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Borgelt L, Wu P. Targeting Ribonucleases with Small Molecules and Bifunctional Molecules. ACS Chem Biol 2023; 18:2101-2113. [PMID: 37382390 PMCID: PMC10594538 DOI: 10.1021/acschembio.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Ribonucleases (RNases) cleave and process RNAs, thereby regulating the biogenesis, metabolism, and degradation of coding and noncoding RNAs. Thus, small molecules targeting RNases have the potential to perturb RNA biology, and RNases have been studied as therapeutic targets of antibiotics, antivirals, and agents for autoimmune diseases and cancers. Additionally, the recent advances in chemically induced proximity approaches have led to the discovery of bifunctional molecules that target RNases to achieve RNA degradation or inhibit RNA processing. Here, we summarize the efforts that have been made to discover small-molecule inhibitors and activators targeting bacterial, viral, and human RNases. We also highlight the emerging examples of RNase-targeting bifunctional molecules and discuss the trends in developing such molecules for both biological and therapeutic applications.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max
Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
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2
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Chung H, Kim J, Lee YJ, Choi KR, Jeong KJ, Kim GJ, Lee SY. Enhanced production of difficult-to-express proteins through knocking down rnpA gene expression. Biotechnol J 2023; 18:e2200641. [PMID: 37285237 DOI: 10.1002/biot.202200641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/21/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Escherichia coli has been employed as a workhorse for the efficient production of recombinant proteins. However, some proteins were found to be difficult to produce in E. coli. The stability of mRNA has been considered as one of the important factors affecting recombinant protein production. Here we report a generally applicable and simple strategy for enhancing mRNA stability, and consequently improving recombinant protein production in E. coli. RNase P, a ribozyme comprising an RNA subunit (RnpB) and a protein subunit (RnpA), is involved in tRNA maturation. Based on the finding that purified RnpA can digest rRNA and mRNA in vitro, it was reasoned that knocking down the level of RnpA might enhance recombinant protein production. For this, the synthetic small regulatory RNA-based knockdown system was applied to reduce the expression level of RnpA. The developed RnpA knockdown system allowed successful overexpression of 23 different recombinant proteins of various origins and sizes, including Cas9 protein, antibody fragment, and spider silk protein. Notably, a 284.9-kDa ultra-high molecular weight, highly repetitive glycine-rich spider silk protein, which is one of the most difficult proteins to produce, could be produced to 1.38 g L-1 , about two-fold higher than the highest value previously achieved, by a fed-batch culture of recombinant E. coli strain employing the RnpA knockdown system. The RnpA-knockdown strategy reported here will be generally useful for the production of recombinant proteins including those that have been difficult to produce.
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Affiliation(s)
- Hannah Chung
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
| | - Jiyong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
| | - Yong Jae Lee
- Protein Engineering Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ki Jun Jeong
- Protein Engineering Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
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Knackstedt LA, Wu L, Rothstein J, Vidensky S, Gordon J, Ramanjulu M, Dunman P, Blass B, Childers W, Abou-Gharbia M. MC-100093, a Novel β-Lactam Glutamate Transporter-1 Enhancer Devoid of Antimicrobial Properties, Attenuates Cocaine Relapse in Rats. J Pharmacol Exp Ther 2021; 378:51-59. [PMID: 33986035 PMCID: PMC8407531 DOI: 10.1124/jpet.121.000532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/11/2021] [Indexed: 11/22/2022] Open
Abstract
Cocaine use disorder currently lacks Food and Drug Administration-approved treatments. In rodents, the glutamate transporter-1 (GLT-1) is downregulated in the nucleus accumbens after cocaine self-administration, and increasing the expression and function of GLT-1 reduces the reinstatement of cocaine seeking. The β-lactam antibiotic ceftriaxone upregulates GLT-1 and attenuates cue- and cocaine-induced cocaine seeking without affecting motivation for natural rewards. Although ceftriaxone shows promise for treating cocaine use disorder, it possesses characteristics that limit successful translation from bench to bedside, including poor brain penetration, a lack of oral bioavailability, and a risk of bacterial resistance when used chronically. Thus, we aimed to develop novel molecules that retained the GLT-1-enhancing effects of ceftriaxone but displayed superior drug-like properties. Here, we describe a new monocyclic β-lactam, MC-100093, as a potent upregulator of GLT-1 that is orally bioavailable and devoid of antimicrobial properties. MC-100093 was synthesized and tested in vitro and in vivo to determine physiochemical, pharmacokinetic, and pharmacodynamic properties. Next, adult male rats underwent cocaine self-administration and extinction training. During extinction training, rats received one of four doses of MC-100093 for 6-8 days prior to a single cue-primed reinstatement test. Separate cohorts of rats were used to assess nucleus accumbens GLT-1 expression and MC-100093 effects on sucrose self-administration. We found that 50 mg/kg MC-100093 attenuated cue-primed reinstatement of cocaine seeking while upregulating GLT-1 expression in the nucleus accumbens core. This dose did not produce sedation, nor did it decrease sucrose consumption or body weight. Thus, MC-100093 represents a potential treatment to reduce cocaine relapse. SIGNIFICANCE STATEMENT: Increasing GLT-1 activity reliably reduces drug-seeking across classes of drugs; however, existing GLT1-enhancers have side effects and lack oral bioavailability. To address this issue, novel GLT-1 enhancers were synthesized, and the compound with the most favorable pharmacokinetic and pharmacodynamic properties, MC-100093, was selected for further testing. MC-100093 attenuated cued cocaine seeking without reducing food seeking or locomotion and upregulated GLT-1 expression in the nucleus accumbens.
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Affiliation(s)
- Lori A Knackstedt
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Lizhen Wu
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Jeffrey Rothstein
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Svetlana Vidensky
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - John Gordon
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Mercy Ramanjulu
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Paul Dunman
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Benjamin Blass
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Wayne Childers
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
| | - Magid Abou-Gharbia
- Psychology Department (L.A.K., L.W.) and Center for Addiction Research (L.A.K.), University of Florida, Gainesville, Florida; Moulder Center for Drug Discovery Research, Temple University, Philadelphia, Pennsylvania (J.G, M.R., B.B., W.C., M.A.-G.); Department of Neurology, Johns Hopkins University, Baltimore, Maryland (J.R., S.V.); and Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York (P.D.)
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4
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RNase P Inhibitors Identified as Aggregators. Antimicrob Agents Chemother 2021; 65:e0030021. [PMID: 33972249 DOI: 10.1128/aac.00300-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNase P is an essential enzyme responsible for tRNA 5'-end maturation. In most bacteria, the enzyme is a ribonucleoprotein consisting of a catalytic RNA subunit and a small protein cofactor termed RnpA. Several studies have reported small-molecule inhibitors directed against bacterial RNase P that were identified by high-throughput screenings. Using the bacterial RNase P enzymes from Thermotoga maritima, Bacillus subtilis, and Staphylococcus aureus as model systems, we found that such compounds, including RNPA2000 (and its derivatives), iriginol hexaacetate, and purpurin, induce the formation of insoluble aggregates of RnpA rather than acting as specific inhibitors. In the case of RNPA2000, aggregation was induced by Mg2+ ions. These findings were deduced from solubility analyses by microscopy and high-performance liquid chromatography (HPLC), RnpA-inhibitor co-pulldown experiments, detergent addition, and RnpA titrations in enzyme activity assays. Finally, we used a B. subtilis RNase P depletion strain, whose lethal phenotype could be rescued by a protein-only RNase P of plant origin, for inhibition zone analyses on agar plates. These cell-based experiments argued against RNase P-specific inhibition of bacterial growth by RNPA2000. We were also unable to confirm the previously reported nonspecific RNase activity of S. aureus RnpA itself. Our results indicate that high-throughput screenings searching for bacterial RNase P inhibitors are prone to the identification of "false positives" that are also termed pan-assay interference compounds (PAINS).
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Suigo L, Chojnacki M, Zanotto C, Sebastián-Pérez V, Morghen CDG, Casiraghi A, Dunman PM, Valoti E, Straniero V. Staphylococcus aureus RnpA Inhibitors: Computational-Guided Design, Synthesis and Initial Biological Evaluation. Antibiotics (Basel) 2021; 10:antibiotics10040438. [PMID: 33920000 PMCID: PMC8071009 DOI: 10.3390/antibiotics10040438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance is spreading worldwide and it has become one of the most important issues in modern medicine. In this context, the bacterial RNA degradation and processing machinery are essential processes for bacterial viability that may be exploited for antimicrobial therapy. In Staphylococcus aureus, RnpA has been hypothesized to be one of the main players in these mechanisms. S. aureus RnpA is able to modulate mRNA degradation and complex with a ribozyme (rnpB), facilitating ptRNA maturation. Corresponding small molecule screening campaigns have recently identified a few classes of RnpA inhibitors, and their structure activity relationship (SAR) has only been partially explored. Accordingly, in the present work, using computational modeling of S. aureus RnpA we identified putative crucial interactions of known RnpA inhibitors, and we used this information to design, synthesize, and biologically assess new potential RnpA inhibitors. The present results may be beneficial for the overall knowledge about RnpA inhibitors belonging to both RNPA2000-like thiosemicarbazides and JC-like piperidine carboxamides molecular classes. We evaluated the importance of the different key moieties, such as the dichlorophenyl and the piperidine of JC2, and the semithiocarbazide, the furan, and the i-propylphenyl ring of RNPA2000. Our efforts could provide a foundation for further computational-guided investigations.
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Affiliation(s)
- Lorenzo Suigo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133 Milano, Italy; (L.S.); (A.C.); (E.V.)
| | - Michaelle Chojnacki
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Ave., Rochester, NY 14642, USA; (M.C.); (P.M.D.)
| | - Carlo Zanotto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Vanvitelli 32, 20129 Milano, Italy;
| | | | - Carlo De Giuli Morghen
- Department of Chemical—Pharmaceutical and Biomolecular Technologies, Catholic University “Our Lady of Good Counsel”, Rr. Dritan Hoxha, 1025 Tirana, Albania;
| | - Andrea Casiraghi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133 Milano, Italy; (L.S.); (A.C.); (E.V.)
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Ave., Rochester, NY 14642, USA; (M.C.); (P.M.D.)
| | - Ermanno Valoti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133 Milano, Italy; (L.S.); (A.C.); (E.V.)
| | - Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133 Milano, Italy; (L.S.); (A.C.); (E.V.)
- Correspondence: ; Tel.: +39-0250319361
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Optimization of 2-Acylaminocycloalkylthiophene Derivatives for Activity against Staphylococcus aureus RnpA. Antibiotics (Basel) 2021; 10:antibiotics10040369. [PMID: 33807357 PMCID: PMC8066339 DOI: 10.3390/antibiotics10040369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus is well-recognized to cause debilitating bacterial infections that are difficult to treat due to the emergence of antibiotic resistance. As such, there is a need to develop new antimicrobials for the therapeutic intervention of S. aureus disease. To that end, S. aureus RnpA is an essential enzyme that is hypothesized to participate in two required cellular processes, precursor tRNA (ptRNA) maturation and mRNA degradation. Corresponding high throughput screening campaigns have identified the phenylcarbamoyl cyclic thiopenes as a chemical class of RnpA inhibitors that display promising antibacterial effects by reducing RnpA ptRNA and mRNA degradation activities and low human cell toxicity. Herein, we perform a structure activity relationship study of the chemical scaffold. Results revealed that the cycloalkane ring size and trifluoroacetamide moiety are required for antibacterial activity, whereas modifications of the para and/or meta positions of the pharmacophore’s phenyl group allowed tuning of the scaffold’s antimicrobial performance and RnpA inhibitory activity. The top performing compounds with respect to antimicrobial activity also did not exhibit cytotoxicity to human cell lines at concentrations up to 100 µM, greater than 100-fold the minimum inhibitory concentration (MIC). Focused studies of one analog, RNP0012, which exhibited the most potent antimicrobial and inhibition of cellular RnpA activities revealed that the compound reduced bacterial burden in a murine model of S. aureus disease. Taken together, the results presented are expected to provide an early framework for optimization of next-generation of RnpA inhibitor analogues that may represent progenitors of a new class of antimicrobials.
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Schaffer AE, Pinkard O, Coller JM. tRNA Metabolism and Neurodevelopmental Disorders. Annu Rev Genomics Hum Genet 2019; 20:359-387. [PMID: 31082281 DOI: 10.1146/annurev-genom-083118-015334] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
tRNAs are short noncoding RNAs required for protein translation. The human genome includes more than 600 putative tRNA genes, many of which are considered redundant. tRNA transcripts are subject to tightly controlled, multistep maturation processes that lead to the removal of flanking sequences and the addition of nontemplated nucleotides. Furthermore, tRNAs are highly structured and posttranscriptionally modified. Together, these unique features have impeded the adoption of modern genomics and transcriptomics technologies for tRNA studies. Nevertheless, it has become apparent from human neurogenetic research that many tRNA biogenesis proteins cause brain abnormalities and other neurological disorders when mutated. The cerebral cortex, cerebellum, and peripheral nervous system show defects, impairment, and degeneration upon tRNA misregulation, suggesting that they are particularly sensitive to changes in tRNA expression or function. An integrated approach to identify tRNA species and contextually characterize tRNA function will be imperative to drive future tool development and novel therapeutic design for tRNA-associated disorders.
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Affiliation(s)
- Ashleigh E Schaffer
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Otis Pinkard
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Jeffery M Coller
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
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Colquhoun JM, Ha L, Beckley A, Meyers B, Flaherty DP, Dunman PM. Identification of Small Molecule Inhibitors of Staphylococcus aureus RnpA. Antibiotics (Basel) 2019; 8:antibiotics8020048. [PMID: 31035380 PMCID: PMC6627331 DOI: 10.3390/antibiotics8020048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus RnpA is thought to be a unique dual functional antimicrobial target that is required for two essential cellular processes, precursor tRNA processing and messenger RNA degradation. Herein, we used a previously described whole cell-based mupirocin synergy assay to screen members of a 53,000 compound small molecule diversity library and simultaneously enrich for agents with cellular RnpA inhibitory activity. A medicinal chemistry-based campaign was launched to generate a preliminary structure activity relationship and guide early optimization of two novel chemical classes of RnpA inhibitors identified, phenylcarbamoyl cyclic thiophene and piperidinecarboxamide. Representatives of each chemical class displayed potent anti-staphylococcal activity, limited the protein’s in vitro ptRNA processing and mRNA degradation activities, and exhibited favorable therapeutic indexes. The most potent piperidinecarboxamide RnpA inhibitor, JC2, displayed inhibition of cellular RnpA mRNA turnover, RnpA-depletion strain hypersusceptibility, and exhibited antimicrobial efficacy in a wax worm model of S. aureus infection. Taken together, these results establish that the whole cell screening assay used is amenable to identifying small molecule RnpA inhibitors within large chemical libraries and that the chemical classes identified here may represent progenitors of new classes of antimicrobials that target RnpA.
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Affiliation(s)
- Jennifer M Colquhoun
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Lisha Ha
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47906, USA.
| | - Andrew Beckley
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Brinkley Meyers
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47906, USA.
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47906, USA.
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47906, USA.
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
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9
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Novel berberine derivatives: Design, synthesis, antimicrobial effects, and molecular docking studies. Chin J Nat Med 2018; 16:774-781. [PMID: 30322611 DOI: 10.1016/s1875-5364(18)30117-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 01/07/2023]
Abstract
A series of berberine derivatives were synthesized by introducing substituted benzyl groups at C-9. All these synthesized compounds (4a-4m) were screened for their in vitro antibacterial activity against four Gram-positive bacteria and four Gram-negative bacteria and evaluated for their antifungal activity against three pathogenic fungal strains. All these compounds displayed good antibacterial and antifungal activities, compared to reference drugs including Ciprofloxacin and Fluconazole; Compounds 4f, 4g, and 4l showed the highest antibacterial and antifungal activities. Moreover, all the synthesized compounds were docked into topoisomerase II-DNA complex, which is a crucial drug target for the treatment of microbial infections. Docking results showed that H-bond, π-π stacked, π-cationic, and π-anionic interactions were responsible for the strong binding of the compounds with the target protein-DNA complex.
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10
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Ha L, Colquhoun J, Noinaj N, Das C, Dunman PM, Flaherty DP. Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus. Acta Crystallogr F Struct Biol Commun 2018; 74:632-637. [PMID: 30279314 PMCID: PMC6168776 DOI: 10.1107/s2053230x18011512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 02/03/2023] Open
Abstract
Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target that is a key protein component for two essential cellular processes, RNA degradation and transfer-RNA (tRNA) maturation. The first crystal structure of RnpA from the pathogenic bacterial species, S. aureus, is reported at 2.0 Å resolution. The structure presented maintains key similarities with previously reported RnpA structures from bacteria and archaea, including the highly conserved RNR-box region and aromatic residues in the precursor-tRNA 5'-leader-binding domain. This structure will be instrumental in the pursuit of structure-based designed inhibitors targeting RnpA-mediated RNA processing as a novel therapeutic approach for treating S. aureus infections.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Catalytic Domain
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Kinetics
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonuclease P/chemistry
- Ribonuclease P/genetics
- Ribonuclease P/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Staphylococcus aureus/chemistry
- Staphylococcus aureus/enzymology
- Substrate Specificity
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Affiliation(s)
- Lisha Ha
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer Colquhoun
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
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Novel inhibitors of Staphylococcus aureus RnpA that synergize with mupirocin. Bioorg Med Chem Lett 2018; 28:1127-1131. [PMID: 29463447 DOI: 10.1016/j.bmcl.2018.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 11/23/2022]
Abstract
We recently discovered RnpA as a promising new drug discovery target for methicillin-resistant S. aureus (MRSA). RnpA is an essential protein that is thought to perform two required cellular processes. As part of the RNA degrasome Rnpa mediates RNA degradation. In combination with rnpB it forms RNase P haloenzymes which are required for tRNA maturation. A high throughput screen identified RNPA2000 as an inhibitor of both RnpA-associated activities that displayed antibacterial activity against clinically relevant strains of S. aureus, including MRSA. Structure-activity studies aimed at improving potency and replacing the potentially metabotoxic furan moiety led to the identification of a number of more potent analogs. Many of these new analogs possessed overt cellular toxicity that precluded their use as antibiotics but two derivatives, including compound 5o, displayed an impressive synergy with mupirocin, an antibiotic used for decolonizing MSRA whose effectiveness has recently been jeopardized by bacterial resistance. Based on our results, compounds like 5o may ultimately find use in resensitizing mupirocin-resistant bacteria to mupirocin.
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12
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Roberts CA, Al-Tameemi HM, Mashruwala AA, Rosario-Cruz Z, Chauhan U, Sause WE, Torres VJ, Belden WJ, Boyd JM. The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils. Infect Immun 2017; 85:e00100-17. [PMID: 28320837 PMCID: PMC5442634 DOI: 10.1128/iai.00100-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/16/2017] [Indexed: 01/30/2023] Open
Abstract
Staphylococcus aureus remains a causative agent for morbidity and mortality worldwide. This is in part a result of antimicrobial resistance, highlighting the need to uncover novel antibiotic targets and to discover new therapeutic agents. In the present study, we explored the possibility that iron-sulfur (Fe-S) cluster synthesis is a viable antimicrobial target. RNA interference studies established that Suf (sulfur mobilization)-dependent Fe-S cluster synthesis is essential in S. aureus We found that sufCDSUB were cotranscribed and that suf transcription was positively influenced by sigma factor B. We characterized an S. aureus strain that contained a transposon inserted in the intergenic space between sufC and sufD (sufD*), resulting in decreased transcription of sufSUB Consistent with the transcriptional data, the sufD* strain had multiple phenotypes associated with impaired Fe-S protein maturation. They included decreased activities of Fe-S cluster-dependent enzymes, decreased growth in media lacking metabolites that require Fe-S proteins for synthesis, and decreased flux through the tricarboxylic acid (TCA) cycle. Decreased Fe-S cluster synthesis resulted in sensitivity to reactive oxygen and reactive nitrogen species, as well as increased DNA damage and impaired DNA repair. The sufD* strain also exhibited perturbed intracellular nonchelated Fe pools. Importantly, the sufD* strain did not exhibit altered exoprotein production or altered biofilm formation, but it was attenuated for survival upon challenge by human polymorphonuclear leukocytes. The results presented are consistent with the hypothesis that Fe-S cluster synthesis is a viable target for antimicrobial development.
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Affiliation(s)
- Christina A Roberts
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hassan M Al-Tameemi
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ameya A Mashruwala
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Zuelay Rosario-Cruz
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Unnati Chauhan
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - William E Sause
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - William J Belden
- Department of Animal Sciences, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
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13
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Matos RG, Casinhas J, Bárria C, dos Santos RF, Silva IJ, Arraiano CM. The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens. Front Microbiol 2017; 8:910. [PMID: 28579982 PMCID: PMC5437115 DOI: 10.3389/fmicb.2017.00910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/04/2017] [Indexed: 12/02/2022] Open
Abstract
Contaminated food is the source of many severe infections in humans. Recent advances in food science have discovered new foodborne pathogens and progressed in characterizing their biology, life cycle, and infection processes. All this knowledge has been contributing to prevent food contamination, and to develop new therapeutics to treat the infections caused by these pathogens. RNA metabolism is a crucial biological process and has an enormous potential to offer new strategies to fight foodborne pathogens. In this review, we will summarize what is known about the role of bacterial ribonucleases and sRNAs in the virulence of several foodborne pathogens and how can we use that knowledge to prevent infection.
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Affiliation(s)
- Rute G. Matos
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de LisboaOeiras, Portugal
| | | | | | | | | | - Cecília M. Arraiano
- Control of Gene Expression Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de LisboaOeiras, Portugal
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14
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Gone S, Alfonso-Prieto M, Paudyal S, Nicholson AW. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation. Sci Rep 2016; 6:25448. [PMID: 27150669 PMCID: PMC4858673 DOI: 10.1038/srep25448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/15/2016] [Indexed: 12/15/2022] Open
Abstract
Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.
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Affiliation(s)
- Swapna Gone
- Department of Chemistry, Philadelphia PA, 19122, USA
| | | | - Samridhdi Paudyal
- Department of Biology, Temple University, Philadelphia PA, 19122, USA
| | - Allen W Nicholson
- Department of Chemistry, Philadelphia PA, 19122, USA.,Department of Biology, Temple University, Philadelphia PA, 19122, USA
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15
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Neomycin Sulfate Improves the Antimicrobial Activity of Mupirocin-Based Antibacterial Ointments. Antimicrob Agents Chemother 2015; 60:862-72. [PMID: 26596945 DOI: 10.1128/aac.02083-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/15/2015] [Indexed: 12/18/2022] Open
Abstract
In the midst of the current antimicrobial pipeline void, alternative approaches are needed to reduce the incidence of infection and decrease reliance on last-resort antibiotics for the therapeutic intervention of bacterial pathogens. In that regard, mupirocin ointment-based decolonization and wound maintenance practices have proven effective in reducing Staphylococcus aureus transmission and mitigating invasive disease. However, the emergence of mupirocin-resistant strains has compromised the agent's efficacy, necessitating new strategies for the prevention of staphylococcal infections. Herein, we set out to improve the performance of mupirocin-based ointments. A screen of a Food and Drug Administration (FDA)-approved drug library revealed that the antibiotic neomycin sulfate potentiates the antimicrobial activity of mupirocin, whereas other library antibiotics did not. Preliminary mechanism of action studies indicate that neomycin's potentiating activity may be mediated by inhibition of the organism's RNase P function, an enzyme that is believed to participate in the tRNA processing pathway immediately upstream of the primary target of mupirocin. The improved antimicrobial activity of neomycin and mupirocin was maintained in ointment formulations and reduced S. aureus bacterial burden in murine models of nasal colonization and wound site infections. Combination therapy improved upon the effects of either agent alone and was effective in the treatment of contemporary methicillin-susceptible, methicillin-resistant, and high-level mupirocin-resistant S. aureus strains. From these perspectives, combination mupirocin-and-neomycin ointments appear to be superior to that of mupirocin alone and warrant further development.
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