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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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2
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Wu SY, Lai HT, Sanjib Banerjee N, Ma Z, Santana JF, Wei S, Liu X, Zhang M, Zhan J, Chen H, Posner B, Chen Y, Price DH, Chow LT, Zhou J, Chiang CM. IDR-targeting compounds suppress HPV genome replication via disruption of phospho-BRD4 association with DNA damage response factors. Mol Cell 2024; 84:202-220.e15. [PMID: 38103559 PMCID: PMC10843765 DOI: 10.1016/j.molcel.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Compounds binding to the bromodomains of bromodomain and extra-terminal (BET) family proteins, particularly BRD4, are promising anticancer agents. Nevertheless, side effects and drug resistance pose significant obstacles in BET-based therapeutics development. Using high-throughput screening of a 200,000-compound library, we identified small molecules targeting a phosphorylated intrinsically disordered region (IDR) of BRD4 that inhibit phospho-BRD4 (pBRD4)-dependent human papillomavirus (HPV) genome replication in HPV-containing keratinocytes. Proteomic profiling identified two DNA damage response factors-53BP1 and BARD1-crucial for differentiation-associated HPV genome amplification. pBRD4-mediated recruitment of 53BP1 and BARD1 to the HPV origin of replication occurs in a spatiotemporal and BRD4 long (BRD4-L) and short (BRD4-S) isoform-specific manner. This recruitment is disrupted by phospho-IDR-targeting compounds with little perturbation of the global transcriptome and BRD4 chromatin landscape. The discovery of these protein-protein interaction inhibitors (PPIi) not only demonstrates the feasibility of developing PPIi against phospho-IDRs but also uncovers antiviral agents targeting an epigenetic regulator essential for virus-host interaction and cancer development.
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Affiliation(s)
- Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hsien-Tsung Lai
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - N Sanjib Banerjee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Shuguang Wei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xisheng Liu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meirong Zhang
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Jian Zhan
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yadong Chen
- State Key Laboratory of Natural Medicines, Department of Organic Chemistry, China Pharmaceutical University, Nanjing 210009, P.R. China
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Louise T Chow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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3
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Sellner H, Chapeau E, Furet P, Voegtle M, Salem B, Le Douget M, Bordas V, Groell JM, Le Goff AL, Rouzet C, Wietlisbach T, Zimmermann T, McKenna J, Brocklehurst C, Chène P, Wartmann M, Scheufler C, Kallen J, Williams G, Harlfinger S, Traebert M, Dumotier B, Schmelzle T, Soldermann N. Optimization of a Class of Dihydrobenzofurane Analogs Toward Orally Efficacious YAP-TEAD Protein-Protein Interaction Inhibitors. ChemMedChem 2023:e202300051. [PMID: 36988034 DOI: 10.1002/cmdc.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 03/30/2023]
Abstract
The inhibition of the YAP-TEAD protein-protein interaction constitutes a promising therapeutic approach for the treatment of cancers linked to the dysregulation of the Hippo signaling pathway. The identification of a class of small molecules which potently inhibit the YAP-TEAD interaction by binding tightly to the Ω-loop pocket of TEAD has previously been communicated. This report details the further multi-parameter optimization of this class of compounds resulting in advanced analogs combining nanomolar cellular potency with a balanced ADME and off-target profile, and efficacy of these compounds in tumor bearing mice is demonstrated for the first time.
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Affiliation(s)
- Holger Sellner
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, Novartis Pharma AG, WSJ-386.01.14.25, 4002, Basel, SWITZERLAND
| | - Emilie Chapeau
- Novartis Institutes for BioMedical Research Basel, Oncology, SWITZERLAND
| | - Pascal Furet
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Markus Voegtle
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Bahaa Salem
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Mickael Le Douget
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Vincent Bordas
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Jean-Marc Groell
- Novartis Institutes for BioMedical Research Basel, Globasl Discovery Chemistry, SWITZERLAND
| | - Anne-Laure Le Goff
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Christine Rouzet
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Thomas Wietlisbach
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Thomas Zimmermann
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Joseph McKenna
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Cara Brocklehurst
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Patrick Chène
- Novartis Institutes for BioMedical Research Basel, Oncology, SWITZERLAND
| | - Markus Wartmann
- Novartis Institutes for BioMedical Research Basel, Oncology, SWITZERLAND
| | - Clemens Scheufler
- Novartis Institutes for BioMedical Research Basel, Chemical Biology & Therapeutics, SWITZERLAND
| | - Joerg Kallen
- Novartis Institutes for BioMedical Research Basel, Chemical Biology & Therapeutics, SWITZERLAND
| | - Gareth Williams
- Novartis Institutes for BioMedical Research Basel, Pharmacokinetics Sciences, SWITZERLAND
| | - Stephanie Harlfinger
- Novartis Institutes for BioMedical Research Basel, Pharmacokinetics Sciences, SWITZERLAND
| | - Martin Traebert
- Novartis Institutes for BioMedical Research Basel, Preclinical Safety, SWITZERLAND
| | - Bérengère Dumotier
- Novartis Institutes for BioMedical Research Basel, Preclinical Safety, SWITZERLAND
| | - Tobias Schmelzle
- Novartis Institutes for BioMedical Research Basel, Oncology, SWITZERLAND
| | - Nicolas Soldermann
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
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4
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Vaaltyn MC, Mateos‐Jimenez M, Müller R, Mackay CL, Edkins AL, Clarke DJ, Veale CGL. Native Mass Spectrometry-Guided Screening Identifies Hit Fragments for HOP-HSP90 PPI Inhibition. Chembiochem 2022; 23:e202200322. [PMID: 36017658 PMCID: PMC9826382 DOI: 10.1002/cbic.202200322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Contemporary medicinal chemistry considers fragment-based drug discovery (FBDD) and inhibition of protein-protein interactions (PPI) as important means of expanding the volume of druggable chemical space. However, the ability to robustly identify valid fragments and PPI inhibitors is an enormous challenge, requiring the application of sensitive biophysical methodology. Accordingly, in this study, we exploited the speed and sensitivity of nanoelectrospray (nano-ESI) native mass spectrometry to identify a small collection of fragments which bind to the TPR2AB domain of HOP. Follow-up biophysical assessment of a small selection of binding fragments confirmed binding to the single TPR2A domain, and that this binding translated into PPI inhibitory activity between TPR2A and the HSP90 C-terminal domain. An in-silico assessment of binding fragments at the PPI interfacial region, provided valuable structural insight for future fragment elaboration strategies, including the identification of losartan as a weak, albeit dose-dependent inhibitor of the target PPI.
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Affiliation(s)
- Michaelone C. Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - Maria Mateos‐Jimenez
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Ronel Müller
- School of Chemistry and PhysicsUniversity of KwaZulu-NatalScottsville3209South Africa
| | - C. Logan Mackay
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - David J. Clarke
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Clinton G. L. Veale
- Department of ChemistryUniversity of Cape Town RondeboschCape Town7700South Africa
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5
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Furet P, Bordas V, Le Douget M, Salem B, Mesrouze Y, Imbach-Weese P, Sellner H, Voegtle M, Soldermann N, Chapeau E, Wartmann M, Scheufler C, Fernandez C, Kallen J, Guagnano V, Chène P, Schmelzle T. The First Class of Small Molecules Potently Disrupting the YAP-TEAD Interaction by Direct Competition. ChemMedChem 2022; 17:e202200303. [PMID: 35950546 DOI: 10.1002/cmdc.202200303] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/10/2022] [Indexed: 11/08/2022]
Abstract
Inhibition of the YAP-TEAD protein protein interaction is an attractive therapeutic concept under intense investigation with the objective to treat cancers associated with a dysregulation of the Hippo pathway. However, owing to the very extended surface of interaction of the two proteins, the identification of small drug-like molecules able to efficiently prevent YAP from binding to TEAD by direct competition has been elusive so far. We disclose here the discovery of the first class of small molecules potently inhibiting the YAP-TEAD interaction by binding at one of the main interaction sites of YAP at the surface of TEAD. These inhibitors, providing a path forward to pharmacological intervention in the Hippo pathway, evolved from a weakly active virtual screening hit advanced to high potency by structure-based design.
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Affiliation(s)
- Pascal Furet
- Novartis Pharma AG, Biomedical Research, 4002, Basel, SWITZERLAND
| | - Vincent Bordas
- Novartis Institutes for BioMedical Research Basel, GDC, SWITZERLAND
| | | | - Bahaa Salem
- Novartis Institutes for BioMedical Research Basel, GDC, SWITZERLAND
| | - Yannick Mesrouze
- Novartis Institutes for BioMedical Research Basel, ODD, SWITZERLAND
| | | | - Holger Sellner
- Novartis Institutes for BioMedical Research Basel, GDC, SWITZERLAND
| | - Markus Voegtle
- Novartis Institutes for BioMedical Research Basel, GDC, SWITZERLAND
| | | | - Emilie Chapeau
- Novartis Institutes for BioMedical Research Basel, ODD, SWITZERLAND
| | - Markus Wartmann
- Novartis Institutes for BioMedical Research Basel, ODD, SWITZERLAND
| | | | - Cesar Fernandez
- Novartis Institutes for BioMedical Research Basel, CBT, SWITZERLAND
| | - Joerg Kallen
- Novartis Institutes for BioMedical Research Basel, CBT, SWITZERLAND
| | - Vito Guagnano
- Novartis Institutes for BioMedical Research Basel, GDC, SWITZERLAND
| | - Patrick Chène
- Novartis Institutes for BioMedical Research Basel, ODD, SWITZERLAND
| | - Tobias Schmelzle
- Novartis Institutes for BioMedical Research Basel, ODD, SWITZERLAND
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6
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Li M, Gaussmann S, Tippler B, Ott J, Popowicz GM, Schliebs W, Sattler M, Erdmann R, Kalel VC. Novel Trypanocidal Inhibitors that Block Glycosome Biogenesis by Targeting PEX3-PEX19 Interaction. Front Cell Dev Biol 2022; 9:737159. [PMID: 34988071 PMCID: PMC8721105 DOI: 10.3389/fcell.2021.737159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Human pathogenic trypanosomatid parasites harbor a unique form of peroxisomes termed glycosomes that are essential for parasite viability. We and others previously identified and characterized the essential Trypanosoma brucei ortholog TbPEX3, which is the membrane-docking factor for the cytosolic receptor PEX19 bound to the glycosomal membrane proteins. Knockdown of TbPEX3 expression leads to mislocalization of glycosomal membrane and matrix proteins, and subsequent cell death. As an early step in glycosome biogenesis, the PEX3–PEX19 interaction is an attractive drug target. We established a high-throughput assay for TbPEX3–TbPEX19 interaction and screened a compound library for small-molecule inhibitors. Hits from the screen were further validated using an in vitro ELISA assay. We identified three compounds, which exhibit significant trypanocidal activity but show no apparent toxicity to human cells. Furthermore, we show that these compounds lead to mislocalization of glycosomal proteins, which is toxic to the trypanosomes. Moreover, NMR-based experiments indicate that the inhibitors bind to PEX3. The inhibitors interfering with glycosomal biogenesis by targeting the TbPEX3–TbPEX19 interaction serve as starting points for further optimization and anti-trypanosomal drug development.
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Affiliation(s)
- Mengqiao Li
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan Gaussmann
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Bettina Tippler
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Julia Ott
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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7
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Nichols C, Ng J, Keshu A, Fraternali F, De Nicola GF. A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface. Front Pharmacol 2020; 11:615211. [PMID: 33381049 PMCID: PMC7768231 DOI: 10.3389/fphar.2020.615211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
In-crystal fragment screening is a powerful tool to chemically probe the surfaces used by proteins to interact, and identify the chemical space worth exploring to design protein-protein inhibitors. A crucial prerequisite is the identification of a crystal form where the target area is exposed and accessible to be probed by fragments. Here we report a crystal form of the SARS-CoV-2 Receptor Binding Domain in complex with the CR3022 antibody where the ACE2 binding site on the Receptor Binding Domain is exposed and accessible. This crystal form of the complex is a valuable tool to develop antiviral molecules that could act by blocking the virus entry in cells.
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Affiliation(s)
- Charlie Nichols
- British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom.,The Randall Centre for Cell and Molecular Biophysics, New Hunt's House, King's College London, London, United Kingdom
| | - Joseph Ng
- British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom
| | - Annika Keshu
- British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom
| | - Franca Fraternali
- British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom
| | - Gian F De Nicola
- British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom.,The Randall Centre for Cell and Molecular Biophysics, New Hunt's House, King's College London, London, United Kingdom
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8
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Vallet C, Aschmann D, Beuck C, Killa M, Meiners A, Mertel M, Ehlers M, Bayer P, Schmuck C, Giese M, Knauer SK. Functional Disruption of the Cancer-Relevant Interaction between Survivin and Histone H3 with a Guanidiniocarbonyl Pyrrole Ligand. Angew Chem Int Ed Engl 2020; 59:5567-5571. [PMID: 31916356 PMCID: PMC7155087 DOI: 10.1002/anie.201915400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 12/21/2022]
Abstract
The protein Survivin is highly upregulated in most cancers and considered to be a key player in carcinogenesis. We explored a supramolecular approach to address Survivin as a drug target by inhibiting the protein-protein interaction of Survivin and its functionally relevant binding partner Histone H3. Ligand L1 is based on the guanidiniocarbonyl pyrrole cation and serves as a highly specific anion binder in order to target the interaction between Survivin and Histone H3. NMR titration confirmed binding of L1 to Survivin's Histone H3 binding site. The inhibition of the Survivin-Histone H3 interaction and consequently a reduction of cancer cell proliferation were demonstrated by microscopic and cellular assays.
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Affiliation(s)
- Cecilia Vallet
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Dennis Aschmann
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Christine Beuck
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Matthias Killa
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Annika Meiners
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Marcel Mertel
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Martin Ehlers
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Peter Bayer
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Carsten Schmuck
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Michael Giese
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Shirley K. Knauer
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
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9
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Abstract
Introduction: The transcription factor Nrf2 (nuclear factor erythroid 2-related factor 2) is the first line of defense against a plethora of environmental or endogenous deviations in redox metabolism, proteostasis, inflammation, etc. Therefore, pharmacological activation of Nrf2 is a potential therapeutic approach for several diseases related to oxidative stress and inflammation, such as cancer, cardiovascular, and neurodegenerative diseases.Areas covered: The authors first describe the biological function of Nrf2 and the molecular regulatory mechanism of Keap1-Nrf2-ARE ((Kelch-like ECH-Associating protein 1)-Nrf2-(antioxidant response element)). Then, they review recent progress of covalent activators and non-covalent Keap1-Nrf2 protein-protein interaction (PPI) inhibitors from patents and publications in 2017-present, consisting of new chemical molecules, structure optimization of reported activators and progress in preclinical or clinical trials.Expert opinion: Despite significant achievements in the development of Nrf2 activators, the selectivity is the primary consideration. Due to reacting with redox-sensitive cysteines in proteins except for Keap1, electrophilic activators often exhibit off-target effects. For Keap1-Nrf2 PPI inhibitors, how to enhance in vivo efficacy and/or penetrate blood-brain barrier (BBB) to reach central nervous system (CNS) is also challenging. Fragment-based drug discovery (FBDD), carboxylic acid bioisosteric replacement and prodrug approach might be used to circumvent this challenge. Moreover, the possibility of cancer risk caused by Nrf2 activation needs to be considered carefully.
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Affiliation(s)
- Haishan Zhou
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yan Wang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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10
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Zhang G, Andersen J, Gerona-Navarro G. Peptidomimetics Targeting Protein-Protein Interactions for Therapeutic Development. Protein Pept Lett 2019; 25:1076-1089. [PMID: 30381055 DOI: 10.2174/0929866525666181101100842] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/04/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Interactions between proteins play a key role in nearly all cellular process, and therefore, its dysregulation may lead to many different types of cellular dysfunctions. Hence, pathologic Protein-Protein Interactions (PPIs) constitute highly attractive drug targets and hold great potential for developing novel therapeutic agents for the treatment of incurable human diseases. Unfortunately, the identification of PPI inhibitors is an extremely challenging task, since traditionally used small molecules ligands are mostly unable to cover and anchor on the extensive and flat surfaces that define those binary protein complexes. In contrast, large biomolecules such as proteins or peptides are ideal fits for this so-called "undruggable" sites. However, their poor pharmacokinetic properties have also limited their applications as therapeutics. In this context, peptidomimetic molecules have emerged as an alternative and viable solution to this problem, since they conserve the architectural and structural features of peptides and also exhibit substantially improved pharmacokinetic profiles. CONCLUSION In the last decades, a wide array of chemical approaches granting access to conformationally constrained peptides with substantially improved pharmacokinetic profiles have been described, with a special focus on those affording stapled peptides and allowing large-scale macrocyclizations. These peptidomimetic molecules have been successfully applied to target a plethora of biological hosts, which highlights their promising future as novel therapeutics for the treatment of incurable human diseases.
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Affiliation(s)
- Gan Zhang
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Jessica Andersen
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States
| | - Guillermo Gerona-Navarro
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States.,Department of Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
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11
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Mercurio FA, Pirone L, Di Natale C, Marasco D, Pedone EM, Leone M. Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2. Bioorg Chem 2018; 80:602-610. [PMID: 30036816 DOI: 10.1016/j.bioorg.2018.07.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Abstract
Sam (Sterile alpha motif) domains represent small helical protein-protein interaction modules which play versatile functions in different cellular processes. The Sam domain from the EphA2 receptor binds the Sam domain of the lipid phosphatase Ship2 and this interaction modulates receptor endocytosis and degradation primarily generating pro-oncogenic effects in cell. To identify molecule antagonists of the EphA2-Sam/Ship2-Sam complex with anti-cancer activity, we focused on hydrocarbon helical stapled peptides. EphA2-Sam and one of its interactors (i.e., the first Sam domain of the adaptor protein Odin) were used as model systems for peptide design. Increase in helicity in the stapled peptides, with respect to the corresponding linear/native-like regions, was proved by structural studies conducted through CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance). Interestingly, interaction assays by means of NMR, SPR (Surface Plasmon Resonance) and MST (MicroScale Thermophoresis) techniques led to the discovery of a novel ligand of Ship2-Sam.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | | | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy; University of Naples Federico II, Department of Pharmacy, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy.
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12
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Morimoto J, Hosono Y, Sando S. Isolation of a peptide containing d-amino acid residues that inhibits the α-helix-mediated p53-MDM2 interaction from a one-bead one-compound library. Bioorg Med Chem Lett 2018; 28:231-234. [PMID: 29326019 DOI: 10.1016/j.bmcl.2018.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/29/2017] [Accepted: 01/01/2018] [Indexed: 11/19/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets in biological research and drug development. Peptides containing d-amino acid residues are attractive molecules for inhibiting α-helix-mediated PPIs because of their wide surface area and high protease resistance. In this study, a peptide library was constructed using a one-bead one-compound format designed to isolate left-handed α-helical peptides, which are promising molecules as inhibitors of α-helix-mediated PPIs. Screening of the library against an α-helix-mediated PPI between MDM2 and p53 yielded an inhibitor of the PPI. Design and screening of the library, and biochemical and spectroscopic studies of the discovered peptide are presented.
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Affiliation(s)
- 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.
| | - Yuki Hosono
- 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.
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13
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Callegari D, Pala D, Scalvini L, Tognolini M, Incerti M, Rivara S, Mor M, Lodola A. Comparative Analysis of Virtual Screening Approaches in the Search for Novel EphA2 Receptor Antagonists. Molecules 2015; 20:17132-51. [PMID: 26393553 PMCID: PMC6331951 DOI: 10.3390/molecules200917132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022] Open
Abstract
The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aimed at finding novel EphA2 antagonists, we investigated the ability of both ligand-based and structure-based approaches to retrieve known EphA2 antagonists from libraries of decoys with similar molecular properties. While ligand-based VSs were conducted using UniPR129 and ephrin-A1 ligand as reference structures, structure-based VSs were performed with Glide, using the X-ray structure of the EphA2 receptor/ephrin-A1 complex. A comparison of enrichment factors showed that ligand-based approaches outperformed the structure-based ones, suggesting ligand-based methods using the G-H loop of ephrin-A1 ligand as template as the most promising protocols to search for novel EphA2 antagonists.
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Affiliation(s)
- Donatella Callegari
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Laura Scalvini
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | | | - Matteo Incerti
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Silvia Rivara
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Marco Mor
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma 43124, Italy.
- Department of Applied Sciences, Northumbria University at Newcastle, Newcastle-Upon-Tyne, NE1 8ST, UK.
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Ivanenkov YA, Vasilevski SV, Beloglazkina EK, Kukushkin ME, Machulkin AE, Veselov MS, Chufarova NV, Chernyaginab ES, Vanzcool AS, Zyk NV, Skvortsov DA, Khutornenko AA, Rusanov AL, Tonevitsky AG, Dontsova OA, Majouga AG. Design, synthesis and biological evaluation of novel potent MDM2/p53 small-molecule inhibitors. Bioorg Med Chem Lett 2014; 25:404-9. [PMID: 25479770 DOI: 10.1016/j.bmcl.2014.09.070] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 09/15/2014] [Accepted: 09/24/2014] [Indexed: 11/18/2022]
Abstract
Regioselective synthesis, biological evaluation and 3D-molecular modeling for a series of novel diastereomeric 2-thioxo-5H-dispiro[imidazolidine-4,3-pyrrolidine-2,3-indole]-2,5(1H)-diones are described. The studied compounds have been tentatively identified as potent small molecule MDM2/p53 PPI inhibitors and can therefore be reasonably regarded as promising anticancer therapeutics.
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Affiliation(s)
- Yan A Ivanenkov
- ChemDiv, Inc., 6605 Nancy Ridge Drive, San Diego, CA 92121, USA; Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, InstitutskiPereulok 9, Moskovskaya Oblast, Russia; Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia.
| | - Sergei V Vasilevski
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia
| | - Elena K Beloglazkina
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia; Moscow State University of Mechanical Engineering (MAMI), Moscow, Russia
| | - Maksim E Kukushkin
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia
| | - Alexey E Machulkin
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia; Moscow State University of Mechanical Engineering (MAMI), Moscow, Russia
| | - Mark S Veselov
- Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, InstitutskiPereulok 9, Moskovskaya Oblast, Russia.
| | - Nina V Chufarova
- Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, InstitutskiPereulok 9, Moskovskaya Oblast, Russia; National University of Science and Technology MISiS, Moscow 119049, Russia
| | - Elizaveta S Chernyaginab
- Moscow Institute of Physics and Technology (MIPT), Dolgoprudny, InstitutskiPereulok 9, Moskovskaya Oblast, Russia
| | | | - Nikolay V Zyk
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia
| | - Dmitry A Skvortsov
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia
| | - Anastasia A Khutornenko
- Belozersky Institute, Lomonosov Moscow State University, Leninskie Gory, 1/40, 119992, Moscow, Russia
| | | | - Alexander G Tonevitsky
- SRC Bioclinicum, Ugreshskaya str 2/85, Moscow 115088, Russia; P.A. Hertsen Moscow Research Oncology Institute, 2nd Botkinsky st., 125284 Moscow, Russia
| | - Olga A Dontsova
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia; Belozersky Institute, Lomonosov Moscow State University, Leninskie Gory, 1/40, 119992, Moscow, Russia
| | - Alexander G Majouga
- Moscow State University, Chemistry Dept., Leninskie Gory, Building 1/3, GSP-1, 119991 Moscow, Russia; National University of Science and Technology MISiS, Moscow 119049, Russia.
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15
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Affiliation(s)
- Ralf Jockers
- U1016, INSERM, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- University of Paris Descartes, Paris, France
- *Correspondence:
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