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Bissaro M, Sturlese M, Moro S. Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? Front Chem 2020; 8:107. [PMID: 32175307 PMCID: PMC7057144 DOI: 10.3389/fchem.2020.00107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/04/2020] [Indexed: 11/30/2022] Open
Abstract
Although proteins have represented the molecular target of choice in the development of new drug candidates, the pharmaceutical importance of ribonucleic acids has gradually been growing. The increasing availability of structural information has brought to light the existence of peculiar three-dimensional RNA arrangements, which can, contrary to initial expectations, be recognized and selectively modulated through small chemical entities or peptides. The application of classical computational methodologies, such as molecular docking, for the rational development of RNA-binding candidates is, however, complicated by the peculiarities characterizing these macromolecules, such as the marked conformational flexibility, the singular charges distribution, and the relevant role of solvent molecules. In this work, we have thus validated and extended the applicability domain of SuMD, an all-atoms molecular dynamics protocol that allows to accelerate the sampling of molecular recognition events on a nanosecond timescale, to ribonucleotide targets of pharmaceutical interest. In particular, we have proven the methodological ability by reproducing the binding mode of viral or prokaryotic ribonucleic complexes, as well as that of artificially engineered aptamers, with an impressive degree of accuracy.
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Affiliation(s)
- Maicol Bissaro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
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Perkins KR, Atilho RM, Moon MH, Breaker RR. Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen. ACS Chem Biol 2019; 14:2841-2850. [PMID: 31609568 DOI: 10.1021/acschembio.9b00713] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Various riboswitch classes are being discovered that precisely monitor the status of important biological processes, including metabolic pathway function, signaling for physiological adaptations, and responses to toxic agents. Biochemical components for some of these processes might make excellent targets for the development of novel antibacterial molecules, which can be broadly sought by using phenotypic drug discovery (PDD) methods. However, PDD data do not normally provide clues regarding the target for each hit compound. We have developed and validated a robust fluorescent reporter system based on a ZTP riboswitch that identifies numerous folate biosynthesis inhibitors with high sensitivity and precision. The utility of the riboswitch-based PDD strategy was evaluated using Escherichia coli bacteria by conducting a 128 310-compound high-throughput screen, which identified 78 sulfanilamide derivatives among the many initial hits. Similarly, representatives of other riboswitch classes could be employed to rapidly match antibacterial hits with the biological processes they target.
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Affiliation(s)
- Kevin R. Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Ruben M. Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Michelle H. Moon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, United States
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, United States
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Mangoni AA, Eynde JJV, Jampilek J, Hadjipavlou-Litina D, Liu H, Reynisson J, Sousa ME, Gomes PAC, Prokai-Tatrai K, Tuccinardi T, Sabatier JM, Luque FJ, Rautio J, Karaman R, Vasconcelos MH, Gemma S, Galdiero S, Hulme C, Collina S, Gütschow M, Kokotos G, Siciliano C, Capasso R, Agrofoglio LA, Ragno R, Muñoz-Torrero D. Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes-5. Molecules 2019; 24:molecules24132415. [PMID: 31262039 PMCID: PMC6650823 DOI: 10.3390/molecules24132415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/04/2023] Open
Affiliation(s)
- Arduino A Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University and Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Jean Jacques Vanden Eynde
- Formerly head of the Department of Organic Chemistry (FS), University of Mons-UMONS, 7000 Mons, Belgium
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Dimitra Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Jóhannes Reynisson
- School of Pharmacy, Keele University, Hornbeam building, Staffordshire ST5 5BG, UK
| | - Maria Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências, Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N 4450-208 Matosinhos, Portugal
| | - Paula A C Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Jean-Marc Sabatier
- Institute of NeuroPhysiopathology, UMR 7051, Faculté de Médecine Secteur Nord, 51, Boulevard Pierre Dramard - CS80011, 13344 Marseille CEDEX 15, France
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Jarkko Rautio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Rafik Karaman
- Pharmaceutical & Medicinal Chemistry Department, Faculty of Pharmacy, Al-Quds University, POB 20002 Jerusalem, Palestine
- Department of Sciences, University of Basilicata, Viadell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - M Helena Vasconcelos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Cancer Drug Resistance Group-IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal
- Department of Biological Sciences, FFUP-Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sandra Gemma
- Department of Biotechnology, chemistry and pharmacy, University of Siena via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Christopher Hulme
- Department of Pharmacology and Toxicology, and Department of Chemistry and Biochemistry, College of Pharmacy, The University of Arizona, Biological Sciences West Room 351, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Pharmaceutical Technology Section, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53115 Bonn, Germany
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Carlo Siciliano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, I-87036 Arcavacata di Rende, Italy
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Luigi A Agrofoglio
- ICOA, CNRS UMR 7311, Universite d'Orleans, Rue de Chartres, 45067 Orleans CEDEX 2, France
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.
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Calabrese DR, Connelly CM, Schneekloth JS. Ligand-observed NMR techniques to probe RNA-small molecule interactions. Methods Enzymol 2019; 623:131-149. [PMID: 31239044 DOI: 10.1016/bs.mie.2019.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A growing understanding of the structure and function of RNA has revealed it as a key regulator of gene expression and disease. A multitude of noncoding functions apart from the central roles of RNA in coding for and facilitating protein biogenesis has stimulated research into RNA as a pharmacological target. Despite many exciting advances, RNA remains an understudied target for small molecules, and techniques to investigate RNA-binding molecules are still emerging. A key stumbling block in this area has been validation of RNA-small molecule interactions. Our laboratory has recently used multiple ligand-observed NMR techniques in this regard, including CPMG and WaterLOGSY. This work describes methods to use these techniques in the context of studying RNA-ligand interactions.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States.
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