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Walter I, Adam S, Gentilini MV, Kany AM, Brengel C, Thomann A, Sparwasser T, Köhnke J, Hartmann RW. Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors. ChemMedChem 2021; 16:2786-2801. [PMID: 34010508 PMCID: PMC8519103 DOI: 10.1002/cmdc.202100283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/29/2022]
Abstract
CYP121 of Mycobacterium tuberculosis (Mtb) is an essential target for the development of novel potent drugs against tuberculosis (TB). Besides known antifungal azoles, further compounds of the azole class were recently identified as CYP121 inhibitors with antimycobacterial activity. Herein, we report the screening of a similarity-oriented library based on the former hit compound, the evaluation of affinity toward CYP121, and activity against M. bovis BCG. The results enabled a comprehensive SAR study, which was extended through the synthesis of promising compounds and led to the identification of favorable features for affinity and/or activity and hit compounds with 2.7-fold improved potency. Mode of action studies show that the hit compounds inhibit substrate conversion and highlighted CYP121 as the main antimycobacterial target of our compounds. Exemplified complex crystal structures of CYP121 with three inhibitors reveal a common binding site. Engaging in both hydrophobic interactions as well as hydrogen bonding to the sixth iron ligand, our compounds block a solvent channel leading to the active site heme. Additionally, we report the first CYP inhibitors that are able to reduce the intracellular replication of M. bovis BCG in macrophages, emphasizing their potential as future drug candidates against TB.
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Affiliation(s)
- Isabell Walter
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Sebastian Adam
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Maria Virginia Gentilini
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Andreas M. Kany
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Christian Brengel
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Andreas Thomann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Tim Sparwasser
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Jesko Köhnke
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Rolf W. Hartmann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2.366123SaarbrückenGermany
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2
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Brengel C, Thomann A, Schifrin A, Allegretta G, Kamal AAM, Haupenthal J, Schnorr I, Cho SH, Franzblau SG, Empting M, Eberhard J, Hartmann RW. Biophysical Screening of a Focused Library for the Discovery of CYP121 Inhibitors as Novel Antimycobacterials. ChemMedChem 2017; 12:1616-1626. [DOI: 10.1002/cmdc.201700363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Giuseppe Allegretta
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Ahmed A. M. Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Isabell Schnorr
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Sang Hyun Cho
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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Brengel C, Thomann A, Schifrin A, Eberhard J, Hartmann RW. Back Cover: Discovery and Biophysical Evaluation of First Low Nanomolar Hits Targeting CYP125 of M. tuberculosis
(ChemMedChem 21/2016). ChemMedChem 2016. [DOI: 10.1002/cmdc.201600532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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4
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Thomann A, Brengel C, Börger C, Kail D, Steinbach A, Empting M, Hartmann RW. Structure-Activity Relationships of 2-Sufonylpyrimidines as Quorum-Sensing Inhibitors to Tackle Biofilm Formation and eDNA Release ofPseudomonas aeruginosa. ChemMedChem 2016; 11:2522-2533. [DOI: 10.1002/cmdc.201600419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/27/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Carsten Börger
- PharmBioTec GmbH; Science Park 1 66123 Saarbrücken Germany
| | - Dagmar Kail
- PharmBioTec GmbH; Science Park 1 66123 Saarbrücken Germany
| | - Anke Steinbach
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E 8.1 66123 Saarbrücken Germany
- Saarland University; Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Campus C 2.3 66123 Saarbrücken Germany
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Brengel C, Thomann A, Schifrin A, Eberhard J, Hartmann RW. Discovery and Biophysical Evaluation of First Low Nanomolar Hits Targeting CYP125 ofM. tuberculosis. ChemMedChem 2016; 11:2385-2391. [DOI: 10.1002/cmdc.201600361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/01/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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Thomann A, de Mello Martins AGG, Brengel C, Empting M, Hartmann RW. Application of Dual Inhibition Concept within Looped Autoregulatory Systems toward Antivirulence Agents against Pseudomonas aeruginosa Infections. ACS Chem Biol 2016; 11:1279-86. [PMID: 26882081 DOI: 10.1021/acschembio.6b00117] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pseudomonas aeruginosa quorum-sensing (QS) is a sophisticated network of genome-wide regulation triggered in response to population density. A major component is the self-inducing pseudomonas quinolone signal (PQS) QS system that regulates the production of several nonvital virulence- and biofilm-related determinants. Hence, QS circuitry is an attractive target for antivirulence agents with lowered resistance development potential and a good model to study the concept of polypharmacology in autoloop-regulated systems per se. Based on the finding that a combination of PqsR antagonist and PqsD inhibitor synergistically lowers pyocyanin, we have developed a dual-inhibitor compound of low molecular weight and high solubility that targets PQS transcriptional regulator (PqsR) and PqsD, a key enzyme in the biosynthesis of PQS-QS signal molecules (HHQ and PQS). In vitro, this compound markedly reduced virulence factor production and biofilm formation accompanied by a diminished content of extracellular DNA (eDNA). Additionally, coadministration with ciprofloxacin increased susceptibility of PA14 to antibiotic treatment under biofilm conditions. Finally, disruption of pathogenicity mechanisms was also assessed in vivo, with significantly increased survival of challenged larvae in a Galleria mellonella infection model. Favorable physicochemical properties and effects on virulence/biofilm establish a promising starting point for further optimization. In particular, the ability to address two targets of the PQS autoinduction cycle at the same time with a single compound holds great promise in achieving enhanced synergistic cellular effects while potentially lowering rates of resistance development.
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Affiliation(s)
- Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Antonio G. G. de Mello Martins
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
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7
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Hutter MC, Brengel C, Negri M, Henn C, Zimmer C, Hartmann RW, Empting M, Steinbach A. Mechanistic details for anthraniloyl transfer in PqsD: the initial step in HHQ biosynthesis. J Mol Model 2014; 20:2255. [PMID: 24842325 DOI: 10.1007/s00894-014-2255-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/21/2014] [Indexed: 11/25/2022]
Abstract
PqsD mediates the conversion of anthraniloyl-coenzyme A (ACoA) to 2-heptyl-4-hydroxyquinoline (HHQ), a precursor of the Pseudomonas quinolone signal (PQS) molecule. Due to the role of the quinolone signaling pathway of Pseudomonas aeruginosa in the expression of several virulence factors and biofilm formation, PqsD is a potential target for controlling this nosocomial pathogen, which exhibits a low susceptibility to standard antibiotics. PqsD belongs to the β-ketoacyl-ACP synthase family and is similar in structure to homologous FabH enzymes in E. coli and Mycobacterium tuberculosis. Here, we used molecular dynamics simulations to obtain the structural position of the substrate ACoA in the binding pocket of PqsD, and semiempirical molecular orbital calculations to study the reaction mechanism for the catalytic cleavage of ACoA. Our findings suggest a nucleophilic attack of the deprotonated sulfur of Cys112 at the carbonyl carbon of ACoA and a switch in the protonation pattern of His257 whereby Nδ is protonated and the proton of Nε is shifted to the sulfur of CoA during the reaction. This is in agreement with the experimentally determined decreased catalytic activity of the Cys112Ser mutant, whereas the Cys112Ala, His257Phe, and Asn287Ala mutants are all inactive. ESI mass-spectrometric measurements of the Asn287Ala mutant show that anthraniloyl remains covalently bound to Cys112, thus further supporting the inference from our computed mechanism that Asn287 does not take part in the cleavage of ACoA. Since this mutant is inactive, we suggest instead that Asn287 must play an essential role in the subsequent formation of HHQ in vitro.
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Affiliation(s)
- Michael C Hutter
- Center for Bioinformatics, Saarland University, Campus Building E2.1, 66123, Saarbrücken, Germany,
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8
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Storz MP, Brengel C, Weidel E, Hoffmann M, Hollemeyer K, Steinbach A, Müller R, Empting M, Hartmann RW. Biochemical and biophysical analysis of a chiral PqsD inhibitor revealing tight-binding behavior and enantiomers with contrary thermodynamic signatures. ACS Chem Biol 2013; 8:2794-801. [PMID: 24099650 DOI: 10.1021/cb400530d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antivirulence strategies addressing bacterial pathogenicity without exhibiting growth inhibition effects represent a novel approach to overcome today's crisis in antibiotic development. In recent studies, we examined various inhibitors of PqsD, an enzyme involved in formation of Pseudomonas aeruginosa cell-to-cell signaling molecules, and observed desired cellular effects for 2-nitrophenyl derivatives. Herein, we investigated the binding characteristics of this interesting compound class using several biochemical and biophysical methods. The inhibitors showed time-dependent activity, tight-binding behavior, and interactions with the catalytic center. Furthermore, isothermal titration calorimetry (ITC) experiments with separated enantiomers revealed contrary thermodynamic signatures showing either enthalpy- or entropy-driven affinity. A combination of site-directed mutagenesis and thermodynamic profiling was used to identify key residues involved in inhibitor binding. This information allowed the proposal of experimentally confirmed docking poses. Although originally designed as transition state analogs, our results suggest an altered position for both enantiomers. Interestingly, the main difference between stereoisomers was found in the orientation of the hydroxyl group at the stereogenic center. The predicted binding modes are in accordance with experimental data and, thus, allow future structure-guided optimization.
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Affiliation(s)
- Michael P. Storz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Christian Brengel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Elisabeth Weidel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Michael Hoffmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Microbial Natural Products, Campus C2.3, 66123 Saarbrücken, Germany
| | - Klaus Hollemeyer
- Biochemical
Engineering, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
| | - Anke Steinbach
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Microbial Natural Products, Campus C2.3, 66123 Saarbrücken, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
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Sahner JH, Brengel C, Storz MP, Groh M, Plaza A, Müller R, Hartmann RW. Combining in silico and biophysical methods for the development of Pseudomonas aeruginosa quorum sensing inhibitors: an alternative approach for structure-based drug design. J Med Chem 2013; 56:8656-64. [PMID: 24083807 DOI: 10.1021/jm401102e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present work deals with the optimization of an inhibitor of PqsD, an enzyme essential for Pseudomonas aeruginosa quorum sensing apparatus. Molecular docking studies, supported by biophysical methods (surface plasmon resonance, isothermal titration calorimetry, saturation transfer difference NMR), were used to illuminate the binding mode of the 5-aryl-ureidothiophene-2-carboxylic acids. Enabled to make profound predictions, structure-based optimization led to increased inhibitory potency. Finally a covalent inhibitor was obtained. Binding to the active site was confirmed by LC-ESI-MS and MALDI-TOF-MS experiments. Following this rational approach, potent PqsD inhibitors were efficiently developed within a short period of time. This example shows that a combination and careful application of in silico and biophysical methods represents a powerful complement to cocrystallography.
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Affiliation(s)
- J Henning Sahner
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Drug Design and Optimization & Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2 3, 66123 Saarbrücken, Germany
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Steinbach A, Maurer CK, Weidel E, Henn C, Brengel C, Hartmann RW, Negri M. Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies. BMC Biophys 2013; 6:10. [PMID: 23916145 PMCID: PMC3734052 DOI: 10.1186/2046-1682-6-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 07/25/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND PQS (PseudomonasQuinolone Signal) and its precursor HHQ are signal molecules of the P. aeruginosa quorum sensing system. They explicate their role in mammalian pathogenicity by binding to the receptor PqsR that induces virulence factor production and biofilm formation. The enzyme PqsD catalyses the biosynthesis of HHQ. RESULTS Enzyme kinetic analysis and surface plasmon resonance (SPR) biosensor experiments were used to determine mechanism and substrate order of the biosynthesis. Comparative analysis led to the identification of domains involved in functionality of PqsD. A kinetic cycle was set up and molecular dynamics (MD) simulations were used to study the molecular bases of the kinetics of PqsD. Trajectory analysis, pocket volume measurements, binding energy estimations and decompositions ensured insights into the binding mode of the substrates anthraniloyl-CoA and β-ketodecanoic acid. CONCLUSIONS Enzyme kinetics and SPR experiments hint at a ping-pong mechanism for PqsD with ACoA as first substrate. Trajectory analysis of different PqsD complexes evidenced ligand-dependent induced-fit motions affecting the modified ACoA funnel access to the exposure of a secondary channel. A tunnel-network is formed in which Ser317 plays an important role by binding to both substrates. Mutagenesis experiments resulting in the inactive S317F mutant confirmed the importance of this residue. Two binding modes for β-ketodecanoic acid were identified with distinct catalytic mechanism preferences.
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Affiliation(s)
- Anke Steinbach
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany
| | - Christine K Maurer
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany
| | | | - Claudia Henn
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany.,Current address: MIP Pharma GmbH, Kirkelerstr. 41, 66440,Blieskastel-Niederwürzbach, Germany
| | - Christian Brengel
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany
| | - Rolf W Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany.,Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Matthias Negri
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C2.3, 66123, Saarbrücken, Germany
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11
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Weidel E, de Jong JC, Brengel C, Storz MP, Braunshausen A, Negri M, Plaza A, Steinbach A, Müller R, Hartmann RW. Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking. J Med Chem 2013; 56:6146-55. [PMID: 23834469 DOI: 10.1021/jm4006302] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pseudomonas aeruginosa employs a characteristic pqs quorum sensing (QS) system that functions via the signal molecules PQS and its precursor HHQ. They control the production of a number of virulence factors and biofilm formation. Recently, we have shown that sulfonamide substituted 2-benzamidobenzoic acids, which are known FabH inhibitors, are also able to inhibit PqsD, the enzyme catalyzing the last and key step in the biosynthesis of HHQ. Here, we describe the further optimization and characterization of this class of compounds as PqsD inhibitors. Structural modifications showed that both the carboxylic acid ortho to the amide and 3'-sulfonamide are essential for binding. Introduction of substituents in the anthranilic part of the molecule resulted in compounds with IC50 values in the low micromolar range. Binding mode investigations by SPR with wild-type and mutated PqsD revealed that this compound class does not bind into the active center of PqsD but in the ACoA channel, preventing the substrate from accessing the active site. This binding mode was further confirmed by docking studies and STD NMR.
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Affiliation(s)
- Elisabeth Weidel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Department of Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
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12
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Storz MP, Maurer CK, Zimmer C, Wagner N, Brengel C, de Jong JC, Lucas S, Müsken M, Häussler S, Steinbach A, Hartmann RW. Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors. J Am Chem Soc 2012; 134:16143-6. [PMID: 22992202 DOI: 10.1021/ja3072397] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Heptyl-4-hydroxyquinoline (HHQ) and Pseudomonas quinolone signal (PQS) are involved in the regulation of virulence factor production and biofilm formation in Pseudomonas aeruginosa. PqsD is a key enzyme in the biosynthesis of these signal molecules. Using a ligand-based approach, we have identified the first class of PqsD inhibitors. Simplification and rigidization led to fragments with high ligand efficiencies. These small molecules repress HHQ and PQS production and biofilm formation in P. aeruginosa. This validates PqsD as a target for the development of anti-infectives.
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Affiliation(s)
- Michael P Storz
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus C23, 66123 Saarbrücken, Germany
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