Ensemble-based, high-throughput virtual screening of potential inhibitor targeting putative farnesol dehydrogenase of Metisa plana (Lepidoptera: Psychidae)

Zifruddin, Anis Nadyra; Yusoff, Mohamad Ariff Mohamad; Ghani, Nur Syatila Abd; Muhammad, Nor Azlan Nor; Lam, Kok Wai; Hassan, Mohd Rohaizat

doi:10.1016/j.compbiolchem.2023.107811

Cited by 4 publications

(2 citation statements)

References 59 publications

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“…The final predicted structure was selected based on the conformation having the lowest energy. A per-residue estimate of its confidence on a scale from 0 to 100 was measured using a scale called pLDDT, with a value >90 referring to high accuracy, and 70 or above expected to be modeled well ( Zifruddin et al, 2023 ). The structure was minimized using the OPLS3e force field in the software package Maestro ( van Zundert et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

Mashraqi,

Alzamami,

Alturki

et al. 2023

Front. Mol. Biosci.

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Kingella kingae is a Gram-negative bacterium that primarily causes pediatric infections such as septicemia, endocarditis, and osteoarticular infections. Its virulence is attributed to the outer membrane proteins having implications in bacterial adhesion, invasion, nutrition, and host tissue damage. TonB-dependent receptors (TBDRs) play an important role in nutrition and were previously implicated as vaccine targets in other bacteria. Therefore, we targeted the conserved β-barrel TBDR domain of these proteins for designing a vaccine construct that could elicit humoral and cellular immune responses. We used bioinformatic tools to mine TBDR-containing proteins from K. kingae ATCC 23330 and then predict B- and T-cell epitopes from their conserved β-barrel TDR domain. A chimeric vaccine construct was designed using three antigenic epitopes, covering >98% of the world population and capable of inciting humoral and adaptive immune responses. The final construct elicited a robust immune response. Docking and dynamics simulation showed good binding affinity of the vaccine construct to various receptors of the immune system. Additionally, the vaccine was predicted to be safe and non-allergenic, making it a promising candidate for further development. In conclusion, our study demonstrates the potential of immunoinformatics approaches in designing chimeric vaccines against K. kingae infections. The chimeric vaccine we designed can serve as a blueprint for future experimental studies to develop an effective vaccine against this pathogen, which can serve as a potential strategy to prevent K. kingae infections.

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Section: Methodsmentioning

confidence: 99%

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

Mashraqi,

Alzamami,

Alturki

et al. 2023

Front. Mol. Biosci.

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“…A biorational insecticide interferes with all activities involved in that location, making it more specific and safer than a conventional insecticide. The target is ideally a mosquito-specific protein to minimize toxicity to humans and other animals [19,40].…”

Section: Introductionmentioning

confidence: 99%

Exploring Natural Alkaloids from Brazilian Biodiversity as Potential Inhibitors of the Aedes aegypti Juvenile Hormone Enzyme: A Computational Approach for Vector Mosquito Control

Costa,

Rocha

et al. 2023

Molecules

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This study explores the potential inhibitory activity of alkaloids, a class of natural compounds isolated from Brazilian biodiversity, against the mJHBP enzyme of the Aedes aegypti mosquito. This mosquito is a significant vector of diseases such as dengue, zika, and chikungunya. The interactions between the ligands and the enzyme at the molecular level were evaluated using computational techniques such as molecular docking, molecular dynamics (MD), and molecular mechanics with generalized Born surface area (MMGBSA) free energy calculation. The findings suggest that these compounds exhibit a high binding affinity with the enzyme, as confirmed by the binding free energies obtained in the simulation. Furthermore, the specific enzyme residues that contribute the most to the stability of the complex with the compounds were identified: specifically, Tyr33, Trp53, Tyr64, and Tyr129. Notably, Tyr129 residues were previously identified as crucial in the enzyme inhibition process. This observation underscores the significance of the research findings and the potential of the evaluated compounds as natural insecticides against Aedes aegypti mosquitoes. These results could stimulate the development of new vector control agents that are more efficient and environmentally friendly.

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Integrating Computational Approaches from Non-synonymous Sequence Variations to Molecular Structure for Drug Repositioning Targeting the SARS-CoV-2 Spike Protein

Costa,

Guedes,

Fanticelli

et al. 2024

Computer-Aided Drug Discovery and Design

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Ensemble-based, high-throughput virtual screening of potential inhibitor targeting putative farnesol dehydrogenase of Metisa plana (Lepidoptera: Psychidae)

Cited by 4 publications

References 59 publications

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330

Exploring Natural Alkaloids from Brazilian Biodiversity as Potential Inhibitors of the Aedes aegypti Juvenile Hormone Enzyme: A Computational Approach for Vector Mosquito Control

Integrating Computational Approaches from Non-synonymous Sequence Variations to Molecular Structure for Drug Repositioning Targeting the SARS-CoV-2 Spike Protein

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