1
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Ellenbroek BD, Kahler JP, Evers SR, Pomplun SJ. Synthetic Peptides: Promising Modalities for the Targeting of Disease-Related Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202401704. [PMID: 38456368 DOI: 10.1002/anie.202401704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
DNA and RNA play pivotal roles in life processes by storing and transferring genetic information, modulating gene expression, and contributing to essential cellular machinery such as ribosomes. Dysregulation and mutations in nucleic acid-related processes are implicated in numerous diseases. Despite the critical impact on health of nucleic acid mutations or dysregulation, therapeutic compounds addressing these biomolecules remain limited. Peptides have emerged as a promising class of molecules for biomedical research, offering potential solutions for challenging drug targets. This review focuses on the use of synthetic peptides to target disease-related nucleic acids. We discuss examples of peptides targeting double-stranded DNA, including the clinical candidate Omomyc, and compounds designed for regulatory G-quadruplexes. Further, we provide insights into both library-based screenings and the rational design of peptides to target regulatory human RNA scaffolds and viral RNAs, emphasizing the potential of peptides in addressing nucleic acid-related diseases.
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Affiliation(s)
| | | | - Sophie R Evers
- Leiden University, 2333 CC, Leiden, The Netherlands
- Present address, Department of Chemistry, University of Zurich, Wintherthurerstrasse 190, 8057, Zurich, Switzerland
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2
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Bhatta S, Senapati BK, Patra SK, Nanda S. A sequential Friedländer and anionic benzannulation strategy for the regiodefined assembly of unsymmetrical acridines. Org Biomol Chem 2023; 21:8727-8738. [PMID: 37870846 DOI: 10.1039/d3ob01470c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
An efficient sequential double-annulation strategy has been developed to afford a series of unsymmetrical acridines with high yield and regioselectivity for the first time. This simple protocol enables the sequential assembly of two aromatic rings from simple starting materials. The reaction proceeds via modified Friedländer annulation and subsequent base-mediated benzannulation with acrylates as Michael acceptors. A range of substrate scope and functional group tolerance is observed. Late-stage synthetic modification is also explored to access novel unsymmetrical acridines in good yield.
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Affiliation(s)
- Suman Bhatta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Bidyut Kumar Senapati
- Department of Chemistry, Midnapore College (Autonomous), Midnapore, West Bengal, 721101, India
| | - Sanjib Kumar Patra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Samik Nanda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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3
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Jenne F, Berezkin I, Tempel F, Schmidt D, Popov R, Nesterov-Mueller A. Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays. Life (Basel) 2023; 13:life13030796. [PMID: 36983951 PMCID: PMC10053474 DOI: 10.3390/life13030796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work.
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Affiliation(s)
- Felix Jenne
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Ivan Berezkin
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Frank Tempel
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Dimitry Schmidt
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | | | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
- Correspondence: ; Tel.: +49-721-608-29253
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4
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Cataldi E, Raschig M, Gutmann M, Geppert PT, Ruopp M, Schock M, Gerwe H, Bertermann R, Meinel L, Finze M, Nowak-Król A, Decker M, Lühmann T. Amber Light Control of Peptide Secondary Structure by a Perfluoroaromatic Azobenzene Photoswitch. Chembiochem 2023; 24:e202200570. [PMID: 36567253 DOI: 10.1002/cbic.202200570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
The incorporation of photoswitches into the molecular structure of peptides and proteins enables their dynamic photocontrol in complex biological systems. Here, a perfluorinated azobenzene derivative triggered by amber light was site-specifically conjugated to cysteines in a helical peptide by perfluoroarylation chemistry. In response to the photoisomerization (trans→cis) of the conjugated azobenzene with amber light, the secondary structure of the peptide was modulated from a disorganized into an amphiphilic helical structure.
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Affiliation(s)
- Eleonora Cataldi
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Martina Raschig
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marcus Gutmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Patrick T Geppert
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Matthias Ruopp
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marvin Schock
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Hubert Gerwe
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Rüdiger Bertermann
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Lorenz Meinel
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), 97080, Würzburg, Germany
| | - Maik Finze
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Agnieszka Nowak-Król
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Michael Decker
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Tessa Lühmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
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5
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Lin Y, Zhao M, Bai L, Li H, Xu Y, Li X, Xie J, Zhang Y, Zheng D. Renal-targeting peptide-microRNA nanocomplex for near IR imaging and therapy of renal ischemia/reperfusion injury. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Zhang W, Sun J, Zhu H, Yue R, Zhang Y, Niu F, Rong L. An efficient synthesis of spiroacridinone derivatives from the facile reaction of isatins, dimedone, and 5‐aminoindazole (6‐aminoindazole or 5‐aminoindole). J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Wen‐Ting Zhang
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
- Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials, School of Chemistry and Materials ScienceJiangsu Normal University Xuzhou China
| | - Jian Sun
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
| | - Hong Zhu
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
| | - Rui‐Xue Yue
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
| | - Yi Zhang
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
| | - Fu‐Xiang Niu
- Xuzhou Institute of Agricultural Sciences in Xuhuai Region of Jiangsu/Sweet Potato Research InstituteChinese Academy of Agricultural Sciences Xuzhou China
| | - Liangce Rong
- Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials, School of Chemistry and Materials ScienceJiangsu Normal University Xuzhou China
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7
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Peralta AN, Dai Y, Sherpa C, Le Grice SFJ, Santos WL. Molecular recognition of HIV-1 RNAs with branched peptides. Methods Enzymol 2019; 623:373-400. [PMID: 31239054 DOI: 10.1016/bs.mie.2019.04.021] [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: 02/02/2023]
Abstract
Targeting RNA offers the potential in many diseases of a therapeutic treatment. Due to its large surface area and ability to adopt different conformations, targeting RNA has proven challenging. Medium-sized branched peptides are of the size to competitively bind RNA while remaining cell permeable, stable in vivo, and non-toxic. Additionally, the ease in generating a large library followed by high-throughput screening provides a way to suggest a scaffold with high diversity that is capable of targeting the structure and sequence of RNA. The ability to select various types of amino acid modifications in the branched peptide allows for variable structures and interactions of the branched peptide but can result in too large a task if not approached properly. In this chapter, we discuss a strategy to selectively recognize RNAs of interest through high throughput screening of branched peptides, validation of hits and biophysical characterization, leading by example with our experience in targeting HIV-1 RNAs with branched peptides.
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Affiliation(s)
- Ashley N Peralta
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Yumin Dai
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Webster L Santos
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
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8
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Wu H, Zhang Z, Ma N, Liu Q, Liu T, Zhang G. Synthesis of Acridines from o-Aminoaryl Ketones and Arylboronic Acids by Copper Trifluoroacetate-Mediated Relay Reactions. J Org Chem 2018; 83:12880-12886. [PMID: 30232875 DOI: 10.1021/acs.joc.8b01828] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An efficient and practical method for the synthesis of medicinally important acridines from readily available o-aminoaryl ketones and arylboronic acids was developed using copper(II)-mediated relay reactions that involve intermolecular Chan-Lam cross-coupling and subsequent intramolecular Friedel-Crafts-type reactions. A sole promoter, i.e., Cu(OTf)2, was used; therefore, strongly acidic and basic conditions, nonreadily available or expensive substrates, additives, and noble-metal catalysts were not needed.
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Affiliation(s)
- Hao Wu
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
| | - Zhiguo Zhang
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
| | - Nana Ma
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
| | - Qingfeng Liu
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
| | - Tongxin Liu
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
| | - Guisheng Zhang
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering , Henan Normal University , Xinxiang , Henan 453007 , China
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9
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Bayat M, Amiri Z. Catalyst-free Synthesis of Tetrahydroacenaphtho[1,2- b
]indolone Derivatives via
One-pot Four-component Reaction. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mohammad Bayat
- Department of Chemistry, Faculty of Science; Imam Khomeini International University; Qazvin Iran
| | - Zeinab Amiri
- Department of Chemistry, Faculty of Science; Imam Khomeini International University; Qazvin Iran
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10
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Hyun S, Choi Y, Lee HN, Lee C, Oh D, Lee DK, Lee C, Lee Y, Yu J. Construction of histidine-containing hydrocarbon stapled cell penetrating peptides for in vitro and in vivo delivery of siRNAs. Chem Sci 2018; 9:3820-3827. [PMID: 29780514 PMCID: PMC5939838 DOI: 10.1039/c8sc00074c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/12/2018] [Indexed: 12/14/2022] Open
Abstract
A hydrocarbon stapled peptide based strategy was used to develop an optimized cell penetrating peptide for siRNA delivery. Various stapled peptides, having amphipathic Leu- and Lys-rich regions, were prepared and their cell penetrating potentials were evaluated. One peptide, stEK, was found to have high cell penetration and siRNA delivery abilities at low nanomolar concentrations. In order to improve its ability to promote gene silencing, stEK was modified by replacing several Lys residues with His moieties. The modified peptide, LKH-stEK, was found to facilitate endosomal escape and to display >90% knock-down with 50 nM of a siRNA targeting cyclophilin B in HeLa cells. The results of an in vivo animal wound healing model study demonstrate that LKH-stEK promotes delivery of an siRNA, which targets the connective tissue growth factor, and that this process leads to efficient gene silencing by the siRNA at a nanomolar level in mouse skin.
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Affiliation(s)
- Soonsil Hyun
- Institute of Molecular Biology and Genetics , Seoul National University , Seoul 08826 , Korea
| | - Yoonhwa Choi
- Department of Chemistry & Education , Seoul National University , Seoul 08826 , Korea .
| | | | | | | | - Dong-Ki Lee
- Department of Chemistry , Sungkyunkwan University , Suwon , Korea
| | | | - Yan Lee
- Department of Chemistry , Seoul National University , Seoul 08826 , Korea .
| | - Jaehoon Yu
- Institute of Molecular Biology and Genetics , Seoul National University , Seoul 08826 , Korea
- Department of Chemistry & Education , Seoul National University , Seoul 08826 , Korea .
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11
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Mu WL, Wang M, Li HJ, Huang DM, Zhang YY, Li CY, Liu Y, Wu YC. Palladium-Catalyzed Regioselective Oxidative Annulation of Cyclohexanones and 2-Aminophenyl Ketones Using Molecular Oxygen as the Sole Oxidant. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wan-Lu Mu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Meirong Wang
- School of Materials Science and Engineering; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Hui-Jing Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Deng-Ming Huang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yi-Yun Zhang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Chao-Yi Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Ying Liu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yan-Chao Wu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry Chinese Academy of Sciences; Beijing 100190 People's Republic of China
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12
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Effect of intercalator and Lewis acid-base branched peptide complex formation: boosting affinity towards HIV-1 RRE RNA. MEDCHEMCOMM 2016; 7:1436-1440. [PMID: 27453773 DOI: 10.1039/c6md00171h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High throughput screening of a 4096 compound library of boronic acid and acridine containing branched peptides revealed compounds that have dissociation constants in the low nanomolar regime for HIV-1 RRE IIB RNA. We demonstrate that branched peptide boronic acids A5, A6, and A7 inhibit the production of p24, an HIV-1 capsid protein, in a dose-dependent manner.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Denis M Tebit
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Laurie R Gray
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - David Rekosh
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
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13
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Chen XB, Wang XQ, Hong Y, Liu W. Site-Selective Convergent Synthesis of Spiroacridines through a Cascade Reaction of Enaminones with Acenaphthoquinone: An Efficient Construction of Multiple C−C and C-Heteroatom Bonds. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Xue-Bing Chen
- Key Laboratory of Natural Pharmaceutical and Chemical Biology of Yunnan Province; School of Science; Honghe University; Mengzi Yunnan 661199 P. R. China
- Local Characteristic Resource Utilization and New Materials Key Laboratory of Universities in Yunnan; Honghe University; Mengzi 661199 Yunan China
| | - Xue-Quan Wang
- Key Laboratory of Natural Pharmaceutical and Chemical Biology of Yunnan Province; School of Science; Honghe University; Mengzi Yunnan 661199 P. R. China
- Local Characteristic Resource Utilization and New Materials Key Laboratory of Universities in Yunnan; Honghe University; Mengzi 661199 Yunan China
| | - Yong Hong
- Key Laboratory of Natural Pharmaceutical and Chemical Biology of Yunnan Province; School of Science; Honghe University; Mengzi Yunnan 661199 P. R. China
- Local Characteristic Resource Utilization and New Materials Key Laboratory of Universities in Yunnan; Honghe University; Mengzi 661199 Yunan China
| | - Wei Liu
- Key Laboratory of Natural Pharmaceutical and Chemical Biology of Yunnan Province; School of Science; Honghe University; Mengzi Yunnan 661199 P. R. China
- Local Characteristic Resource Utilization and New Materials Key Laboratory of Universities in Yunnan; Honghe University; Mengzi 661199 Yunan China
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14
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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15
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Recent advances in the identification of Tat-mediated transactivation inhibitors: progressing toward a functional cure of HIV. Future Med Chem 2016; 8:421-42. [PMID: 26933891 DOI: 10.4155/fmc.16.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The current anti-HIV combination therapy does not eradicate the virus that persists mainly in quiescent infected CD4(+) T cells as a latent integrated provirus that resumes after therapy interruption. The Tat-mediated transactivation (TMT) is a critical step in the HIV replication cycle that could give the opportunity to reduce the size of latent reservoirs. More than two decades of research led to the identification of various TMT inhibitors. While none of them met the criteria to reach the market, the search for a suitable TMT inhibitor is still actively pursued. Really promising compounds, including one in a Phase III clinical trial, have been recently identified, thus warranting an update.
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16
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Pai J, Hyun S, Hyun JY, Park SH, Kim WJ, Bae SH, Kim NK, Yu J, Shin I. Screening of Pre-miRNA-155 Binding Peptides for Apoptosis Inducing Activity Using Peptide Microarrays. J Am Chem Soc 2016; 138:857-67. [PMID: 26771315 DOI: 10.1021/jacs.5b09216] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MicroRNA-155, one of the most potent miRNAs that suppress apoptosis in human cancer, is overexpressed in numerous cancers, and it displays oncogenic activity. Peptide microarrays, constructed by immobilizing 185 peptides containing the C-terminal hydrazide onto epoxide-derivatized glass slides, were employed to evaluate peptide binding properties of pre-miRNA-155 and to identify its binding peptides. Two peptides, which were identified based on the results of peptide microarray and in vitro Dicer inhibition studies, were found to inhibit generation of mature miRNA-155 catalyzed by Dicer and to enhance expression of miRNA-155 target genes in cells. In addition, the results of cell experiments indicate that peptide inhibitors promote apoptotic cell death via a caspase-dependent pathway. Finally, observations made in NMR and molecular modeling studies suggest that a peptide inhibitor preferentially binds to the upper bulge and apical stem-loop region of pre-miRNA-155, thereby suppressing Dicer-mediated miRNA-155 processing.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Soonsil Hyun
- Department of Chemistry and Education, Seoul National University , Seoul 08826, Korea
| | - Ji Young Hyun
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Seong-Hyun Park
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Won-Je Kim
- Advanced Analysis Center, Korea Institute of Science and Technology , Seoul 02792, Korea
| | - Sung-Hun Bae
- CKD Research Institute , 315-20, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17006, Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology , Seoul 02792, Korea
| | - Jaehoon Yu
- Department of Chemistry and Education, Seoul National University , Seoul 08826, Korea
| | - Injae Shin
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University , Seoul 03722, Korea
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17
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Ghasemzadeh MA, Mirhosseini-Eshkevari B. Fe3O4@silica Sulfonic Acid Nanocomposite as a Magnetically Separable Catalyst for the Synthesis of 2-Arylpyrrolo[2,3,4-kl]Acridin-1(2H)-Ones. JOURNAL OF CHEMICAL RESEARCH 2015. [DOI: 10.3184/174751915x14355930432579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The synthesis of a series of 2-arylpyrrolo[2,3,4-kl]acridin-1(2H)-ones, three of which are novel, though a one-pot three-component reaction of dimedone, various anilines, and isatin has been achieved in the presence of magnetite nanoparticles supported silica-sulfonic acid as catalyst under solvent-free conditions at 80 °C. The procedure avoids hazardous reagents/solvents and is more eco-friendly than existing methods. Fe3O4@silica-sulfonic acid is shown to be a highly efficient catalyst, and could be readily recovered using a simple external magnet and reused several times without any significant loss in activity. The catalyst was fully characterised by FTIR, SEM, XRD, EDX and VSM.
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18
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Chen J, Poddar NK, Tauzin LJ, Cooper D, Kolomeisky AB, Landes CF. Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics. J Phys Chem B 2014; 118:12130-9. [PMID: 25254491 PMCID: PMC4207534 DOI: 10.1021/jp507067p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States
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19
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Jang S, Hyun S, Kim S, Lee S, Lee IS, Baba M, Lee Y, Yu J. Cell-Penetrating, Dimeric α-Helical Peptides: Nanomolar Inhibitors of HIV-1 Transcription. Angew Chem Int Ed Engl 2014; 53:10086-9. [DOI: 10.1002/anie.201404684] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 11/10/2022]
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20
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Jang S, Hyun S, Kim S, Lee S, Lee IS, Baba M, Lee Y, Yu J. Cell-Penetrating, Dimeric α-Helical Peptides: Nanomolar Inhibitors of HIV-1 Transcription. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404684] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Hyun S, Han A, Jo MH, Hohng S, Yu J. Dicer Nuclease-Promoted Production of Let7a-1 MicroRNA Is Enhanced in the Presence of Tryptophan-Containing Amphiphilic Peptides. Chembiochem 2014; 15:1651-9. [DOI: 10.1002/cbic.201402126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 11/07/2022]
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22
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Zhang W, Bryson DI, Crumpton JB, Wynn J, Santos WL. Targeting folded RNA: a branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA. Org Biomol Chem 2014; 11:6263-71. [PMID: 23925474 DOI: 10.1039/c3ob41053f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On-bead high-throughput screening of a medium-sized (1000-2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a K(d) of 1.4 μM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and "branching" in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB.
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Affiliation(s)
- Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA
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23
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Abstract
The therapeutic importance of microRNA (miRNA) regulation has recently been realized as these small, noncoding RNAs have been demonstrated to be involved with a plethora of diseases and disorders. Due to the complex miRNA maturation process, the expression of these important biomolecules can be manipulated at various stages of the pathway. This review examines both in vivo and in vitro mechanisms and assays that have been developed to regulate miRNA levels. Modulation of miRNA maturation can be accomplished via several therapeutic agents, including small molecules and oligonucleotides, in both specific and nonspecific fashions. Due to the relevance of miRNAs, these novel therapeutic approaches represent new tools for the treatment of various cancers and other deleterious disorders.
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Affiliation(s)
- Valerie T Tripp
- Integrated Science Center, College of William and Mary, Williamsburg, VA, USA
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24
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Ranjan N, Kumar S, Watkins D, Wang D, Appella DH, Arya DP. Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates. Bioorg Med Chem Lett 2013; 23:5689-93. [PMID: 24012122 PMCID: PMC4048829 DOI: 10.1016/j.bmcl.2013.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Derrick Watkins
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
| | - Deyun Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
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25
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Microwave-assisted improved synthesis of pyrrolo[2,3,4-kl]acridine and dihydropyrrolo[2,3,4-kl]acridine derivatives catalyzed by silica sulfuric acid. Molecules 2013; 18:1613-25. [PMID: 23358320 PMCID: PMC6269803 DOI: 10.3390/molecules18021613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/21/2012] [Accepted: 01/05/2013] [Indexed: 11/16/2022] Open
Abstract
An improved synthesis of multifunctionalized pyrrolo[2,3,4-kl]acridine derivatives with different substituted patterns using silica sulfuric acid (SSA) as a heterogeneous catalyst under microwave irradiation conditions was developed. The reaction could be conducted by using readily available and inexpensive substrates within short periods of 12–15 min. under microwave irradiation. Compared with the conventional methods, the remarkable advantages of this method are milder reaction conditions, operational simplicity, higher yields, short reaction times, and an environmentally friendly procedure.
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26
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Pai J, Yoon T, Kim ND, Lee IS, Yu J, Shin I. High-throughput profiling of peptide-RNA interactions using peptide microarrays. J Am Chem Soc 2012; 134:19287-96. [PMID: 23110629 DOI: 10.1021/ja309760g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid and quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays has been developed. The microarray technology was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants (K(d)) of RNA-peptide complexes. Our results reveal that both hydrophobic and hydrophilic faces of amphiphilic peptides are likely involved in interactions with RNAs. Furthermore, these results also show that most of the tested peptides bind hairpin RNAs with submicromolar K(d) values. One of the peptides identified by using this method was found to have good inhibitory activity against TAR-Tat interactions in cells. Because of their great applicability to evaluation of nearly all types of RNA-peptide interactions, peptide microarrays are expected to serve as robust tools for rapid assessment of peptide-RNA interactions and development of peptide ligands against RNA targets.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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27
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Shukla SP, Tiwari R, Verma AK. Silver-catalyzed regioselective synthesis of acridines, quinolines, and naphthalenes from 3-(2-alkynyl)aryl-β-ketoesters. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.068] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Han XD, Zhao YL, Meng J, Ren CQ, Liu Q. Synthesis of Acridines and Persubstituted Phenols from Cyclobutenones and Active Methylene Ketones. J Org Chem 2012; 77:5173-8. [DOI: 10.1021/jo300615t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Xiao-Dan Han
- Department
of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China
| | - Yu-Long Zhao
- Department
of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China
| | - Jia Meng
- Department
of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China
| | - Chuan-Qing Ren
- Department
of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China
| | - Qun Liu
- Department
of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China
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29
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Neubacher S, Dojahn CM, Arenz C. A Rapid Assay for miRNA Maturation by Using Unmodified pre-miRNA. Chembiochem 2011; 12:2302-5. [DOI: 10.1002/cbic.201100445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Indexed: 01/20/2023]
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30
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Rogness DC, Larock RC. Synthesis of acridines by the [4 + 2] annulation of arynes and 2-aminoaryl ketones. J Org Chem 2010; 75:2289-95. [PMID: 20222700 PMCID: PMC2852258 DOI: 10.1021/jo1000687] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The reaction of 2-aminoaryl ketones and arynes generated by the treatment of various o-(trimethylsilyl)aryl triflates with CsF results in [4 + 2] annulation to afford substituted acridines in good yields.
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31
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Hyun S, Na J, Lee SJ, Park S, Yu J. RNA Grooves Can Accommodate Disulfide-Bridged Bundles of α-Helical Peptides. Chembiochem 2010; 11:767-70. [DOI: 10.1002/cbic.201000072] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009; 48:4372-5. [DOI: 10.1002/anie.200900758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Lee SJ, Hyun S, Kieft JS, Yu J. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc 2009; 131:2224-30. [PMID: 19199621 DOI: 10.1021/ja807609m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hairpin RNA motif is one of the most frequently observed secondary structures and is often targeted by therapeutic agents. An amphiphilic peptide with seven lysine and eight leucine residues and its derivatives were designed for use as ligands against RNA hairpin motifs. We hypothesized that variations in both the hydrophobic leucine-rich and hydrophilic lysine-rich spheres of these amphiphilic peptides would create extra attractive interactions with hairpin RNA targets. A series of alanine-scanned peptides were probed to identify the most influential lysine residues in the hydrophilic sphere. The binding affinities of these modified peptides with several hairpins, such as RRE, TAR from HIV, a short hairpin from IRES of HCV, and a hairpin from the 16S A-site stem from rRNA, were determined. Since the hairpin from IRES of HCV was the most susceptible to the initial series of alanine-scanned peptides, studies investigating how further variations in the peptides effect binding employed the IRES hairpin. Next, the important Lys residues were substituted by shorter chain amines, such as ornithine, to place the peptide deeper into the hairpin groove. In a few cases, a 70-fold improved binding was observed for peptides that contained the specifically located shorter amine side chains. To further explore changes in binding affinities brought about by alterations in the hydrophobic sphere, tryptophan residues were introduced in place of leucine. A few peptides with tryptophan in specific positions also displayed 70-fold improved binding affinities. Finally, double mutant peptides incorporating both specifically located shorter amine side chains in the hydrophilic region and tryptophan residues in the hydrophobic region were synthesized. The binding affinities of peptides containing the simple double modification were observed to be 80 times lower, and their binding specificities were increased 40-fold. The results of this effort provide important information about strategies that can be used to prepare peptides that both strongly and selectively target hairpin RNAs. Specifically, the findings indicate that tailor-made amphiphilic peptide ligands against certain hairpin RNAs can be obtained if the RNA target possesses a deep groove in which both the hydrophobic and hydrophilic spheres of the peptide interact.
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Affiliation(s)
- Su Jin Lee
- Department of Chemistry and Education, Seoul National University, Seoul 151-748, Korea
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35
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Hyun S, Han A, Yu J. Photocrosslinking of RNA and photoMet-containing amphiphilic alpha-helical peptides. Chembiochem 2009; 10:987-9. [PMID: 19308928 DOI: 10.1002/cbic.200900100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Discovering RNA-protein interactions: A library of photoMet-containing peptides was synthesized by using an Arg- and Leu-rich alpha-helical amphiphilic peptide. Irradiation of mixtures of these peptides and Rev-responsive element (RRE) hairpin RNA promoted formation of covalent adducts. Analysis of one adduct showed that U26 in the bulged stem is responsible for covalent bond formation with the carbene intermediate. This strategy can provide important structural information about RNA-peptide interactions.
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Affiliation(s)
- Soonsil Hyun
- Department of Chemistry and Education, Seoul National University, Korea
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