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Kovachka S, Panosetti M, Grimaldi B, Azoulay S, Di Giorgio A, Duca M. Small molecule approaches to targeting RNA. Nat Rev Chem 2024; 8:120-135. [PMID: 38278932 DOI: 10.1038/s41570-023-00569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.
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Affiliation(s)
- Sandra Kovachka
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Marc Panosetti
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Benedetto Grimaldi
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Stéphane Azoulay
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France.
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2
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Abadi B, Ilaghi M, Shahsavani Y, Faramarzpour M, Oghazian MB, Rahimi HR. Antibiotics with Antiviral and Anti-Inflammatory Potential Against Covid-19: A Review. Curr Rev Clin Exp Pharmacol 2023; 18:51-63. [PMID: 34994339 DOI: 10.2174/2772432817666220106162013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023]
Abstract
In Covid-19 cases, elderly patients in long-term care facilities, children younger than five years with moderate symptoms, and patients admitted to ICU or with comorbidities are at a high risk of coinfection, as suggested by the evidence. Thus, in these patients, antibiotic therapy based on empirical evidence is necessary. Finding appropriate antimicrobial agents, especially with antiviral and anti-inflammatory properties, is a promising approach to target the virus and its complications, hyper-inflammation, and microorganisms resulting in co-infection. Moreover, indiscriminate use of antibiotics can be accompanied by Clostridioides difficile colitis, the emergence of resistant microorganisms, and adverse drug reactions, particularly kidney damage and QT prolongation. Therefore, rational administration of efficient antibiotics is an important issue. The main objective of the present review is to provide a summary of antibiotics with possible antiviral activity against SARS-CoV-2 and anti-immunomodulatory effects to guide scientists for further research. Besides, the findings can help health professionals in the rational prescription of antibiotics in Covid-19 patients with a high risk of co-infection.
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Affiliation(s)
- Banafshe Abadi
- Brain Cancer Research Core (BCRC), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehran Ilaghi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Department of Infectious Diseases, Afzalipour Hospital, Kerman University of Medical Sciences, Kerman, Iran
| | - Yasamin Shahsavani
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahsa Faramarzpour
- Brain Cancer Research Core (BCRC), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Bagher Oghazian
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hamid-Reza Rahimi
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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3
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Tevyashova AN, Shapovalova KS. Potential for the Development of a New Generation of Aminoglycoside Antibiotics. Pharm Chem J 2022; 55:860-875. [PMID: 35039693 PMCID: PMC8754558 DOI: 10.1007/s11094-021-02510-0] [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: 07/11/2021] [Indexed: 11/29/2022]
Abstract
The present review summarizes recent publications devoted to aminoglycosides that study the main types of resistance to antibiotics of this class and the main directions of chemical modification aimed at overcoming the resistance or changing the spectrum of biological activity. Conjugates of aminoglycosides with various pharmacophores including amino acids, peptides, peptide nucleic acids, nucleic bases, and several other biologically active molecules and modifications resulting in other types of biological activity of this class of antibiotics are described. It is concluded that a promising research direction aimed at increasing the activity of antibiotics against resistant strains is the search for selective inhibitors of aminoglycoside-modifying enzymes. This would allow renewal of the use of antibiotics already meeting widespread resistance and would increase the potential of a new generation of antibiotics.
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Affiliation(s)
- A. N. Tevyashova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
| | - K. S. Shapovalova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
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4
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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5
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Bernacchi S, Ennifar E. Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry. Methods Mol Biol 2020; 2113:237-250. [PMID: 32006318 DOI: 10.1007/978-1-0716-0278-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Isothermal titration calorimetry (ITC) provides a sensitive, powerful, and accurate tool to suitably analyze the thermodynamic of RNA binding events. This approach does not require any modification or labeling of the system under analysis and is performed in solution. ITC is a very convenient technique that provides an accurate determination of binding parameters, as well as a complete thermodynamic profile of the molecular interactions. Here we show how this approach can be used to characterize the interactions between the dimerization initiation site (DIS) RNA localized within the HIV-1 viral genome and aminoglycoside antibiotics. Our ITC study showed that the 4,5-disubstituted 2-desoxystreptamine (2-DOS) aminoglycosides can bind the DIS with a nanomolar affinity and a high specificity.
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Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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6
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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7
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Dubois N, Marquet R, Paillart JC, Bernacchi S. Retroviral RNA Dimerization: From Structure to Functions. Front Microbiol 2018; 9:527. [PMID: 29623074 PMCID: PMC5874298 DOI: 10.3389/fmicb.2018.00527] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/08/2018] [Indexed: 01/18/2023] Open
Abstract
The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA) molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…), the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.
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Affiliation(s)
- Noé Dubois
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Serena Bernacchi
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
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8
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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9
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Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics. Biochem Pharmacol 2017; 134:56-73. [DOI: 10.1016/j.bcp.2016.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
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10
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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11
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Kamal A, Nekkanti S, Shankaraiah N, Sathish M. Future of Drug Discovery. DRUG RESISTANCE IN BACTERIA, FUNGI, MALARIA, AND CANCER 2017:609-629. [DOI: 10.1007/978-3-319-48683-3_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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12
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Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein. Biochemistry 2016; 55:6221-6229. [PMID: 27766833 DOI: 10.1021/acs.biochem.6b00748] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by systematic evolution of ligands by exponential enrichment. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used. A thermodynamic study using isothermal titration calorimetry (ITC) showed that the aptamer-RD interaction is driven by a large enthalpy change, and its unfavorable entropy change is compensated by a favorable enthalpy change. Furthermore, the binding heat capacity change was identified from the ITC data at various temperatures. The aptamer binding showed a large negative heat capacity change, which suggests that a large apolar surface is buried upon such binding. Thus, we proposed that the aptamer binds to RD with long-range electrostatic force in the early stage of the association and then changes its conformation and recognizes a large surface area of RD. These findings about the biophysics of aptamer binding should be useful for understanding the mechanism of RNA-protein interaction and optimizing and modifying RNA aptamers.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education, Instrumental Analysis Center, Yokohama National University , 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo , Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Ribomic Inc. , 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology , Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Jiménez-Moreno E, Montalvillo-Jiménez L, Santana AG, Gómez AM, Jiménez-Osés G, Corzana F, Bastida A, Jiménez-Barbero J, Cañada FJ, Gómez-Pinto I, González C, Asensio JL. Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders. J Am Chem Soc 2016; 138:6463-74. [DOI: 10.1021/jacs.6b00328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ester Jiménez-Moreno
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Andrés G. Santana
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
- Institute of Biocomputation and Physics of Complex Systems
(BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Bizkaia, Spain
- Basque Foundation for Science, Ikerbasque, 48013 Bilbao, Bizkaia, Spain
| | | | - Irene Gómez-Pinto
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes. Methods Mol Biol 2016; 1320:127-43. [PMID: 26227041 DOI: 10.1007/978-1-4939-2763-0_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The success rate of nucleic acids/ligands co-crystallization can be significantly improved by performing preliminary biophysical analyses. Among suitable biophysical approaches, isothermal titration calorimetry (ITC) is certainly a method of choice. ITC can be used in a wide range of experimental conditions to monitor in real time the formation of the RNA- or DNA-ligand complex, with the advantage of providing in addition the complete binding profile of the interaction. Following the ITC experiment, the complex is ready to be concentrated for crystallization trials. This chapter describes a detailed experimental protocol for using ITC as a tool for monitoring RNA/small molecule binding, followed by co-crystallization.
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Zhan P, Pannecouque C, De Clercq E, Liu X. Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends. J Med Chem 2015; 59:2849-78. [PMID: 26509831 DOI: 10.1021/acs.jmedchem.5b00497] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The early effectiveness of combinatorial antiretroviral therapy (cART) in the treatment of HIV infection has been compromised to some extent by rapid development of multidrug-resistant HIV strains, poor bioavailability, and cumulative toxicities, and so there is a need for alternative strategies of antiretroviral drug discovery and additional therapeutic agents with novel action modes or targets. From this perspective, we first review current strategies of antiretroviral drug discovery and optimization, with the aid of selected examples from the recent literature. We highlight the development of phosphate ester-based prodrugs as a means to improve the aqueous solubility of HIV inhibitors, and the introduction of the substrate envelope hypothesis as a new approach for overcoming HIV drug resistance. Finally, we discuss future directions for research, including opportunities for exploitation of novel antiretroviral targets, and the strategy of activation of latent HIV reservoirs as a means to eradicate the virus.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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16
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Alguacil J, Robles J, Ràfols C, Bosch E. Binding thermodynamics of paromomycin, neomycin, neomycin-dinucleotide and -diPNA conjugates to bacterial and human rRNA. J Mol Recognit 2015; 29:142-50. [DOI: 10.1002/jmr.2513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 09/18/2015] [Accepted: 09/19/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Javier Alguacil
- Departament de Química Orgànica; Facultat de Química and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
| | - Jordi Robles
- Departament de Química Orgànica; Facultat de Química and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
| | - Clara Ràfols
- Departament de Química Analítica; Facultat de Química and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
| | - Elisabeth Bosch
- Departament de Química Analítica; Facultat de Química and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona; Martí i Franquès, 1-11 08028 Barcelona Spain
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17
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Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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Le Grice SFJ. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol 2015; 389:147-69. [PMID: 25735922 PMCID: PMC7120518 DOI: 10.1007/82_2015_434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Small molecules targeting the enzymes responsible for human immunodeficiency virus (HIV) maturation, DNA synthesis and its subsequent chromosomal integration as ribonucleotide-free double-stranded DNA remain the mainstay of combination antiretroviral therapy. For infected individuals harboring drug-susceptible virus, this approach has afforded complete or near-complete viral suppression. However, in the absence of a curative strategy, the predictable emergence of drug-resistant variants requires continued development of improved antiviral strategies, inherent to which is the necessity of identifying novel targets. Regulatory elements that mediate transcription, translation, nucleocytoplasmic transport, dimerization, packaging and reverse transcription of the (+) strand RNA genome should now be considered viable targets for small molecule, peptide- and oligonucleotide-based therapeutics. Where target specificity and cellular penetration and toxicity have been the primary obstacle to successful “macromolecule therapeutics”, this chapter summarizes (a) novel approaches targeting RNA motifs whose three-dimensional structure is critical for biological function and consequently may be less prone to resistance-conferring mutations and (b) improved methods for delivery.
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Affiliation(s)
- Stuart F J Le Grice
- RT Biochemistry Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA,
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19
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Leeder WM, Reuss AJ, Brecht M, Kratz K, Wachtveitl J, Göringer HU. Charge reduction and thermodynamic stabilization of substrate RNAs inhibit RNA editing. PLoS One 2015; 10:e0118940. [PMID: 25742417 PMCID: PMC4350841 DOI: 10.1371/journal.pone.0118940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/07/2015] [Indexed: 01/04/2023] Open
Abstract
African trypanosomes cause a parasitic disease known as sleeping sickness. Mitochondrial transcript maturation in these organisms requires a RNA editing reaction that is characterized by the insertion and deletion of U-nucleotides into otherwise non-functional mRNAs. Editing represents an ideal target for a parasite-specific therapeutic intervention since the reaction cycle is absent in the infected host. In addition, editing relies on a macromolecular protein complex, the editosome, that only exists in the parasite. Therefore, all attempts to search for editing interfering compounds have been focused on molecules that bind to proteins of the editing machinery. However, in analogy to other RNA-driven biochemical pathways it should be possible to stall the reaction by targeting its substrate RNAs. Here we demonstrate inhibition of editing by specific aminoglycosides. The molecules bind into the major groove of the gRNA/pre-mRNA editing substrates thereby causing a stabilization of the RNA molecules through charge compensation and an increase in stacking. The data shed light on mechanistic details of the editing process and identify critical parameters for the development of new trypanocidal compounds.
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Affiliation(s)
- W.-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Andreas J. Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Michael Brecht
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Katja Kratz
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - H. Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
- * E-mail:
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Blond A, Ennifar E, Tisné C, Micouin L. The design of RNA binders: targeting the HIV replication cycle as a case study. ChemMedChem 2014; 9:1982-96. [PMID: 25100137 DOI: 10.1002/cmdc.201402259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Indexed: 01/08/2023]
Abstract
The human immunodeficiency virus 1 (HIV-1) replication cycle is finely tuned with many important steps involving RNA-RNA or protein-RNA interactions, all of them being potential targets for the development of new antiviral compounds. This cycle can also be considered as a good benchmark for the evaluation of early-stage strategies aiming at designing drugs that bind to RNA, with the possibility to correlate in vitro activities with antiviral properties. In this review, we highlight different approaches developed to interfere with four important steps of the HIV-1 replication cycle: the early stage of reverse transcription, the transactivation of viral transcription, the nuclear export of partially spliced transcripts and the dimerization step.
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Affiliation(s)
- Aurélie Blond
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 Rue des Saints Pères, 75006 Paris (France)
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21
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Mundigala H, Michaux JB, Feig AL, Ennifar E, Rueda D. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Nucleic Acids Res 2014; 42:7281-9. [PMID: 24813449 PMCID: PMC4066764 DOI: 10.1093/nar/gku332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The HIV-1 dimerization initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin motif in the 5′-untranslated region of its RNA genome. DIS hairpin plays an important role in genome dimerization by forming a ‘kissing complex’ between two complementary hairpins. Understanding the kinetics of this interaction is key to exploiting DIS as a possible human immunodeficiency virus (HIV) drug target. Here, we present a single-molecule Förster resonance energy transfer (smFRET) study of the dimerization reaction kinetics. Our data show the real-time formation and dissociation dynamics of individual kissing complexes, as well as the formation of the mature extended duplex complex that is ultimately required for virion packaging. Interestingly, the single-molecule trajectories reveal the presence of a previously unobserved bent intermediate required for extended duplex formation. The universally conserved A272 is essential for the formation of this intermediate, which is stabilized by Mg2+, but not by K+ cations. We propose a 3D model of a possible bent intermediate and a minimal dimerization pathway consisting of three steps with two obligatory intermediates (kissing complex and bent intermediate) and driven by Mg2+ ions.
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Affiliation(s)
- Hansini Mundigala
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | | | - Andrew L Feig
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA Department of Medicine, Section of Virology, Imperial College, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College, London W12 0NN, UK
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