In-Silico Prediction and Modeling of the Quorum Sensing LuxS Protein and Inhibition of AI-2 Biosynthesis in Aeromonas hydrophila

Abstract

luxS is conserved in several bacterial species, including A. hydrophila, which causes infections in prawn, fish, and shrimp, and is consequently a great risk to the aquaculture industry and public health. luxS plays a critical role in the biosynthesis of the autoinducer-2 (AI-2), which performs wide-ranging functions in bacterial communication, and especially in quorum sensing (QS). The prediction of a 3D structure of the QS-associated LuxS protein is thus essential to better understand and control A. hydrophila pathogenecity. Here, we predicted the structure of A. hydrophila LuxS and characterized it structurally and functionally with in silico methods. The predicted structure of LuxS provides a framework to develop more complete structural and functional insights and will aid the mitigation of A. hydrophila infection, and the development of novel drugs to control infections. In addition to modeling, the suitable inhibitor was identified by high through put screening (HTS) against drug like subset of ZINC database and inhibitor ((−)-Dimethyl 2,3-O-isopropylidene-l-tartrate) molecule was selected based on the best drug score. Molecular docking studies were performed to find out the best binding affinity between LuxS homologous or predicted model of LuxS protein for the ligand selection. Remarkably, this inhibitor molecule establishes agreeable interfaces with amino acid residues LYS 23, VAL 35, ILE76, and SER 90, which are found to play an essential role in inhibition mechanism. These predictions were suggesting that the proposed inhibitor molecule may be considered as drug candidates against AI-2 biosynthesis of A. hydrophila. Therefore, (−)-Dimethyl 2,3-O-isopropylidene-l-tartrate inhibitor molecule was studied to confirm its potency of AI-2 biosynthesis inhibition. The results shows that the inhibitor molecule had a better efficacy in AI-2 inhibition at 40 μM concentration, which was further validated using Western blotting at a protein expression level. The AI-2 bioluminescence assay showed that the decreased amount of AI-2 biosynthesis and downregulation of LuxS protein play an important role in the AI-2 inhibition. Lastly, these experiments were conducted with the supplementation of antibiotics via cocktail therapy of AI-2 inhibitor plus OXY antibiotics, in order to determine the possibility of novel cocktail drug treatments of A. hydrophila infection.

LuxS/AI-2 Quorum Sensing System in Edwardsiella piscicida Promotes Biofilm Formation and Pathogenicity

“…These results suggested that the luxS gene promoted AI-2 production and that the luxS gene deletion led to an inability to synthesize AI-2. A LuxS/AI-2 system was reported to exist in C. jejuni, Aeromonas hydrophila (A. hydrophila), E. coli, Actinobacillus pleuropneumoniae (A. pleuropneumoniae), Lactobacillus paraplantarum, A. actinomycetemcomitans, S. pneumoniae, and H. parasuis, etc., and LuxS inactivation affected the growth and/or virulence of the above-mentioned strains (2,3,8,18,21,22,25,26).…”

“…These results suggested that the luxS gene could enhance the biofilm formation ability and that the product of the luxS gene could secrete outside the cell and could enhance biofilm formation ability, too. A similar study reported that inhibition of luxS gene expression could inhibit biofilm in E. coli and A. hydrophila (25,37). It is well known that bacterial biofilms increase cell survival through the improved defense of the immune system, increased availability of nutrients, resistance to antibiotics, and better opportunities for cellular communication and transfer of genetic material.…”

Evaluation of gene expression and protein structural modeling involved in persister cell formation in Salmonella Typhimurium

“…In a study by Mohammadzadeh et al, after protein modeling of three TA systems and prediction their interaction in Listeria monocytogenes, they designed in silico-derived peptides to inhibit TA systems and the proteins involved in formation persister cells [17]. In another study, considering the importance of LuxS protein in the biosynthesis of autoinducer-2, which plays a significant role in bacterial communication and in particular in the induction of quorum sensing, in silico prediction and modeling of the LuxS in Aeromonas hydrophila was performed and then, the suitable inhibitor for inhibition of AI-2 was identified [39]. These studies provide new knowledge for developing novel therapeutic strategies against bacterial infections.…”

In silico Selection and Experimental Validation of FDA-Approved Drugs as Anti-quorum Sensing Agents

“…Most pqs-inhibitors have been identified via costly and timeconsuming biosensor-based screenings or via the rational design and experimental validation of AQ analogs or precursors based on the structure of PqsR and of AQ biosynthetic enzymes. Virtual screenings could reduce the time and costs associated to conventional drug discovery programs, hence in silico techniques have been extensively applied for the identification of molecules hampering the las QS system of P. aeruginosa (Yang et al, 2009;Skovstrup et al, 2013;Tan et al, 2013;Soheili et al, 2015;Gökalsın et al, 2017;Kalia et al, 2017;Xu et al, 2017) or QS systems in other bacteria (Zhu et al, 2012;Ali et al, 2018;Ding et al, 2018Ding et al, , 2019Medarametla et al, 2018). To the best of our knowledge, only synthetic quinoline-based molecules have so far been identified as PqsR antagonists by means of in silico docking analyses (Soukarieh et al, 2018a).…”