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Trebino MA, Shingare RD, MacMillan JB, Yildiz FH. Strategies and Approaches for Discovery of Small Molecule Disruptors of Biofilm Physiology. Molecules 2021; 26:molecules26154582. [PMID: 34361735 PMCID: PMC8348372 DOI: 10.3390/molecules26154582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Biofilms, the predominant growth mode of microorganisms, pose a significant risk to human health. The protective biofilm matrix, typically composed of exopolysaccharides, proteins, nucleic acids, and lipids, combined with biofilm-grown bacteria’s heterogenous physiology, leads to enhanced fitness and tolerance to traditional methods for treatment. There is a need to identify biofilm inhibitors using diverse approaches and targeting different stages of biofilm formation. This review discusses discovery strategies that successfully identified a wide range of inhibitors and the processes used to characterize their inhibition mechanism and further improvement. Additionally, we examine the structure–activity relationship (SAR) for some of these inhibitors to optimize inhibitor activity.
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Affiliation(s)
- Michael A. Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA;
| | - Rahul D. Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA;
| | - John B. MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA;
- Correspondence: (J.B.M.); (F.H.Y.)
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA;
- Correspondence: (J.B.M.); (F.H.Y.)
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Mantoni F, Paiardini A, Brunotti P, D'Angelo C, Cervoni L, Paone A, Cappellacci L, Petrelli R, Ricciutelli M, Leoni L, Rampioni G, Arcovito A, Rinaldo S, Cutruzzolà F, Giardina G. Insights into the GTP-dependent allosteric control of c-di-GMP hydrolysis from the crystal structure of PA0575 protein from Pseudomonas aeruginosa. FEBS J 2018; 285:3815-3834. [PMID: 30106221 DOI: 10.1111/febs.14634] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/25/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022]
Abstract
Bis-(3'-5')-cyclic diguanylic acid (c-di-GMP) belongs to the class of cyclic dinucleotides, key carriers of cellular information in prokaryotic and eukaryotic signal transduction pathways. In bacteria, the intracellular levels of c-di-GMP and their complex physiological outputs are dynamically regulated by environmental and internal stimuli, which control the antagonistic activities of diguanylate cyclases (DGCs) and c-di-GMP specific phosphodiesterases (PDEs). Allostery is one of the major modulators of the c-di-GMP-dependent response. Both the c-di-GMP molecule and the proteins interacting with this second messenger are characterized by an extraordinary structural plasticity, which has to be taken into account when defining and possibly predicting c-di-GMP-related processes. Here, we report a structure-function relationship study on the catalytic portion of the PA0575 protein from Pseudomonas aeruginosa, bearing both putative DGC and PDE domains. The kinetic and structural studies indicate that the GGDEF-EAL portion is a GTP-dependent PDE. Moreover, the crystal structure confirms the high degree of conformational flexibility of this module. We combined structural analysis and protein engineering studies to propose the possible molecular mechanism guiding the nucleotide-dependent allosteric control of catalysis; we propose that the role exerted by GTP via the GGDEF domain is to allow the two EAL domains to form a dimer, the species competent to enter PDE catalysis.
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Affiliation(s)
- Federico Mantoni
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Paolo Brunotti
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Cecilia D'Angelo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Laura Cervoni
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | | | - Riccardo Petrelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Italy
| | | | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
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