Structure‐Based Virtual Screening of LsrK Kinase Inhibitors to Target Quorum Sensing

Medarametla, Prasanthi; Gatta, Viviana; Kajander, Tommi; Laitinen, Tuomo; Tammela, Päivi; Poso, Antti

doi:10.1002/cmdc.201800548

Cited by 17 publications

(29 citation statements)

References 24 publications

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“…Accordingly, we further explored the 1,3,5-trisubstituted pyrazole series (series E), applying our synthetic protocol which permits an easy access to molecular diversity at three different diversification points, as outlined in All the prepared 1,3,5-trisubstituted pyrazoles-Het-DPD were assayed for inhibitory activity against LsrK at 200 µM concentration, according to the protocol previously described. 54 The obtained results confirmed that the presence of the dioxolane ring at position 5 of the pyrazole moiety is essential for the binding to LsrK and that acetals derivatives have a better profile respect to the corresponding diols.…”

Section: Structure-activity Relationship (Sar) Studies Of Pyrazole-cosupporting

confidence: 68%

DPD-Inspired Discovery of Novel LsrK Kinase Inhibitors: An Opportunity To Fight Antimicrobial Resistance

et al. 2019

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Antibiotic resistance is posing a continuous threat to global public health and represents a huge burden for society as a whole. In the last decade, the interference with bacterial Quorum Sensing (QS) (i.e., cell-cell communication) mechanisms has extensively been investigated as a valid therapeutic approach in the pursuit of a next generation of antimicrobials. (S)-4,5-dihydroxy-2,3pentanedione, commonly known as (S)-DPD, a small signaling molecule that modulates QS in both Gram-negative and Gram-positive bacteria, is phosphorylated by LsrK and the resulting phospho-DPD activates QS. We designed and prepared a small library of DPD derivatives, characterized by five different scaffolds and evaluated their LsrK inhibition in the context of QS interference. SAR studies highlighted the pyrazole moiety as an essential structural element for LsrK inhibition. Particularly, four compounds were found to be micromolar LsrK inhibitors (IC50 ranging between 100 µM and 500 µM) encouraging further exploration of novel analogues as potential new antimicrobials. imination reagent and then deprotected (Scheme 1). Briefly, alkyne 1 was dissolved in DMF and then Pd(OAc)2, PPh3, KOAc and the appropriate o-bromoaldehyde were added. The reaction mixtures were irradiated at 80 °C for 1-2 hours, ammonium acetate was added and the resulting mixtures were irradiated again at 150 °C, thus affording the desired protected products 3a-g (Scheme 1). Heteroaromatic o-bromoaldehydes (i.e., 3-bromofuran-2-carbaldehyde 2e, 3-bromothiophene-2carbaldehyde 2f and 5-bromo-2-methyl-4-thiazolecarboxaldehyde 2g) led to isolation of the corresponding furopyridine, thienopyridine and thiazolopyridine derivatives 3e-f. Final acidic treatment yielded the monosubstituted annulated pyridines-Het-DPD derivatives 4a-g (Scheme 1). Scheme 1: Synthesis of monosubstituted annulated pyridines-Het-DPD derivatives 4a-g. Reagents and conditions: (a) 2a-g (0.9 eq), Pd(OAc)2 (1.8% mol), PPh3 (3.6% mol), KOAc (1.8 eq), DMF, mw, 80 °C, 1h-2h; (a') NH4OAc (1.8 eq), MW, 150 °C, 2h-3h; (b) 12M HCl (cat.), 1,4-dioxane, 0 °C to rt, 1h-3h Sonogashira coupling 43 of terminal alkyne 1 with acyl chlorides, followed by addition of amidinium salts to the corresponding ynones and final acidic removal of the acetal protecting group provided rapid access to 2,4,6-trisubstituted pyrimidines-Het-DPD derivatives (Figure 2, series B). Benzoyl chloride 5a was selected to screen three different conditions for the synthesis of ynone 6a. Surprisingly, copper-, ligand-and solvent-free acylation 51 as well as the use of a mixture of PdCl2(CH3CN)2, Sphos and Cs2CO3 26 did not furnish the desired product. Good results were obtained with the copper-and palladium-catalyzed system proposed by Karpov et al. 50 which allowed us to obtain compound 6a with a yield of 87%. 52 Three different ynones (6a-c) were reacted with six different amidinium salts and the resulting products 7a-f treated under acidic conditions (i.e., Scheme 2, conditions c) to afford the 2,4,6trisubstituted pyrimidines-Het-DPD derivat...

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Section: Structure-activity Relationship (Sar) Studies Of Pyrazole-cosupporting

confidence: 68%

DPD-Inspired Discovery of Novel LsrK Kinase Inhibitors: An Opportunity To Fight Antimicrobial Resistance

et al. 2019

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“…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).…”

Section: Discussionmentioning

confidence: 99%

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

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The emergence of antibiotic resistant bacterial pathogens is increasing at an unprecedented pace, calling for the development of new therapeutic options. Small molecules interfering with virulence processes rather than growth hold promise as an alternative to conventional antibiotics. Anti-virulence agents are expected to decrease bacterial virulence and to pose reduced selective pressure for the emergence of resistance. In the opportunistic pathogen Pseudomonas aeruginosa the expression of key virulence traits is controlled by quorum sensing (QS), an intercellular communication process that coordinates gene expression at the population level. Hence, QS inhibitors represent promising anti-virulence agents against P. aeruginosa. Virtual screenings allow fast and cost-effective selection of target ligands among vast libraries of molecules, thus accelerating the time and limiting the cost of conventional drug-discovery processes, while the drug-repurposing approach is based on the identification of off-target activity of FDA-approved drugs, likely endowed with low cytotoxicity and favorable pharmacological properties. This study aims at combining the advantages of virtual screening and drug-repurposing approaches to identify new QS inhibitors targeting the pqs QS system of P. aeruginosa. An in silico library of 1,467 FDA-approved drugs has been screened by molecular docking, and 5 hits showing the highest predicted binding affinity for the pqs QS receptor PqsR (also known as MvfR) have been selected. In vitro experiments have been performed by engineering ad hoc biosensor strains, which were used to verify the ability of hit compounds to decrease PqsR activity in P. aeruginosa. Phenotypic analyses confirmed the impact of the most promising hit, the antipsychotic drug pimozide, on the expression of P. aeruginosa PqsR-controlled virulence traits. Overall, this study highlights the potential of virtual screening campaigns of FDA-approved drugs to rapidly select new inhibitors of important bacterial functions.

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“…Thus, homology models were further used to identify LsrK inhibitors using structure-based virtual screening. The detailed procedures of the homology modelling, virtual screening and experimental bioassays can be found in our previous paper 17 .…”

Section: Cs (Atp Hez) Cs (Apo) Cs (Adp) Open Model Closed Model C) Dmentioning

confidence: 99%

“…LsrK phosphorylates the AI-2 precursor, DPD (4,5dihydroxy-2,3-Pentanedione) and thus regulates the AI-2 signalling and QS process. Implying the role of LsrK in QS signalling and virulence regulation, we explored LsrK to identify anti-virulence agents by employing the homology modelling and virtual screening approaches 17 . Recently, LsrK crystal structure (E. coli) was published by Ha JH et al with a phosphocarrier protein, HPr.…”

Section: Introductionmentioning

confidence: 99%

Structural characterization of LsrK to target quorum sensing and comparison between X-ray and homology model

Medarametla

Laitinen

Poso

2020

Preprint

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Quorum sensing is being investigated as an alternative therapeutic strategy in antibacterial drug discovery to combat bacterial resistance. LsrK is an autoinducer-2 kinase, playing a key role in the phosphorylation of autoinducer-2 (AI-2) signalling molecules involved in quorum sensing. Inhibiting LsrK could result in reduced pathogenicity by interfering with the quorum sensing signalling. Previously, we have generated homology models to identify LsrK inhibitors using structure-based virtual screening and successfully found the first class of LsrK inhibitors. While conducting these studies, the crystal structure of LsrK was released providing us an opportunity to inspect the reliability and quality of our models. Structural analysis of crystal structure and homology models revealed the consistencies of constructed models with crystal structure in the structural fold and binding site. Further, binding characteristics and conformational changes are investigated using molecular dynamics. These simulations provided us insights into the protein function and flexibility that need to be considered during the structure-based drug design studies targeting LsrK.

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Structure‐Based Virtual Screening of LsrK Kinase Inhibitors to Target Quorum Sensing

Cited by 17 publications

References 24 publications

DPD-Inspired Discovery of Novel LsrK Kinase Inhibitors: An Opportunity To Fight Antimicrobial Resistance

DPD-Inspired Discovery of Novel LsrK Kinase Inhibitors: An Opportunity To Fight Antimicrobial Resistance

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

Structural characterization of LsrK to target quorum sensing and comparison between X-ray and homology model

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