Dockey: a modern integrated tool for large-scale molecular docking and virtual screening

Du, Lianming; Geng, Chaoyue; Zeng, Qianglin; Huang, Ting; Tang, Jie; Chu, Yiwen; Zhao, Kelei

doi:10.1093/bib/bbad047

Cited by 16 publications

(6 citation statements)

References 51 publications

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“…Subsequently, we evaluated the structural disparities among the LasR mutant models to pinpoint unique features associated with each variant. Following model generation, we conducted molecular docking experiments with Dockey v0.8.2 (Du et al, 2023 ). Twenty docking runs were performed for each LasR mutant with self-inducing ligands to evaluate differences in binding free energies and interaction sites.…”

Section: Methodsmentioning

confidence: 99%

Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates

Yang,

Zeng,

Gou

et al. 2024

Front. Microbiol.

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Colonization of Pseudomonas aeruginosa in the lung environments frequently leads to the enrichment of strains displaying enhanced antibiotic resistance and reduced production of quorum-sensing (QS) controlled products. However, the relationship between the emergence of QS deficient variants and antibiotic resistance remains less understood. In this study, 67 P. aeruginosa strains were isolated from the lungs of 14 patients with chronic obstructive pulmonary disease, followed by determining their genetic relationship, QS-related phenotypes and resistance to commonly used antibiotics. The integrity of P. aeruginosa QS system was checked by DNA sequencing. The relationship between the QS system and antibiotic resistance was then assessed by correlation analyses. The function of the LasR protein and bacterial virulence were evaluated through homology modeling and nematode-infection assay. The influence of antibiotic on the development of extracellular protease production ability of P. aeruginosa was tested by an evolutionary experiment. The results showed that P. aeruginosa clinical strains displayed abundant diversity in phenotype and genotype. The production of extracellular proteases was significantly negatively correlated with antibiotic resistance. The strains with enhanced antibiotic resistance also showed a notable overlap with the mutation of lasR gene, which is the core regulatory gene of P. aeruginosa QS system. Molecular docking and Caenorhabditis elegans infection assays further suggested that P. aeruginosa with impaired LasR protein could also have varying pathogenicity. Moreover, in vitro evolution experiments demonstrated that antibiotic-mediated selective pressure, particularly from Levofloxacin contributed to the emergence of extracellular protease-negative strains. Therefore, this study provides evidence for the connection of P. aeruginosa QS system and antibiotic resistance, and holds significance for developing targeted strategies to address antibiotic resistance and improving the management of antibiotic-resistant infections in chronic respiratory diseases.

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Section: Methodsmentioning

confidence: 99%

Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates

Yang,

Zeng,

Gou

et al. 2024

Front. Microbiol.

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“…Molecular docking was performed by using AutoDock 4 and Dockey, following standard protocols (Du et al 2023 ). The crystal structure of LasR (PDB ID: 3IX3) and PqsR (PDB ID:6B8A) was downloaded from the RCSB PDB ( https://www.rcsb.org/ ).…”

Section: Methodsmentioning

confidence: 99%

Discovery of psoralen as a quorum sensing inhibitor suppresses Pseudomonas aeruginosa virulence

Wen,

Wu,

Yuan

et al. 2024

Appl Microbiol Biotechnol

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Pseudomonas aeruginosa is a common opportunistic pathogen with growing resistance and presents heightened treatment challenges. Quorum sensing (QS) is a cell-to-cell communication system that contributes to the production of a variety of virulence factors and is also related to biofilm formation of P. aeruginosa. Compared to traditional antibiotics which kill bacteria directly, the anti-virulence strategy by targeting QS is a promising strategy for combating pseudomonal infections. In this study, the QS inhibition potential of the compounds derived from the Traditional Chinese Medicines was evaluated by using in silico, in vitro, and in vivo analyses. The results showed that psoralen, a natural furocoumarin compound derived from Psoralea corylifolia L., was capable of simultaneously inhibiting the three main QS regulators, LasR, RhlR, and PqsR of P. aeruginosa. Psoralen had no bactericidal activity but could widely inhibit the production of extracellular proteases, pyocyanin, and biofilm, and the cell motilities of the model and clinical P. aeruginosa strains. RNA-sequencing and quantitative PCR analyses further demonstrated that a majority of QS-activated genes in P. aeruginosa were suppressed by psoralen. The supplementation of psoralen could protect Caenorhabditis elegans from P. aeruginosa challenge, especially for the hypervirulent strain PA14. Moreover, psoralen showed synergistic antibacterial effects with polymyxin B, levofloxacin, and kanamycin. In conclusions, this study identifies the anti-QS and antibiofilm effects of psoralen against P. aeruginosa strains and sheds light on the discovery of anti-pseudomonal drugs among Traditional Chinese Medicines. Key points • Psoralen derived from Psoralea corylifolia L. inhibits the virulence-related phenotypes of P. aeruginosa. • Psoralen simultaneously targets the three core regulators of P. aeruginosa QS system and inhibits the expression of a large part of downstream genes. • Psoralen protects C. elegans from P. aeruginosa challenge and enhances the susceptibility of P. aeruginosa to antibiotics.

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“…Available tools are Auto Dock, Dockey, Openeye, Mosoft, etc. ( 94 ). Gromacs and VMD are also used in molecular dynamics simulation ( 95 ).…”

Section: Development Of Computational Biology For Sars-cov-2 Inhibito...mentioning

confidence: 99%

Recent advances in the exploration and discovery of SARS-CoV-2 inhibitory peptides from edible animal proteins

Kong,

Wang,

Zhong

et al. 2024

Front. Nutr.

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The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), is spreading worldwide. Although the COVID-19 epidemic has passed its peak of transmission, the harm it has caused deserves our attention. Scientists are striving to develop medications that can effectively treat COVID-19 symptoms without causing any adverse reactions. SARS-CoV-2 inhibitory peptides derived from animal proteins have a wide range of functional activities in addition to safety. Identifying animal protein sources is crucial to obtaining SARS-CoV-2 inhibitory peptides from animal sources. This review aims to reveal the mechanisms of action of these peptides on SARS-CoV-2 and the possibility of animal proteins as a material source of SARS-CoV-2 inhibitory peptides. Also, it introduces the utilization of computer-aided design methods, phage display, and drug delivery strategies in the research on SARS-CoV-2 inhibitor peptides from animal proteins. In order to identify new antiviral peptides and boost their efficiency, we recommend investigating the interaction between SARS-CoV-2 inhibitory peptides from animal protein sources and non-structural proteins (Nsps) using a variety of technologies, including computer-aided drug approaches, phage display techniques, and drug delivery techniques. This article provides useful information for the development of novel anti-COVID-19 drugs.

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Dockey: a modern integrated tool for large-scale molecular docking and virtual screening

Cited by 16 publications

References 51 publications

Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates

Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates

Discovery of psoralen as a quorum sensing inhibitor suppresses Pseudomonas aeruginosa virulence

Recent advances in the exploration and discovery of SARS-CoV-2 inhibitory peptides from edible animal proteins

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