal <em>Salmonella </em>(iNTS) Through Immunoinformatic Approaches

Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach

Discovery of GPX4 inhibitor by molecular docking simulation as a potential ferroptosis inducer

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