1
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Pattelli ON, Valdivia EM, Beyersdorf MS, Regan CS, Rivas M, Hebert KA, Merajver SD, Cierpicki T, Mapp AK. A Lipopeptidomimetic of Transcriptional Activation Domains Selectively Disrupts the Coactivator Med25 Protein-Protein Interactions. Angew Chem Int Ed Engl 2024; 63:e202400781. [PMID: 38527936 PMCID: PMC11134611 DOI: 10.1002/anie.202400781] [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: 01/11/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium-chain, branched fatty acid to the N-terminus of one such heptameric lipopeptidomimetic (LPPM-8) increases the affinity for the coactivator Med25 >20-fold (Ki >100 μM to 4 μM), rendering it an effective inhibitor of Med25 protein-protein interactions (PPIs). The lipid structure, the peptide sequence, and the C-terminal functionalization of the lipopeptidomimetic each influence the structural propensity of LPPM-8 and its effectiveness as an inhibitor. LPPM-8 engages Med25 through interaction with the H2 face of its activator interaction domain and in doing so stabilizes full-length protein in the cellular proteome. Further, genes regulated by Med25-activator PPIs are inhibited in a cell model of triple-negative breast cancer. Thus, LPPM-8 is a useful tool for studying Med25 and mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator-coactivator complexes.
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Affiliation(s)
- Olivia N. Pattelli
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Estefanía Martínez Valdivia
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Matthew S. Beyersdorf
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Clint S. Regan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mónica Rivas
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Sofia D. Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Tomasz Cierpicki
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
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2
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Claussen ER, Renfrew PD, Müller CL, Drew K. Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds. Proteins 2024; 92:343-355. [PMID: 37874196 PMCID: PMC10873094 DOI: 10.1002/prot.26619] [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: 06/19/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
The design of protein interaction inhibitors is a promising approach to address aberrant protein interactions that cause disease. One strategy in designing inhibitors is to use peptidomimetic scaffolds that mimic the natural interaction interface. A central challenge in using peptidomimetics as protein interaction inhibitors, however, is determining how best the molecular scaffold aligns to the residues of the interface it is attempting to mimic. Here we present the Scaffold Matcher algorithm that aligns a given molecular scaffold onto hotspot residues from a protein interaction interface. To optimize the degrees of freedom of the molecular scaffold we implement the covariance matrix adaptation evolution strategy (CMA-ES), a state-of-the-art derivative-free optimization algorithm in Rosetta. To evaluate the performance of the CMA-ES, we used 26 peptides from the FlexPepDock Benchmark and compared with three other algorithms in Rosetta, specifically, Rosetta's default minimizer, a Monte Carlo protocol of small backbone perturbations, and a Genetic algorithm. We test the algorithms' performance on their ability to align a molecular scaffold to a series of hotspot residues (i.e., constraints) along native peptides. Of the 4 methods, CMA-ES was able to find the lowest energy conformation for all 26 benchmark peptides. Additionally, as a proof of concept, we apply the Scaffold Match algorithm with CMA-ES to align a peptidomimetic oligooxopiperazine scaffold to the hotspot residues of the substrate of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our implementation of CMA-ES into Rosetta allows for an alternative optimization method to be used on macromolecular modeling problems with rough energy landscapes. Finally, our Scaffold Matcher algorithm allows for the identification of initial conformations of interaction inhibitors that can be further designed and optimized as high-affinity reagents.
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Affiliation(s)
- Erin R. Claussen
- Department of Biological Sciences, University of Illinois
at Chicago, Chicago, Il, 60607, USA
| | - P. Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New
York, NY, 10010, USA
| | - Christian L. Müller
- Ludwig-Maximilians-Universität München
- Helmholtz Munich, München
- Center for Computational Mathematics, Flatiron Institute,
New York
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois
at Chicago, Chicago, Il, 60607, USA
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3
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Splandesci M, Wróbel MZ, Madura ID, Dawidowski M. Ugi 5-center-4-component reaction of α-amino aldehydes and its application in synthesis of 2-oxopiperazines. Mol Divers 2024; 28:229-248. [PMID: 38104301 PMCID: PMC10876754 DOI: 10.1007/s11030-023-10760-1] [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: 02/20/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023]
Abstract
A synthetic route leading to densely functionalized 2-oxopiperazines is presented. The strategy employs a 5-center-4-component variant of Ugi multicomponent reaction followed by a deprotection/cyclization sequence. N-Boc-α-amino aldehydes were used for the first time as carbonyl components in a key Ugi 5-center-4-component reaction (U-5C-4CR). It is shown that the presented synthetic route can lead to rigid, heterocyclic scaffolds, as demonstrated by the synthesis of tetrahydro-2H-pyrazino[1,2-a]pyrazine-3,6,9(4H)-trione β-turn mimetic and derivatives of 1,6-dioxooctahydropyrrolo[1,2-a]pyrazine and 3,8-dioxohexahydro-3H-oxazolo[3,4-a]pyrazine.
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Affiliation(s)
- Marta Splandesci
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Martyna Z Wróbel
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Izabela D Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland.
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4
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Gabizon R, Tivon B, Reddi RN, van den Oetelaar MCM, Amartely H, Cossar PJ, Ottmann C, London N. A simple method for developing lysine targeted covalent protein reagents. Nat Commun 2023; 14:7933. [PMID: 38040731 PMCID: PMC10692228 DOI: 10.1038/s41467-023-42632-5] [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: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters-electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.
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Affiliation(s)
- Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maxime C M van den Oetelaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Hadar Amartely
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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5
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Kwok JG, Yuan Z, Arora PS. An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA. Angew Chem Int Ed Engl 2023; 62:e202308650. [PMID: 37548640 PMCID: PMC10528708 DOI: 10.1002/anie.202308650] [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: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.
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Affiliation(s)
- Jonathan G. Kwok
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Zhi Yuan
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
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6
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McCann S, Roe WE, Agnew HE, Knipe PC. Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers. Angew Chem Int Ed Engl 2023; 62:e202307180. [PMID: 37414732 PMCID: PMC10952507 DOI: 10.1002/anie.202307180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.
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Affiliation(s)
- Sinead McCann
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - William E. Roe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Hannah E. Agnew
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Peter C. Knipe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
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7
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Marciniak M, Mróz P, Napolitano V, Kalel VC, Fino R, Pykacz E, Schliebs W, Plettenburg O, Erdmann R, Sattler M, Popowicz GM, Dawidowski M. Development of novel PEX5-PEX14 protein-protein interaction (PPI) inhibitors based on an oxopiperazine template. Eur J Med Chem 2023; 258:115587. [PMID: 37406382 DOI: 10.1016/j.ejmech.2023.115587] [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: 03/28/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Protein-protein interactions (PPIs) constitute an important but challenging class of molecular targets for small molecules. The PEX5-PEX14 PPI has been shown to play a critical role in glycosome biogenesis and its disruption impairs the metabolism in Trpanosoma parasites, eventually leading to their death. Therefore, this PPI is a potential molecular target for new drugs against diseases caused by Trypanosoma infections. Here, we report a new class of peptidomimetic scaffolds to target the PEX5-PEX14 PPI. The molecular design was based on an oxopiperazine template for the α-helical mimetics. A structural simplification along with modifications of the central oxopiperazine scaffold and addressing the lipophilic interactions led to the development of peptidomimetics that inhibit PEX5-TbPEX14 PPI and display cellular activity against T. b. brucei. This approach provides an alternative approach towards the development of trypanocidal agents and may be generally useful for the design of helical mimetics as PPI inhibitors.
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Affiliation(s)
- Monika Marciniak
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Piotr Mróz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Valeria Napolitano
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Roberto Fino
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Emilia Pykacz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany; Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1b, Hannover, 30167, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland.
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8
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Haque M, Flack T, Singh R, Wall A, de Castro GV, Jiang L, White AJP, Barnard A. Aromatic oligoesters as novel helix mimetic scaffolds. Bioorg Med Chem 2023; 87:117311. [PMID: 37182518 DOI: 10.1016/j.bmc.2023.117311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023]
Abstract
The design, synthesis, and conformational analysis of a novel aromatic oligoester helix mimetic scaffold is reported. A range of amino acid-type side-chain functionality can be readily incorporated into monomer building blocks over three facile synthetic steps. Analysis of representative dimers revealed a stable conformer capable of effective mimicry of a canonical α-helix and the scaffold was found to be surprisingly stable to degradation in aqueous solutions at acidic and neutral pH.
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Affiliation(s)
- Muhammed Haque
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Theo Flack
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Ravi Singh
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Archie Wall
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | | | - Lishen Jiang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Andrew J P White
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
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9
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Pattelli ON, Valdivia EM, Beyersdorf MS, Regan CS, Rivas M, Merajver SD, Cierpicki T, Mapp AK. A lipopeptidomimetic of transcriptional activation domains selectively disrupts Med25 PPIs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534168. [PMID: 36993479 PMCID: PMC10055422 DOI: 10.1101/2023.03.24.534168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium-chain, branched fatty acid to the N-terminus of one such heptameric lipopeptidomimetic (34913-8) increases the affinity for the coactivator Med25 >10-fold ( Ki >>100 μM to 10 μM). Importantly, the selectivity of 34913-8 for Med25 compared to other coactivators is excellent. 34913-8 engages Med25 through interaction with the H2 face of its Ac tivator I nteraction D omain and in doing so stabilizes full-length protein in the cellular proteome. Further, genes regulated by Med25-activator PPIs are inhibited in a cell model of triple-negative breast cancer. Thus, 34913-8 is a useful tool for studying Med25 and the Mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator-coactivator complexes.
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10
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Himiyama T, Hamaguchi T, Yonekura K, Nakamura T. Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins. Bioconjug Chem 2023. [PMID: 36888722 DOI: 10.1021/acs.bioconjchem.3c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from Thermococcus kodakaraensis, which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations.
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Affiliation(s)
- Tomoki Himiyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31, Ikeda, Osaka 563-8577, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Sendai, Miyagi 980-8577, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Sendai, Miyagi 980-8577, Japan
- Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Tsutomu Nakamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31, Ikeda, Osaka 563-8577, Japan
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11
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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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12
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Kell S, Wang Z, Ji H. Common Structural Features of Hydrophobic α-Helical Hot Spots: Insights for the Design of Novel α-Helix Mimetics. ACS Med Chem Lett 2022; 13:1670-1677. [PMID: 36262397 PMCID: PMC9575182 DOI: 10.1021/acsmedchemlett.2c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/28/2022] Open
Abstract
The binding conformations of α-helical hydrophobic hot spots are convergent into two spatial areas in protein-protein complex structures. The physical basis for convergence was disclosed, which allows the development of pharmacophore models for i/i + 4/i + 7 or i/i + 3/i + 4 α-helical hot spots. Further investigation revealed that this convergence of binding conformations is common among all hydrophobic hot spots regardless of their α-helical positions. This observation led to a streamlined generation of pharmacophore models for hydrophobic hot spots at any positions along the α-helix. These successfully evaluated pharmacophore models may be useful for designing novel α-helical hot spot mimetics.
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Affiliation(s)
- Shelby
R. Kell
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Zhen Wang
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Haitao Ji
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center & Research Institute, Tampa, Florida 33612, United States
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Oncologic Sciences, University of South
Florida, Tampa, Florida 33620, United
States
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13
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Wang Z, Ji H. Characterization of Hydrophilic α-Helical Hot Spots on the Protein-Protein Interaction Interfaces for the Design of α-Helix Mimetics. J Chem Inf Model 2022; 62:1873-1890. [PMID: 35385659 DOI: 10.1021/acs.jcim.1c01556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cooperativity index, Kc, was developed to examine the binding synergy between hot spots of the ligand-protein. For the first time, the convergence of the side-chain spatial arrangements of hydrophilic α-helical hot spots Thr, Tyr, Asp, Asn, Ser, Cys, and His in protein-protein interaction (PPI) complex structures was disclosed and quantified by developing novel clustering models. In-depth analyses revealed the driving force for the protein-protein binding conformation convergence of hydrophilic α-helical hot spots. This observation allows deriving pharmacophore models to design new mimetics for hydrophilic α-helical hot spots. A computational protocol was developed to search amino acid analogues and small-molecule mimetics for each hydrophilic α-helical hot spot. As a pilot study, diverse building blocks of commercially available nonstandard L-type α-amino acids and the phenyl ring-containing small-molecule fragments were obtained, which serve as a fragment collection to mimic hydrophilic α-helical hot spots for the improvement of binding affinity, selectivity, physicochemical properties, and synthesis accessibility of α-helix mimetics.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612-9497, United States.,Departments of Chemistry and Oncologic Sciences, University of South Florida, Tampa, Florida 33620-9497, United States
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14
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Singh MK, Lakshman MK. Recent developments in the utility of saturated azaheterocycles in peptidomimetics. Org Biomol Chem 2022; 20:963-979. [PMID: 35018952 DOI: 10.1039/d1ob01329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To a large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules to modulate conformational flexibility, improve bioavailability, and fine-tune electronics, and in order to achieve potency similar to or better than that of the natural peptide ligand. This mini-review delineates recent developments, limited to the past five years, in the utility of selected saturated 3- to 6-membered heterocyclic moieties in peptidomimetic design. Also discussed is the chemistry involved in the synthesis of the azaheterocyclic scaffolds and the structural implications of the introduction of these azaheterocycles in peptide backbones as well as side chains of the peptide mimics.
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Affiliation(s)
- Manish K Singh
- Department of Science, Technology, and Mathematics, Lincoln University, 820 Chestnut Street, Jefferson City, Missouri 65101, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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15
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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16
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Yin H, Zhou X, Huang YH, King GJ, Collins BM, Gao Y, Craik DJ, Wang CK. Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy. J Am Chem Soc 2021; 143:18536-18547. [PMID: 34661406 DOI: 10.1021/jacs.1c08132] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptides have potential to be developed into immune checkpoint inhibitors, but the target interfaces are difficult to inhibit. Here, we explored an approach to mimic the binding surface of PD-1 to design inhibitors. Mimicking native PD-1 resulted in a mimetic with no activity. However, mimicking an affinity-optimized PD-1 resulted in the peptide mimetic MOPD-1 that displayed nanomolar affinity to PD-L1 and could inhibit PD-1:PD-L1 interactions in both protein- and cell-based assays. Mutagenesis and structural characterization using NMR spectroscopy and X-ray crystallography revealed that binding residues from the high affinity PD-1 are crucial for the bioactivity of MOPD-1. Furthermore, MOPD-1 was extremely stable in human serum and inhibited tumor growth in vivo, suggesting it has potential for use in cancer immunotherapy. The successful design of an inhibitor of PD-1:PD-L1 using the mimicry approach described herein illustrates the value of placing greater emphasis on optimizing the target interface before inhibitor design and is an approach that could have broader utility for the design of peptide inhibitors for other complex protein-protein interactions.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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17
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Das A, Yadav A, Gupta M, R P, Terse VL, Vishvakarma V, Singh S, Nandi T, Banerjee A, Mandal K, Gosavi S, Das R, Ainavarapu SRK, Maiti S. Rational Design of Protein-Specific Folding Modifiers. J Am Chem Soc 2021; 143:18766-18776. [PMID: 34724378 DOI: 10.1021/jacs.1c09611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The principle is based on constructing a "xenonucleus", which is a prefolded peptide that mimics the folding nucleus of a protein. Using stopped-flow kinetics, NMR spectroscopy, Förster resonance energy transfer, single-molecule force measurements, and molecular dynamics simulations, we demonstrate that a xenonucleus can make the refolding of ubiquitin faster by 33 ± 5%, while variants of the same peptide have little or no effect. Our approach provides a novel method for constructing specific, genetically encodable folding catalysts for suitable proteins that have a well-defined contiguous folding nucleus.
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Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Anju Yadav
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Purushotham R
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Vishram L Terse
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sameer Singh
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Tathagata Nandi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Arkadeep Banerjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Shachi Gosavi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | | | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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18
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Fukuda Y, Yokomine M, Kuroda D, Tsumoto K, Morimoto J, Sando S. Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions. Chem Sci 2021; 12:13292-13300. [PMID: 34777747 PMCID: PMC8528041 DOI: 10.1039/d1sc01560e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022] Open
Abstract
The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors. A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.![]()
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Affiliation(s)
- Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan.,Institute of Medical Science, The University of Tokyo 4-6-1, Shirokanedai, Minato-ku Tokyo 108-8639 Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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19
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Takashima H, Yoshimori A, Honda E, Taguri T, Ozawa J, Kasai M, Shuto S, Takehara D. Visualized and Quantitative Conformational Analysis of Peptidomimetics. ACS OMEGA 2021; 6:26601-26612. [PMID: 34661014 PMCID: PMC8515614 DOI: 10.1021/acsomega.1c03967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Protein-protein interactions (PPIs) are fundamentally important and challenging drug targets. Peptidomimetic molecules of various types have been developed to modulate PPIs. A particularly promising drug discovery strategy, structural peptidomimetics, was designed based on special mimicking of side-chain Cα-Cβ bonds. It is simple and versatile. Nevertheless, no quantitative method has been established to evaluate its similarity to a target peptide motif. We developed two methods that enable visual, comprehensive, and quantitative analysis of peptidomimetics: peptide conformation distribution (PCD) plot and peptidomimetic analysis (PMA) map. These methods specifically examine multiple side-chain Cα-Cβ bonds of a peptide fragment motif and their corresponding bonds (pseudo-Cα-Cβ bonds) in a mimetic molecule instead of φ and ψ angles of a single amino acid in the traditional Ramachandran plot. The PCD plot is an alignment-free method, whereas the PMA map is an alignment-based method providing distinctive and complementary analysis. Results obtained from analysis using these two methods indicate our multifacial α-helix mimetic scaffold 12 as an excellent peptidomimetic that can precisely mimic the spatial positioning of side-chain functional groups of α-helix. These methods are useful for visualized and quantified evaluation of peptidomimetics and for the rational design of new mimetic scaffolds.
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Affiliation(s)
- Hajime Takashima
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Atsushi Yoshimori
- Chemoinformatics
& AI Research Group, Institute for Theoretical
Medicine, Inc., BW3M-20B, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Eiji Honda
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Tomonori Taguri
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Jun Ozawa
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Masaji Kasai
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Satoshi Shuto
- Faculty
of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6,
Kita-ku, Sapporo, Hokkaido 060-0812, Japan
| | - Dai Takehara
- Research
and Development Department, PRISM BioLab
Co., Ltd., C21F-4110, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
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20
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Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods Enzymol 2021; 656:1-25. [PMID: 34325784 DOI: 10.1016/bs.mie.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Examination of complexes of proteins with biomolecular ligands reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices comprising the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acid interactions. We have demonstrated a unique strategy for stabilization of the α-helical conformation that involves replacement of one of the main chain i and i+4 hydrogen bonds in the target α-helix with a covalent bond. We termed this synthetic strategy a hydrogen bond surrogate (HBS) approach. Two salient features of this approach are: (1) the internal placement of the crosslink allows development of helices such that none of the solvent-exposed surfaces are blocked by the constraining element, i.e., all side chains of the constrained helices remain available for molecular recognition. (2) This approach can be deployed to constrain very short peptides (<10 amino acid residues) into highly stable α-helices. This chapter presents the biophysical basis for the development of the hydrogen bond surrogate approach, as well as methods for the synthesis and conformational analysis of the artificial helices.
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Affiliation(s)
- Ganesh S Jedhe
- Department of Chemistry, New York University, New York, NY, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, United States.
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21
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Wang X, Ni D, Liu Y, Lu S. Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions. Front Chem 2021; 9:682675. [PMID: 34017824 PMCID: PMC8128998 DOI: 10.3389/fchem.2021.682675] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are well-established as a class of promising drug targets for their implications in a wide range of biological processes. However, drug development toward PPIs is inevitably hampered by their flat and wide interfaces, which generally lack suitable pockets for ligand binding, rendering most PPI systems "undruggable." Here, we summarized drug design strategies for developing peptide-based PPI inhibitors. Importantly, several quintessential examples toward well-established PPI targets such as Bcl-2 family members, p53-MDM2, as well as APC-Asef are presented to illustrate the detailed schemes for peptide-based PPI inhibitor development and optimizations. This review supplies a comprehensive overview of recent progresses in drug discovery targeting PPIs through peptides or peptidomimetics, and will shed light on future therapeutic agent development toward the historically "intractable" PPI systems.
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Affiliation(s)
- Xuefei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Yaqin Liu
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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22
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Salkovski M, Pavlinov I, Gao Q, Aldrich LN. Development of a High-Throughput, Compound-Multiplexed Fluorescence Polarization Assay to Identify ATG5-ATG16L1 Protein-Protein Interaction Inhibitors. SLAS DISCOVERY 2021; 26:933-943. [PMID: 33783243 DOI: 10.1177/24725552211000679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Macroautophagy is a catabolic process wherein cytosolic cargo is engulfed in an autophagosome that fuses with a lysosome to degrade the cargo for recycling. Autophagy maintains cellular homeostasis and is involved in a myriad of illnesses ranging from cancer to neurodegenerative diseases, but its therapeutic potential remains elusive due to a lack of potent and specific autophagy modulators. To identify specific inhibitors of early autophagy, a target-based, compound-multiplexed, fluorescence polarization, high-throughput screen that targets the ATG5-ATG16L1 protein-protein interaction was developed. This interaction is critical for the formation of LC3-II, which is involved in phagophore maturation, and its disruption should inhibit autophagy. This assay is based on the polarization of light emitted by a fluorescent rhodamine tag conjugated to a peptide corresponding to the N-terminal region of ATG16L1 (ATG16L1-N). It was confirmed that this peptide binds specifically to ATG5, and the assay was validated by rapidly screening 4800 molecules through compound multiplexing. Through these initial screening efforts, a molecule was identified that disrupts the ATG5-ATG16L1 protein-protein interaction with micromolar potency, and this molecule will serve as a starting point for chemical optimization as an autophagy inhibitor.
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Affiliation(s)
- Maryna Salkovski
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Qiwen Gao
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
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23
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Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A. Front Mol Biosci 2021; 8:650881. [PMID: 33842550 PMCID: PMC8032985 DOI: 10.3389/fmolb.2021.650881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 12/01/2022] Open
Abstract
Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.
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Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
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24
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maritess Arancillo
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
| | | | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases Institute of Biosciences and Technology Texas A&M Health Science Center Houston TX 77030 USA
| | - Kevin Burgess
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
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25
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021; 60:6653-6659. [PMID: 33319463 PMCID: PMC7940574 DOI: 10.1002/anie.202015203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Small molecule probe development is pivotal in biomolecular science. Research described here was undertaken to develop a non-peptidic chemotype, piptides, that is amenable to convenient, iterative solid-phase syntheses, and useful in biomolecular probe discovery. Piptides can be made from readily accessible pip acid building blocks and have good proteolytic and pH stabilities. An illustrative application of piptides against a protein-protein interaction (PPI) target was explored. The Exploring Key Orientations (EKO) strategy was used to evaluate piptide candidates for this. A library of only 14 piptides contained five members that disrupted epidermal growth factor (EGF) and its receptor, EGFR, at low micromolar concentrations. These piptides also caused apoptotic cell death, and antagonized EGF-induced phosphorylation of intracellular tyrosine residues in EGFR.
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Affiliation(s)
- Maritess Arancillo
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Jaru Taechalertpaisarn
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, 77030, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
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Bari KJ, Prakashchand DD. Fundamental Challenges and Outlook in Simulating Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins. J Phys Chem Lett 2021; 12:1644-1656. [PMID: 33555894 DOI: 10.1021/acs.jpclett.0c03404] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intrinsically disordered proteins (IDPs) populate an ensemble of dynamic conformations, making their structural characterization by experiments challenging. Many IDPs undergo liquid-liquid phase separation into dense membraneless organelles with myriad cellular functions. Multivalent interactions in low-complexity IDPs promote the formation of these subcellular coacervates. While solution NMR, Förster resonance energy transfer (FRET), and small-angle X-ray scattering (SAXS) studies on IDPs have their own challenges, recent computational methods draw a rational trade-off to characterize the driving forces underlying phase separation. In this Perspective, we critically evaluate the scope of approximation-free field theoretic simulations, well-tempered ensemble methods, enhanced sampling techniques, coarse-grained force fields, and slab simulation approaches to offer an improved understanding of phase separation. A synergy between simulation length scale and model resolution would reduce the existing caveats and enable theories of polymer physics to elucidate finer details of liquid-liquid phase separation (LLPS). These computational advances offer promise for rigorous characterization of the IDP proteome and designing peptides with tunable material and self-assembly properties.
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Affiliation(s)
- Khandekar Jishan Bari
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad 500107, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Dube Dheeraj Prakashchand
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad 500107, India
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Zwillinger M, Reddy PS, Wicher B, Mandal PK, Csékei M, Fischer L, Kotschy A, Huc I. Aromatic Foldamer Helices as α-Helix Extended Surface Mimetics. Chemistry 2020; 26:17366-17370. [PMID: 32910480 PMCID: PMC7839445 DOI: 10.1002/chem.202004064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 12/15/2022]
Abstract
Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α-helices and are not obvious candidates for α-helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α-helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α-helix-like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.
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Affiliation(s)
- Márton Zwillinger
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityBudapestHungary
| | - Post Sai Reddy
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660780PoznanPoland
| | - Pradeep K. Mandal
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Márton Csékei
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Lucile Fischer
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
| | - András Kotschy
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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Cussol L, Mauran‐Ambrosino L, Buratto J, Belorusova AY, Neuville M, Osz J, Fribourg S, Fremaux J, Dolain C, Goudreau SR, Rochel N, Guichard G. Structural Basis for α‐Helix Mimicry and Inhibition of Protein–Protein Interactions with Oligourea Foldamers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Léonie Cussol
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Laura Mauran‐Ambrosino
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
- Ureka Pharma SAS 2 rue Robert Escarpit F-33607 Pessac France
| | - Jérémie Buratto
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) INSERM U1258/CNRS UMR 7104/ Univ. Strasbourg 67404 Illkirch France
| | - Maxime Neuville
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
- Ureka Pharma SAS 2 rue Robert Escarpit F-33607 Pessac France
| | - Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) INSERM U1258/CNRS UMR 7104/ Univ. Strasbourg 67404 Illkirch France
| | - Sébastien Fribourg
- ARNA Laboratory INSERM U1212 UMR CNRS 5320 Univ. Bordeaux Bordeaux France
| | | | - Christel Dolain
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | | | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) INSERM U1258/CNRS UMR 7104/ Univ. Strasbourg 67404 Illkirch France
| | - Gilles Guichard
- Univ. Bordeaux CNRS Bordeaux INP CBMN UMR 5248 Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
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29
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Structural Basis for α‐Helix Mimicry and Inhibition of Protein–Protein Interactions with Oligourea Foldamers. Angew Chem Int Ed Engl 2020; 60:2296-2303. [DOI: 10.1002/anie.202008992] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/19/2020] [Indexed: 12/16/2022]
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30
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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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31
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Shi Y, Sang P, Lu J, Higbee P, Chen L, Yang L, Odom T, Daughdrill G, Chen J, Cai J. Rational Design of Right-Handed Heterogeneous Peptidomimetics as Inhibitors of Protein-Protein Interactions. J Med Chem 2020; 63:13187-13196. [PMID: 33140956 DOI: 10.1021/acs.jmedchem.0c01638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptidomimetics have gained great attention for their function as protein-protein interaction (PPI) inhibitors. Herein, we report the design and investigation of a series of right-handed helical heterogeneous 1:1 α/Sulfono-γ-AA peptides as unprecedented inhibitors for p53-MDM2 and p53-MDMX. The most potent helical heterogeneous 1:1 α/Sulfono-γ-AA peptides were shown to bind tightly to MDM2 and MDMX, with Kd of 19.3 and 66.8 nM, respectively. Circular dichroism spectra, 2D-NMR spectroscopy, and the computational simulations suggested that these helical sulfono-γ-AA peptides could mimic the critical side chains of p53 and disrupt p53/MDM2 PPI effectively. It was noted that these 1:1 α/Sulfono-γ-AA peptides were completely resistant to proteolytic degradation, boosting their potential for biomedical applications. Furthermore, effective cellular activity is achieved by the stapled 1:1 α/Sulfono-γ-AA peptides, evidenced by significantly enhanced p53 transcriptional activity and much more induced level of MDM2 and p21. The 1:1 α/Sulfono-γ-AA peptides could be an alternative strategy to antagonize a myriad of PPIs.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Junhao Lu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Pirada Higbee
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Lihong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Leixiang Yang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Jiandong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
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32
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Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem 2020; 207:112764. [PMID: 32871340 DOI: 10.1016/j.ejmech.2020.112764] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) play a pivotal role in extensive biological processes and are thus crucial to human health and the development of disease states. Due to their critical implications, PPIs have been spotlighted as promising drug targets of broad-spectrum therapeutic interests. However, owing to the general properties of PPIs, such as flat surfaces, featureless conformations, difficult topologies, and shallow pockets, previous attempts were faced with serious obstacles when targeting PPIs and almost portrayed them as "intractable" for decades. To date, rapid progress in computational chemistry and structural biology methods has promoted the exploitation of PPIs in drug discovery. These techniques boost their cost-effective and high-throughput traits, and enable the study of dynamic PPI interfaces. Thus, computational methods represent an alternative strategy to target "undruggable" PPI interfaces and have attracted intense pharmaceutical interest in recent years, as exemplified by the accumulating number of successful cases. In this review, we first introduce a diverse set of computational methods used to design PPI modulators. Herein, we focus on the recent progress in computational strategies and provide a comprehensive overview covering various methodologies. Importantly, a list of recently-reported successful examples is highlighted to verify the feasibility of these computational approaches. Finally, we conclude the general role of computational methods in targeting PPIs, and also discuss future perspectives on the development of such aids.
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33
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Nucleic acid recognition and antiviral activity of 1,4-substituted terphenyl compounds mimicking all faces of the HIV-1 Rev protein positively-charged α-helix. Sci Rep 2020; 10:7190. [PMID: 32346097 PMCID: PMC7188855 DOI: 10.1038/s41598-020-64120-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/09/2020] [Indexed: 11/08/2022] Open
Abstract
Small synthetic molecules mimicking the three-dimensional structure of α-helices may find applications as inhibitors of therapeutically relevant protein-protein and protein-nucleic acid interactions. However, the design and use of multi-facial helix mimetics remains in its infancy. Here we describe the synthesis and application of novel bilaterally substituted p-terphenyl compounds containing positively-charged aminoalkyl groups in relative 1,4 positions across the aromatic scaffold. These compounds were specifically designed to mimic all faces of the arginine-rich α-helix of the HIV-1 protein Rev, which forms deeply embedded RNA complexes and plays key roles in the virus replication cycle. Two of these molecules recognized the Rev site in the viral RNA and inhibited the formation of the RRE-Rev ribonucleoprotein complex, a currently unexploited target in HIV chemotherapy. Cellular assays revealed that the most active compounds blocked HIV-1 replication with little toxicity, and likely exerted this effect through a multi-target mechanism involving inhibition of viral LTR promoter-dependent transcription and Rev function. Further development of this scaffold may open new avenues for targeting nucleic acids and may complement current HIV therapies, none of which involve inhibitors interfering with the gene regulation processes of the virus.
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34
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Pavlinov I, Salkovski M, Aldrich LN. Beclin 1-ATG14L Protein-Protein Interaction Inhibitor Selectively Inhibits Autophagy through Disruption of VPS34 Complex I. J Am Chem Soc 2020; 142:8174-8182. [PMID: 32320221 DOI: 10.1021/jacs.9b12705] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy, a catabolic recycling process, has been implicated as a critical pathway in cancer. Its role in maintaining cellular homeostasis helps to nourish hypoxic, nutrient-starved tumors and protects them from chemotherapy-induced death. Recent efforts to target autophagy in cancer have focused on kinase inhibition, which has led to molecules that lack specificity due to the multiple roles of key kinases in this pathway. For example, the lipid kinase VPS34 is present in two multiprotein complexes responsible for the generation of phosphatidylinositol-3-phosphate. Complex I generates the autophagosome, and Complex II is crucial for endosomal trafficking. Molecules targeting VPS34 inhibit both complexes, which inhibits autophagy but causes undesirable defects in vesicle trafficking. The lack of specific autophagy modulators has limited the utility of autophagy inhibition as a therapeutic strategy. We hypothesize that disruption of the Beclin 1-ATG14L protein-protein interaction, which is required for the formation, proper localization, and function of VPS34 Complex I but not Complex II, will disrupt Complex I formation and selectively inhibit autophagy. To this end, a high-throughput, cellular NanoBRET assay was developed targeting this interaction. An initial screen of 2560 molecules yielded 19 hits that effectively disrupted the interaction, and it was confirmed that one hit disrupted VPS34 Complex I formation and inhibited autophagy. In addition, the molecule did not disrupt the Beclin 1-UVRAG interaction, critical for VPS34 Complex II, and thus had little impact on vesicle trafficking. This molecule is a promising new tool that is critical for understanding how modulation of the Beclin 1-ATG14L interaction affects autophagy. More broadly, its discovery demonstrates that targeting protein-protein interactions found within the autophagy pathway is a viable strategy for the discovery of autophagy-specific probes and therapeutics.
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Affiliation(s)
- Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
| | - Maryna Salkovski
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago Illinois 60607, United States
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35
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Sadek J, Wuo MG, Rooklin D, Hauenstein A, Hong SH, Gautam A, Wu H, Zhang Y, Cesarman E, Arora PS. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat Commun 2020; 11:1786. [PMID: 32286300 PMCID: PMC7156456 DOI: 10.1038/s41467-020-15576-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein. NF-κB signalling involves the scaffold protein NEMO, which can be bound by the oncoprotein vFLIP to promote cell survival and oncogenic transformation. Here the authors rationally engineer a tertiary protein mimic of NEMO to disrupt the vFLIP-NEMO interaction to induce cell death.
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Affiliation(s)
- Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Michael G Wuo
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - David Rooklin
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Arthur Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Archana Gautam
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, USA.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, 200122, Shanghai, China
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, 10003, USA.
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36
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Sang P, Shi Y, Lu J, Chen L, Yang L, Borcherds W, Abdulkadir S, Li Q, Daughdrill G, Chen J, Cai J. α-Helix-Mimicking Sulfono-γ-AApeptide Inhibitors for p53-MDM2/MDMX Protein-Protein Interactions. J Med Chem 2020; 63:975-986. [PMID: 31971801 PMCID: PMC7025332 DOI: 10.1021/acs.jmedchem.9b00993] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The use of peptidomimetic scaffolds is a promising strategy for the inhibition of protein-protein interactions (PPIs). Herein, we demonstrate that sulfono-γ-AApeptides can be rationally designed to mimic the p53 α-helix and inhibit p53-MDM2 PPIs. The best inhibitor, with Kd and IC50 values of 26 nM and 0.891 μM toward MDM2, respectively, is among the most potent unnatural peptidomimetic inhibitors disrupting the p53-MDM2/MDMX interaction. Using fluorescence polarization assays, circular dichroism, nuclear magnetic resonance spectroscopy, and computational simulations, we demonstrate that sulfono-γ-AApeptides adopt helical structures resembling p53 and competitively inhibit the p53-MDM2 interaction by binding to the hydrophobic cleft of MDM2. Intriguingly, the stapled sulfono-γ-AApeptides showed promising cellular activity by enhancing p53 transcriptional activity and inducing expression of MDM2 and p21. Moreover, sulfono-γ-AApeptides exhibited remarkable resistance to proteolysis, augmenting their biological potential. Our results suggest that sulfono-γ-AApeptides are a new class of unnatural helical foldamers that disrupt PPIs.
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Affiliation(s)
- Peng Sang
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Yan Shi
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Junhao Lu
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Lihong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Leixiang Yang
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Sami Abdulkadir
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Qi Li
- Department of Medical Oncology , Shuguang Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Jiandong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Jianfeng Cai
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
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37
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Wang Z, Ji H. Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7. J Med Chem 2019; 62:9906-9917. [PMID: 31593458 DOI: 10.1021/acs.jmedchem.9b01324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated protein-protein interaction (PPI) complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. These provide the foundation for designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivities between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 1 was disclosed. The close positioning of this small molecule to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule inhibitors for α-helix-mediated PPIs.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
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38
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Ganeshpurkar A, Swetha R, Kumar D, Gangaram GP, Singh R, Gutti G, Jana S, Kumar D, Kumar A, Singh SK. Protein-Protein Interactions and Aggregation Inhibitors in Alzheimer's Disease. Curr Top Med Chem 2019; 19:501-533. [PMID: 30836921 DOI: 10.2174/1568026619666190304153353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alzheimer's Disease (AD), a multifaceted disorder, involves complex pathophysiology and plethora of protein-protein interactions. Thus such interactions can be exploited to develop anti-AD drugs. OBJECTIVE The interaction of dynamin-related protein 1, cellular prion protein, phosphoprotein phosphatase 2A and Mint 2 with amyloid β, etc., studied recently, may have critical role in progression of the disease. Our objective has been to review such studies and their implications in design and development of drugs against the Alzheimer's disease. METHODS Such studies have been reviewed and critically assessed. RESULTS Review has led to show how such studies are useful to develop anti-AD drugs. CONCLUSION There are several PPIs which are current topics of research including Drp1, Aβ interactions with various targets including PrPC, Fyn kinase, NMDAR and mGluR5 and interaction of Mint2 with PDZ domain, etc., and thus have potential role in neurodegeneration and AD. Finally, the multi-targeted approach in AD may be fruitful and opens a new vista for identification and targeting of PPIs in various cellular pathways to find a cure for the disease.
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Affiliation(s)
- Ankit Ganeshpurkar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Devendra Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gore P Gangaram
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Dileep Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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Cicaloni V, Trezza A, Pettini F, Spiga O. Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019; 19:534-554. [PMID: 30836920 DOI: 10.2174/1568026619666190304153901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/02/2019] [Accepted: 01/25/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Identification of Protein-Protein Interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. OBJECTIVE Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. METHODS Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. RESULTS In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/ inhibitor molecules. CONCLUSION A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention.
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Affiliation(s)
- Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy.,Toscana Life Sciences Foundation, via Fiorentina 1, 53100 Siena, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Francesco Pettini
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
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40
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Taechalertpaisarn J, Lyu RL, Arancillo M, Lin CM, Perez LM, Ioerger TR, Burgess K. Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis. Org Biomol Chem 2019; 17:3267-3274. [PMID: 30847453 PMCID: PMC6863600 DOI: 10.1039/c9ob00204a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An active segment of the research community designing small molecules ("minimalist mimics" of peptide fragments) to interfere with protein-protein interactions have based their studies on an implicit hypothesis. Here we refer to this as the Secondary Structure Hypothesis, that might be defined as, "If a small molecule can orient amino acid side-chains in directions that resemble side-chains of the parent secondary structure at the interface, then that small molecule is a candidate to perturb the protein-protein interaction". Rigorous tests of this hypothesis require co-crystallization of minimalist mimics with protein receptors, and comparison of the bound conformations with the interface secondary structures they were designed to resemble. Unfortunately, to the best of our knowledge, there is no such analysis in the literature, and it is unlikely that enough examples will emerge in the near future to test the hypothesis. Research described here was designed to challenge this hypothesis from a different perspective. In a previous study, preferred conformations of a series of novel minimalist mimics were simulated then systematically overlaid on >240 000 crystallographically characterized protein-protein interfaces. Select data from that overlay procedure revealed chemotypes that overlay side chains on various PPI interfaces with a relatively high frequency of occurrence. The first aim of this work was to determine if good secondary structure mimics overlay frequently on PPI interfaces. The second aim of this work was to determine if overlays of preferred conformers at interface regions involve secondary structures. Thus situations where these conformations overlaid extremely well on PPI interfaces were analyzed to determine if secondary structures featured the PPI regions where these molecules overlaid in the previous study. Combining conclusions from these two studies enabled us to formulate a hypothesis that is complementary to the Secondary Structure Hypothesis, but, unlike this, is supported by abundant data. We call this the Interface Mimicry Hypothesis.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
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Olajos G, Hetényi A, Wéber E, Szögi T, Fülöp L, Martinek TA. Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches. Org Biomol Chem 2019; 16:5492-5499. [PMID: 30024580 DOI: 10.1039/c8ob01322e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary.
| | - Titanilla Szögi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Li J, Xi W, Li X, Sun H, Li Y. Advances in inhibition of protein-protein interactions targeting hypoxia-inducible factor-1 for cancer therapy. Bioorg Med Chem 2019; 27:1145-1158. [PMID: 30819620 DOI: 10.1016/j.bmc.2019.01.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/23/2022]
Abstract
Hypoxia is a common characteristic of many types of solid tumors and is associated with tumor propagation, malignant progression, and resistance to anti-cancer therapy. HIF-1 pathway is one of the survival pathways activated in tumor in response to hypoxia. In hypoxic condition, hypoxia-inducible factor-1α (HIF-1α) is stabilized and translocated into nucleus where it forms heterodimer with HIF-1β and regulates the expression of a plethora of genes involved in different processes, such as cell proliferation, differentiation, apoptosis, vascularization/angiogenesis, tumor invasion and metastasis. Recruitment of co-activator p300 or CBP to HIF-1α is critical to the transactivation activity of HIF-1 dimer, therefore, small molecules which can block the dimerization of HIF-1α and HIF-1β or inhibit the interaction between HIF-1α and p300 can function as inhibitors of HIF-1 and have the potential to be developed as novel therapies for the treatment of human cancers. In this review, recent progress of small molecular inhibitors of protein-protein interactions targeting HIF-1 is summarized, the mechanism of functions of these compounds and their potential usage as anti-cancer agents have also been discussed.
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Affiliation(s)
- Jia Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Wanlin Xi
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaofang Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
| | - Yuyan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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45
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Burnside D, Schoenrock A, Moteshareie H, Hooshyar M, Basra P, Hajikarimlou M, Dick K, Barnes B, Kazmirchuk T, Jessulat M, Pitre S, Samanfar B, Babu M, Green JR, Wong A, Dehne F, Biggar KK, Golshani A. In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences. iScience 2018; 11:375-387. [PMID: 30660105 PMCID: PMC6348295 DOI: 10.1016/j.isci.2018.11.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/19/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
Synthetic proteins with high affinity and selectivity for a protein target can be used as research tools, biomarkers, and pharmacological agents, but few methods exist to design such proteins de novo. To this end, the In-Silico Protein Synthesizer (InSiPS) was developed to design synthetic binding proteins (SBPs) that bind pre-determined targets while minimizing off-target interactions. InSiPS is a genetic algorithm that refines a pool of random sequences over hundreds of generations of mutation and selection to produce SBPs with pre-specified binding characteristics. As a proof of concept, we design SBPs against three yeast proteins and demonstrate binding and functional inhibition of two of three targets in vivo. Peptide SPOT arrays confirm binding sites, and a permutation array demonstrates target specificity. Our foundational approach will support the field of de novo design of small binding polypeptide motifs and has robust applicability while offering potential advantages over the limited number of techniques currently available. InSiPS engineers synthetic binding proteins (SBPs) using primary protein sequence SBPs are designed to a bind a target protein and avoid “off-target” interactions Binding and functional inhibition of two of three target proteins in yeast is demonstrated Our new approach offers advantages over alternative tools that rely on 3D models
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Affiliation(s)
- Daniel Burnside
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Andrew Schoenrock
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Prabh Basra
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Maryam Hajikarimlou
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Brad Barnes
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Tom Kazmirchuk
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Matthew Jessulat
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C5, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Kyle K Biggar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Institute of Biochemistry, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Institute of Biochemistry, Carleton University, Ottawa, ON K1S5B6, Canada.
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Jiang T, Renfrew PD, Drew K, Youngs N, Butterfoss GL, Bonneau R, Shasha DN. An adaptive geometric search algorithm for macromolecular scaffold selection. Protein Eng Des Sel 2018; 31:345-354. [PMID: 30407584 PMCID: PMC6373690 DOI: 10.1093/protein/gzy028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/05/2018] [Indexed: 11/14/2022] Open
Abstract
A wide variety of protein and peptidomimetic design tasks require matching functional 3D motifs to potential oligomeric scaffolds. For example, during enzyme design, one aims to graft active-site patterns-typically consisting of 3-15 residues-onto new protein surfaces. Identifying protein scaffolds suitable for such active-site engraftment requires costly searches for protein folds that provide the correct side chain positioning to host the desired active site. Other examples of biodesign tasks that require similar fast exact geometric searches of potential side chain positioning include mimicking binding hotspots, design of metal binding clusters and the design of modular hydrogen binding networks for specificity. In these applications, the speed and scaling of geometric searches limits the scope of downstream design to small patterns. Here, we present an adaptive algorithm capable of searching for side chain take-off angles, which is compatible with an arbitrarily specified functional pattern and which enjoys substantive performance improvements over previous methods. We demonstrate this method in both genetically encoded (protein) and synthetic (peptidomimetic) design scenarios. Examples of using this method with the Rosetta framework for protein design are provided. Our implementation is compatible with multiple protein design frameworks and is freely available as a set of python scripts (https://github.com/JiangTian/adaptive-geometric-search-for-protein-design).
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Affiliation(s)
- Tian Jiang
- Computer ScienceDepartment, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - P Douglas Renfrew
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Kevin Drew
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Noah Youngs
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Richard Bonneau
- Computer ScienceDepartment, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Den Nis Shasha
- Computer ScienceDepartment, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
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Fletcher JM, Horner KA, Bartlett GJ, Rhys GG, Wilson AJ, Woolfson DN. De novo coiled-coil peptides as scaffolds for disrupting protein-protein interactions. Chem Sci 2018; 9:7656-7665. [PMID: 30393526 PMCID: PMC6182421 DOI: 10.1039/c8sc02643b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023] Open
Abstract
Homo- and hetero-dimeric coiled coils as scaffolds for the presentation of α-helical protein-binding motifs.
Protein–protein interactions (PPIs) play pivotal roles in the majority of biological processes. Therefore, improved approaches to target and disrupt PPIs would provide tools for chemical biology and leads for therapeutic development. PPIs with α-helical components are appealing targets given that the secondary structure is well understood and can be mimicked or stabilised to render small-molecule and constrained-peptide-based inhibitors. Here we present a strategy to target α-helix-mediated PPIs that exploits de novo coiled-coil assemblies and test this using the MCL-1/NOXA-B PPI. First, computational alanine scanning is used to identify key α-helical residues from NOXA-B that contribute to the interface. Next, these residues are grafted onto the exposed surfaces of de novo designed homodimeric or heterodimeric coiled-coil peptides. The resulting synthetic peptides selectively inhibit a cognate MCL-1/BID complex in the mid-nM range. Furthermore, the heterodimeric system affords control as inhibition occurs only when both the grafted peptide and its designed partner are present. This establishes proof of concept for exploiting peptides stabilised in de novo coiled coils as inhibitors of PPIs. This dependence on supramolecular assembly introduces new possibilities for regulation and control.
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Affiliation(s)
- Jordan M Fletcher
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Katherine A Horner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Gail J Bartlett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; .,School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , UK.,BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol , BS8 1TQ , UK
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48
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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49
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Wuo MG, Arora PS. Engineered protein scaffolds as leads for synthetic inhibitors of protein-protein interactions. Curr Opin Chem Biol 2018; 44:16-22. [PMID: 29803113 DOI: 10.1016/j.cbpa.2018.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 11/18/2022]
Abstract
Rationally designed protein-protein interaction inhibitors mimic interfacial binding epitopes, specifically residues that contribute significantly to binding. However, direct mimicry often does not lead to high affinity ligands because the natural complexes themselves are functionally transient and of low affinity. The mimics typically need to be optimized for potency. Engineered proteins displaying conformationally-defined epitopes may serve as attractive alternatives to natural protein partners as they can be strictly screened for tight binding. The advantage of focused screens with conformationally-defined protein scaffolds is that conservation of the geometry of the natural binding epitopes may preserve binding site specificity while allowing direct mimicry by various synthetic secondary structure scaffolds. Here we review different classes of engineered proteins for their binding epitope geometry and as leads for synthetic secondary and tertiary structure mimics.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA.
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50
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Kumar S, Henning-Knechtel A, Magzoub M, Hamilton AD. Peptidomimetic-Based Multidomain Targeting Offers Critical Evaluation of Aβ Structure and Toxic Function. J Am Chem Soc 2018; 140:6562-6574. [PMID: 29648815 DOI: 10.1021/jacs.7b13401] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The prevailing hypothesis stipulates that the preamyloid oligomers of Aβ are the main culprits associated with the onset and progression of Alzheimer's disease (AD), which has prompted efforts to search for therapeutic agents with the ability to inhibit Aβ oligomerization and amyloidogenesis. However, clinical progress is impeded by the limited structural information about the neurotoxic oligomers. To address this issue, we have adopted a synthetic approach, where a library of oligopyridylamide-based small molecules was tested against various microscopic events implicated in the self-assembly of Aβ. Two oligopyridylamides bind to different domains of Aβ and affect distinct microscopic events in Aβ self-assembly. The study lays the foundations for a dual recognition strategy to simultaneously target different domains of Aβ for further improvement in antiamyloidogenic activity. The data demonstrate that one of the most effective oligopyridylamides forms a high affinity complex with Aβ, which sustains the compound's activity in cellular milieu. The oligopyridylamide was able to rescue cells when introduced 24 h after the incubation of Aβ. The rescue of Aβ toxicity is potentially a consequence of the colocalization of the oligopyridylamide with Aβ. The synthetic tools utilized here provide a straightforward strategic framework to identify a range of potent antagonists of Aβ-mediated toxic functions. This approach could be a powerful route to the design of candidate drugs for various amyloid diseases that have so far proven to be "untargetable".
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Affiliation(s)
- Sunil Kumar
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Anja Henning-Knechtel
- 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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