1
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Nepravishta R, Ramírez-Cárdenas J, Rocha G, Walpole S, Hicks T, Monaco S, Muñoz-García JC, Angulo J. Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy. J Med Chem 2024; 67:10025-10034. [PMID: 38848103 PMCID: PMC11215723 DOI: 10.1021/acs.jmedchem.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor-ligand interactions enabling binding detection and structural characterization. Comparison of relaxation and exchange matrix calculations with 1H STD NMR experimental data is essential for the validation of 3D structures of protein-ligand complexes. In this work, we present a new approach based on the calculation of a reduced relaxation matrix, in combination with funnel metadynamics MD simulations, that allows a very fast generation of experimentally STD-NMR-validated 3D structures of low-affinity protein-ligand complexes.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Cancer Research Horizons, CRUK Scotland Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, U.K
| | - Jonathan Ramírez-Cárdenas
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Gabriel Rocha
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Juan C Muñoz-García
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
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2
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Girardini M, Ferlenghi F, Annunziato G, Degiacomi G, Papotti B, Marchi C, Sammartino JC, Rasheed SS, Contini A, Pasca MR, Vacondio F, Evans JC, Dick T, Müller R, Costantino G, Pieroni M. Expanding the knowledge around antitubercular 5-(2-aminothiazol-4-yl)isoxazole-3-carboxamides: Hit-to-lead optimization and release of a novel antitubercular chemotype via scaffold derivatization. Eur J Med Chem 2023; 245:114916. [PMID: 36399878 PMCID: PMC10583863 DOI: 10.1016/j.ejmech.2022.114916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Tuberculosis is one of the deadliest infectious diseases in the world, and the increased number of multidrug-resistant and extensively drug-resistant strains is a reason for concern. We have previously reported a series of substituted 5-(2-aminothiazol-4-yl)isoxazole-3-carboxamides with growth inhibitory activity against Mycobacterium tuberculosis strains and low propensity to be substrate of efflux pumps. Encouraged by these preliminary results, we have undertaken a medicinal chemistry campaign to determine the metabolic fate of these compounds and to delineate a reliable body of Structure-Activity Relationships. Keeping intact the (thiazol-4-yl)isoxazole-3-carboxamide core, as it is deemed to be the pharmacophore of the molecule, we have extensively explored the structural modifications able to confer good activity and avoid rapid clearance. Also, a small set of analogues based on isostere manipulation of the 2-aminothiazole were prepared and tested, with the aim to disclose novel antitubercular chemotypes. These studies, combined, were instrumental in designing improved compounds such as 42g and 42l, escaping metabolic degradation by human liver microsomes and, at the same time, maintaining good antitubercular activity against both drug-susceptible and drug-resistant strains.
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Affiliation(s)
- Miriam Girardini
- P4T Group, Italy; Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Francesca Ferlenghi
- Department of Food and Drug, University of Parma, 43124, Parma, Italy; Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma, Parma, Italy
| | | | - Giulia Degiacomi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Bianca Papotti
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Cinzia Marchi
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - José Camilla Sammartino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Sari S Rasheed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123, Saarbrücken, Germany; German Centre for Infection Research, partner site Hannover-Braunschweig, Germany
| | - Anna Contini
- P4T Group, Italy; Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, 43124, Parma, Italy; Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma, Parma, Italy
| | - Joanna C Evans
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA; Department of Microbiology and Immunology, Georgetown University, Washington DC, USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123, Saarbrücken, Germany; German Centre for Infection Research, partner site Hannover-Braunschweig, Germany
| | - Gabriele Costantino
- P4T Group, Italy; Department of Food and Drug, University of Parma, 43124, Parma, Italy; Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma, Parma, Italy; Centro Interdipartimentale Misure (CIM) 'G. Casnati', University of Parma, Parma, Italy
| | - Marco Pieroni
- P4T Group, Italy; Department of Food and Drug, University of Parma, 43124, Parma, Italy; Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma, Parma, Italy.
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3
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Annunziato G, Spadini C, Marchetti M, Franko N, Pavone M, Iannarelli M, Bruno A, Pieroni M, Bettati S, Cabassi CS, Campanini B, Costantino G. Inhibitors of O-Acetylserine Sulfhydrylase with a Cyclopropane-Carboxylic Acid Scaffold Are Effective Colistin Adjuvants in Gram Negative Bacteria. Pharmaceuticals (Basel) 2022; 15:ph15060766. [PMID: 35745685 PMCID: PMC9227781 DOI: 10.3390/ph15060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Antibacterial adjuvants are of great significance, since they allow one to downscale the therapeutic dose of conventional antibiotics and reduce the insurgence of antibacterial resistance. Herein, we report that O-acetylserine sulfhydrylase (OASS) inhibitors could be used as colistin adjuvants to treat infections caused by critical pathogens spreading worldwide, Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella pneumoniae. Starting from a hit compound endowed with a nanomolar dissociation constant, we have rationally designed and synthesized a series of derivatives to be tested against S. Typhimurium OASS isoenzymes, StOASS-A and StOASS-B. All acidic derivatives have shown good activities in the nanomolar range against both OASS isoforms in vitro. Minimal Inhibitory Concentrations (MICs) were then evaluated, as well as compounds’ toxicity. The compounds endowed with good activity in vitro and low cytotoxicity have been challenged as a potential colistin adjuvant against pathogenic bacteria in vitro and the fractional inhibitory concentration (FIC) index has been calculated to define additive or synergistic effects. Finally, the target engagement inside the S. Typhimurium cells was confirmed by using a mutant strain in which the OASS enzymes were inactivated. Our results provide a robust proof of principle supporting OASS as a potential nonessential antibacterial target to develop a new class of adjuvants.
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Affiliation(s)
- Giannamaria Annunziato
- P4T Group, Food and Drug Department, University of Parma, 43124 Parma, Italy; (M.P.); (A.B.); (M.P.); (G.C.)
- Correspondence:
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.); (M.I.); (C.S.C.)
| | - Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (M.M.); (S.B.)
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Food and Drug Department, University of Parma, 43124 Parma, Italy; (N.F.); (B.C.)
| | - Marialaura Pavone
- P4T Group, Food and Drug Department, University of Parma, 43124 Parma, Italy; (M.P.); (A.B.); (M.P.); (G.C.)
| | - Mattia Iannarelli
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.); (M.I.); (C.S.C.)
| | - Agostino Bruno
- P4T Group, Food and Drug Department, University of Parma, 43124 Parma, Italy; (M.P.); (A.B.); (M.P.); (G.C.)
| | - Marco Pieroni
- P4T Group, Food and Drug Department, University of Parma, 43124 Parma, Italy; (M.P.); (A.B.); (M.P.); (G.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (M.M.); (S.B.)
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.); (M.I.); (C.S.C.)
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Food and Drug Department, University of Parma, 43124 Parma, Italy; (N.F.); (B.C.)
| | - Gabriele Costantino
- P4T Group, Food and Drug Department, University of Parma, 43124 Parma, Italy; (M.P.); (A.B.); (M.P.); (G.C.)
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4
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Wu X, Xu LY, Li EM, Dong G. Application of molecular dynamics simulation in biomedicine. Chem Biol Drug Des 2022; 99:789-800. [PMID: 35293126 DOI: 10.1111/cbdd.14038] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 02/05/2023]
Abstract
Molecular dynamics (MD) simulation has been widely used in the field of biomedicine to study the conformational transition of proteins caused by mutation or ligand binding/unbinding. It provides some perspectives those are difficult to find in traditional biochemical or pathological experiments, for example, detailed effects of mutations on protein structure and protein-protein/ligand interaction at the atomic level. In this review, a broad overview on conformation changes and drug discovery by MD simulation is given. We first discuss the preparation of protein structure for MD simulation, which is a key step that determines the accuracy of the simulation. Then, we summarize the applications of commonly used force fields and MD simulations in scientific research. Finally, enhanced sampling methods and common applications of these methods are introduced. In brief, MD simulation is a powerful tool and it can be used to guide experimental study. The combination of MD simulation and experimental techniques is an a priori means to solve the biomedical problems and give a deep understanding on the relationship between protein structure and function.
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Affiliation(s)
- Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
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5
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Pavone M, Raboni S, Marchetti M, Annunziato G, Bettati S, Papotti B, Marchi C, Carosati E, Pieroni M, Campanini B, Costantino G. Exploring the chemical space around N-(5-nitrothiazol-2-yl)-1,2,3-thiadiazole-4-carboxamide, a hit compound with serine acetyltransferase (SAT) inhibitory properties. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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6
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Abd El-Aleam RH, George RF, Georgey HH, Abdel-Rahman HM. Bacterial virulence factors: a target for heterocyclic compounds to combat bacterial resistance. RSC Adv 2021; 11:36459-36482. [PMID: 35494393 PMCID: PMC9043591 DOI: 10.1039/d1ra06238g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance is one of the most important challenges of the 21st century. However, the growing understanding of bacterial pathogenesis and cell-to-cell communication has revealed many potential strategies for the discovery of drugs that can be used for the treatment of bacterial infections. Interfering with bacterial virulence and/or quorum sensing could be a particularly interesting approach, because it is believed to exert less selective pressure on the bacterial resistance than with traditional strategies, geared toward killing bacteria or preventing their growth. Here, we discuss the mechanism of bacterial virulence, presenting promising strategies and recently synthesized heterocyclic compounds to combat future bacterial infections.
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Affiliation(s)
- Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI Cairo 11571 Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University Cairo 11786 Egypt
| | - Hamdy M Abdel-Rahman
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University Beni Suef Egypt
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7
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Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Armao S, Spadini C, Cabassi CS, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Discovery of Substituted (2-Aminooxazol-4-yl)Isoxazole-3-carboxylic Acids as Inhibitors of Bacterial Serine Acetyltransferase in the Quest for Novel Potential Antibacterial Adjuvants. Pharmaceuticals (Basel) 2021; 14:ph14020174. [PMID: 33672408 PMCID: PMC7931047 DOI: 10.3390/ph14020174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Many bacteria and actinomycetales use L-cysteine biosynthesis to increase their tolerance to antibacterial treatment and establish a long-lasting infection. In turn, this might lead to the onset of antimicrobial resistance that currently represents one of the most menacing threats to public health worldwide. The biosynthetic machinery required to synthesise L-cysteine is absent in mammals; therefore, its exploitation as a drug target is particularly promising. In this article, we report a series of inhibitors of Salmonella thyphimurium serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of L-cysteine biosynthesis. The development of such inhibitors started with the virtual screening of an in-house library of compounds that led to the selection of seven structurally unrelated hit derivatives. A set of molecules structurally related to hit compound 5, coming either from the original library or from medicinal chemistry efforts, were tested to determine a preliminary structure–activity relationship and, especially, to improve the inhibitory potency of the derivatives, that was indeed ameliorated by several folds compared to hit compound 5 Despite these progresses, at this stage, the most promising compound failed to interfere with bacterial growth when tested on a Gram-negative model organism, anticipating the need for further research efforts.
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Affiliation(s)
- Joana Magalhães
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Samanta Raboni
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
| | - Giannamaria Annunziato
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland;
| | - Agostino Bruno
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
| | - Stefano Bettati
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- Department of Medicine and Surgery, University of Parma, Via Volturno, 39, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Stefano Armao
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy; (C.S.); (C.S.C.)
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
- Institute of Biophysics, CNR, 56124 Pisa, Italy;
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905054
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (N.F.); (S.R.); (S.A.); (A.M.); (B.C.)
| | - Gabriele Costantino
- P4T Group, Department of Food and Drug, University of Parma, 43124 Parma, Italy; (J.M.); (G.A.); (A.B.); (G.C.)
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
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8
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Annunziato G, Spadini C, Franko N, Storici P, Demitri N, Pieroni M, Flisi S, Rosati L, Iannarelli M, Marchetti M, Magalhaes J, Bettati S, Mozzarelli A, Cabassi CS, Campanini B, Costantino G. Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O-Acetylserine Sulfhydrylase as a Colistin Adjuvant. ACS Infect Dis 2021; 7:281-292. [PMID: 33513010 DOI: 10.1021/acsinfecdis.0c00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibacterial adjuvants are of great significance, since they allow the therapeutic dose of conventional antibiotics to be lowered and reduce the insurgence of antibiotic resistance. Herein, we report that an O-acetylserine sulfhydrylase (OASS) inhibitor can be used as a colistin adjuvant to treat infections caused by Gram-positive and Gram-negative pathogens. A compound that binds OASS with a nM dissociation constant was tested as an adjuvant of colistin against six critical pathogens responsible for infections spreading worldwide, Escherichia coli, Salmonella enterica serovar Typhimurium, Klebisiella pneumoniae, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Staphylococcus pseudintermedius. The compound showed promising synergistic or additive activities against all of them. Knockout experiments confirmed the intracellular target engagement supporting the proposed mechanism of action. Moreover, compound toxicity was evaluated by means of its hemolytic activity against sheep defibrinated blood cells, showing a good safety profile. The 3D structure of the compound in complex with OASS was determined at 1.2 Å resolution by macromolecular crystallography, providing for the first time structural insights about the nature of the interaction between the enzyme and this class of competitive inhibitors. Our results provide a robust proof of principle supporting OASS as a potential nonessential antibacterial target to develop a new class of adjuvants and the structural basis for further structure-activity relationship studies.
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Affiliation(s)
- Giannamaria Annunziato
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Paola Storici
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Sara Flisi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Lucrezia Rosati
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Mattia Iannarelli
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Joana Magalhaes
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, via Volturno, 39, 43125 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Gabriele Costantino
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
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9
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Abstract
Introduction: Antimicrobial peptides are a large class of compounds that are part of innate immune response found among all classes of life and are considered promising compounds to deal with antimicrobial resistance. These AMPs have been demonstrated to have some advantages over the traditional antibiotics with a broad spectrum of antimicrobial activities and even overcome bacterial drug-resistance. Areas covered: The present review represents a comprehensive analysis of patents and patent applications available on Espacenet, from the year 2015 to 2020 referring to the therapeutic use of AMPs. Expert opinion: There are important examples about the use of antimicrobial peptides in clinical practice (e.g. polimixin b, colistin, etc.). AMPs are usually inspired by nature being produced by different living organisms as defensive and/or competition mechanisms. Despite limitations related to their development in classical drug discovery pipeline, they are endowed with relevant advantages, such as an unlimited reservoir of organisms able to produce new AMPs and they represent good starting point upon which to develop new antimicrobials.
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10
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Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Inhibition of Nonessential Bacterial Targets: Discovery of a Novel Serine O-Acetyltransferase Inhibitor. ACS Med Chem Lett 2020; 11:790-797. [PMID: 32435386 DOI: 10.1021/acsmedchemlett.9b00627] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/13/2020] [Indexed: 11/29/2022] Open
Abstract
In ϒ-proteobacteria and Actinomycetales, cysteine biosynthetic enzymes are indispensable during persistence and become dispensable during growth or acute infection. The biosynthetic machinery required to convert inorganic sulfur into cysteine is absent in mammals; therefore, it is a suitable drug target. We searched for inhibitors of Salmonella serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of l-cysteine biosynthesis. The virtual screening of three ChemDiv focused libraries containing 91 243 compounds was performed to identify potential SAT inhibitors. Scaffold similarity and the analysis of the overall physicochemical properties allowed the selection of 73 compounds that were purchased and evaluated on the recombinant enzyme. Six compounds displaying an IC50 <100 μM were identified via an indirect assay using Ellman's reagent and then tested on a Gram-negative model organism, with one of them being able to interfere with bacterial growth via SAT inhibition.
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Affiliation(s)
| | | | | | | | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Marco Pieroni
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
| | | | - Gabriele Costantino
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
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11
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Annunziato G. Strategies to Overcome Antimicrobial Resistance (AMR) Making Use of Non-Essential Target Inhibitors: A Review. Int J Mol Sci 2019; 20:E5844. [PMID: 31766441 PMCID: PMC6928725 DOI: 10.3390/ijms20235844] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/23/2022] Open
Abstract
Antibiotics have always been considered as one of the most relevant discoveries of the twentieth century. Unfortunately, the dawn of the antibiotic era has sadly corresponded to the rise of the phenomenon of antimicrobial resistance (AMR), which is a natural process whereby microbes evolve in such a way to withstand the action of drugs. In this context, the identification of new potential antimicrobial targets and/or the identification of new chemical entities as antimicrobial drugs are in great demand. To date, among the many possible approaches used to deal with antibiotic resistance is the use of antibiotic adjuvants that hit bacterial non-essential targets. In this review, the author focuses on the discovery of antibiotic adjuvants and on new tools to study and reduce the prevalence of resistant bacterial infections.
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Affiliation(s)
- Giannamaria Annunziato
- Probes for Targets Group (P4T group), Department of food and Drug, University of Parma, 43124 Parma, Italy
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12
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Bruno A, Barresi E, Simola N, Da Pozzo E, Costa B, Novellino E, Da Settimo F, Martini C, Taliani S, Cosconati S. Unbinding of Translocator Protein 18 kDa (TSPO) Ligands: From in Vitro Residence Time to in Vivo Efficacy via in Silico Simulations. ACS Chem Neurosci 2019; 10:3805-3814. [PMID: 31268683 DOI: 10.1021/acschemneuro.9b00300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Translocator protein 18 kDa (TSPO) is a validated pharmacological target for the development of new treatments for neurological disorders. N,N-Dialkyl-2-phenylindol-3-ylglyoxylamides (PIGAs) are effective TSPO modulators and potentially useful therapeutics for the treatment of anxiety, central nervous system pathologies featuring astrocyte loss, and inflammatory-based neuropathologies. For this class of compounds, no correlation exists between the TSPO binding affinity and the corresponding functional efficacy. Rather, their biological effectiveness correlates with the kinetics of the unbinding events and more specifically with the residence time (RT). So far, the structural reasons for the different recorded RT of congeneric PIGAs remain elusive. Here, to understand the different kinetics of PIGAs, their unbinding paths were studied by employing enhanced-sampling molecular dynamics simulations. Results of these studies revealed how subtle structural differences between PIGAs have a substantial effect on the unbinding energetics. In particular, during the egress from the TSPO binding site, slow-dissociating PIGAs find tight interactions with the protein LP1 region thereby determining a long RT. Further support to these findings was achieved by in vivo studies, which demonstrated how the anxiolytic effect observed for the inspected PIGAs correlated with their RT to TSPO.
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Affiliation(s)
- Agostino Bruno
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Elisabetta Barresi
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Nicola Simola
- Department of Biomedical Sciences, University of Cagliari, Monserrato University Campus, 09042 Monserrato, Italy
| | - Eleonora Da Pozzo
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Barbara Costa
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Federico Da Settimo
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Claudia Martini
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
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13
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Magalhães J, Franko N, Annunziato G, Pieroni M, Benoni R, Nikitjuka A, Mozzarelli A, Bettati S, Karawajczyk A, Jirgensons A, Campanini B, Costantino G. Refining the structure-activity relationships of 2-phenylcyclopropane carboxylic acids as inhibitors of O-acetylserine sulfhydrylase isoforms. J Enzyme Inhib Med Chem 2018; 34:31-43. [PMID: 30362368 PMCID: PMC6217552 DOI: 10.1080/14756366.2018.1518959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The lack of efficacy of current antibacterials to treat multidrug resistant bacteria poses a life-threatening alarm. In order to develop enhancers of the antibacterial activity, we carried out a medicinal chemistry campaign aiming to develop inhibitors of enzymes that synthesise cysteine and belong to the reductive sulphur assimilation pathway, absent in mammals. Previous studies have provided a novel series of inhibitors for O-acetylsulfhydrylase – a key enzyme involved in cysteine biosynthesis. Despite displaying nanomolar affinity, the most active representative of the series was not able to interfere with bacterial growth, likely due to poor permeability. Therefore, we rationally modified the structure of the hit compound with the aim of promoting their passage through the outer cell membrane porins. The new series was evaluated on the recombinant enzyme from Salmonella enterica serovar Typhimurium, with several compounds able to keep nanomolar binding affinity despite the extent of chemical manipulation.
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Affiliation(s)
- Joana Magalhães
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Nina Franko
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | | | - Marco Pieroni
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Roberto Benoni
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | - Anna Nikitjuka
- c Latvian Institute of Organic Synthesis , Riga , Latvia
| | - Andrea Mozzarelli
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,d National Institute of Biostructures and Biosystems , Rome , Italy.,e Institute of Biophysics , Pisa , Italy
| | - Stefano Bettati
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,f Department of Neurosciences , University of Parma , Parma , Italy
| | | | | | - Barbara Campanini
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | - Gabriele Costantino
- a P4T group, Department of Food and Drug, University of Parma, Parma, Italy.,h Centro Interdipartimentale Misure (CIM)'G. Casnati', University of Parma , Parma , Italy
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14
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Annunziato G, Giovati L, Angeli A, Pavone M, Del Prete S, Pieroni M, Capasso C, Bruno A, Conti S, Magliani W, Supuran CT, Costantino G. Discovering a new class of antifungal agents that selectively inhibits microbial carbonic anhydrases. J Enzyme Inhib Med Chem 2018; 33:1537-1544. [PMID: 30284487 PMCID: PMC6179086 DOI: 10.1080/14756366.2018.1516652] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Infections caused by pathogens resistant to the available antimicrobial treatments represent nowadays a threat to global public health. Recently, it has been demonstrated that carbonic anhydrases (CAs) are essential for the growth of many pathogens and their inhibition leads to growth defects. Principal drawbacks in using CA inhibitors (CAIs) as antimicrobial agents are the side effects due to the lack of selectivity toward human CA isoforms. Herein we report a new class of CAIs, which preferentially interacts with microbial CA active sites over the human ones. The mechanism of action of these inhibitors was investigated against an important fungal pathogen, Cryptococcus neoformans, revealing that they are also able to inhibit CA in microbial cells growing in vitro. At our best knowledge, this is the first report on newly designed synthetic compounds selectively targeting β-CAs and provides a proof of concept of microbial CAs suitability as an antimicrobial drug target.
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Affiliation(s)
| | - Laura Giovati
- b Department of Medicine and Surgery, Ospedale Maggiore di Parma , University of Parma , Parma , Italy
| | - Andrea Angeli
- c Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Firenze , Italy
| | - Marialaura Pavone
- a Department of Food and Drugs , University of Parma , Parma , Italy
| | - Sonia Del Prete
- c Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Firenze , Italy
| | - Marco Pieroni
- a Department of Food and Drugs , University of Parma , Parma , Italy
| | - Clemente Capasso
- d National Council of Research (CNR) , Istituto di Bioscenze e Biorisorse , Napoli , Italy
| | - Agostino Bruno
- a Department of Food and Drugs , University of Parma , Parma , Italy.,e Experimental Therapeutics Program , IFOM the FIRC Institute for Molecular Oncology Foundation , Milano , Italy
| | - Stefania Conti
- b Department of Medicine and Surgery, Ospedale Maggiore di Parma , University of Parma , Parma , Italy
| | - Walter Magliani
- b Department of Medicine and Surgery, Ospedale Maggiore di Parma , University of Parma , Parma , Italy
| | - Claudiu T Supuran
- c Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , Firenze , Italy
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15
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Magalhães J, Franko N, Annunziato G, Welch M, Dolan SK, Bruno A, Mozzarelli A, Armao S, Jirgensons A, Pieroni M, Costantino G, Campanini B. Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand-based drug design. J Enzyme Inhib Med Chem 2018; 33:1444-1452. [PMID: 30221554 PMCID: PMC6147075 DOI: 10.1080/14756366.2018.1512596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several bacteria rely on the reductive sulphur assimilation pathway, absent in mammals, to synthesise cysteine. Reduction of virulence and decrease in antibiotic resistance have already been associated with mutations on the genes that codify cysteine biosynthetic enzymes. Therefore, inhibition of cysteine biosynthesis has emerged as a promising strategy to find new potential agents for the treatment of bacterial infection. Following our previous efforts to explore OASS inhibition and to expand and diversify our library, a scaffold hopping approach was carried out, with the aim of identifying a novel fragment for further development. This novel chemical tool, endowed with favourable pharmacological characteristics, was successfully developed, and a preliminary Structure–Activity Relationship investigation was carried out.
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Affiliation(s)
- Joana Magalhães
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Nina Franko
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | | | - Martin Welch
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Stephen K Dolan
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Agostino Bruno
- d Experimental Therapeutics Program , IFOM - The FIRC Institute for Molecular Oncology Foundation , Milano , Italy
| | - Andrea Mozzarelli
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,e National Institute of Biostructures and Biosystems , Rome , Italy.,f Institute of Biophysics, CNR , Pisa , Italy
| | - Stefano Armao
- g Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma , Parma , Italy
| | | | - Marco Pieroni
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Gabriele Costantino
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy.,i Centro Interdipartimentale Misure (CIM)'G. Casnati', University of Parma , Parma , Italy
| | - Barbara Campanini
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
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