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Kasana S, Kumar S, Patel P, Kurmi BD, Jain S, Sahu S, Vaidya A. Caspase inhibitors: a review on recently patented compounds (2016-2023). Expert Opin Ther Pat 2024:1-26. [PMID: 39206873 DOI: 10.1080/13543776.2024.2397732] [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: 03/06/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Caspases are a family of protease enzymes that play a crucial role in apoptosis. Dysregulation of caspase activity has been implicated in various pathological conditions, making caspases an important focus of research in understanding cell death mechanisms and developing therapeutic strategies for diseases associated with abnormal apoptosis. AREAS COVERED It is a comprehensive review of caspase inhibitors that have been comprising recently granted patents from 2016 to 2023. It includes peptide and non-peptide caspase inhibitors with their application for different diseases. EXPERT OPINION This review categorizes and analyses recently patented caspase inhibitors on various diseases. Diseases linked to caspase dysregulation, including neurodegenerative disorders, and autoimmune conditions, are highlighted to accentuate the therapeutic relevance of the patented caspase inhibitors. This paper serves as a valuable resource for researchers, clinicians, and pharmaceutical developers seeking an up-to-date understanding of recently patented caspase inhibitors. The integration of recent patented compounds, structural insights, and mechanistic details provides a holistic view of the progress in caspase inhibitor research and its potential impact on addressing various diseases.
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Affiliation(s)
- Shivani Kasana
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, India
| | - Shivam Kumar
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, India
| | - Preeti Patel
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, India
| | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, India
| | - Shweta Jain
- Sir Madanlal Institute of Pharmacy, Etawah, India
| | - Sanjeev Sahu
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Ankur Vaidya
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences, Etawah, India
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2
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Lamson DR, Tarpley M, Addo K, Ji X, Abu Rabe D, Ehe B, Hughes M, Smith GR, Daye LR, Musso DL, Zheng W, Williams KP. Identification of small molecule antagonists of sonic hedgehog/heparin binding with activity in hedgehog functional assays. Biochim Biophys Acta Gen Subj 2024; 1868:130692. [PMID: 39151833 DOI: 10.1016/j.bbagen.2024.130692] [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: 03/10/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
Sonic hedgehog (Shh) is a morphogen with important roles in embryonic development and in the development of a number of cancers. Its activity is modulated by interactions with binding partners and co-receptors including heparin and heparin sulfate proteoglycans (HSPG). To identify antagonists of Shh/heparin binding, a diverse collection of 34,560 chemicals was screened in single point 384-well format. We identified and confirmed twenty six novel small molecule antagonists with diverse structures including four scaffolds that gave rise to multiple hits. Nineteen of the confirmed hits blocked binding of the N-terminal fragment of Shh (ShhN) to heparin with IC50 values < 50 μM. In the Shh-responsive C3H10T1/2 cell model, four of the compounds demonstrated the ability to block ShhN-induced alkaline phosphatase activity. To demonstrate a direct and selective effect on ShhN ligand mediated activity, two of the compounds were able to block induction of Gli1 mRNA, a primary downstream marker for Shh signaling activity, in Shh-mediated but not Smoothened agonist (SAG)-mediated C3H10T1/2 cells. Direct binding of the two compounds to ShhN was confirmed by thermal shift assay and molecular docking simulations, with both compounds docking with the N-terminal heparin binding domain of Shh. Overall, our findings indicate that small molecule compounds that block ShhN binding to heparin and act to inhibit Shh mediated activity in vitro can be identified. We propose that the interaction between Shh and HSPGs provides a novel target for identifying small molecules that bind Shh, potentially leading to novel tool compounds to probe Shh ligand function.
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Affiliation(s)
- David R Lamson
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Michael Tarpley
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Kezia Addo
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Xiaojia Ji
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Dina Abu Rabe
- Biomanufacturing Research Institute and Technology Enterprise, USA; INBS PhD Program, USA
| | - Ben Ehe
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Mark Hughes
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Ginger R Smith
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Laura R Daye
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - David L Musso
- Biomanufacturing Research Institute and Technology Enterprise, USA
| | - Weifan Zheng
- Biomanufacturing Research Institute and Technology Enterprise, USA; Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA
| | - Kevin P Williams
- Biomanufacturing Research Institute and Technology Enterprise, USA; Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA.
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3
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Botticelli L, Bakhtina AA, Kaiser NK, Keller A, McNutt S, Bruce JE, Chu F. Chemical cross-linking and mass spectrometry enabled systems-level structural biology. Curr Opin Struct Biol 2024; 87:102872. [PMID: 38936319 PMCID: PMC11283951 DOI: 10.1016/j.sbi.2024.102872] [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: 04/06/2024] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Structural information on protein-protein interactions (PPIs) is essential for improved understanding of regulatory interactome networks that confer various physiological and pathological responses. Additionally, maladaptive PPIs constitute desirable therapeutic targets due to inherently high disease state specificity. Recent advances in chemical cross-linking strategies coupled with mass spectrometry (XL-MS) have positioned XL-MS as a promising technology to not only elucidate the molecular architecture of individual protein assemblies, but also to characterize proteome-wide PPI networks. Moreover, quantitative in vivo XL-MS provides a new capability for the visualization of cellular interactome dynamics elicited by drug treatments, disease states, or aging effects. The emerging field of XL-MS based complexomics enables unique insights on protein moonlighting and protein complex remodeling. These techniques provide complimentary information necessary for in-depth structural interactome studies to better comprehend how PPIs mediate function in living systems.
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Affiliation(s)
- Luke Botticelli
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Anna A Bakhtina
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Nathan K Kaiser
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Seth McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle WA, USA.
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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4
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Khan ES, Däinghaus T. HSP47 in human diseases: Navigating pathophysiology, diagnosis and therapy. Clin Transl Med 2024; 14:e1755. [PMID: 39135385 PMCID: PMC11319607 DOI: 10.1002/ctm2.1755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 08/16/2024] Open
Abstract
Heat shock protein 47 (HSP47) is a chaperone protein responsible for regulating collagen maturation and transport, directly impacting collagen synthesis levels. Aberrant HSP47 expression or malfunction has been associated with collagen-related disorders, most notably fibrosis. Recent reports have uncovered new functions of HSP47 in various cellular processes. Hsp47 dysregulation in these alternative roles has been linked to various diseases, such as cancer, autoimmune and neurodegenerative disorders, thereby highlighting its potential as both a diagnostic biomarker and a therapeutic target. In this review, we discuss the pathophysiological roles of HSP47 in human diseases, its potential as a diagnostic tool, clinical screening techniques and its role as a target for therapeutic interventions.
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Affiliation(s)
- Essak. S. Khan
- Posttranscriptional Gene RegulationCancer Research and Experimental HemostasisUniversity Medical Center Mainz (UMCM)MainzGermany
- Center for Thrombosis and Hemostasis (CTH)UMCMMainzGermany
- German Consortium for Translational Cancer Research (DKTK)DKFZ Frankfurt‐MainzFrankfurt am MainGermany
| | - Tobias Däinghaus
- Posttranscriptional Gene RegulationCancer Research and Experimental HemostasisUniversity Medical Center Mainz (UMCM)MainzGermany
- Center for Thrombosis and Hemostasis (CTH)UMCMMainzGermany
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5
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Engelhardt PM, Strippel J, Albat D, Chiha S, Rojas Pión J, Plein L, Kühne R, Müller M, Schmalz HG. C-Terminal Decarboxylation of Proline-Derived Building Blocks for Protein-Binding Peptides. Chemistry 2024; 30:e202401678. [PMID: 38770931 DOI: 10.1002/chem.202401678] [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: 04/29/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
Using a set of conformationally restricted Proline-derived Modules (ProMs), our group has recently succeeded in developing inhibitors for the enabled/vasodilator-stimulated phosphoprotein homology 1 (EVH1) domain, which is a key mediator of cell migration and plays an important role in tumor metastasis. While these (formally) pentapeptidic compounds show nanomolecular binding affinities towards EVH1, their drug-like properties and cell permeability need to be further optimized before they can be clinically tested as therapeutic agents against metastasis. In this study, we sought to improve these properties by removing the C-terminal carboxylic acid function of our peptoids, either by late-stage decarboxylation or by direct synthesis. For late-stage decarboxylation of ProM-like systems, a method for reductive halo decarboxylation was optimized and applied to several proline-derived substrates. In this way, a series of new decarboxy ProMs suitable as building blocks for decarboxy EVH1 inhibitors were obtained. In addition, we incorporated decarboxy-ProM-1 into the pentapeptide-like compound Ac[2ClF][ProM-2][Decarb-ProM-1], which showed similar affinity towards EVH1 as the methyl ester derivative (Ac[2Cl-F][ProM-2][ProM1]OMe). However, despite better calculated drug-like properties, this compound did not inhibit chemotaxis in a cellular assay.
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Affiliation(s)
- Pascal M Engelhardt
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Julian Strippel
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Dominik Albat
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | - Slim Chiha
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | | | - Laura Plein
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
| | - Ronald Kühne
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Matthias Müller
- Prosion Therapeutics GmbH, Luxemburger Str. 90, 50939, Köln, Germany
| | - Hans-Günther Schmalz
- University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany
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6
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Lyu Y, Yang F, Sundaresh B, Rosconi F, van Opijnen T, Gao J. Covalent Inhibition of a Host-Pathogen Protein-Protein Interaction Reduces the Infectivity of Streptococcus pneumoniae. JACS AU 2024; 4:2484-2491. [PMID: 39055144 PMCID: PMC11267552 DOI: 10.1021/jacsau.4c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
Abstract
The ever-expanding antibiotic resistance urgently calls for novel antibacterial therapeutics, especially those with a new mode of action. We report herein our exploration of protein-protein interaction (PPI) inhibition as a new mechanism to thwart bacterial pathogenesis. Specifically, we describe potent and specific inhibitors of the pneumococcal surface protein PspC, an important virulence factor that facilitates the infection of Streptococcus pneumoniae. Specifically, PspC has been documented to recruit human complement factor H (hFH) to suppress host complement activation and/or promote the bacterial attachment to host tissues. The CCP9 domain of hFH was recombinantly expressed to inhibit the PspC-hFH interaction as demonstrated on live pneumococcal cells. The inhibitor allowed for the first pharmacological intervention of the PspC-hFH interaction. This PPI inhibition reduced pneumococci's attachment to epithelial cells and also resensitized the D39 strain of S. pneumoniae for opsonization. Importantly, we have further devised covalent versions of CCP9, which afforded long-lasting PspC inhibition with low nanomolar potency. Overall, our results showcase the promise of PPI inhibition for combating bacterial infections as well as the power of covalent inhibitors.
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Affiliation(s)
- Yuhan Lyu
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
| | - Fan Yang
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
| | - Bharathi Sundaresh
- Department
of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Federico Rosconi
- Department
of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Broad
Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, United States
| | - Jianmin Gao
- Department
of Chemistry, Merkert Chemistry Center, Boston College, Chestnut
Hill, Massachusetts 02467, United States
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7
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Cawood EE, Baker E, Edwards TA, Woolfson DN, Karamanos TK, Wilson AJ. Understanding β-strand mediated protein-protein interactions: tuning binding behaviour of intrinsically disordered sequences by backbone modification. Chem Sci 2024; 15:10237-10245. [PMID: 38966365 PMCID: PMC11220606 DOI: 10.1039/d4sc02240h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/24/2024] [Indexed: 07/06/2024] Open
Abstract
A significant challenge in chemical biology is to understand and modulate protein-protein interactions (PPIs). Given that many PPIs involve a folded protein domain and a peptide sequence that is intrinsically disordered in isolation, peptides represent powerful tools to understand PPIs. Using the interaction between small ubiquitin-like modifier (SUMO) and SUMO-interacting motifs (SIMs), here we show that N-methylation of the peptide backbone can effectively restrict accessible peptide conformations, predisposing them for protein recognition. Backbone N-methylation in appropriate locations results in faster target binding, and thus higher affinity, as shown by relaxation-based NMR experiments and computational analysis. We show that such higher affinities occur as a consequence of an increase in the energy of the unbound state, and a reduction in the entropic contribution to the binding and activation energies. Thus, backbone N-methylation may represent a useful modification within the peptidomimetic toolbox to probe β-strand mediated interactions.
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Affiliation(s)
- Emma E Cawood
- 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
| | - Emily Baker
- 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
| | - 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
- College of Biomedical Sciences, Larkin University 18301 N Miami Ave #1 Miami FL 33169 USA
| | - Derek N Woolfson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS 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
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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8
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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA.
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9
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Chen H, Revennaugh B, Fu H, Ivanov AA. AVERON notebook to discover actionable cancer vulnerabilities enabled by neomorph protein-protein interactions. iScience 2024; 27:110035. [PMID: 38883827 PMCID: PMC11179073 DOI: 10.1016/j.isci.2024.110035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/30/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Genomic alterations, such as missense mutations, often lead to the activation of oncogenic pathways and cell transformation by rewiring protein-protein interaction (PPI) networks. Understanding how mutant-directed neomorph PPIs (neoPPIs) drive cancer is vital to developing new personalized clinical strategies. However, the experimental interrogation of neoPPI functions in patients with cancer is highly challenging. To address this challenge, we developed a computational platform, termed AVERON for discovering actionable vulnerabilities enabled by rewired oncogenic networks. AVERON enables rapid systematic profiling of the clinical significance of neomorph PPIs across different cancer types, informing molecular mechanisms of neoPPI-driven tumorigenesis, and revealing therapeutically actionable neoPPI-regulated genes. We demonstrated the application of the AVERON platform by evaluating the biological functions and clinical significance of 130 neomorph interactions, experimentally determined for oncogenic BRAFV600E. The AVERON application to broad sets of mutant-directed PPIs may inform new testable biological models and clinical strategies in cancer.
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Affiliation(s)
- Hongyue Chen
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Brian Revennaugh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Emory University, Atlanta, GA, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
- Department of Hematology, Medical Oncology Emory University, Atlanta, GA, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Emory University, Atlanta, GA, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
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Konstantinidou M, Arkin MR. Molecular glues for protein-protein interactions: Progressing toward a new dream. Cell Chem Biol 2024; 31:1064-1088. [PMID: 38701786 PMCID: PMC11193649 DOI: 10.1016/j.chembiol.2024.04.002] [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: 01/04/2024] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
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11
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Taya T, Kami D, Teruyama F, Matoba S, Gojo S. Peptide-encoding gene transfer to modulate intracellular protein-protein interactions. Mol Ther Methods Clin Dev 2024; 32:101226. [PMID: 38516692 PMCID: PMC10952081 DOI: 10.1016/j.omtm.2024.101226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/24/2024] [Indexed: 03/23/2024]
Abstract
Peptide drug discovery has great potential, but the cell membrane is a major obstacle when the target is an intracellular protein-protein interaction (PPI). It is difficult to target PPIs with small molecules; indeed, there are no intervention tools that can target any intracellular PPI. In this study, we developed a platform that enables the introduction of peptides into cells via mRNA-based gene delivery. Peptide-length nucleic acids do not enable stable ribosome binding and exhibit little to no translation into protein. In this study, a construct was created in which the sequence encoding dihydrofolate reductase (DHFR) was placed in front of the sequence encoding the target peptide, together with a translation skipping sequence, as a sequence that meets the requirements of promoting ribosome binding and rapid decay of the translated protein. This enabled efficient translation from the mRNA encoding the target protein while preventing unnecessary protein residues. Using this construct, we showed that it can inhibit Drp1/Fis1 binding, one of the intracellular PPIs, which governs mitochondrial fission, an important aspect of mitochondrial dynamics. In addition, it was shown to inhibit pathological hyperfission, normalize mitochondrial dynamics and metabolism, and inhibit apoptosis of the mitochondrial pathway.
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Affiliation(s)
- Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Fumiya Teruyama
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Pharmacology Research Department, Tokyo New Drug Research Laboratories, Kowa Company, Ltd, Tokyo, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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12
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna G, Montelione GT, Roth MJ, Perez A. A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. Angew Chem Int Ed Engl 2024; 63:e202405767. [PMID: 38588243 DOI: 10.1002/anie.202405767] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners but often include false positives. Furthermore, they provide no information about what the binding region is (e.g., the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competitive Binding Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment and the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies of AF and AF-CBA to help users identify scenarios where the approach will be most useful. Given the method's speed and accuracy, we anticipate its broad applicability to identify binding epitope regions among potential partners, setting the stage for experimental verification.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Roland H Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gvt Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Monica J Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [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: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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14
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Funke FJ, Schlee S, Sterner R. Validation of aminodeoxychorismate synthase and anthranilate synthase as novel targets for bispecific antibiotics inhibiting conserved protein-protein interactions. Appl Environ Microbiol 2024; 90:e0057224. [PMID: 38700332 PMCID: PMC11107160 DOI: 10.1128/aem.00572-24] [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: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Multi-resistant bacteria are a rapidly emerging threat to modern medicine. It is thus essential to identify and validate novel antibacterial targets that promise high robustness against resistance-mediating mutations. This can be achieved by simultaneously targeting several conserved function-determining protein-protein interactions in enzyme complexes from prokaryotic primary metabolism. Here, we selected two evolutionary related glutamine amidotransferase complexes, aminodeoxychorismate synthase and anthranilate synthase, that are required for the biosynthesis of folate and tryptophan in most prokaryotic organisms. Both enzymes rely on the interplay of a glutaminase and a synthase subunit that is conferred by a highly conserved subunit interface. Consequently, inhibiting subunit association in both enzymes by one competing bispecific inhibitor has the potential to suppress bacterial proliferation. We comprehensively verified two conserved interface hot-spot residues as potential inhibitor-binding sites in vitro by demonstrating their crucial role in subunit association and enzymatic activity. For in vivo target validation, we generated genomically modified Escherichia coli strains in which subunit association was disrupted by modifying these central interface residues. The growth of such strains was drastically retarded on liquid and solid minimal medium due to a lack of folate and tryptophan. Remarkably, the bacteriostatic effect was observed even in the presence of heat-inactivated human plasma, demonstrating that accessible host metabolite concentrations do not compensate for the lack of folate and tryptophan within the tested bacterial cells. We conclude that a potential inhibitor targeting both enzyme complexes will be effective against a broad spectrum of pathogens and offer increased resilience against antibiotic resistance. IMPORTANCE Antibiotics are indispensable for the treatment of bacterial infections in human and veterinary medicine and are thus a major pillar of modern medicine. However, the exposure of bacteria to antibiotics generates an unintentional selective pressure on bacterial assemblies that over time promotes the development or acquisition of resistance mechanisms, allowing pathogens to escape the treatment. In that manner, humanity is in an ever-lasting race with pathogens to come up with new treatment options before resistances emerge. In general, antibiotics with novel modes of action require more complex pathogen adaptations as compared to chemical derivates of existing entities, thus delaying the emergence of resistance. In this contribution, we use modified Escherichia coli strains to validate two novel targets required for folate and tryptophan biosynthesis that can potentially be targeted by one and the same bispecific protein-protein interaction inhibitor and promise increased robustness against bacterial resistances.
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Affiliation(s)
- Franziska Jasmin Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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15
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Xie X, Zhang O, Yeo MJR, Lee C, Harry SA, Paul L, Li Y, Payne NC, Nam E, Kwok HS, Jiang H, Mao H, Hadley JL, Lin H, Batts M, Gosavi PM, D'Angiolella V, Cole PA, Mazitschek R, Northcott PA, Zheng N, Liau BB. KBTBD4 Cancer Hotspot Mutations Drive Neomorphic Degradation of HDAC1/2 Corepressor Complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.593970. [PMID: 38798357 PMCID: PMC11118371 DOI: 10.1101/2024.05.14.593970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cancer mutations can create neomorphic protein-protein interactions to drive aberrant function 1 . As a substrate receptor of the CULLIN3-RBX1 E3 ubiquitin ligase complex, KBTBD4 is recurrently mutated in medulloblastoma (MB) 2 , the most common embryonal brain tumor in children, and pineoblastoma 3 . These mutations impart gain-of-function to KBTBD4 to induce aberrant degradation of the transcriptional corepressor CoREST 4 . However, their mechanism of action remains unresolved. Here, we elucidate the mechanistic basis by which KBTBD4 mutations promote CoREST degradation through engaging HDAC1/2, the direct neomorphic target of the substrate receptor. Using deep mutational scanning, we systematically map the mutational landscape of the KBTBD4 cancer hotspot, revealing distinct preferences by which insertions and substitutions can promote gain-of-function and the critical residues involved in the hotspot interaction. Cryo-electron microscopy (cryo-EM) analysis of two distinct KBTBD4 cancer mutants bound to LSD1-HDAC1-CoREST reveals that a KBTBD4 homodimer asymmetrically engages HDAC1 with two KELCH-repeat propeller domains. The interface between HDAC1 and one of the KBTBD4 propellers is stabilized by the MB mutations, which directly insert a bulky side chain into the active site pocket of HDAC1. Our structural and mutational analyses inform how this hotspot E3-neo-substrate interface can be chemically modulated. First, our results unveil a converging shape complementarity-based mechanism between gain-of-function E3 mutations and a molecular glue degrader, UM171. Second, we demonstrate that HDAC1/2 inhibitors can block the mutant KBTBD4-HDAC1 interface, the aberrant degradation of CoREST, and the growth of KBTBD4-mutant MB models. Altogether, our work reveals the structural and mechanistic basis of cancer mutation-driven neomorphic protein-protein interactions and pharmacological strategies to modulate their action for therapeutic applications.
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16
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Ghosh A, Sharma M, Zhao Y. Cell-penetrating protein-recognizing polymeric nanoparticles through dynamic covalent chemistry and double imprinting. Nat Commun 2024; 15:3731. [PMID: 38702306 PMCID: PMC11068882 DOI: 10.1038/s41467-024-48131-5] [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: 06/20/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
Molecular recognition of proteins is key to their biological functions and processes such as protein-protein interactions (PPIs). The large binding interface involved and an often relatively flat binding surface make the development of selective protein-binding materials extremely challenging. A general method is reported in this work to construct protein-binding polymeric nanoparticles from cross-linked surfactant micelles. Preparation involves first dynamic covalent chemistry that encodes signature surface lysines on a protein template. A double molecular imprinting procedure fixes the binding groups on the nanoparticle for these lysine groups, meanwhile creating a binding interface complementary to the protein in size, shape, and distribution of acidic groups on the surface. These water-soluble nanoparticles possess excellent specificities for target proteins and sufficient affinities to inhibit natural PPIs such as those between cytochrome c (Cytc) and cytochrome c oxidase (CcO). With the ability to enter cells through a combination of energy-dependent and -independent pathways, they intervene apoptosis by inhibiting the PPI between Cytc and the apoptotic protease activating factor-1 (APAF1). Generality of the preparation and the excellent molecular recognition of the materials have the potential to make them powerful tools to probe protein functions in vitro and in cellulo.
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Affiliation(s)
- Avijit Ghosh
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
| | - Mansi Sharma
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA.
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17
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Chen FJ, Pinnette N, Gao J. Strategies for the Construction of Multicyclic Phage Display Libraries. Chembiochem 2024; 25:e202400072. [PMID: 38466139 DOI: 10.1002/cbic.202400072] [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: 01/27/2024] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
Peptide therapeutics have gained great interest due to their multiple advantages over small molecule and antibody-based drugs. Peptide drugs are easier to synthesize, have the potential for oral bioavailability, and are large enough to target protein-protein interactions that are undruggable by small molecules. However, two major limitations have made it difficult to develop novel peptide therapeutics not derived from natural products, including the metabolic instability of peptides and the difficulty of reaching antibody-like potencies and specificities. Compared to linear and disulfide-monocyclized peptides, multicyclic peptides can provide increased conformational rigidity, enhanced metabolic stability, and higher potency in inhibiting protein-protein interactions. The identification of novel multicyclic peptide binders can be difficult, however, recent advancements in the construction of multicyclic phage libraries have greatly advanced the process of identifying novel multicyclic peptide binders for therapeutically relevant protein targets. This review will describe the current approaches used to create multicyclic peptide libraries, highlighting the novel chemistries developed and the proof-of-concept work done on validating these libraries against different protein targets.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Nicole Pinnette
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center 2609 Beacon Street, Chestnut Hill, MA-02467, USA
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18
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Stillman NH, Joseph JA, Ahmed J, Baysah CZ, Dohoney RA, Ball TD, Thomas AG, Fitch TC, Donnelly CM, Kumar S. Protein mimetic 2D FAST rescues alpha synuclein aggregation mediated early and post disease Parkinson's phenotypes. Nat Commun 2024; 15:3658. [PMID: 38688913 PMCID: PMC11061149 DOI: 10.1038/s41467-024-47980-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Abberent protein-protein interactions potentiate many diseases and one example is the toxic, self-assembly of α-Synuclein in the dopaminergic neurons of patients with Parkinson's disease; therefore, a potential therapeutic strategy is the small molecule modulation of α-Synuclein aggregation. In this work, we develop an Oligopyridylamide based 2-dimensional Fragment-Assisted Structure-based Technique to identify antagonists of α-Synuclein aggregation. The technique utilizes a fragment-based screening of an extensive array of non-proteinogenic side chains in Oligopyridylamides, leading to the identification of NS132 as an antagonist of the multiple facets of α-Synuclein aggregation. We further identify a more cell permeable analog (NS163) without sacrificing activity. Oligopyridylamides rescue α-Synuclein aggregation mediated Parkinson's disease phenotypes in dopaminergic neurons in early and post disease Caenorhabditis elegans models. We forsee tremendous potential in our technique to identify lead therapeutics for Parkinson's disease and other diseases as it is expandable to other oligoamide scaffolds and a larger array of side chains.
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Affiliation(s)
- Nicholas H Stillman
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Johnson A Joseph
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Jemil Ahmed
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA
| | - Charles Zuwu Baysah
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Ryan A Dohoney
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tyler D Ball
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Alexandra G Thomas
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Tessa C Fitch
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Courtney M Donnelly
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA
| | - Sunil Kumar
- Department of Chemistry and Biochemistry, F.W. Olin Hall, 2190 E Iliff Ave, University of Denver, Denver, CO, 80210, USA.
- The Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave, Suite 579, University of Denver, Denver, CO, 80208, USA.
- Molecular and Cellular Biophysics Program, Boettcher West, Room 228, 2050 E. Iliff Ave, University of Denver, Denver, CO, 80210, USA.
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19
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Chen S, Li M, Xue C, Zhou X, Wei J, Zheng L, Duan Y, Deng H, Tang F, Xiong W, Xiang B, Zhou M. Validation of Core Ingredients and Molecular Mechanism of Cinobufotalin Injection Against Liver Cancer. Drug Des Devel Ther 2024; 18:1321-1338. [PMID: 38681206 PMCID: PMC11055549 DOI: 10.2147/dddt.s443305] [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: 10/27/2023] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Cinobufotalin injection has obvious curative effects on liver cancer patients with less toxicity and fewer side effects than other therapeutic approaches. However, the core ingredients and mechanism underlying these anti-liver cancer effects have not been fully clarified due to its complex composition. Methods Multidimensional network analysis was used to screen the core ingredients, key targets and pathways underlying the therapeutic effects of cinobufotalin injection on liver cancer, and in vitro and in vivo experiments were performed to confirm the findings. Results By construction of ingredient networks and integrated analysis, eight core ingredients and ten key targets were finally identified in cinobufotalin injection, and all of the core ingredients are tightly linked with the key targets, and these key targets are highly associated with the cell cycle-related pathways, supporting that both cinobufotalin injection and its core ingredients exert anti-liver cancer roles by blocking cell cycle-related pathways. Moreover, in vitro and in vivo experiments confirmed that either cinobufotalin injection or one of its core ingredients, cinobufagin, significantly inhibited cell proliferation, colony formation, cell cycle progression and xenograft tumor growth, and the key target molecules involved in the cell cycle pathway such as CDK1, CDK4, CCNB1, CHEK1 and CCNE1, exhibit consistent changes in expression after treatment with cinobufotalin injection or cinobufagin. Interestingly, some key targets CDK1, CDK4, PLK1, CHEK1, TTK were predicted to bind with multiple of core ingredients of cinobufotalin injection, and the affinity between one of the critical ingredients cinobufagin and key target CDK1 was further confirmed by SPR assay. Conclusion Cinobufotalin injection was confirmed to includes eight core ingredients, and they play therapeutic effects in liver cancer by blocking cell cycle-related pathways, which provides important insights for the mechanism of cinobufotalin injection antagonizing liver cancer and the development of novel small molecule anti-cancer drugs.
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MESH Headings
- Bufanolides/pharmacology
- Bufanolides/chemistry
- Bufanolides/administration & dosage
- Humans
- Animals
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Cell Proliferation/drug effects
- Mice
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Drug Screening Assays, Antitumor
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Liver Neoplasms, Experimental/metabolism
- Mice, Inbred BALB C
- Cell Cycle/drug effects
- Mice, Nude
- Dose-Response Relationship, Drug
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/pathology
- Neoplasms, Experimental/metabolism
- Tumor Cells, Cultured
- Structure-Activity Relationship
- Molecular Structure
- Injections
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Affiliation(s)
- Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Xiangting Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, People’s Republic of China
- Cancer Research Institute, Central South University, Changsha, 410078, People’s Republic of China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, People’s Republic of China
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20
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Jumppanen M, Kinnunen SM, Zore M, Välimäki MJ, Talman V, Gennäs GBA, Ruskoaho HJ, Yli-Kauhaluoma J. Affinity chromatography reveals direct binding of the GATA4-NKX2-5 interaction inhibitor (3i-1000) with GATA4. Sci Rep 2024; 14:8938. [PMID: 38637629 PMCID: PMC11026519 DOI: 10.1038/s41598-024-59418-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Heart failure is a serious medical condition with a poor prognosis. Current treatments can only help manage the symptoms and slow the progression of heart failure. However, there is currently no cure to prevent and reverse cardiac remodeling. Transcription factors are in a central role in various cellular processes, and in the heart, GATA4 and NKX2-5 transcription factors mediate hypertrophic responses and remodeling. We have identified compounds that modulate the synergistic interaction of GATA4 and NKX2-5 and shown that the most promising compound (1, 3i-1000) is cardioprotective in vitro and in vivo. However, direct evidence of its binding site and mechanism of action has not been available. Due to the disordered nature of transcription factors, classical target engagement approaches cannot be utilized. Here, we synthesized a small-molecule ligand-binding pulldown probe of compound 1 to utilize affinity chromatography alongside CETSA, AlphaScreen, and molecular modeling to study ligand binding. These results provide the first evidence of direct physical binding of compound 1 selectively to GATA4. While developing drugs that target transcription factors presents challenges, advances in technologies and knowledge of intrinsically disordered proteins enable the identification of small molecules that can selectively target transcription factors.
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Affiliation(s)
- Mikael Jumppanen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Sini M Kinnunen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Matej Zore
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Mika J Välimäki
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Virpi Talman
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Gustav Boije Af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Heikki J Ruskoaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, (P.O. Box 56), FI-00014, Helsinki, Finland.
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21
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Craig RA, De Vicente J, Estrada AA, Feng JA, Lexa KW, Canet MJ, Dowdle WE, Erickson RI, Flores BN, Haddick PCG, Kane LA, Lewcock JW, Moerke NJ, Poda SB, Sweeney Z, Takahashi RH, Tong V, Wang J, Yulyaningsih E, Solanoy H, Scearce-Levie K, Sanchez PE, Tang L, Xu M, Zhang R, Osipov M. Discovery of DNL343: A Potent, Selective, and Brain-Penetrant eIF2B Activator Designed for the Treatment of Neurodegenerative Diseases. J Med Chem 2024; 67:5758-5782. [PMID: 38511649 DOI: 10.1021/acs.jmedchem.3c02422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Eukaryotic translation initiation factor 2B (eIF2B) is a key component of the integrated stress response (ISR), which regulates protein synthesis and stress granule formation in response to cellular insult. Modulation of the ISR has been proposed as a therapeutic strategy for treatment of neurodegenerative diseases such as vanishing white matter (VWM) disease and amyotrophic lateral sclerosis (ALS) based on its ability to improve cellular homeostasis and prevent neuronal degeneration. Herein, we report the small-molecule discovery campaign that identified potent, selective, and CNS-penetrant eIF2B activators using both structure- and ligand-based drug design. These discovery efforts culminated in the identification of DNL343, which demonstrated a desirable preclinical drug profile, including a long half-life and high oral bioavailability across preclinical species. DNL343 was progressed into clinical studies and is currently undergoing evaluation in late-stage clinical trials for ALS.
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Affiliation(s)
- Robert A Craig
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Javier De Vicente
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Anthony A Estrada
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Jianwen A Feng
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Katrina W Lexa
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Mark J Canet
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - William E Dowdle
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Rebecca I Erickson
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Brittany N Flores
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Patrick C G Haddick
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Lesley A Kane
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Joseph W Lewcock
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Nathan J Moerke
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Suresh B Poda
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Zachary Sweeney
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Ryan H Takahashi
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Vincent Tong
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Jing Wang
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Ernie Yulyaningsih
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Hilda Solanoy
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | | | - Pascal E Sanchez
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
| | - Liwei Tang
- Department of Chemistry, WuXi AppTec Co., Ltd., Tianjin 300457, China
| | - Musheng Xu
- Department of Chemistry, WuXi AppTec Co., Ltd., Tianjin 300457, China
| | - Rui Zhang
- Department of Chemistry, WuXi AppTec Co., Ltd., Tianjin 300457, China
| | - Maksim Osipov
- Denali Therapeutics Inc., South San Francisco, California 94080, United States
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22
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Zhang Z, Zhao L, Gao M, Chen Y, Wang J, Wang C. PPII-AEAT: Prediction of protein-protein interaction inhibitors based on autoencoders with adversarial training. Comput Biol Med 2024; 172:108287. [PMID: 38503089 DOI: 10.1016/j.compbiomed.2024.108287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
Protein-protein interactions (PPIs) have shown increasing potential as novel drug targets. The design and development of small molecule inhibitors targeting specific PPIs are crucial for the prevention and treatment of related diseases. Accordingly, effective computational methods are highly desired to meet the emerging need for the large-scale accurate prediction of PPI inhibitors. However, existing machine learning models rely heavily on the manual screening of features and lack generalizability. Here, we propose a new PPI inhibitor prediction method based on autoencoders with adversarial training (named PPII-AEAT) that can adaptively learn molecule representation to cope with different PPI targets. First, Extended-connectivity fingerprints and Mordred descriptors are employed to extract the primary features of small molecular compounds. Then, an autoencoder architecture is trained in three phases to learn high-level representations and predict inhibitory scores. We evaluate PPII-AEAT on nine PPI targets and two different tasks, including the PPI inhibitor identification task and inhibitory potency prediction task. The experimental results show that our proposed PPII-AEAT outperforms state-of-the-art methods.
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Affiliation(s)
- Zitong Zhang
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Lingling Zhao
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Mengyao Gao
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Yuanlong Chen
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China
| | - Junjie Wang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, 150001, China.
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23
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Gaikwad V, Choudhury AR, Chakrabarti R. Decoding the dynamics of BCL9 triazole stapled peptide. Biophys Chem 2024; 307:107197. [PMID: 38335808 DOI: 10.1016/j.bpc.2024.107197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
BCL9 is a key protein in Wnt signaling pathway. It acts as a transcriptional co-activator to β-catenin, and dysregulation in this pathway leads to tumor growth. Inhibiting such a protein-protein interaction is considered as a therapeutic challenge. The interaction between β-catenin and BCL9 is facilitated by a 23-residue helical domain from BCL9 and a hydrophobic groove of β-catenin. To prevent this interaction, a peptide that mimics the alpha-helical domain of BCL9 can be designed. Stapling is considered a successful strategy in the pursuit of designing such peptides in which amino acids side are stitched together using chemical moieties. Among the various types of cross-linkers, triazole is the most rapid and effective one synthesized via click reaction. However, the underlying interactions behind maintaining the secondary structure of stapled peptides remain less explored. In the current work, we employed the molecular dynamics simulation to study the conformational behavior of the experimentally synthesized single and double triazole stapled BCL9 peptide. Upon the addition of a triazole staple, there is a significant reduction in the conformational space of BCL9. The helical character of the stapled peptide increases with an increase in separation between the triazole cross-linkers. Also, we encompassed the Replica Exchange with Solute Tempering (REST2) simulation to validate the high-temperature response of the stapled peptide. From REST2, the PCA and t-SNE show the reduction in distinct cluster formation on the addition of triazole staple. Our study infers further development of these triazole-stapled BCL9 peptides into effective inhibitors to target the interaction between β-catenin and BCL9.
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Affiliation(s)
- Vikram Gaikwad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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24
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Shen L, Fang J, Liu L, Yang F, Jenkins JL, Kutchukian PS, Wang H. Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery. J Cheminform 2024; 16:33. [PMID: 38515171 PMCID: PMC10958880 DOI: 10.1186/s13321-024-00829-w] [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: 10/17/2023] [Accepted: 03/16/2024] [Indexed: 03/23/2024] Open
Abstract
We present a user-friendly molecular generative pipeline called Pocket Crafter, specifically designed to facilitate hit finding activity in the drug discovery process. This workflow utilized a three-dimensional (3D) generative modeling method Pocket2Mol, for the de novo design of molecules in spatial perspective for the targeted protein structures, followed by filters for chemical-physical properties and drug-likeness, structure-activity relationship analysis, and clustering to generate top virtual hit scaffolds. In our WDR5 case study, we acquired a focused set of 2029 compounds after a targeted searching within Novartis archived library based on the virtual scaffolds. Subsequently, we experimentally profiled these compounds, resulting in a novel chemical scaffold series that demonstrated activity in biochemical and biophysical assays. Pocket Crafter successfully prototyped an effective end-to-end 3D generative chemistry-based workflow for the exploration of new chemical scaffolds, which represents a promising approach in early drug discovery for hit identification.
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Affiliation(s)
- Lingling Shen
- Novartis Biomedical Research, Cambridge, MA, 02139, USA.
| | - Jian Fang
- Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Lulu Liu
- Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Fei Yang
- Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | | | | | - He Wang
- Novartis Biomedical Research, Cambridge, MA, 02139, USA.
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25
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Du B, Ru J, Zhan Z, Lin C, Liu Y, Mao W, Zhang J. Insight into small-molecule inhibitors targeting extracellular nucleotide pyrophosphatase/phosphodiesterase1 for potential multiple human diseases. Eur J Med Chem 2024; 268:116286. [PMID: 38432057 DOI: 10.1016/j.ejmech.2024.116286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/06/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Extracellular nucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) has been identified as a type II transmembrane glycoprotein. It plays a crucial role in various biological processes, such as bone mineralization, cancer cell proliferation, and immune regulation. Consequently, ENPP1 has garnered attention as a promising target for pharmacological interventions. Despite its potential, the development of clinical-stage ENPP1 inhibitors for solid tumors, diabetes, and silent rickets remains limited. However, there are encouraging findings from preclinical trials involving small molecules exhibiting favorable therapeutic effects and safety profiles. This perspective aims to shed light on the structural properties, biological functions and the relationship between ENPP1 and diseases. Additionally, it focuses on the structure-activity relationship of ENPP1 inhibitors, with the intention of guiding the future development of new and effective ENPP1 inhibitors.
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Affiliation(s)
- Baochan Du
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinxiao Ru
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zixuan Zhan
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yang Liu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China
| | - Wuyu Mao
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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26
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Asano W, Hantani R, Uhara T, Debaene F, Nomura A, Yamaguchi K, Adachi T, Otake K, Harada K, Hantani Y. Screening approaches for the identification of Nrf2-Keap1 protein-protein interaction inhibitors targeting hot spot residues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100125. [PMID: 37935317 DOI: 10.1016/j.slasd.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
Protein-protein interactions (PPIs) play a crucial role in most biological processes and are important targets in the development of therapeutic agents. However, small molecule drug discovery that targets PPIs remains very challenging. Targeting hot spot residues is considered the best option for inhibiting such interactions, but there are few examples of how knowledge of hot spots can be used in high throughput screening to find hit compounds. A substrate adaptor protein for a ubiquitin ligase complex, Kelch-like ECH-associated protein 1 (Keap1), negatively modulates the expression of genes involved in cellular protection against oxidative stress. Here, we focused on three arginine hot spot residues in the Keap1 substrate binding pocket (Arg380, Arg415, and Arg483), and screened the carboxylic acid library owned by Japan Tobacco Inc. for compounds that interact with the arginine residues in differential scanning fluorescence assays. Furthermore, we identified several small molecule compounds that specifically bind to the Keap1 Kelch domain hot spots by comparing binding to alanine mutant proteins (R380A, R415A, and R483A) with binding to the wild-type protein using surface plasmon resonance (SPR) screening. These compounds inhibited the protein-protein interaction between the Keap1 Kelch domain and the nuclear factor erythroid 2-related factor 2 (Nrf2) peptide, and the ubiquitination of Nrf2 catalyzed by the Cul3/RINGBox 1 E3 ligase. In addition, the binding mode of one compound (Compound 4) was determined by X-ray crystallography after validation of binding by isothermal titration calorimetry, native mass spectrometry, and nuclear magnetic resonance. Compound 4 had favorable thermodynamic properties, and noncovalently bound to Keap1 with a stoichiometry of 1:1. Our results suggest that Compound 4 could potentially be developed into effective therapeutic or preventive agents for a variety of diseases and conditions such as oxidative stress response, inflammation, and carcinogenesis. We believe that the use of a set of complementary biophysical techniques including the SPR assay with single alanine mutant of hot spots provides opportunities to identify hit compounds for developing inhibitors of PPIs.
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Affiliation(s)
- Wataru Asano
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Rie Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Uhara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - François Debaene
- Biophysics Dpt/ MS Platform, NovAliX, 16 rue d'Ankara, Strasbourg 67000, France
| | - Akihiro Nomura
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Keishi Yamaguchi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuki Otake
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuhito Harada
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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27
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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28
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Ahmed MS, Nguyen NUN, Nakada Y, Hsu CC, Farag A, Lam NT, Wang P, Thet S, Menendez-Montes I, Elhelaly WM, Lou X, Secco I, Tomczyk M, Zentilin L, Pei J, Cui M, Dos Santos M, Liu X, Liu Y, Zaha D, Walcott G, Tomchick DR, Xing C, Zhang CC, Grishin NV, Giacca M, Zhang J, Sadek HA. Identification of FDA-approved drugs that induce heart regeneration in mammals. NATURE CARDIOVASCULAR RESEARCH 2024; 3:372-388. [PMID: 39183959 PMCID: PMC11343477 DOI: 10.1038/s44161-024-00450-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/06/2024] [Indexed: 08/27/2024]
Abstract
Targeting Meis1 and Hoxb13 transcriptional activity could be a viable therapeutic strategy for heart regeneration. In this study, we performd an in silico screening to identify FDA-approved drugs that can inhibit Meis1 and Hoxb13 transcriptional activity based on the resolved crystal structure of Meis1 and Hoxb13 bound to DNA. Paromomycin (Paro) and neomycin (Neo) induced proliferation of neonatal rat ventricular myocytes in vitro and displayed dose-dependent inhibition of Meis1 and Hoxb13 transcriptional activity by luciferase assay and disruption of DNA binding by electromobility shift assay. X-ray crystal structure revealed that both Paro and Neo bind to Meis1 near the Hoxb13-interacting domain. Administration of Paro-Neo combination in adult mice and in pigs after cardiac ischemia/reperfusion injury induced cardiomyocyte proliferation, improved left ventricular systolic function and decreased scar formation. Collectively, we identified FDA-approved drugs with therapeutic potential for induction of heart regeneration in mammals.
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Affiliation(s)
- Mahmoud Salama Ahmed
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- These authors contributed equally: Mahmoud Salama Ahmed, Ngoc Uyen Nhi Nguyen
| | - Ngoc Uyen Nhi Nguyen
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- These authors contributed equally: Mahmoud Salama Ahmed, Ngoc Uyen Nhi Nguyen
| | - Yuji Nakada
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ching-Cheng Hsu
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ayman Farag
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicholas T. Lam
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ping Wang
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Suwannee Thet
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Menendez-Montes
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Waleed M. Elhelaly
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xi Lou
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ilaria Secco
- School of Cardiovascular and Metabolic Medicine & Sciences and British Heart Foundation Centre of Research Excellence, King’s College London, London, UK
| | - Mateusz Tomczyk
- School of Cardiovascular and Metabolic Medicine & Sciences and British Heart Foundation Centre of Research Excellence, King’s College London, London, UK
| | - Lorena Zentilin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Jimin Pei
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Miao Cui
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthieu Dos Santos
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoye Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Liu
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David Zaha
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gregory Walcott
- Division of Cardiovascular Diseases, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diana R. Tomchick
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V. Grishin
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mauro Giacca
- School of Cardiovascular and Metabolic Medicine & Sciences and British Heart Foundation Centre of Research Excellence, King’s College London, London, UK
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hesham A. Sadek
- Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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29
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Wei Y, Chen AX, Lin Y, Wei T, Qiao B. Allosteric regulation in SARS-CoV-2 spike protein. Phys Chem Chem Phys 2024; 26:6582-6589. [PMID: 38329233 DOI: 10.1039/d4cp00106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Allosteric regulation is common in protein-protein interactions and is thus promising in drug design. Previous experimental and simulation work supported the presence of allosteric regulation in the SARS-CoV-2 spike protein. Here the route of allosteric regulation in SARS-CoV-2 spike protein is examined by all-atom explicit solvent molecular dynamics simulations, contrastive machine learning, and the Ohm approach. It was found that peptide binding to the polybasic cleavage sites, especially the one at the first subunit of the trimeric spike protein, activates the fluctuation of the spike protein's backbone, which eventually propagates to the receptor-binding domain on the third subunit that binds to ACE2. Remarkably, the allosteric regulation routes starting from the polybasic cleavage sites share a high fraction (39-67%) of the critical amino acids with the routes starting from the nitrogen-terminal domains, suggesting the presence of an allosteric regulation network in the spike protein. Our study paves the way for the rational design of allosteric antibody inhibitors.
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Affiliation(s)
- Yong Wei
- Department of Computer Science, High Point University, High Point, NC 27268, USA
| | - Amy X Chen
- Thomas Jefferson High School for Science and Technology, Alexandria, VA 22312, USA
| | - Yuewei Lin
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tao Wei
- Department of Chemical Engineering and Department of Biomedical Engineering, University of South Carolina, Columbia, SC 29208, USA.
| | - Baofu Qiao
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY 10010, USA.
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30
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Hong JY, Lin SC, Kehn-Hall K, Zhang KM, Luo SY, Wu HY, Chang SY, Hou MH. Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2. Biophys J 2024; 123:478-488. [PMID: 38234090 PMCID: PMC10912909 DOI: 10.1016/j.bpj.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs.
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Affiliation(s)
- Jhen-Yi Hong
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Shih-Chao Lin
- Bachelor Degree Program in Marine Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Kai-Min Zhang
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Shun-Yuan Luo
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University. Taichung, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; PhD Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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Choudhury AA, Arumugam M, Ponnusamy N, Sivaraman D, Sertsemariam W, Thiruvengadam M, Pandiaraj S, Rahaman M, Devi Rajeswari V. Anti-diabetic drug discovery using the bioactive compounds of Momordica charantia by molecular docking and molecular dynamics analysis. J Biomol Struct Dyn 2024:1-15. [PMID: 38334124 DOI: 10.1080/07391102.2024.2313156] [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: 06/06/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Diabetes mellitus (DM) is a multifactorial life-threatening endocrine disease characterized by abnormalities in glucose metabolism. It is a chronic metabolic disease that involves multiple enzymes such as α-amylase and α-glucosidases. Inhibition of these enzymes has been identified as a promising method for managing diabetes, and researchers are currently focusing on discovering novel α-amylase and α-glucosidase inhibitors for diabetes therapy. Hence, we have selected 12 bioactive compounds from the Momordica charantia (MC) plant and performed a virtual screening and molecular dynamics investigation to identify natural inhibitors of α-amylase and α-glucosidases. Our in silico result revealed that phytocompound Rutin showed the highest binding affinity against α-amylase (1HNY) enzymes at (-11.68 kcal/mol), followed by Karaviloside II (-9.39), Momordicoside F (-9.19), Campesterol (-9.11. While docking against α-glucosidases (4J5T), Rutin again showed the greatest binding affinity (-11.93 kcal/mol), followed by Momordicine (-9.89), and Campesterol (-8.99). Molecular dynamics (MD) simulation research is currently the gold standard for drug design and discovery. Consequently, we conducted simulations of 100 nanoseconds (ns) to assess the stability of protein-ligand complexes based on parameters like RMSD, RMSF, RG, PCA, and FEL. The significance of our findings indicates that rutin from MC might serve as an effective natural therapeutic agent for diabetes management due to its strongest binding affinities with α-amylase and α-glucosidase enzymes. Further research in animals and humans is essential to validate the efficacy of these drug molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abbas Alam Choudhury
- Department of Biomedical Sciences, School of Bio Sciences and Technology, VIT, Vellore, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Bio Sciences and Technology, VIT, Vellore, India
| | - Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Bio Sciences and Technology, VIT, Vellore, India
| | | | - Woldie Sertsemariam
- Department of Biomedical Sciences, School of Bio Sciences and Technology, VIT, Vellore, India
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, Konkuk University, Seoul, Republic of Korea
| | - Saravanan Pandiaraj
- Department of Self-Development Skills, King Saud University, Riyadh, Saudi Arabia
| | - Mostafizur Rahaman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - V Devi Rajeswari
- Department of Biomedical Sciences, School of Bio Sciences and Technology, VIT, Vellore, India
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Zhang X, Zhang M, Sun H, Wang X, Wang X, Sheng W, Xu M. The role of transcription factors in the crosstalk between cancer-associated fibroblasts and tumor cells. J Adv Res 2024:S2090-1232(24)00046-8. [PMID: 38309692 DOI: 10.1016/j.jare.2024.01.033] [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: 11/29/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Transcription factors (TFs) fulfill a critical role in the formation and maintenance of different cell types during the developmental process as well as disease. It is believed that cancer-associated fibroblasts (CAFs) are activation status of tissue-resident fibroblasts or derived from form other cell types via transdifferentiation or dedifferentiation. Despite a subgroup of CAFs exhibit anti-cancer effects, most of them are reported to exert effects on tumor progression, further indicating their heterogeneous origin. AIM OF REVIEW This review aimed to summarize and review the roles of TFs in the reciprocal crosstalk between CAFs and tumor cells, discuss the emerging mechanisms, and their roles in cell-fate decision, cellular reprogramming and advancing our understanding of the gene regulatory networks over the period of cancer initiation and progression. KEY SCIENTIFIC CONCEPTS OF REVIEW This manuscript delves into the key contributory factors of TFs that are involved in activating CAFs and maintaining their unique states. Additionally, it explores how TFs play a pivotal and multifaceted role in the reciprocal crosstalk between CAFs and tumor cells. This includes their involvement in processes such as epithelial-mesenchymal transition (EMT), proliferation, invasion, and metastasis, as well as metabolic reprogramming. TFs also have a role in constructing an immunosuppressive microenvironment, inducing resistance to radiation and chemotherapy, facilitating angiogenesis, and even 'educating' CAFs to support the malignancies of tumor cells. Furthermore, this manuscript delves into the current status of TF-targeted therapy and considers the future directions of TFs in conjunction with anti-CAFs therapies to address the challenges in clinical cancer treatment.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Meng Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Hui Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xu Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xin Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Weiqi Sheng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
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Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
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Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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Kailasam Natesan V, Kuppannagounder Pitchaimuthu E. Structure-based drug design and molecular dynamics studies of an allosteric modulator targeting the protein-protein interaction site of PDK1. J Mol Model 2024; 30:51. [PMID: 38277080 DOI: 10.1007/s00894-024-05842-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024]
Abstract
CONTEXT Protein-protein interaction interfaces play a major role in cell signaling pathways. There is always a great interest in developing protein-protein interaction (PPI) inhibitors of kinases, as they are challenging due to their hydrophobicity, flat surface, specificity, potency, etc. 3 Phosphoinositide-dependent kinase-1 (PDK1), which is involved in the PI3K/PDK1/AKT pathway, is a cancer target that has gained insight for the past two decades. PDK1 possesses a protein interaction fragment (PIF) pocket, which is a well-known PPI that targets allosteric modulators. This work focusses on energy-based pharmacophore model development which on virtual screening could yield novel scaffolds towards the drug designing objective for the kind of PDK1 modulators. A novel pyrazolo pyridine molecule was identified as an allosteric modulator that binds to the PPI site. The metadynamics simulations with free energy profiles further revealed the conformational allosteric changes stimulated on the protein structure upon ligand binding. The cytotoxic activity (IC50-20 μM) of the identified compound against five different cancer cell lines and cell cycle analysis supported the anticancer activity of the identified compound. METHODS All the computational works were carried out by the most commonly used Schrodinger Suite software. The pharmacophore was validated by Receiver Operation Characteristics (ROC) and screening against allosteric Enamine database library. The Optimized Potential Liquid Simulations (OPLS-2005) was used to minimize the structures for molecular docking calculations, and inbuilt scoring method of ranking the compounds based on docking score and Glide energy was used. Molecular dynamics simulations were conducted by Desmond implemented in Maestro. The hit compound was purchased from Enamine and tested against different cancer cell lines by MTT assay, apoptosis by western blotting technique, and by flow cytometry analysis.
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna GVT, Montelione GT, Roth MJ, Perez A. Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576374. [PMID: 38328039 PMCID: PMC10849530 DOI: 10.1101/2024.01.20.576374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners, but often include false positives. Furthermore, they provide no information about what the binding region is (e.g. the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competition Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment, along with the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies to AF and AF-CBA, to help users identify scenarios where the approach will be most useful. Given the speed and accuracy of the methodology, we expect it to be generally applicable to facilitate target selection for experimental verification starting from high-throughput protein libraries.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Roland H. Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - GVT Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Monica J. Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
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Raevsky A, Kovalenko O, Bulgakov E, Sharifi M, Volochnyuk D, Tukalo M. Developing a comprehensive solution aimed to disrupt LARS1/RagD protein-protein interaction. J Biomol Struct Dyn 2024; 42:747-758. [PMID: 36995308 DOI: 10.1080/07391102.2023.2194996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/18/2023] [Indexed: 03/31/2023]
Abstract
Aminoacyl-tRNA synthetases are crucial enzymes involved in protein synthesis and various cellular physiological reactions. Aside from their standard role in linking amino acids to the corresponding tRNAs, they also impact protein homeostasis by controlling the level of soluble amino acids within the cell. For instance, leucyl-tRNA synthetase (LARS1) acts as a leucine sensor for the mammalian target of rapamycin complex 1 (mTORC1), and may also function as a probable GTPase-activating protein (GAP) for the RagD subunit of the heteromeric activator of mTORC1. In turn, mTORC1 regulates cellular processes, such as protein synthesis, autophagy, and cell growth, and is implicated in various human diseases including cancer, obesity, diabetes, and neurodegeneration. Hence, inhibitors of mTORC1 or a deregulated mTORC1 pathway may offer potential cancer therapies. In this study, we investigated the structural requirements for preventing the sensing and signal transmission from LARS to mTORC1. Building upon recent studies on mTORC1 regulation activation by leucine, we lay the foundation for the development of chemotherapeutic agents against mTORC1 that can overcome resistance to rapamycin. Using a combination of in-silico approaches to develop and validate an alternative interaction model, discussing its benefits and advancements. Finally, we identified a set of compounds ready for testing to prevent LARS1/RagD protein-protein interactions. We establish a basis for creating chemotherapeutic drugs targeting mTORC1, which can conquer resistance to rapamycin. We utilize in-silico methods to generate and confirm an alternative interaction model, outlining its advantages and improvements, and pinpoint a group of novel substances that can prevent LARS1/RagD interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexey Raevsky
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Enamine Ltd, Kyiv, Ukraine
| | - Oksana Kovalenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Elijah Bulgakov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | - Dmityi Volochnyuk
- Enamine Ltd, Kyiv, Ukraine
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Michael Tukalo
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Odunitan TT, Saibu OA, Apanisile BT, Omoboyowa DA, Balogun TA, Awe AV, Ajayi TM, Olagunju GV, Mahmoud FM, Akinboade M, Adeniji CB, Abdulazeez WO. Integrating biocomputational techniques for Breast cancer drug discovery via the HER-2, BCRA, VEGF and ER protein targets. Comput Biol Med 2024; 168:107737. [PMID: 38000249 DOI: 10.1016/j.compbiomed.2023.107737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Computational modelling remains an indispensable technique in drug discovery. With myriad of high computing resources, and improved modelling algorithms, there has been a high-speed in the drug development cycle with promising success rate compared to the traditional route. For example, lapatinib; a well-known anticancer drug with clinical applications was discovered with computational drug design techniques. Similarly, molecular modelling has been applied to various disease areas ranging from cancer to neurodegenerative diseases. The techniques ranges from high-throughput virtual screening, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) to molecular dynamics simulation. This review focuses on the application of computational modelling tools in the identification of drug candidates for Breast cancer. First, we begin with a succinct overview of molecular modelling in the drug discovery process. Next, we take note of special efforts on the developments and applications of combining these techniques with particular emphasis on possible breast cancer therapeutic targets such as estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), vascular endothelial growth factor (VEGF), breast cancer gene 1 (BRCA1), and breast cancer gene 2 (BRCA2). Finally, we discussed the search for covalent inhibitors against these receptors using computational techniques, advances, pitfalls, possible solutions, and future perspectives.
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Affiliation(s)
- Tope T Odunitan
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Oluwatosin A Saibu
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA.
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Oyo State, Nigeria
| | - Toheeb A Balogun
- Department of Biological Sciences, University of California, San Diego, CA, USA
| | - Adeyoola V Awe
- Department of Medical Laboratory Science, Lead City, University, Ibadan, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Grace V Olagunju
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, USA
| | - Fatimah M Mahmoud
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, USA
| | - Modinat Akinboade
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Catherine B Adeniji
- Department of Environmental Management and Toxicology, Lead City University, Ibadan, Oyo State, Nigeria
| | - Waliu O Abdulazeez
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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38
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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39
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Roth JR, Rush T, Thompson SJ, Aldaher AR, Dunn TB, Mesina JS, Cochran JN, Boyle NR, Dean HB, Yang Z, Pathak V, Ruiz P, Wu M, Day JJ, Bostwick JR, Suto MJ, Augelli-Szafran CE, Roberson ED. Development of small-molecule Tau-SH3 interaction inhibitors that prevent amyloid-β toxicity and network hyperexcitability. Neurotherapeutics 2024; 21:e00291. [PMID: 38241154 PMCID: PMC10903085 DOI: 10.1016/j.neurot.2023.10.001] [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: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 01/21/2024] Open
Abstract
Alzheimer's disease (AD) is the leading cause of dementia and lacks highly effective treatments. Tau-based therapies hold promise. Tau reduction prevents amyloid-β-induced dysfunction in preclinical models of AD and also prevents amyloid-β-independent dysfunction in diverse disease models, especially those with network hyperexcitability, suggesting that strategies exploiting the mechanisms underlying Tau reduction may extend beyond AD. Tau binds several SH3 domain-containing proteins implicated in AD via its central proline-rich domain. We previously used a peptide inhibitor to demonstrate that blocking Tau interactions with SH3 domain-containing proteins ameliorates amyloid-β-induced dysfunction. Here, we identify a top hit from high-throughput screening for small molecules that inhibit Tau-FynSH3 interactions and describe its optimization with medicinal chemistry. The resulting lead compound is a potent cell-permeable Tau-SH3 interaction inhibitor that binds Tau and prevents amyloid-β-induced dysfunction, including network hyperexcitability. These data support the potential of using small molecule Tau-SH3 interaction inhibitors as a novel therapeutic approach to AD.
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Affiliation(s)
- Jonathan R Roth
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Travis Rush
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha J Thompson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adam R Aldaher
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Trae B Dunn
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob S Mesina
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Nicholas Cochran
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicholas R Boyle
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hunter B Dean
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zhengrong Yang
- Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vibha Pathak
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Pedro Ruiz
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Mousheng Wu
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Mark J Suto
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | | | - Erik D Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Calabretta MM, Michelini E. Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years. Expert Opin Drug Discov 2024; 19:85-95. [PMID: 37814480 DOI: 10.1080/17460441.2023.2266989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability. AREAS COVERED This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models. EXPERT OPINION The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, Bologna, Italy
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Wu Z, Wu Y, Zhu C, Wu X, Zhai S, Wang X, Su Z, Duan H. Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides. J Chem Inf Model 2023; 63:7655-7668. [PMID: 38049371 DOI: 10.1021/acs.jcim.3c01385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
The development of potentially active peptides for specific targets is critical for the modern pharmaceutical industry's growth. In this study, we present an efficient computational framework for the discovery of active peptides targeting a specific pharmacological target, which combines a conditional variational autoencoder (CVAE) and a classifier named TCPP based on the Transformer and convolutional neural network. In our example scenario, we constructed an active cyclic peptide library targeting interleukin-17C (IL-17C) through a library-based in vitro selection strategy. The CVAE model is trained on the preprocessed peptide data sets to generate potentially active peptides and the TCPP further screens the generated peptides. Ultimately, six candidate peptides predicted by the model were synthesized and assayed for their activity, and four of them exhibited promising binding affinity to IL-17C. Our study provides a one-stop-shop for target-specific active peptide discovery, which is expected to boost up the process of peptide drug development.
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Affiliation(s)
- Zhipeng Wu
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yejian Wu
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Cheng Zhu
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinyi Wu
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Silong Zhai
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinqiao Wang
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhihao Su
- Artificial Intelligence Aided Drug Discovery Institute, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
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Zerihun M, Rubin SJS, Silnitsky S, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part II: Peptides as Allosteric Protein Kinase C Modulators Targeting Protein-Protein Interactions. Int J Mol Sci 2023; 24:17504. [PMID: 38139336 PMCID: PMC10743673 DOI: 10.3390/ijms242417504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Human protein kinases are highly-sought-after drug targets, historically harnessed for treating cancer, cardiovascular disease, and an increasing number of autoimmune and inflammatory conditions. Most current treatments involve small molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP-binding pocket. As a result, these compounds are often poorly selective and highly toxic. Part I of this series reviews the role of PKC isoforms in various human diseases, featuring cancer and cardiovascular disease, as well as translational examples of PKC modulation applied to human health and disease. In the present Part II, we discuss alternative allosteric binding mechanisms for targeting PKC, as well as novel drug platforms, such as modified peptides. A major goal is to design protein kinase modulators with enhanced selectivity and improved pharmacological properties. To this end, we use molecular docking analysis to predict the mechanisms of action for inhibitor-kinase interactions that can facilitate the development of next-generation PKC modulators.
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Affiliation(s)
- Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
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43
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Atanda H, Balogun TA, Alshehri MM, Olivos-Ramirez G, Vilca-Quispe J, Chenet-Zuta M, Cárdenas-Cárdenas R, Delgado Wong H, Ropón-Palacios G, Umar HI. In silico study revealed the inhibitory activity of selected phytomolecules of C. rotundus against VacA implicated in gastric ulcer. J Biomol Struct Dyn 2023; 41:10713-10724. [PMID: 36571437 DOI: 10.1080/07391102.2022.2160814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022]
Abstract
Gastric ulcer is associated with weakening of the mucous coating of the stomach and damages to the intestinal lining. It is caused by H. pylori assisted by enzymes including VacA, which necessitates the need for inhibitors of VacA. Bioactive compounds from Cyperus rotundus have been documented to have anti-inflammatory activities. However, the mechanism of action of the phytochemicals is not characterized. This research aimed to assess, in silico, the potential of selected bioactive compounds against VacA based on the binding to its active sites. VacA and bioactive compounds structures were obtained from protein database and PubChem webserver, respectively. All compounds, including 2 controls, omeprazole and cimetidine were docked against the protein using AutoDock Vina and screened based on the binding energy. The selected complexes were subjected to pharmacokinetics and toxicity screening. Finally, molecular dynamics simulation and MMPBSA were carried out on two best compounds. 17 compounds interacted with the active site of VacA with higher binding affinities, with 7 of them - aureusidine, catechin, chlorogenic acid, isorhamnetin, isovitexin, oreintin, and vitexin having the best behaviours based on ADMET and druglikeness screening. Molecular dynamics and MMPBSA experiments of two of the hits corroborated good stability and binding energy for Ellagic Acid and Scirpusin B (ΔG = -14.38 and -13.20 kcal mol-1, respectively). These phytochemicals showed good pharmacokinetic profiles with respect to the control drugs. This study revealed that the identified compounds of C. rotundus may serve as VacA inhibitors and may be potent candidates for novel drug formulations in gastric ulcer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Halimat Atanda
- Department of Biotechnology, Federal University of Technology, Akure, Ondo State, Nigeria
- Computer-Aided Therapeutic Discovery and Design Group, FUTA, Akure, Ondo State, Nigeria
| | - Toheeb Adewale Balogun
- Computer-Aided Therapeutic Discovery and Design Group, FUTA, Akure, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Mohammed M Alshehri
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Gustavo Olivos-Ramirez
- Laboratório de Modelagem Computacional - LaModel, Instituto de Ciências Exatas - ICEx, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Brasil
| | - Julissa Vilca-Quispe
- Laboratório de Modelagem Computacional - LaModel, Instituto de Ciências Exatas - ICEx, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Brasil
| | - Manuel Chenet-Zuta
- Universidad Nacional Tecnológica de Lima Sur UNTELS, Villa el Salvador, Perú
| | - Reyna Cárdenas-Cárdenas
- Facultad de Farmacia y Bioquímica, Universidad Nacional de la Amazonía Peruana, Iquitos, Peru
| | - Henry Delgado Wong
- Laboratorio de Farmacología y Toxicología de la Facultad de Farmacia y Bioquímica de la Universidad Nacional de la Amazonia Peruana, Villa el Salvador, Perú
| | - Georcki Ropón-Palacios
- Laboratório de Modelagem Computacional - LaModel, Instituto de Ciências Exatas - ICEx, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Brasil
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Group, FUTA, Akure, Ondo State, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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Breen ME, Joy ST, Baruti OJ, Beyersdorf MS, Henley MJ, De Salle SN, Ycas PD, Croskey A, Cierpicki T, Pomerantz WCK, Mapp AK. Garcinolic Acid Distinguishes Between GACKIX Domains and Modulates Interaction Networks. Chembiochem 2023; 24:e202300439. [PMID: 37525583 PMCID: PMC10870240 DOI: 10.1002/cbic.202300439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
Natural products are often uniquely suited to modulate protein-protein interactions (PPIs) due to their architectural and functional group complexity relative to synthetic molecules. Here we demonstrate that the natural product garcinolic acid allosterically blocks the CBP/p300 KIX PPI network and displays excellent selectivity over related GACKIX motifs. It does so via a strong interaction (KD 1 μM) with a non-canonical binding site containing a structurally dynamic loop in CBP/p300 KIX. Garcinolic acid engages full-length CBP in the context of the proteome and in doing so effectively inhibits KIX-dependent transcription in a leukemia model. As the most potent small-molecule KIX inhibitor yet reported, garcinolic acid represents an important step forward in the therapeutic targeting of CBP/p300.
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Affiliation(s)
- Meghan E Breen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Stephen T Joy
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Omari J Baruti
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Matthew S Beyersdorf
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Madeleine J Henley
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Samantha N De Salle
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Peter D Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN-55455, USA
| | - Ayza Croskey
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN-55455, USA
| | - Anna K Mapp
- Department of Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
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46
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Xiang H, Zhou M, Li Y, Zhou L, Wang R. Drug discovery by targeting the protein-protein interactions involved in autophagy. Acta Pharm Sin B 2023; 13:4373-4390. [PMID: 37969735 PMCID: PMC10638514 DOI: 10.1016/j.apsb.2023.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/17/2023] Open
Abstract
Autophagy is a cellular process in which proteins and organelles are engulfed in autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein-protein interactions (PPIs) play a crucial role at many stages of autophagy, which present formidable but attainable targets for autophagy regulation. Moreover, selective regulation of PPIs tends to have a lower risk in causing undesired off-target effects in the context of a complicated biological network. Thus, small-molecule regulators, including peptides and peptidomimetics, targeting the critical PPIs involved in autophagy provide a new opportunity for innovative drug discovery. This article provides general background knowledge of the critical PPIs involved in autophagy and reviews a range of successful attempts on discovering regulators targeting those PPIs. Successful strategies and existing limitations in this field are also discussed.
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Affiliation(s)
- Honggang Xiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Mi Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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Fang Y, Bai Z, Cao J, Zhang G, Li X, Li S, Yan Y, Gao P, Kong X, Zhang Z. Low-intensity ultrasound combined with arsenic trioxide induced apoptosis of glioma via EGFR/AKT/mTOR. Life Sci 2023; 332:122103. [PMID: 37730111 DOI: 10.1016/j.lfs.2023.122103] [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: 02/23/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
AIMS This study aimed to explore whether low-intensity ultrasound (LIUS) combined with low-concentration arsenic trioxide (ATO) could inhibit the proliferation of glioma and, if so, to clarify the potential mechanism. MAIN METHODS The effects of ATO and LIUS alone or in combination on glioma were examined by CCK8, EdU, and flow cytometry assays. Western blot analysis was used to detect changes in expression of apoptosis-related proteins and their effects on the EGFR/AKT/mTOR pathway. The effects of ATO and LIUS were verified in vivo in orthotopic xenograft models, and tumor size, arsenic content in brain tissue, survival, and immunohistochemical changes were observed. KEY FINDINGS LIUS enhanced the inhibitory effect of ATO on the proliferation of glioma, and EGF reversed the proliferation inhibition and protein changes induced by ATO and LIUS. The anti-glioma effect of ATO combined with LIUS was related to downstream AKT/mTOR pathway changes caused by inhibition of EGFR activation, which enhanced apoptosis of U87MG and U373 cells. In vivo experiments showed significant increases in arsenic content in brain tissue, as well as decreased tumor sizes and longer survival times in the combined treatment group compared with other groups. The trends of immunohistochemical protein changes were consistent with the in vitro results. SIGNIFICANCE This study showed that LIUS enables ATO to exert anti-glioma effects at a safe dose by inhibiting the activation of EGFR and the downstream AKT/mTOR pathway to regulate apoptosis. LIUS in combination with ATO is a promising novel method for treating glioma and could improve patient prognosis.
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Affiliation(s)
- Yi Fang
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Zhiqun Bai
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Jibin Cao
- Department of Radiology, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Gaosen Zhang
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Xiang Li
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Shufeng Li
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Yudie Yan
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Peirong Gao
- Department of Ultrasound, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiangkai Kong
- Department of Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
| | - Zhen Zhang
- Department of Ultrasound, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China.
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Tokareva OS, Li K, Travaline TL, Thomson TM, Swiecicki JM, Moussa M, Ramirez JD, Litchman S, Verdine GL, McGee JH. Recognition and reprogramming of E3 ubiquitin ligase surfaces by α-helical peptides. Nat Commun 2023; 14:6992. [PMID: 37914719 PMCID: PMC10620186 DOI: 10.1038/s41467-023-42395-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
Molecules that induce novel interactions between proteins hold great promise for the study of biological systems and the development of therapeutics, but their discovery has been limited by the complexities of rationally designing interactions between three components, and because known binders to each protein are typically required to inform initial designs. Here, we report a general and rapid method for discovering α-helically constrained (Helicon) polypeptides that cooperatively induce the interaction between two target proteins without relying on previously known binders or an intrinsic affinity between the proteins. We show that Helicons are capable of binding every major class of E3 ubiquitin ligases, which are of great biological and therapeutic interest but remain largely intractable to targeting by small molecules. We then describe a phage-based screening method for discovering "trimerizer" Helicons, and apply it to reprogram E3s to cooperatively bind an enzyme (PPIA), a transcription factor (TEAD4), and a transcriptional coactivator (β-catenin).
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Affiliation(s)
| | - Kunhua Li
- FOG Pharmaceuticals Inc., Cambridge, MA, USA
- Kymera Therapeutics, Inc., Watertown, MA, USA
| | | | | | - Jean-Marie Swiecicki
- FOG Pharmaceuticals Inc., Cambridge, MA, USA
- Relay Therapeutics, Inc., Cambridge, MA, USA
| | | | | | | | - Gregory L Verdine
- FOG Pharmaceuticals Inc., Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard, University, Cambridge, MA, USA.
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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Arnold L, Gomez JP, Barry M, Yap M, Jackson L, Ly T, Standing D, Padhye SB, Biersack B, Anant S, Thomas SM. Acryl-3,5-bis(2,4-difluorobenzylidene)-4-piperidone targeting cellular JUN proto-oncogene, AP-1 transcription factor subunit inhibits head and neck squamous cell carcinoma progression. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1104-1121. [PMID: 38023989 PMCID: PMC10651473 DOI: 10.37349/etat.2023.00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/17/2023] [Indexed: 12/01/2023] Open
Abstract
Aim Head and neck squamous cell carcinoma (HNSCC) is the seventh most common cancer worldwide with a survival rate below fifty percent. Addressing meager therapeutic options, a series of small molecule inhibitors were screened for antitumor efficacy. The most potent analog, acryl-3,5-bis(2,4-difluorobenzylidene)-4-piperidone (DiFiD; A-DiFiD), demonstrated strong cellular JUN proto-oncogene, activator protein 1 (AP-1) transcription factor subunit (JUN, c-Jun) antagonism. c-Jun, an oncogenic transcription factor, promotes cancer progression, invasion, and adhesion; high (JUN) mRNA expression correlates with poorer HNSCC survival. Methods Four new small molecules were generated for cytotoxicity screening in HNSCC cell lines. A-DiFiD-treated HNSCC cells were assessed for cytotoxicity, colony formation, invasion, migration, and adhesion. Dot blot array was used to identify targets. Phospho-c-Jun (p-c-Jun) expression was analyzed using immunoblotting. The Cancer Genome Atlas (TCGA) head and neck cancer datasets were utilized to determine overall patient survival. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) datasets interfaced with University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN) were analyzed to determine protein levels of c-Jun in HNSCC patients and correlate levels with patient. Results Of the small molecules tested, A-DiFiD was the most potent in HNSCC lines, while demonstrating low half-maximal drug inhibitory concentration (IC50) in non-malignant Het-1A cells. Additionally, A-DiFiD abrogated cell invasion, migration, and colony formation. Phospho-kinase in vitro array demonstrated A-DiFiD reduced p-c-Jun. Likewise, a time dependent reduction in p-c-Jun was observed starting at 3 min post A-DiFiD treatment. TCGA Firehose Legacy vs. recurrent and metastatic head and neck cancer reveal a nearly 3% DNA amplification in recurrent/metastatic tumor compared to below 1% in primary tumors that had no lymph node metastasis. CPTAC analysis show higher tumor c-Jun levels compared to normal. Patients with high JUN expression had significantly reduced 3-year survival. Conclusions A-DiFiD targets c-Jun, a clinical HNSCC driver, with potent anti-tumor effects.
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Affiliation(s)
- Levi Arnold
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Juan Pineda Gomez
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Michael Barry
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Marrion Yap
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Laura Jackson
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Thuc Ly
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - David Standing
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Subhash B. Padhye
- Interdisciplinary Science and Technology Research Academy, University of Pune, Pune 411007, Maharashtra, India
| | - Bernhard Biersack
- Department of Biology, Chemistry, Earth Sciences, University of Bayreuth, 95440 Bayreuth, Germany
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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50
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Manning D, Huang TY, Berida T, Roy S. The challenges and opportunities of developing small molecule inhibitors of MraY. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2023; 60:1-27. [PMID: 39015353 PMCID: PMC11250723 DOI: 10.1016/bs.armc.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Affiliation(s)
- Destinee Manning
- Department of BioMolecular Sciences, University of Mississippi, University, MS, United States
| | - Tzu-Yu Huang
- Department of BioMolecular Sciences, University of Mississippi, University, MS, United States
| | - Tomayo Berida
- Department of BioMolecular Sciences, University of Mississippi, University, MS, United States
| | - Sudeshna Roy
- Department of BioMolecular Sciences, University of Mississippi, University, MS, United States
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