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Díaz-Casado L, Santana AG, Gómez-Pinto I, Villacampa A, Corzana F, Jiménez-Barbero J, González C, Asensio JL. Binding-driven reactivity attenuation enables NMR identification of selective drug candidates for nucleic acid targets. Commun Chem 2022; 5:137. [PMID: 36697799 PMCID: PMC9814457 DOI: 10.1038/s42004-022-00755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 01/28/2023] Open
Abstract
NMR methods, and in particular ligand-based approaches, are among the most robust and reliable alternatives for binding detection and consequently, they have become highly popular in the context of hit identification and drug discovery. However, when dealing with DNA/RNA targets, these techniques face limitations that have precluded widespread application in medicinal chemistry. In order to expand the arsenal of spectroscopic tools for binding detection and to overcome the existing difficulties, herein we explore the scope and limitations of a strategy that makes use of a binding indicator previously unexploited by NMR: the perturbation of the ligand reactivity caused by complex formation. The obtained results indicate that ligand reactivity can be utilised to reveal association processes and identify the best binders within mixtures of significant complexity, providing a conceptually different reactivity-based alternative within NMR screening methods.
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Affiliation(s)
- Laura Díaz-Casado
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G. Santana
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Irene Gómez-Pinto
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Alejandro Villacampa
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Francisco Corzana
- grid.119021.a0000 0001 2174 6969Dept. Química and Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26005 La Rioja, Spain
| | - Jesús Jiménez-Barbero
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC-bioGUNE). Derio, 48160 Bizkaia, Spain
| | - Carlos González
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Juan Luis Asensio
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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2
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Liu X, Ding F, Guo Y, Jiang K, Fu Y, Zhu L, Li M, Zhu X, Zhang C. Complexing the Pre-assembled Brush-like siRNA with Poly(β-amino ester) for Efficient Gene Silencing. ACS APPLIED BIO MATERIALS 2022; 5:1857-1867. [PMID: 35107256 DOI: 10.1021/acsabm.1c01182] [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: 11/29/2022]
Abstract
Small interfering RNA (siRNA) has been emerging as a highly selective and effective pharmaceutics for treating broad classes of diseases. However, the practical application of siRNA agent is often hampered by its poor crossing of the cellular membrane barrier and ineffective releasing from endosome to cytoplasm, leading to low gene silencing efficacy for clinical purposes. Thus far, cationic lipid and polymer-based vectors have been extensively explored for gene delivery. Yet condensing the rigid and highly negatively charged siRNA duplex to form a stable complex vehicle usually requires a large load of cationic carriers, prone to raising the toxicity issue for delivery. Herein, we develop a simple strategy that can efficiently condense the siRNAs into nanoparticle vehicles for target gene regulation. In this approach, we first employ a DNA-grafted polycaprolactone (DNA-g-PCL) brush as template to organize the small rigid siRNAs into a large brush-like structure (siRNA-brush) through nucleic acid hybridization. Then, the siRNA-brush assembly is condensed by an ionizable and biodegradable polymer (poly(β-amino ester), PBAE) under acidic buffer condition to form a stable nanoparticle for siRNA delivery. Compared to the free siRNAs with poor complexing capability with PBAE, the large brush-like siRNA assemblies with more complicated topological architecture significantly promotes their electrostatic interaction with PBAE, enabling the formation of complexed nanoparticles at low weight ratio of polymer to siRNA. Additionally, PBAE/siRNA-brush complexes exhibit good biocompatibility and stability under physiological condition, as well as enhanced cellular internalization. When equipped with functional siRNAs, the obtained delivery system demonstrates excellent downregulation of target genes both in vitro and in vivo, through which the progression of hypertrophic scars can be retarded with negligible adverse effects in an xenografted mouse model.
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Affiliation(s)
- Xinlong Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Ding
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Guo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Jiang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lijuan Zhu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Ming Li
- Department of Dermatology, Institute of Dermatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Santana AG, Díaz-Casado L, Montalvillo L, Jiménez-Moreno E, Mann E, Asensio JL. Aromatic interactions in Glycochemistry: from molecular recognition to catalysis. Curr Med Chem 2021; 29:1208-1218. [PMID: 34254906 DOI: 10.2174/0929867328666210709120216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 11/22/2022]
Abstract
Aromatic platforms are ubiquitous recognition motifs occurring in protein carbohydrate binding domains (CBDs), RNA receptors and enzymes. They stabilize the glycoside/receptor complexes by participating in stacking CH/π interactions with either the α- or β- face of the corresponding pyranose units. In addition, the role played by aromatic units in the stabilization of glycoside cationic transition states has started being recognized in recent years. Extensive studies carried out during the last decade have allowed to dissect the main contributing forces that stabilize the carbohydrate/aromatic complexes, while helping delineate not only the standing relationship between the glycoside/aromatic chemical structures and the strength of this interaction, but also their potential influence on glycoside reactivity.
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Affiliation(s)
| | | | | | | | - Enrique Mann
- Instituto de Química Orgánica General (IQOG-CSIC), Madrid, Spain
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4
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Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA. Methods Mol Biol 2021; 2105:157-172. [PMID: 32088869 DOI: 10.1007/978-1-0716-0243-0_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the important roles noncoding RNAs play in gene expression, their sequence-specific recognition is important for both fundamental science and the pharmaceutical industry. However, most noncoding RNAs fold in complex helical structures that are challenging problems for molecular recognition. Herein, we describe a method for sequence-specific recognition of double-stranded RNA using peptide nucleic acids (PNAs) that form triple helices in the major grove of RNA under physiologically relevant conditions. We also outline methods for solid-phase conjugation of PNA with cell-penetrating peptides and fluorescent dyes. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.
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5
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Sun LZ, Jiang Y, Zhou Y, Chen SJ. RLDOCK: A New Method for Predicting RNA-Ligand Interactions. J Chem Theory Comput 2020; 16:7173-7183. [PMID: 33095555 DOI: 10.1021/acs.jctc.0c00798] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The ability to accurately predict the binding site, binding pose, and binding affinity for ligand-RNA binding is important for RNA-targeted drug design. Here, we describe a new computational method, RLDOCK, for predicting the binding site and binding pose for ligand-RNA binding. By developing an energy-based scoring function, we sample exhaustively all of the possible binding sites with flexible ligand conformations for a ligand-RNA pair based on the geometric and energetic scores. The model distinguishes from other approaches in three notable features. First, the model enables exhaustive scanning of all of the possible binding sites, including multiple alternative or coexisting binding sites, for a given ligand-RNA pair. Second, the model is based on a new energy-based scoring function developed here. Third, the model employs a novel multistep screening algorithm to improve computational efficiency. Specifically, first, for each binding site, we use a gird-based energy map to rank the binding sites according to the minimum Lennard-Jones potential energy for the different ligand poses. Second, for a given selected binding site, we predict the ligand pose using a two-step algorithm. In the first step, we quickly identify the probable ligand poses using a coarse-grained simplified energy function. In the second step, for each of the probable ligand poses, we predict the ligand poses using a refined energy function. Tests of the RLDOCK for a set of 230 RNA-ligand-bound structures indicate that RLDOCK can successfully predict ligand poses for 27.8, 58.3, and 69.6% of all of the test cases with the root-mean-square deviation within 1.0, 2.0, and 3.0 Å, respectively, for the top three predicted docking poses. The computational method presented here may enable the development of a new, more comprehensive framework for the prediction of ligand-RNA binding with an ensemble of RNA conformations and the metal-ion effects.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.,Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yangwei Jiang
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yuanzhe Zhou
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
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6
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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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7
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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8
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Zárate SG, Bastida A, Santana AG, Revuelta J. Synthesis of Ring II/III Fragment of Kanamycin: A New Minimum Structural Motif for Aminoglycoside Recognition. Antibiotics (Basel) 2019; 8:antibiotics8030109. [PMID: 31382490 PMCID: PMC6783941 DOI: 10.3390/antibiotics8030109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 11/30/2022] Open
Abstract
A novel protocol has been established to prepare the kanamycin ring II/III fragment, which has been validated as a minimum structural motif for the development of new aminoglycosides on the basis of its bactericidal activity even against resistant strains. Furthermore, its ability to act as a AAC-(6′) and APH-(3′) binder, and as a poor substrate for the ravenous ANT-(4′), makes it an excellent candidate for the design of inhibitors of these aminoglycoside modifying enzymes.
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Affiliation(s)
- Sandra G Zárate
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
- Facultad de Tecnología, Carrera de Ingeniería Química, Universidad Mayor, Real y Pontificia de San Francisco Xavier de Chuquisaca, Regimiento Campos 180, Casilla 60-B Sucre, Bolivia
| | - Agatha Bastida
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G Santana
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Julia Revuelta
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
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9
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Arjmand F, Afsan Z, Sharma S, Parveen S, Yousuf I, Sartaj S, Siddique HR, Tabassum S. Recent advances in metallodrug-like molecules targeting non-coding RNAs in cancer chemotherapy. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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10
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Identification of Chemical Inducers of the Phosphate-Starvation Signaling Pathway in A. thaliana Using Chemical Genetics. Methods Mol Biol 2018; 1795:65-84. [PMID: 29846919 DOI: 10.1007/978-1-4939-7874-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In spite of its importance for agriculture and 30 years of genetic studies, the phosphate-starvation signaling pathway, that allows plants to detect, respond, and adapt to changes in the phosphate concentration of the rhizosphere, remains poorly known. Chemical genetics has been increasingly and successfully used as a complementary approach to genetics for the dissection of signaling pathways in diverse organisms. Screens can be designed to identify chemicals interfering specifically with a pathway of interest. We designed a screen that led to the discovery of the first chemical capable to induce specifically the phosphate-starvation signaling pathway in Arabidopsis thaliana. This procedure, described here, can be adapted for the discovery of inducers or repressors of other pathways.
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11
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Ferron F, Weber F, de la Torre JC, Reguera J. Transcription and replication mechanisms of Bunyaviridae and Arenaviridae L proteins. Virus Res 2017; 234:118-134. [PMID: 28137457 PMCID: PMC7114536 DOI: 10.1016/j.virusres.2017.01.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/17/2017] [Accepted: 01/21/2017] [Indexed: 12/15/2022]
Abstract
Bunyavirus and arenavirus are important public health threats. Bunyavirus and arenavirus molecular biology, common and differential features. Implications of LACV L protein structure for understanding viral RNA synthesis. Current state and future perspectives on bunya- and arenavirus antivirals.
Bunyaviridae and Arenaviridae virus families include an important number of highly pathogenic viruses for humans. They are enveloped viruses with negative stranded RNA genomes divided into three (bunyaviruses) or two (arenaviruses) segments. Each genome segment is coated by the viral nucleoproteins (NPs) and the polymerase (L protein) to form a functional ribonucleoprotein (RNP) complex. The viral RNP provides the necessary context on which the L protein carries out the biosynthetic processes of RNA replication and gene transcription. Decades of research have provided a good understanding of the molecular processes underlying RNA synthesis, both RNA replication and gene transcription, for these two families of viruses. In this review we will provide a global view of the common features, as well as differences, of the molecular biology of Bunyaviridae and Arenaviridae. We will also describe structures of protein and protein-RNA complexes so far determined for these viral families, mainly focusing on the L protein, and discuss their implications for understanding the mechanisms of viral RNA replication and gene transcription within the architecture of viral RNPs, also taking into account the cellular context in which these processes occur. Finally, we will discuss the implications of these structural findings for the development of antiviral drugs to treat human diseases caused by members of the Bunyaviridae and Arenaviridae families.
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Affiliation(s)
- François Ferron
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | | | - Juan Reguera
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France; INSERM, AFMB UMR 7257, 13288 Marseille, France.
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12
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rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines. Antimicrob Agents Chemother 2016; 60:4433-41. [PMID: 27246781 DOI: 10.1128/aac.00594-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tetracycline antibiotics are known to be effective in the treatment of both infectious and noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the antibacterial action of the tetracyclines does not explain their activity against viruses, protozoa that lack mitochondria, and noninfectious conditions. Also, the mechanism by which the tetracyclines selectively inhibit microbial protein synthesis against host eukaryotic protein synthesis despite conservation of ribosome structure and functions is still questionable. Many studies have investigated the binding of the tetracyclines to the 16S rRNA using the small ribosomal subunit of different bacterial species, but there seems to be no agreement between various reports on the exact binding site on the 16S rRNA. The wide range of activity of the tetracyclines against a broad spectrum of bacterial pathogens, viruses, protozoa, and helminths, as well as noninfectious conditions, indicates a more generalized effect on RNA. In the light of recent evidence that the tetracyclines bind to various synthetic double-stranded RNAs (dsRNAs) of random base sequences, suggesting that the double-stranded structures may play a more important role in the binding of the tetracyclines to RNA than the specific base pairs, as earlier speculated, it is imperative to consider possible alternative binding modes or sites that could help explain the mechanisms of action of the tetracyclines against various pathogens and disease conditions.
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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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14
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Interaction of the tetracyclines with double-stranded RNAs of random base sequence: new perspectives on the target and mechanism of action. J Antibiot (Tokyo) 2016; 69:622-30. [PMID: 26786504 DOI: 10.1038/ja.2015.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/02/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023]
Abstract
The 16S rRNA binding mechanism proposed for the antibacterial action of the tetracyclines does not explain their mechanism of action against non-bacterial pathogens. In addition, several contradictory base pairs have been proposed as their binding sites on the 16S rRNA. This study investigated the binding of minocycline and doxycycline to short double-stranded RNAs (dsRNAs) of random base sequences. These tetracyclines caused a dose-dependent decrease in the fluorescence intensities of 6-carboxyfluorescein (FAM)-labelled dsRNA and ethidium bromide (EtBr)-stained dsRNA, indicating that both drugs bind to dsRNA of random base sequence in a manner that is competitive with the binding of EtBr and other nucleic acid ligands often used as stains. This effect was observable in the presence of Mg(2+). The binding of the tetracyclines to dsRNA changed features of the fluorescence emission spectra of the drugs and the CD spectra of the RNA, and inhibited RNase III cleavage of the dsRNA. These results indicate that the double-stranded structures of RNAs may have a more important role in their interaction with the tetracyclines than the specific base pairs, which had hitherto been the subject of much investigation. Given the diverse functions of cellular RNAs, the binding of the tetracyclines to their double-stranded helixes may alter the normal processing and functioning of the various biological processes they regulate. This could help to explain the wide range of action of the tetracyclines against various pathogens and disease conditions.
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15
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Santana AG, Zárate SG, Asensio JL, Revuelta J, Bastida A. Selective modification of the 3''-amino group of kanamycin prevents significant loss of activity in resistant bacterial strains. Org Biomol Chem 2016; 14:516-525. [PMID: 26501183 DOI: 10.1039/c5ob01599e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminoglycosides are highly potent, wide-spectrum bactericidals. N-1 modification of aminoglycosides has thus far been the best approach to regain bactericidal efficiency of this class of antibiotics against resistant bacterial strains. In the present study we have evaluated the effect that both, the number of modifications and their distribution on the aminoglycoside amino groups (N-1, N-3, N-6' and N-3''), have on the antibiotic activity. The modification of N-3'' in the antibiotic kanamycin A is the key towards the design of new aminoglycoside antibiotics. This derivative maintains the antibiotic activity against aminoglycoside acetyl-transferase- and nucleotidyl-transferase-expressing strains, which are two of the most prevalent modifying enzymes found in aminoglycoside resistant bacteria.
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Affiliation(s)
- Andrés G Santana
- CSIC, Department of Bioorganic Chemistry, c/Juan de la Cierva, 3, 28006-Madrid, Spain.
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16
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Tumir LM, Radić Stojković M, Piantanida I. Come-back of phenanthridine and phenanthridinium derivatives in the 21st century. Beilstein J Org Chem 2014; 10:2930-54. [PMID: 25550761 PMCID: PMC4273281 DOI: 10.3762/bjoc.10.312] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/21/2014] [Indexed: 12/23/2022] Open
Abstract
Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.
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Affiliation(s)
- Lidija-Marija Tumir
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
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17
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Interactions with polynucleotides and antitumor activity of amidino and imidazolinyl substituted 2-phenylbenzothiazole mesylates. Eur J Med Chem 2014; 86:406-19. [PMID: 25194933 DOI: 10.1016/j.ejmech.2014.08.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/12/2014] [Accepted: 08/30/2014] [Indexed: 11/23/2022]
Abstract
Based on previously reported antiproliferative activity screening, four most promising disubstituted 2-phenylbenzothiazole hydrochlorides were chosen for detailed study. Water solubility, as well as liphophilicity/hydrophilicity balance of organic core were modified by conversion to mesylate salts. For purpose of structure/activity studies their structures were determined by X-ray structure analysis. Detailed analysis of interactions of new compounds with double stranded (ds-) DNA/RNA by UV/Vis and CD titrations, thermal melting and viscometry experiments revealed that most of studied compounds intercalate into ds-RNA but bind into minor groove of AT-DNA, and agglomerate along GC-DNA. Furthermore, compounds also interact with ss-RNA, but only amino-imidazolinyl 2-phenylbenzothiazole, 4b displayed well defined orientation and dominant binding mode (by induced CD signals) with poly A and poly G. Besides, in vitro investigations revealed moderate to high antiproliferative activity of benzothiazoles against seven human cancer cell lines, while in some cases (HTC 116, SW620, MIA PaCa-2) high correlation between the type of the amidino group and cytotoxic activity was observed.
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18
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Henriksen NM, Hayatshahi HS, Davis D, Cheatham TE. Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations. J Chem Inf Model 2014; 54:1758-72. [PMID: 24835734 PMCID: PMC4076022 DOI: 10.1021/ci500132c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 12/15/2022]
Abstract
Despite the many biological functions of RNA, very few drugs have been designed or found to target RNA. Here we report the results of molecular dynamics (MD) simulations and binding energy analyses on hepatitis C virus internal ribosome entry site (IRES) RNA in complex with highly charged 2-aminobenzimidazole inhibitors. Initial coordinates were taken from NMR and crystallography studies that had yielded different binding modes. During MD simulations, the RNA-inhibitor complex is stable in the crystal conformation but not in the NMR conformation. Additionally, we found that existing and standard MD trajectory postprocessing free energy methods, such as the MM-GBSA and MM-PBSA approaches available in AMBER, seem unsuitable to properly rank the binding energies of complexes between highly charged molecules. A better correlation with the experimental data was found using a rather simple binding enthalpy calculation based on the explicitly solvated potential energies. In anticipation of further growth in the use of small molecules to target RNA, we include results addressing the impact of charge assignment on docking, the structural role of magnesium in the IRES-inhibitor complex, the entropic contribution to binding energy, and simulations of a plausible scaffold design for new inhibitors.
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Affiliation(s)
| | - Hamed S. Hayatshahi
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Darrell
R. Davis
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
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19
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Dela-Moss LI, Moss WN, Turner DH. Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C. BMC Res Notes 2014; 7:22. [PMID: 24405943 PMCID: PMC3895672 DOI: 10.1186/1756-0500-7-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/02/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Influenza B and C are single-stranded RNA viruses that cause yearly epidemics and infections. Knowledge of RNA secondary structure generated by influenza B and C will be helpful in further understanding the role of RNA structure in the progression of influenza infection. FINDINGS All available protein-coding sequences for influenza B and C were analyzed for regions with high potential for functional RNA secondary structure. On the basis of conserved RNA secondary structure with predicted high thermodynamic stability, putative structures were identified that contain splice sites in segment 8 of influenza B and segments 6 and 7 of influenza C. The sequence in segment 6 also contains three unused AUG start codon sites that are sequestered within a hairpin structure. CONCLUSIONS When added to previous studies on influenza A, the results suggest that influenza splicing may share common structural strategies for regulation of splicing. In particular, influenza 3' splice sites are predicted to form secondary structures that can switch conformation to regulate splicing. Thus, these RNA structures present attractive targets for therapeutics aimed at targeting one or the other conformation.
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Affiliation(s)
- Lumbini I Dela-Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
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20
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Kulkarni SS, Chi FC, Hung SC. Biologically PotentL-Hexoses and 6-Deoxy-L-Hexoses: Their Syntheses and Applications. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Bellaousov S, Reuter JS, Seetin MG, Mathews DH. RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res 2013; 41:W471-4. [PMID: 23620284 PMCID: PMC3692136 DOI: 10.1093/nar/gkt290] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provided. Additionally, the server can predict secondary structures conserved in either two homologs or more than two homologs. Folding free energy changes can be predicted for a given RNA structure using nearest neighbor rules. Secondary structures can be compared using circular plots or the scoring methods, sensitivity and positive predictive value. Additionally, structure drawings can be rendered as SVG, postscript, jpeg or pdf. The web server is freely available for public use at: http://rna.urmc.rochester.edu/RNAstructureWeb.
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Affiliation(s)
- Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
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22
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Abstract
RNA molecules have highly versatile structures that can fold into myriad conformations, providing many potential pockets for binding small molecules. The increasing number of available RNA structures, in complex with proteins, small ligands and in free form, enables the design of new therapeutically useful RNA-binding ligands. Here we studied RNA ligand complexes from 10 RNA groups extracted from the protein data bank (PDB), including adaptive and non-adaptive complexes. We analyzed the chemical, physical, structural and conformational properties of binding pockets around the ligand. Comparing the properties of ligand-binding pockets to the properties of computed pockets extracted from all available RNA structures and RNA-protein interfaces, revealed that ligand-binding pockets, mainly the adaptive pockets, are characterized by unique properties, specifically enriched in rare conformations of the nucleobase and the sugar pucker. Further, we demonstrate that nucleotides possessing the rare conformations are preferentially involved in direct interactions with the ligand. Overall, based on our comprehensive analysis of RNA-ligand complexes, we suggest that the unique conformations adopted by RNA nucleotides play an important role in RNA recognition by small ligands. We term the recognition of a binding site by a ligand via the unique RNA conformations "RNA conformational readout." We propose that "conformational readout" is a general way by which RNA binding pockets are recognized and selected from an ensemble of different RNA states.
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Affiliation(s)
- Efrat Kligun
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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23
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Frolov L, Dix A, Tor Y, Tesler AB, Chaikin Y, Vaskevich A, Rubinstein I. Direct observation of aminoglycoside-RNA binding by localized surface plasmon resonance spectroscopy. Anal Chem 2013; 85:2200-7. [PMID: 23368968 DOI: 10.1021/ac3029079] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA is involved in fundamental biological functions when bacterial pathogens replicate. Identifying and studying small molecules that can interact with bacterial RNA and interrupt cellular activities is a promising path for drug design. Aminoglycoside (AMG) antibiotics, prominent natural products that recognize RNA specifically, exert their biological functions by binding to prokaryotic ribosomal RNA and interfering with protein translation, ultimately resulting in bacterial cell death. The decoding site, a small internal loop within the 16S rRNA, is the molecular target for the AMG antibiotics. The specificity of neomycin B, a highly potent AMG antibiotic, to the ribosomal decoding RNA site, was previously studied by observing AMG-RNA complexes in solution. Here, we study this interaction using localized surface plasmon resonance (LSPR) transducers comprising gold island films prepared by evaporation on glass and annealing. Small molecule AMG receptors were immobilized on the Au islands via polyethylene glycol (PEG)-thiol linkers, and the interaction with target RNA in solution was studied by monitoring the change in the LSPR optical response upon binding. The results show high-affinity binding of neomycin to 27-nucleotide model A-site RNA sequence in the nanomolar range, while no specific binding is observed for synthetic RNA oligomers (e.g., poly-U). The impact of specific base substitutions in the A-site RNA constructs on binding affinity and selectivity is determined quantitatively. It is concluded that LSPR is a powerful tool for providing molecular insight into small molecule-RNA interactions and for the design and screening of selective antimicrobial drugs.
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Affiliation(s)
- Ludmila Frolov
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One 2012; 7:e38323. [PMID: 22685560 PMCID: PMC3369869 DOI: 10.1371/journal.pone.0038323] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
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Affiliation(s)
- Walter N. Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Salvatore F. Priore
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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25
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Matesanz R, Diaz JF, Corzana F, Santana AG, Bastida A, Asensio JL. Multiple keys for a single lock: the unusual structural plasticity of the nucleotidyltransferase (4')/kanamycin complex. Chemistry 2012; 18:2875-89. [PMID: 22298309 DOI: 10.1002/chem.201101888] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 12/05/2011] [Indexed: 11/09/2022]
Abstract
The most common mode of bacterial resistance to aminoglycoside antibiotics is the enzyme-catalysed chemical modification of the drug. Over the last two decades, significant efforts in medicinal chemistry have been focused on the design of non- inactivable antibiotics. Unfortunately, this strategy has met with limited success on account of the remarkably wide substrate specificity of aminoglycoside-modifying enzymes. To understand the mechanisms behind substrate promiscuity, we have performed a comprehensive experimental and theoretical analysis of the molecular-recognition processes that lead to antibiotic inactivation by Staphylococcus aureus nucleotidyltransferase 4'(ANT(4')), a clinically relevant protein. According to our results, the ability of this enzyme to inactivate structurally diverse polycationic molecules relies on three specific features of the catalytic region. First, the dominant role of electrostatics in aminoglycoside recognition, in combination with the significant extension of the enzyme anionic regions, confers to the protein/antibiotic complex a highly dynamic character. The motion deduced for the bound antibiotic seem to be essential for the enzyme action and probably provide a mechanism to explore alternative drug inactivation modes. Second, the nucleotide recognition is exclusively mediated by the inorganic fragment. In fact, even inorganic triphosphate can be employed as a substrate. Third, ANT(4') seems to be equipped with a duplicated basic catalyst that is able to promote drug inactivation through different reactive geometries. This particular combination of features explains the enzyme versatility and renders the design of non-inactivable derivatives a challenging task.
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Affiliation(s)
- Ruth Matesanz
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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26
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Gupta P, Muse O, Rozners E. Recognition of double-stranded RNA by guanidine-modified peptide nucleic acids. Biochemistry 2011; 51:63-73. [PMID: 22146072 DOI: 10.1021/bi201570a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double-helical RNA has become an attractive target for molecular recognition because many noncoding RNAs play important roles in the control of gene expression. Recently, we discovered that short peptide nucleic acids (PNA) bind strongly and sequence selectively to a homopurine tract of double-helical RNA via formation of a triple helix. Herein, we tested if the molecular recognition of RNA could be enhanced by α-guanidine modification of PNA. Our study was motivated by the discovery of Ly and co-workers that the guanidine modification greatly enhances the cellular delivery of PNA. Isothermal titration calorimetry showed that the guanidine-modified PNA (GPNA) had reduced affinity and sequence selectivity for triple-helical recognition of RNA. The data suggested that in contrast to unmodified PNA, which formed a 1:1 PNA-RNA triple helix, GPNA preferred a 2:1 GPNA-RNA triplex invasion complex. Nevertheless, promising results were obtained for recognition of biologically relevant double-helical RNA. Consistent with enhanced strand invasion ability, GPNA derived from d-arginine recognized the transactivation response element of HIV-1 with high affinity and sequence selectivity, presumably via Watson-Crick duplex formation. On the other hand, strong and sequence selective triple helices were formed by unmodified and nucelobase-modified PNA and the purine-rich strand of the bacterial A-site. These results suggest that appropriate chemical modifications of PNA may enhance molecular recognition of complex noncoding RNAs.
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Affiliation(s)
- Pankaj Gupta
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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27
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Gupta P, Zengeya T, Rozners E. Triple helical recognition of pyrimidine inversions in polypurine tracts of RNA by nucleobase-modified PNA. Chem Commun (Camb) 2011; 47:11125-7. [PMID: 21909545 DOI: 10.1039/c1cc14706d] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids containing 2-pyrimidinone (P) and 3-oxo-2,3-dihydropyridazine (E) heterocycles recognized C-G and U-A inversions in a polypurine tract of double helical RNA with high affinity and sequence selectivity at pH 6.25. E-modified PNA bound strongly to bacterial A-site RNA, while no binding was observed to the human A-site RNA.
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Affiliation(s)
- Pankaj Gupta
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, USA
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28
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Conjugate of neamine and 2-deoxystreptamine mimic connected by an amide bond. Bioorg Med Chem Lett 2011; 21:4713-5. [DOI: 10.1016/j.bmcl.2011.06.084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/16/2011] [Accepted: 06/17/2011] [Indexed: 11/24/2022]
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29
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Moss WN, Priore SF, Turner DH. Identification of potential conserved RNA secondary structure throughout influenza A coding regions. RNA (NEW YORK, N.Y.) 2011; 17:991-1011. [PMID: 21536710 PMCID: PMC3096049 DOI: 10.1261/rna.2619511] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, including two previously described structured regions. Of these predictions, eight have high thermodynamic stability and SSCU, with five of these corresponding to current annotations (e.g., splice sites), while the remaining 12 are predicted by the thermodynamics alone. Secondary structures with high conservation of base-pairing are proposed within the five regions having known function. A combination of thermodynamics, amino acid and nucleotide sequence comparisons along with SSCU was essential for revealing potential secondary structures.
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Affiliation(s)
- Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
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30
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Arenavirus reverse genetics: new approaches for the investigation of arenavirus biology and development of antiviral strategies. Virology 2011; 411:416-25. [PMID: 21324503 PMCID: PMC3057228 DOI: 10.1016/j.virol.2011.01.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 01/12/2011] [Indexed: 10/25/2022]
Abstract
Several arenaviruses, chiefly Lassa virus, cause hemorrhagic fever disease in humans and pose a significant public health problem in their endemic regions. On the other hand the prototypic arenavirus LCMV is a superb workhorse for the investigation of virus-host interactions and associated disease. The development of novel antiviral strategies to combat pathogenic arenaviruses would be facilitated by a detailed understanding of the arenavirus molecular and cell biology. To this end, the development of reverse genetic systems for several arenaviruses has provided investigators with novel and powerful approaches to dissect the functions of arenavirus proteins and their interactions with host factors required to complete each of the steps of the virus life cycle, as well as to cause disease.
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31
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Zengeya T, Li M, Rozners E. PNA containing isocytidine nucleobase: synthesis and recognition of double helical RNA. Bioorg Med Chem Lett 2011; 21:2121-4. [PMID: 21333533 DOI: 10.1016/j.bmcl.2011.01.130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 01/25/2011] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
Abstract
Peptide nucleic acid (PNA1) containing a 5-methylisocytidine (iC) nucleobase has been synthesized. Triple helix formation between PNA1 and RNA hairpins having variable base pairs interacting with iC was studied using isothermal titration calorimetry. The iC nucleobase recognized the proposed target, C-G inversion in polypurine tract of RNA, with slightly higher affinity than the natural nucleobases, though the sequence selectivity of recognition was low. Compared to non-modified PNA, PNA1 had lower affinity for its RNA target.
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Affiliation(s)
- Thomas Zengeya
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
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32
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McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:209-32. [DOI: 10.1002/wrna.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Li M, Zengeya T, Rozners E. Short peptide nucleic acids bind strongly to homopurine tract of double helical RNA at pH 5.5. J Am Chem Soc 2010; 132:8676-81. [PMID: 20527745 DOI: 10.1021/ja101384k] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The important role that noncoding RNA plays in cell biology makes it an attractive target for molecular recognition. However, the discovery of small molecules that bind double helical RNA selectively and may serve as biochemical probes and potential drug leads has been relatively slow. Herein, we show that peptide nucleic acids, as short as six nucleobases, bind very strongly (K(a) > 10(7)) and sequence selectively to a homopurine tract of double helical RNA at pH 5.5. The isothermal titration calorimetry and circular dichroism experiments suggest that the binding mode may be a sequence selective triple helix formation. Our results have implications for development of biochemical probes to study function of noncoding RNAs and design of compounds with potential antibacterial and antiviral activity.
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Affiliation(s)
- Ming Li
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, USA
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34
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Vacas T, Corzana F, Jiménez-Osés G, González C, Gómez AM, Bastida A, Revuelta J, Asensio JL. Role of Aromatic Rings in the Molecular Recognition of Aminoglycoside Antibiotics: Implications for Drug Design. J Am Chem Soc 2010; 132:12074-90. [DOI: 10.1021/ja1046439] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatiana Vacas
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Francisco Corzana
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Carlos González
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Julia Revuelta
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
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35
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Identification of RNA-binding sites in proteins by integrating various sequence information. Amino Acids 2010; 40:239-48. [DOI: 10.1007/s00726-010-0639-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 05/22/2010] [Indexed: 12/12/2022]
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36
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Ramisetty SR, Baranger AM. Cooperative binding of a quinoline derivative to an RNA stem loop containing a dangling end. Bioorg Med Chem Lett 2010; 20:3134-7. [DOI: 10.1016/j.bmcl.2010.03.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/23/2010] [Accepted: 03/26/2010] [Indexed: 11/25/2022]
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37
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Revuelta J, Vacas T, Corzana F, Gonzalez C, Bastida A, Asensio JL. Structure-based design of highly crowded ribostamycin/kanamycin hybrids as a new family of antibiotics. Chemistry 2010; 16:2986-91. [PMID: 20162651 DOI: 10.1002/chem.200903003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Revuelta
- Departamento de Química Bio-orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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38
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Zhang J, Umemoto S, Nakatani K. Fluorescent Indicator Displacement Assay for Ligand−RNA Interactions. J Am Chem Soc 2010; 132:3660-1. [DOI: 10.1021/ja100089u] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinhua Zhang
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
| | - Shiori Umemoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
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39
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Meyer ST, Hergenrother PJ. Small molecule ligands for bulged RNA secondary structures. Org Lett 2010; 11:4052-5. [PMID: 19678613 DOI: 10.1021/ol901478x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.
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Affiliation(s)
- S Todd Meyer
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61801, USA
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40
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Sherer EC. Antibiotics Targeting the Ribosome: Structure-Based Design and the Nobel Prize. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1574-1400(10)06009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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41
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Islam MM, Suresh Kumar G. RNA-binding potential of protoberberine alkaloids: spectroscopic and calorimetric studies on the binding of berberine, palmatine, and coralyne to protonated RNA structures. DNA Cell Biol 2009; 28:637-50. [PMID: 19715476 DOI: 10.1089/dna.2009.0930] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interaction of the protoberberine alkaloids berberine, palmatine, and coralyne with the two double-stranded RNA homopolymers of cytidine-guanosine (CG) and inosine-cytidine (IC) sequences in the protonated conformation was investigated using various biophysical techniques. All the three alkaloids bound polyC(+)G in a cooperative way. The binding of coralyne to both the polyribonucleotides was stronger than that of berberine and palmatine. Evidence for the intercalative binding of coralyne was revealed from fluorescence quenching studies. Isothermal titration calorimetry results suggested that the binding of berberine to both the polymers and palmatine to polyIC(+) was very weak while that of palmatine and coralyne to polyC(+)G and polyIC(+) was predominantly entropy driven. Circular dichroic results provided evidence for the perturbation of the RNA conformation with the bound coralyne in a more deeply intercalated position compared to berberine and palmatine as revealed by induced circular dichroism peaks. Taken together, the present study suggests that planarity of coralyne results in a more favorable and stronger binding to the double-stranded RNA conformations compared to berberine and palmatine that may potentiate its use in RNA-targeted drug design.
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Affiliation(s)
- M M Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata 700032, India.
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42
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Warui DM, Baranger AM. Identification of Specific Small Molecule Ligands for Stem Loop 3 Ribonucleic Acid of the Packaging Signal Ψ of Human Immunodeficiency Virus-1. J Med Chem 2009; 52:5462-73. [DOI: 10.1021/jm900599v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Douglas M. Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Anne M. Baranger
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
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43
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Keene FR, Smith JA, Collins JG. Metal complexes as structure-selective binding agents for nucleic acids. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2009.01.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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44
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Xu Y, Jin H, Yang Z, Zhang L, Zhang L. Synthesis and biological evaluation of novel neamine–nucleoside conjugates potentially targeting to RNAs. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.04.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Synthesis and evaluation of novel neamine derivatives effectively targeting to RNA. Bioorg Med Chem Lett 2009; 19:2103-6. [DOI: 10.1016/j.bmcl.2009.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 02/18/2009] [Accepted: 03/09/2009] [Indexed: 11/21/2022]
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46
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de la Torre JC. Reverse genetics approaches to combat pathogenic arenaviruses. Antiviral Res 2008; 80:239-50. [PMID: 18782590 PMCID: PMC2628465 DOI: 10.1016/j.antiviral.2008.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/11/2008] [Accepted: 08/13/2008] [Indexed: 11/18/2022]
Abstract
Several arenaviruses cause hemorrhagic fever (HF) in humans, and evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. Moreover, arenaviruses pose a biodefense threat. No licensed anti-arenavirus vaccines are available, and current anti-arenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with anemia and other side effects. Therefore, it is important to develop effective vaccines and better antiviral drugs to combat the dual threats of naturally occurring and intentionally introduced arenavirus infections. The development of arenavirus reverse genetic systems is allowing investigators to conduct a detailed molecular characterization of the viral cis-acting signals and trans-acting factors that control each of the steps of the arenavirus life cycle, including RNA synthesis, packaging and budding. Knowledge derived from these studies is uncovering potential novel targets for therapeutic intervention, as well as facilitating the establishment of assays to identify and characterize candidate antiviral drugs capable of interfering with specific steps of the virus life cycle. Likewise, the ability to generate predetermined specific mutations within the arenavirus genome and analyze their phenotypic expression would significantly contribute to the elucidation of arenavirus-host interactions, including the basis of their ability to cause severe HF. This, in turn, could lead to the development of novel, potent and safe arenavirus vaccines.
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Affiliation(s)
- Juan C de la Torre
- Immunology and Microbial Science, IMM-6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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47
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Belousoff MJ, Graham B, Spiccia L, Tor Y. Cleavage of RNA oligonucleotides by aminoglycosides. Org Biomol Chem 2008; 7:30-3. [PMID: 19081939 DOI: 10.1039/b813252f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of aminoglycoside antibiotics, and in particular neomycin B, are demonstrated to promote strand cleavage of RNA oligonucleotides (minimised HIV-1 TAR element and prokaryotic ribosomal A-site), by binding and causing sufficient distortion to the RNA backbone to render it more susceptible to intramolecular transesterification.
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48
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Studies on the synthesis of neamine-dinucleosides and neamine-PNA conjugates and their interaction with RNA. Bioorg Med Chem Lett 2008; 18:5355-8. [PMID: 18829307 DOI: 10.1016/j.bmcl.2008.09.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/13/2008] [Accepted: 09/16/2008] [Indexed: 11/20/2022]
Abstract
Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5'-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.
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Abstract
Understanding how RNA folds and what causes it to unfold has become more important as knowledge of the diverse functions of RNA has increased. Here we review the contributions of single-molecule experiments to providing answers to questions such as: How much energy is required to unfold a secondary or tertiary structure? How fast is the process? How do helicases unwind double helices? Are the unwinding activities of RNA-dependent RNA polymerases and of ribosomes different from other helicases? We discuss the use of optical tweezers to monitor the unfolding activities of helicases, polymerases, and ribosomes, and to apply force to unfold RNAs directly. We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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50
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Lorpitthaya R, Xie ZZ, Kuo JL, Liu XW. Stereocontrolled intramolecular aziridination of glycals: ready access to aminoglycosides and mechanistic insights from DFT studies. Chemistry 2008; 14:1561-70. [PMID: 18046690 DOI: 10.1002/chem.200701288] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Stereocontrolled intramolecular aziridination of the glycal-derived sulfamates offers a highly efficient strategy to divergently prepare aminoglycosides. Rhodium-catalyzed nitrogen-atom transfer to C==C bonds formed semistable aziridines, which were subjected to various nucleophiles (C, O, S, and N) to give cyclic sulfamate-containing aminosugar derivatives selectively. The second nucleophilic displacement of sulfonyloxy moieties of [1,2,3]-oxathiazepane-2,2- dioxides allows straightforward access to aminoglycosides with selective alpha- or beta-linkages. This approach is operationally simple, complements existing methods, and is a versatile protocol for the synthesis of polyfunctionalized amino sugars. In addition, the mechanism of the rhodium-catalyzed intramolecular aziridination of glycals and its ring-opening reaction was extensively studied by using DFT calculations.
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Affiliation(s)
- Rujee Lorpitthaya
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
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