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Hönig SMN, Lemmen C, Rarey M. Small molecule superposition: A comprehensive overview on pose scoring of the latest methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sophia M. N. Hönig
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
- BioSolveIT Sankt Augustin Germany
| | | | - Matthias Rarey
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
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2
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H M Ehrler J, Brunst S, Tjaden A, Kilu W, Heering J, Hernandez-Olmos V, Krommes A, Kramer JS, Steinhilber D, Schubert-Zsilavecz M, Müller-Knapp S, Merk D, Proschak E. Compilation and Evaluation of Fatty Acid Mimetics Screening Library. Biochem Pharmacol 2022; 204:115191. [PMID: 35907497 DOI: 10.1016/j.bcp.2022.115191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/02/2022]
Abstract
Focused compound libraries are well-established tools for hit identification in drug discovery and chemical probe development. We present the compilation and application of a focused screening library of fatty acid mimetics (FAMs), which are compounds designed to bind the orthosteric site proteins that endogenously accommodate natural fatty acids and lipid metabolites. This set complies with chemical properties of FAM and was found suitable for use also in cellular setting. Several hits were retrieved in screening the focused library against diverse fatty acid binding targets including the enzymes soluble epoxide hydrolase (sEH) and leukotriene A4 hydrolase (LTA4H), the nuclear receptors peroxisome proliferator-activated receptor γ (PPARγ) and retinoid X receptor α (RXRα), the carrier proteins fatty acid binding protein 4 and 5 (FABP4 and FABP5), as well as the G-protein coupled receptors leukotriene B4 receptor 1 (BLT1) and free-fatty acid receptor 1 (FFAR1). Thus, the focused FAM library is suitable to obtain chemical starting matter for fatty acid binding proteins and valuable extends available screening collections.
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Affiliation(s)
- Johanna H M Ehrler
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Victor Hernandez-Olmos
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Andrè Krommes
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Susanne Müller-Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Ludwig-Maximilians-Universität München, Department of Pharmacy, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany.
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3
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Schierle S, Brunst S, Helmstädter M, Ebert R, Kramer JS, Steinhilber D, Proschak E, Merk D. Development and in vitro Profiling of Dual FXR/LTA4H Modulators. ChemMedChem 2021; 16:2366-2374. [PMID: 33856122 PMCID: PMC8453936 DOI: 10.1002/cmdc.202100118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 11/10/2022]
Abstract
Designed polypharmacology presents as an attractive strategy to increase therapeutic efficacy in multi-factorial diseases by a directed modulation of multiple involved targets with a single molecule. Such an approach appears particularly suitable in non-alcoholic steatohepatitis (NASH) which involves hepatic steatosis, inflammation and fibrosis as pathological hallmarks. Among various potential pharmacodynamic mechanisms, activation of the farnesoid X receptor (FXRa) and inhibition of leukotriene A4 hydrolase (LTA4Hi) hold promise to counteract NASH according to preclinical and clinical observations. We have developed dual FXR/LTA4H modulators as pharmacological tools, enabling evaluation of this polypharmacology concept to treat NASH and related pathologies. The optimized FXRa/LTA4Hi exhibits well-balanced dual activity on the intended targets with sub-micromolar potency and is highly selective over related nuclear receptors and enzymes rendering it suitable as tool to probe synergies of dual FXR/LTA4H targeting.
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Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Steffen Brunst
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Moritz Helmstädter
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Roland Ebert
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Jan S. Kramer
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Dieter Steinhilber
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Ewgenij Proschak
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Daniel Merk
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
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Qin R, Wang H, Yan A. Classification and QSAR models of leukotriene A4 hydrolase (LTA4H) inhibitors by machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:411-431. [PMID: 33896285 DOI: 10.1080/1062936x.2021.1910862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Leukotriene A4 hydrolase (LTA4H) is an important anti-inflammatory target which can convert leukotriene A4 (LTA4) into pro-inflammatory substance leukotriene B4 (LTB4). In this paper, we built 18 classification models for 463 LTA4H inhibitors by using support vector machine (SVM), random forest (RF) and K-Nearest Neighbour (KNN). The best classification model (Model 2A) was built from RF and MACCS fingerprints. The prediction accuracy of 88.96% and the Matthews correlation coefficient (MCC) of 0.74 had been achieved on the test set. We also divided the 463 LTA4H inhibitors into six subsets using K-Means. We found that the highly active LTA4H inhibitors mostly contained diphenylmethane or diphenyl ether as the scaffold and pyridine or piperidine as the side chain. In addition, six quantitative structure-activity relationship (QSAR) models for 172 LTA4H inhibitors were built by multiple linear regression (MLR) and SVM. The best QSAR model (Model 6A) was built by using SVM and CORINA Symphony descriptors. The coefficients of determination of the training set and the test set were equal to 0.81 and 0.79, respectively. Classification and QSAR models could be used for subsequent virtual screening, and the obtained fragments that were important for highly active inhibitors would be helpful for designing new LTA4H inhibitors.
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Affiliation(s)
- R Qin
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - H Wang
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
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5
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Hefke L, Hiesinger K, Zhu WF, Kramer JS, Proschak E. Computer-Aided Fragment Growing Strategies to Design Dual Inhibitors of Soluble Epoxide Hydrolase and LTA4 Hydrolase. ACS Med Chem Lett 2020; 11:1244-1249. [PMID: 32551007 DOI: 10.1021/acsmedchemlett.0c00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022] Open
Abstract
Multitarget ligands are interesting candidates for drug discovery and development due to improved safety and efficacy. However, rational design and optimization of multitarget ligands is tedious because affinity optimization for two or more targets has to be performed simultaneously. In this study, we demonstrate that, given a molecular fragment, which binds to two targets of interest, computer-aided fragment growing can be applied to optimize compound potency, relying on either ligand- or structure-derived information. This methodology is applied to the design of dual inhibitors of soluble epoxide hydrolase and leukotriene A4 hydrolase.
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Affiliation(s)
- Lena Hefke
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, D-60438 Frankfurt, Germany
| | - Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, D-60438 Frankfurt, Germany
| | - W. Felix Zhu
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, D-60438 Frankfurt, Germany
| | - Jan S. Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, D-60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, D-60438 Frankfurt, Germany
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6
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Hiesinger K, Schott A, Kramer JS, Blöcher R, Witt F, Wittmann SK, Steinhilber D, Pogoryelov D, Gerstmeier J, Werz O, Proschak E. Design of Dual Inhibitors of Soluble Epoxide Hydrolase and LTA 4 Hydrolase. ACS Med Chem Lett 2020; 11:298-302. [PMID: 32184960 DOI: 10.1021/acsmedchemlett.9b00330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/30/2019] [Indexed: 11/30/2022] Open
Abstract
Multitarget anti-inflammatory drugs interfering with the arachidonic acid cascade exhibit superior efficacy. In this study, a prototype dual inhibitor of soluble epoxide hydrolase (sEH) and LTA4 hydrolase (LTA4H) with submicromolar activity toward both targets has been designed and synthesized. Preliminary structure-activity relationship studies were performed to identify optimal substitution patterns. X-ray structure analysis of a promising dual inhibitor in complex with sEH, as well as molecular docking with LTA4H provided a rationale for further optimization. Hereby, scaffold extension was successfully applied to yield potent dual sEH/LTA4H inhibitors. The spectrum of pro- and anti-inflammatory lipid mediators was evaluated in M1 and M2 macrophages, stimulated with LPS, and incubated with the most promising compound 14. The effect of 14 on the inflammatory lipid mediator profile characterizes dual sEH/LTA4H inhibitors as an interesting option for future anti-inflammatory agent investigations.
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Affiliation(s)
- Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Annika Schott
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jan S. Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - René Blöcher
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Finja Witt
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Sandra K. Wittmann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Denys Pogoryelov
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jana Gerstmeier
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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Fehlmann T, Hutter MC. Conservation and Relevance of Pharmacophore Point Types. J Chem Inf Model 2019; 59:1314-1323. [PMID: 30807146 DOI: 10.1021/acs.jcim.8b00757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharmacophore models in general use a variety of features for distinct chemical characteristics, such as hydrogen-bond properties, lipohilicity, and ionizability. Usually, features have to match onto their identical type. To clarify if this stringent one-to-one assignment is justified, we investigated a set of 581 unique ligands from the BindingDB with known orientation inside the respective binding pockets and conducted a statistical analysis of the likelihood of observed exchanges in between the pharmacophore features, respectively their degree of conservation. To find out if certain features are obsolete, we derived a ranking to determine the most relevant ones. We found that the most conserved one-to-one feature is the negative ionizable (acids), followed by hydrogen-bond donor, positive ionizable (basic nitrogens), hydrogen-bond acceptor, aromatic, nonaromatic π-systems, and other lipophilic characteristics. The most likely exchanges were found between carboxylate groups and hydrogen-bond acceptors and likewise between basic nitrogens and hydrogen-bond donors, which reflects the characteristics of Lewis acids and bases. Exchanges between hydrogen-bond donors and hydrogen-bond acceptors are hardly more likely than by chance. The kind of target (e.g., kinase, phosphatase, protease, phosphodiesterase, nuclear receptor, metal-containing, or transmembrane protein) did not show substantial influence on the degree of conservation. The relevance of the actual pharmacophore features was found to be strongly dependent on the applied ranking scheme. Mutual information ranks all hydrophobic features as least important, whereas the aromatic feature is put into second place by using a geometric series. Both ranking schemes see the negative ionizable feature of higher significance than the positively ionizable feature.
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Affiliation(s)
- Tobias Fehlmann
- Center for Bioinformatics , Saarland University , Campus E2.1 , 66123 Saarbruecken , Germany
| | - Michael C Hutter
- Center for Bioinformatics , Saarland University , Campus E2.1 , 66123 Saarbruecken , Germany
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8
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König S, Pace S, Pein H, Heinekamp T, Kramer J, Romp E, Straßburger M, Troisi F, Proschak A, Dworschak J, Scherlach K, Rossi A, Sautebin L, Haeggström JZ, Hertweck C, Brakhage AA, Gerstmeier J, Proschak E, Werz O. Gliotoxin from Aspergillus fumigatus Abrogates Leukotriene B 4 Formation through Inhibition of Leukotriene A 4 Hydrolase. Cell Chem Biol 2019; 26:524-534.e5. [PMID: 30745237 DOI: 10.1016/j.chembiol.2019.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/23/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]
Abstract
The epidithiodioxopiperazine gliotoxin is a virulence factor of Aspergillus fumigatus, the most important airborne fungal pathogen of humans. Gliotoxin suppresses innate immunity in invasive aspergillosis, particularly by compromising neutrophils, but the underlying molecular mechanisms remain elusive. Neutrophils are the first responders among innate immune cells recruited to sites of infection by the chemoattractant leukotriene (LT)B4 that is biosynthesized by 5-lipoxygenase and LTA4 hydrolase (LTA4H). Here, we identified gliotoxin as inhibitor of LTA4H that selectively abrogates LTB4 formation in human leukocytes and in distinct animal models. Gliotoxin failed to inhibit the formation of other eicosanoids and the aminopeptidase activity of the bifunctional LTA4H. Suppression of LTB4 formation by gliotoxin required the cellular environment and/or reducing conditions, and only the reduced form of gliotoxin inhibited LTA4H activity. Conclusively, gliotoxin suppresses the biosynthesis of the potent neutrophil chemoattractant LTB4 by direct interference with LTA4H thereby impairing neutrophil functions in invasive aspergillosis.
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Affiliation(s)
- Stefanie König
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Simona Pace
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Helmut Pein
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany
| | - Jan Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Erik Romp
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Maria Straßburger
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany
| | - Fabiana Troisi
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Anna Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Dworschak
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany
| | - Antonietta Rossi
- Department of Pharmacy, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Lidia Sautebin
- Department of Pharmacy, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Jesper Z Haeggström
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany; Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), 07745 Jena, Germany; Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Jana Gerstmeier
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany.
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Blöcher R, Rodarte Ramírez A, Castro-Escarpulli G, Curiel-Quesada E, Reyes-Arellano A. Design, Synthesis, and Evaluation of Alkyl-Quinoxalin-2(1 H)-One Derivatives as Anti- Quorum Sensing Molecules, Inhibiting Biofilm Formation in Aeromonas caviae Sch3. Molecules 2018; 23:molecules23123075. [PMID: 30477243 PMCID: PMC6321446 DOI: 10.3390/molecules23123075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/18/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2023] Open
Abstract
With the increasing antibiotic resistance of bacterial strains, alternative methods for infection control are in high demand. Quorum sensing (QS) is the bacterial communication system based on small molecules. QS is enables bacterial biofilm formation and pathogenic development. The interruption of QS has become a target for drug discovery, but remains in the early experimental phase. In this study, we synthesized a set of six compounds based on a scaffold (alkyl-quinoxalin-2(1H)-one), new in the anti-QS of Gram-negative bacteria Aeromonas caviae Sch3. By quantifying biofilm formation, we were able to monitor the effect of these compounds from concentrations of 1 to 100 µM. Significant reduction in biofilm formation was achieved by 3-hexylylquinoxalin-2(1H)-one (11), 3-hexylylquinoxalin-2(1H)-one-6-carboxylic acid (12), and 3-heptylylquinoxalin-2(1H)-one-6-carboxylic acid (14), ranging from 11% to 59% inhibition of the biofilm. This pilot study contributes to the development of anti-QS compounds to overcome the clinical challenge of resistant bacteria strains.
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Affiliation(s)
- René Blöcher
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Departamento de Química Orgánica, Ciudad de México 11340, México.
| | - Ariel Rodarte Ramírez
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Ciudad de México 11340, México.
| | - Graciela Castro-Escarpulli
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Ciudad de México 11340, México.
| | - Everardo Curiel-Quesada
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Departamento de Bioquímica, Ciudad de México 11340, México.
| | - Alicia Reyes-Arellano
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Departamento de Química Orgánica, Ciudad de México 11340, México.
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10
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Vázquez J, Deplano A, Herrero A, Ginex T, Gibert E, Rabal O, Oyarzabal J, Herrero E, Luque FJ. Development and Validation of Molecular Overlays Derived from Three-Dimensional Hydrophobic Similarity with PharmScreen. J Chem Inf Model 2018; 58:1596-1609. [PMID: 30010337 DOI: 10.1021/acs.jcim.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular alignment is a standard procedure for three-dimensional (3D) similarity measurements and pharmacophore elucidation. This process is influenced by several factors, such as the physicochemical descriptors utilized to account for the molecular determinants of biological activity and the reference templates. Relying on the hypothesis that the maximal achievable binding affinity for a drug-like molecule is largely due to desolvation, we explore a novel strategy for 3D molecular overlays that exploits the partitioning of molecular hydrophobicity into atomic contributions in conjunction with information about the distribution of hydrogen-bond (HB) donor/acceptor groups. A brief description of the method, as implemented in the software package PharmScreen, including the derivation of the fractional hydrophobic contributions within the quantum mechanical version of the Miertus-Scrocco-Tomasi (MST) continuum model, and the procedure utilized for the optimal superposition between molecules, is presented. The computational procedure is calibrated by using a data set of 402 molecules pertaining to 14 distinct targets taken from the literature and validated against the AstraZeneca test, which comprises 121 experimentally derived sets of molecular overlays. The results point out the suitability of the MST-based hydrophobic parameters for generating molecular overlays, as correct predictions were obtained for 94%, 79%, and 54% of the molecules classified into easy, moderate, and hard sets, respectively. Moreover, the results point out that this accuracy is attained at a much lower degree of identity between the templates used by hydrophobic/HB fields and electrostatic/steric ones. These findings support the usefulness of the hydrophobic/HB descriptors to generate complementary overlays that may be valuable to rationalize structure-activity relationships and for virtual screening campaigns.
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Affiliation(s)
- Javier Vázquez
- Pharmacelera , Plaça Pau Vila, 1, Sector C 2a , Edifici Palau de Mar, Barcelona 08039 , Spain.,Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB) , University of Barcelona , Av. Prat de la Riba 171 , Santa Coloma de Gramenet E-08921 , Spain
| | - Alessandro Deplano
- Pharmacelera , Plaça Pau Vila, 1, Sector C 2a , Edifici Palau de Mar, Barcelona 08039 , Spain
| | - Albert Herrero
- Pharmacelera , Plaça Pau Vila, 1, Sector C 2a , Edifici Palau de Mar, Barcelona 08039 , Spain
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB) , University of Barcelona , Av. Prat de la Riba 171 , Santa Coloma de Gramenet E-08921 , Spain
| | - Enric Gibert
- Pharmacelera , Plaça Pau Vila, 1, Sector C 2a , Edifici Palau de Mar, Barcelona 08039 , Spain
| | - Obdulia Rabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA) , University of Navarra , Avda. Pio XII 55 , Pamplona E-31008 , Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA) , University of Navarra , Avda. Pio XII 55 , Pamplona E-31008 , Spain
| | - Enric Herrero
- Pharmacelera , Plaça Pau Vila, 1, Sector C 2a , Edifici Palau de Mar, Barcelona 08039 , Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB) , University of Barcelona , Av. Prat de la Riba 171 , Santa Coloma de Gramenet E-08921 , Spain
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MolAlign: an algorithm for aligning multiple small molecules. J Comput Aided Mol Des 2017; 31:523-546. [DOI: 10.1007/s10822-017-0023-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022]
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Thermodynamic properties of leukotriene A 4 hydrolase inhibitors. Bioorg Med Chem 2016; 24:5243-5248. [DOI: 10.1016/j.bmc.2016.08.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/20/2016] [Accepted: 08/25/2016] [Indexed: 02/03/2023]
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Lehmann C, Homann J, Ball AK, Blöcher R, Kleinschmidt TK, Basavarajappa D, Angioni C, Ferreirós N, Häfner AK, Rådmark O, Proschak E, Haeggström JZ, Geisslinger G, Parnham MJ, Steinhilber D, Kahnt AS. Lipoxin and resolvin biosynthesis is dependent on 5-lipoxygenase activating protein. FASEB J 2015; 29:5029-43. [PMID: 26289316 DOI: 10.1096/fj.15-275487] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/13/2015] [Indexed: 12/13/2022]
Abstract
Resolution of acute inflammation is an active process coordinated by proresolving lipid mediators (SPMs) such as lipoxins (LXs) and resolvins (Rvs), which are formed by the concerted action of 2 lipoxygenases (LOs). Because the exact molecular mechanisms of SPM biosynthesis are not completely understood, we aimed to investigate LX and D-type Rv formation in human leukocytes and HEK293T cells overexpressing leukotriene (LT) pathway enzymes. Activity assays in precursor (15-hydroxyeicosatetraenoic acids, 17-HDoHE)-treated granulocytes [polymorphonuclear leukocytes (PMNLs)] showed a strict dependence of LXA4/RvD1 biosynthesis on cell integrity, and incubation with recombinant human 5-LO did not lead to LX or Rv formation. Pharmacologic inhibition of 5-LO activating protein (FLAP) by MK-886 inhibited LXA4/RvD1 biosynthesis in precursor-treated PMNLs (drug concentration causing 50% inhibition ∼ 0.3/0.2 µM), as did knockdown of the enzyme in MM6 cells, and precursor-treated HEK293T overexpressing 5-LO produced high amounts of LXA4 only in the presence of FLAP. In addition, inhibition of cytosolic phospholipase A2α (cPLA2α) interfered with LXA4/RvD1 formation from exogenous precursors in PMNLs. Furthermore, inhibition of the LT synthases LTA4 hydrolase and LTC4 synthase in PMNL/platelet coincubations augmented LXA4 levels. These findings show that several enzymes known to be involved in the biosynthesis of proinflammatory LTs, such as FLAP and cPLA2α, also contribute to LX and Rv formation.
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Affiliation(s)
- Christoph Lehmann
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Julia Homann
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Katrin Ball
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - René Blöcher
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Thea K Kleinschmidt
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Devaraj Basavarajappa
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Carlo Angioni
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Nerea Ferreirós
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Kathrin Häfner
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Olof Rådmark
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Ewgenij Proschak
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Z Haeggström
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Gerd Geisslinger
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Michael J Parnham
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Dieter Steinhilber
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
| | - Astrid Stefanie Kahnt
- *Fraunhofer Institute for Molecular Biology and Applied Ecology, Project Group Translational Medicine and Pharmacology, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, and Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany; and Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, Stockholm, Sweden
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