From phylogeny to protein dynamics: A computational hierarchical quest for potent drug identification against an emerging enteropathogen “Yersinia enterocolitica”

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii

Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.

Therapeutic target mapping from the genome of Kingella negevensis and biophysical inhibition assessment through PNP synthase binding with traditional medicinal compounds

Kingella negevensis belongs to the Neisseriaceae family. It is implied that it has significant virulence potential due to RTX toxin production, which can cause hemolysis. It usually colonizes the orophayrynx of pediatric population, along with Kingella kingae but has also been isolated from vagina. Todate no report on its drug targets is present, therefore putative therapeutic targets were identified from its genomic sequence data. Traditional Chinese (n > 36,000) and Indian medicinal compounds (n > 2000) were then screened against its pyridoxine 5'-phosphate synthase, a vital therapeutic target. Prioritized TCM compounds included ZINC02525131, ZINC33833737 and ZINC85486932, and Cadiyenol, 9,11,13-Octadecatrienoic acid and 6-Gingerol from Indian medicinal library. Molecular dynamics simulation of top compounds revealed ZINC02525131 as having best stability for 100 ns, compared to Cadiyenol. ADMET profiling was then done, along with physiologically based pharmacokinetic simulation of these compounds in a population of 200 individuals, for 12 h to see fate of the ingested compound. Additionally, the impact of these compounds in a population with cirrhosis and renal impairment was also simulated. We imply in light of all the studied parameters of safety and bioavailability, etc., that 6-Gingerol from Zingiber officinalis rhizome must be proceeded further for in vitro and in vivo testing for inhibition of K. negevensis.

The biochemical characteristics of viable but nonculturable state Yersinia enterocolitica induced by lactic acid stress and its presence in food systems

The viable but nonculturable (VBNC) state is adopted by many foodborne pathogenic bacteria to survive in adverse conditions. This study found that lactic acid, a widely used food preservative, can induce Yersinia enterocolitica to enter a VBNC state. Y. enterocolitica treated with 2 mg/mL lactic acid completely lost culturability within 20 min, and 10.137 ± 1.693 % of the cells entered a VBNC state. VBNC state cells could be recovered (resuscitated) in tryptic soy broth (TSB), 5 % (v/v) Tween80-TSB, and 2 mg/mL sodium pyruvate-TSB. In the VBNC state of Y. enterocolitica induced by lactic acid, the intracellular adenosine triphosphate (ATP) concentration and various enzyme activities were decreased, and the reactive oxygen species (ROS) level was elevated, compared with uninduced cells. The VBNC state cells were significantly more resistant to heat and simulated gastric fluid than uninduced cells, but their ability to survive in a high-osmotic-pressure environment was significantly less than that of uninduced cells. The VBNC state cells induced by lactic acid changed from long rod-like to short rod-like, with small vacuoles at the cell edges; the genetic material was loosened and the density of cytoplasm was increased. The VBNC state cells had decreased ability to adhere to and invade Caco-2 (human colorectal adenocarcinoma) cells. The transcription levels of genes related to adhesion, invasion, motility, and resistance to adverse environmental stress were downregulated in VBNC state cells relative to uninduced cells. In meat-based broth, all nine tested strains of Y. enterocolitica entered the VBNC state after lactic acid treatment; among these strains, only VBNC state cells of Y. enterocolitica CMCC 52207 and Isolate 36 could not be recovered. Therefore, this study is a wake-up call for food safety problems caused by VBNC state pathogens induced by lactic acid.

Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach

Aurora kinase B plays an important role in the cell cycle to orchestrate the mitotic process. The amplification and overexpression of this kinase have been implicated in several human malignancies. Therefore, Aurora kinase B is a potential drug target for anticancer therapies. Here, we combine atom-based 3D-QSAR analysis and pharmacophore model generation to identify the principal structural features of acylureidoindolin derivatives that could potentially be responsible for the inhibition of Aurora kinase B. The selected CoMFA and CoMSIA model showed significant results with cross-validation values (q²) of 0.68, 0.641 and linear regression values (r²) of 0.971, 0.933 respectively. These values support the statistical reliability of our model. A pharmacophore model was also generated, incorporating features of reported crystal complex structures of Aurora kinase B. The pharmacophore model was used to screen commercial databases to retrieve potential lead candidates. The resulting hits were analyzed at each stage for diversity based on the pharmacophore model, followed by molecular docking and filtering based on their interaction with active site residues and 3D-QSAR predictions. Subsequently, MD simulations and binding free energy calculations were performed to test the predictions and to characterize interactions at the molecular level. The results suggested that the identified compounds retained the interactions with binding residues. Binding energy decomposition identified residues Glu155, Trp156 and Ala157 of site B and Leu83 and Leu207 of site C as major contributors to binding affinity, complementary to 3D-QSAR results. To best of our knowledge, this is the first comparison of WaterSwap field and 3D-QSAR maps. Overall, this integrated strategy provides a basis for the development of new and potential AK-B inhibitors and is applicable to other protein targets.

Mining the Proteome of Streptococcus mutans for Putative Drug Targets

BACKGROUND

Dental caries is the most common and one of the prevalent diseases in the world. Streptococcus mutans is one of the major oral pathogens that cause dental caries by forming a biofilm on dental tissues, degrading dental enamel and consequent cavitation in the tissue. In vitro selection of drug targets is a laborious and expensive process and therefore, computational methods are preferable for target identification at the initial stage.

OBJECTIVE

The present research aims to find new drug targets in S. mutans by using subtractive proteomics analysis, which implements various bioinformatics tools and databases.

METHODS

The proteome of S. mutans UA159 was mined for novel drug targets using computational tools and databases such as: CD-HIT, BLASTP, DEG, KAAS and CELL2GO.

RESULTS

Out of 1953 proteins of S. mutans UA159, proteins that are redundant, homologous to human and non-essential to the pathogen were eliminated. Around 178 proteins already available in drug target repositories were also eliminated. Possible functions and subcellular localization of 32 uncharacterized proteins were predicted. Substantially, 13 proteins were identified as novel drug targets in S. mutans UA159 that can be targeted by various drugs against dental caries.

CONCLUSION

This study will effectuate the development of novel therapeutic agents against dental caries and other Streptococcal infections.

Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors

The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.

A comprehensive review on the prevalence, pathogenesis and detection ofYersinia enterocolitica

Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat. “Yersiniosis” is caused by a pathogen named Yersinia enterocolitica and is characterized by diarrheal, ileitis, and mesenteric lymphadenitis types of sicknesses. This neglected pathogen starts its pathogenic activity by colonizing inside the intestinal tract of the host upon the ingestion of contaminated food. Y. enterocolitica remains a challenge for researchers and food handlers due to its growth habits, low concentrations in samples, morphological similarities with other bacteria and lack of rapid, cost-effective, and accurate detection methods. In this review, we presented recent information about its prevalence, biology, pathogenesis, and existing cultural, immunological, and molecular detection approaches. Our ultimate goal is to provide updated knowledge regarding this pathogen for the development of quick, effective, automated, and sensitive detection methods for the systematic detection of Y. enterocolitica.

Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat.