1
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Xie DD, Song R, Cheng X, Zhang H, Wei YF, Gao F. From Intercalation to External Binding: Ru(II) Complexes with a Spiro Ligand for TAR RNA Selective Binding and HIV-1 Reverse Transcriptase Inhibition. Inorg Chem 2024; 63:12342-12349. [PMID: 38904258 DOI: 10.1021/acs.inorgchem.4c01815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
As a typical RNA virus, the genetic information on HIV-1 is entirely stored in RNA. The reverse transcription activity of HIV-1 reverse transcriptase (RT) plays a crucial role in the replication and transmission of the virus. Non-nucleoside RT inhibitors (NNRTIs) block the function of RT by binding to the RNA binding site on RT, with very few targeting viral RNA. In this study, by transforming planar conjugated ligands into a spiro structure, we convert classical Ru(II) DNA intercalators into a nonintercalator. This enables selective binding to HIV-1 transactivation response (TAR) RNA on the outer side of nucleic acids through dual interactions involving hydrogen bonds and electrostatic attraction, effectively inhibiting HIV-1 RT and serving as a selective fluorescence probe for TAR RNA.
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Affiliation(s)
- Dan-Dan Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Ran Song
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Xiaohong Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Yuan-Fang Wei
- Guangzhou Quality Supervision and Testing Institute, Guangzhou 511400, P. R. China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
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2
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Stillman NH, Joseph JA, Ahmed J, Baysah CZ, Dohoney RA, Ball TD, Thomas AG, Fitch TC, Donnelly CM, Kumar S. Protein mimetic 2D FAST rescues alpha synuclein aggregation mediated early and post disease Parkinson's phenotypes. Nat Commun 2024; 15:3658. [PMID: 38688913 PMCID: PMC11061149 DOI: 10.1038/s41467-024-47980-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Abberent protein-protein interactions potentiate many diseases and one example is the toxic, self-assembly of α-Synuclein in the dopaminergic neurons of patients with Parkinson's disease; therefore, a potential therapeutic strategy is the small molecule modulation of α-Synuclein aggregation. In this work, we develop an Oligopyridylamide based 2-dimensional Fragment-Assisted Structure-based Technique to identify antagonists of α-Synuclein aggregation. The technique utilizes a fragment-based screening of an extensive array of non-proteinogenic side chains in Oligopyridylamides, leading to the identification of NS132 as an antagonist of the multiple facets of α-Synuclein aggregation. We further identify a more cell permeable analog (NS163) without sacrificing activity. Oligopyridylamides rescue α-Synuclein aggregation mediated Parkinson's disease phenotypes in dopaminergic neurons in early and post disease Caenorhabditis elegans models. We forsee tremendous potential in our technique to identify lead therapeutics for Parkinson's disease and other diseases as it is expandable to other oligoamide scaffolds and a larger array of side chains.
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Affiliation(s)
- Nicholas H Stillman
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Johnson A Joseph
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Jemil Ahmed
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA
| | - Charles Zuwu Baysah
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Ryan A Dohoney
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tyler D Ball
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Alexandra G Thomas
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tessa C Fitch
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Courtney M Donnelly
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Sunil Kumar
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA.
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA.
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA.
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3
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Solga D, Wieske LHE, Wilcox S, Zeilinger C, Jansen-Olliges L, Cirnski K, Herrmann J, Müller R, Erdelyi M, Kirschning A. Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids? Chemistry 2024; 30:e202303796. [PMID: 38217886 DOI: 10.1002/chem.202303796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Cystobactamids are aromatic oligoamides that exert their natural antibacterial properties by inhibition of bacterial gyrases. Such aromatic oligoamides were proposed to inhibit α-helix-mediated protein-protein interactions and may serve for specific recognition of DNA. Based on this suggestion, we designed new derivatives that have duplicated cystobactamid triarene units as model systems to decipher the specific binding mode of cystobactamids to double stranded DNA. Solution NMR analyses revealed that natural cystobactamids as well as their elongated analogues show an overall bent shape at their central aliphatic unit, with an average CX-CY-CZ angle of ~110 degrees. Our finding is corroborated by the target-bound structure of close analogues, as established by cryo-EM very recently. Cystobactamid CN-861-2 binds directly to the bacterial gyrase with an affinity of 9 μM, and also exhibits DNA-binding properties with specificity for AT-rich DNA. Elongation/dimerization of the triarene subunit of native cystobactamids is demonstrated to lead to an increase in DNA binding affinity. This implies that cystobactamids' gyrase inhibitory activity necessitates not just interaction with the gyrase itself, but also with DNA via their triarene unit.
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Affiliation(s)
- Danny Solga
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Scott Wilcox
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Carsten Zeilinger
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Linda Jansen-Olliges
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Katarina Cirnski
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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4
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Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
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5
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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6
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Dohoney RA, Joseph JA, Baysah C, Thomas AG, Siwakoti A, Ball TD, Kumar S. "Common-Precursor" Protein Mimetic Approach to Rescue Aβ Aggregation-Mediated Alzheimer's Phenotypes. ACS Chem Biol 2023. [PMID: 37367833 DOI: 10.1021/acschembio.3c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Abberent protein-protein interactions (aPPIs) are associated with an array of pathological conditions, which make them important therapeutic targets. The aPPIs are mediated via specific chemical interactions that spread over a large and hydrophobic surface. Therefore, ligands that can complement the surface topography and chemical fingerprints could manipulate aPPIs. Oligopyridylamides (OPs) are synthetic protein mimetics that have been shown to manipulate aPPIs. However, the previous OP library used to disrupt these aPPIs was moderate in number (∼30 OPs) with very limited chemical diversity. The onus is on the laborious and time-consuming synthetic pathways with multiple chromatography steps. We have developed a novel chromatography-free technique to synthesize a highly diverse chemical library of OPs using a "common-precursor" approach. We significantly expanded the chemical diversity of OPs using a chromatography-free high-yielding method. To validate our novel approach, we have synthesized an OP with identical chemical diversity to a pre-existing OP-based potent inhibitor of Aβ aggregation, a process central to Alzheimer's disease (AD). The newly synthesized OP ligand (RD242) was very potent in inhibiting Aβ aggregation and rescuing AD phenotypes in an in vivo model. Moreover, RD242 was very effective in rescuing AD phenotypes in a post-disease onset AD model. We envision that our "common-precursor" synthetic approach will have tremendous potential as it is expandable for other oligoamide scaffolds to enhance affinity for disease-relevant targets.
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Affiliation(s)
- Ryan A Dohoney
- The Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
| | - Johnson A Joseph
- The Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
| | - Charles Baysah
- The Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
| | - Alexandra G Thomas
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
- The Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Apshara Siwakoti
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
- The Department of Biological Sciences, University of Denver, Denver, Colorado 80210, United States
| | - Tyler D Ball
- The Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
| | - Sunil Kumar
- The Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80210, United States
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7
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Maity D. Inhibition of Amyloid Protein Aggregation Using Selected Peptidomimetics. ChemMedChem 2023; 18:e202200499. [PMID: 36317359 DOI: 10.1002/cmdc.202200499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Aberrant protein aggregation leads to the formation of amyloid fibrils. This phenomenon is linked to the development of more than 40 irremediable diseases such as Alzheimer's disease, Parkinson's disease, type 2 diabetes, and cancer. Plenty of research efforts have been given to understanding the underlying mechanism of protein aggregation, associated toxicity, and the development of amyloid inhibitors. Recently, the peptidomimetic approach has emerged as a potential tool to modulate several protein-protein interactions (PPIs). In this review, we discussed selected peptidomimetic-based approaches for the modulation of important amyloid proteins (Islet Amyloid Polypeptide, Amyloid Beta, α-synuclein, mutant p53, and insulin) aggregation. This approach holds a powerful platform for creating an essential stepping stone for the vital development of anti-amyloid therapeutic agents.
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Affiliation(s)
- Debabrata Maity
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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8
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Trobe M, Schreiner T, Vareka M, Grimm S, Wölfl B, Breinbauer R. A Modular Synthesis of Teraryl-Based α-Helix Mimetics, Part 5: A Complete Set of Pyridine Boronic Acid Pinacol Esters Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101280. [PMID: 35910461 PMCID: PMC9304165 DOI: 10.1002/ejoc.202101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 11/30/2022]
Abstract
Teraryl-based α-helix mimetics have proven to be useful compounds for the inhibition of protein-protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl-based α-helix mimetics using pyridine containing boronic acid building blocks to increase the water solubility. Following our initial publication in which we have introduced the methodology in combination with sequential Pd-catalyzed cross-coupling for teraryl assembly, we can now report a complete set of pyridine based boronic acid building blocks decorated with side chains of all proteinogenic amino acids relevant for PPI (Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr, Val) to complement the core fragment set. For a representative set of teraryls we have studied the influence of the pyridine rings on the solubility of the assembled oligoarenes.
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Affiliation(s)
- Melanie Trobe
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Till Schreiner
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Martin Vareka
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Sebastian Grimm
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Bernhard Wölfl
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
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9
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Targeting Tat-TAR RNA Interaction for HIV-1 Inhibition. Viruses 2021; 13:v13102004. [PMID: 34696435 PMCID: PMC8536978 DOI: 10.3390/v13102004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 Tat protein interacts with TAR RNA and recruits CDK9/cyclin T1 and other host factors to induce HIV-1 transcription. Thus, Tat–TAR RNA interaction, which is unique for HIV-1, represents an attractive target for anti-HIV-1 therapeutics. To target Tat–TAR RNA interaction, we used a crystal structure of acetylpromazine bound to the bulge of TAR RNA, to dock compounds from the Enamine database containing over two million individual compounds. The docking procedure identified 173 compounds that were further analyzed for the inhibition of HIV-1 infection. The top ten inhibitory compounds with IC50 ≤ 6 µM were selected and the three least toxic compounds, T6780107 (IC50 = 2.97 μM), T0516-4834 (IC50 = 0.2 μM) and T5628834 (IC50 = 3.46 μM), were further tested for HIV-1 transcription inhibition. Only the T0516-4834 compound showed selective inhibition of Tat-induced HIV-1 transcription, whereas the T6780107 compound inhibited equally basal and Tat-induced transcription and the T5628834 compound only inhibited basal HIV-1 transcription. The compounds were tested for the inhibition of translation and showed minimal (<25%) effect. The T0516-4834 compound also showed the strongest inhibition of HIV-1 RNA expression and p24 production in CEM T cells and peripheral blood mononuclear cells infected with HIV-1 IIIB. Of the three compounds, only the T0516-4834 compound significantly disrupted Tat–TAR RNA interaction. Additionally, of the three tested compounds, T5628834 and, to a lesser extent, T0516-4834 disrupted Tat–CDK9/cyclin T1 interaction. None of the three compounds showed significant inhibition of the cellular CDK9 and cyclin T1 levels. In silico modelling showed that the T0516-4834 compound interacted with TAR RNA by binding to the bulge formed by U23, U25, C39, G26,C39 and U40 residues. Taken together, our study identified a novel benzoxazole compound that disrupted Tat–TAR RNA interaction and inhibited Tat-induced transcription and HIV-1 infection, suggesting that this compound might serve as a new lead for anti-HIV-1 therapeutics.
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10
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Maity D, Hamilton AD. The helical supramolecular assembly of oligopyridylamide foldamers in aqueous media can be guided by adenosine diphosphates. Chem Commun (Camb) 2021; 57:9192-9195. [PMID: 34519293 DOI: 10.1039/d1cc02704b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A metal-free and achiral tri-pyridylamide foldamer, DM 11, containing a critical naphthalimide side chain self-assembles in a left-handed helical manner in the presence of chiral adenosine phosphates, under physiological conditions. Surprisingly, a very high degree of helicity in the foldamer assemblies was observed with ADP compared to other nucleoside phosphates, including ATP.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University, New York, NY 10003, USA.
| | - Andrew D Hamilton
- Department of Chemistry, New York University, New York, NY 10003, USA.
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11
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Seedorf T, Kirschning A, Solga D. Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications. Chemistry 2021; 27:7321-7339. [PMID: 33481284 PMCID: PMC8251530 DOI: 10.1002/chem.202005086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
The term "privileged structure" refers to a single molecular substructure or scaffold that can serve as a starting point for high-affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well-defined scaffolds capable of specifically binding to conformationally well-defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein-protein and nucleic acid-protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications.
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Affiliation(s)
- Tim Seedorf
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Danny Solga
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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12
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Melidis L, Styles IB, Hannon MJ. Targeting structural features of viral genomes with a nano-sized supramolecular drug. Chem Sci 2021; 12:7174-7184. [PMID: 34123344 PMCID: PMC8153246 DOI: 10.1039/d1sc00933h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022] Open
Abstract
RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Iain B Styles
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Computer Science, University of Birmingham Edgbaston Birmingham B15 2TT UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham The Midlands UK
- Alan Turing Institute London UK
| | - Michael J Hannon
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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13
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Maity D, Howarth M, Vogel MC, Magzoub M, Hamilton AD. Peptidomimetic-Based Vesicles Inhibit Amyloid-β Fibrillation and Attenuate Cytotoxicity. J Am Chem Soc 2021; 143:3086-3093. [PMID: 33600171 DOI: 10.1021/jacs.0c09967] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An interruption in Aβ homeostasis leads to the deposit of neurotoxic amyloid plaques and is associated with Alzheimer's disease. A supramolecular strategy based on the assembly of peptidomimetic agents into functional vesicles has been conceived for the simultaneous inhibition of Aβ42 fibrillation and expedited clearance of Aβ42 aggregates. Tris-pyrrolamide peptidomimetic, ADH-353, contains one hydrophobic N-butyl and two hydrophilic N-propylamine side chains and readily forms vesicles under physiological conditions. These vesicles completely rescue both mouse neuroblastoma N2a and human neuroblastoma SH-SY5Y cells from the cytotoxicity that follows from Aβ42 misfolding likely in mitochondria. Biophysical studies, including confocal imaging, demonstrate the biocompatibility and selectivity of the approach toward this aberrant protein assembly in cellular milieu.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Madeline Howarth
- Biology Program, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Maria C Vogel
- Biology Program, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Biology Program, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Andrew D Hamilton
- Department of Chemistry, New York University, New York, New York 10003, United States
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14
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Mockler N, Ramberg KO, Guagnini F, Raston CL, Crowley PB. Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with α-Helical Recognition Properties. CRYSTAL GROWTH & DESIGN 2021; 21:1424-1427. [PMID: 34054353 PMCID: PMC8154262 DOI: 10.1021/acs.cgd.0c01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Water-soluble, anionic calix[n]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene (sclx 8 ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger receptor would have increased capacity for protein masking/encapsulation. A cocrystal structure of p-benzyl-sulfonato-calix[8]arene (b-sclx 8 ) and cytochrome c (cyt c) revealed a surprising assembly. A pseudorotaxane comprising a stack of three b-sclx 8 molecules threaded by polyethylene glycol (PEG) was bound to the protein. The trimeric b-sclx 8 stack, a tubelike structure with a highly charged surface, mediated assembly via a new mode of protein recognition. The calixarene stack presents four hydrophobic grooves, each of which binds to one cyt c by accommodating the N-terminal α-helix. This unprecedented binding mode suggests new possibilities for supramolecular protein chemistry.
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Affiliation(s)
- Niamh
M. Mockler
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Kiefer O. Ramberg
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Francesca Guagnini
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
| | - Colin L. Raston
- Flinders
Institute for Nanoscale Science and Technology, College of Science
and Engineering, Flinders University, Bedford Park, South 5042, Australia
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland
Galway, University Road, Galway, H91 TK33, Ireland
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15
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Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020; 211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
Abstract
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
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Affiliation(s)
- Sergio Algar
- Instituto de Química Médica, IQM-CSIC, Juan de La Cierva 3, 28006, Madrid, Spain
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16
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Maity D, Kumar S, AlHussein R, Gremer L, Howarth M, Karpauskaite L, Hoyer W, Magzoub M, Hamilton AD. Sub-stoichiometric inhibition of IAPP aggregation: a peptidomimetic approach to anti-amyloid agents. RSC Chem Biol 2020; 1:225-232. [PMID: 34458762 PMCID: PMC8341728 DOI: 10.1039/d0cb00086h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Membrane-catalysed misfolding of islet amyloid polypeptide is associated with the death of β-cells in type II diabetes (T2D). Most active compounds so far reported require high doses for inhibition of membrane bound IAPP fibrillation. Here, we describe a naphthalimide-appended oligopyridylamide-based α-helical mimetic, DM 1, for targeting membrane bound IAPP. DM 1 completely inhibits the aggregation of IAPP at doses of 0.2 equivalents. DM 1 is also effective at similarly low doses for inhibition of seed-catalyzed secondary nucleation. An NMR based study demonstrates that DM 1 modulates IAPP self-assembly by stabilizing and/or perturbing the N-terminus helix conformation. DM 1 at substoichiometric doses rescues rat insulinoma cells from IAPP-mediated cytotoxicity. Most importantly, 0.2 equivalents of DM 1 disaggregate preformed oligomers and fibrils and can reverse cytotoxicity by modulating toxic preformed oligomers and fibrils of IAPP into non-toxic conformations.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University New York New York 10003 USA
| | - Sunil Kumar
- Department of Chemistry, New York University New York New York 10003 USA
| | - Ruyof AlHussein
- Department of Chemistry, New York University New York New York 10003 USA
| | - Lothar Gremer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany.,Institute of Complex Systems, Structural Biochemistry (ICS-6) Forschungszentrum Jülich 52425 Jülich Germany
| | - Madeline Howarth
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Laura Karpauskaite
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany.,Institute of Complex Systems, Structural Biochemistry (ICS-6) Forschungszentrum Jülich 52425 Jülich Germany
| | - Mazin Magzoub
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Andrew D Hamilton
- Department of Chemistry, New York University New York New York 10003 USA
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17
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Alex JM, Corvaglia V, Hu X, Engilberge S, Huc I, Crowley PB. Crystal structure of a protein–aromatic foldamer composite: macromolecular chiral resolution. Chem Commun (Camb) 2019; 55:11087-11090. [DOI: 10.1039/c9cc05330a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A protein–foldamer crystal structure illustrates protein assembly by a sulfonated aromatic oligoamide, and chiral resolution of the foldamer helix handedness.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Valentina Corvaglia
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | - Xiaobo Hu
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | | | - Ivan Huc
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
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