1
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Hayward D, Beekman AM. Strategies for converting turn-motif and cyclic peptides to small molecules for targeting protein-protein interactions. RSC Chem Biol 2024; 5:198-208. [PMID: 38456035 PMCID: PMC10915966 DOI: 10.1039/d3cb00222e] [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: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
The development of small molecules that interact with protein-protein interactions is an ongoing challenge. Peptides offer a starting point in the drug discovery process for targeting protein-interactions due to their larger, more flexible structure and the structurally diverse properties that allow for a greater interaction with the protein. The techniques for rapidly identifying potent cyclic peptides and turn-motif peptides are highly effective, but this potential has not yet transferred to approved drug candidates. By applying the properties of the peptide-protein interaction the development of small molecules for drug discovery has the potential to be more efficient. In this review, we discuss the methods that allow for the unique binding properties of peptides to proteins, and the methods deployed to transfer these qualities to potent small molecules.
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Affiliation(s)
- Deanne Hayward
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Andrew M Beekman
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
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2
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Yin G, Lv G, Zhang J, Jiang H, Lai T, Yang Y, Ren Y, Wang J, Yi C, Chen H, Huang Y, Xiao C. Early-stage structure-based drug discovery for small GTPases by NMR spectroscopy. Pharmacol Ther 2022; 236:108110. [PMID: 35007659 DOI: 10.1016/j.pharmthera.2022.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Small GTPase or Ras superfamily, including Ras, Rho, Rab, Ran and Arf, are fundamental in regulating a wide range of cellular processes such as growth, differentiation, migration and apoptosis. They share structural and functional similarities for binding guanine nucleotides and hydrolyzing GTP. Dysregulations of Ras proteins are involved in the pathophysiology of multiple human diseases, however there is still a stringent need for effective treatments targeting these proteins. For decades, small GTPases were recognized as 'undruggable' targets due to their complex regulatory mechanisms and lack of deep pockets for ligand binding. NMR has been critical in deciphering the structural and dynamic properties of the switch regions that are underpinning molecular switch functions of small GTPases, which pave the way for developing new effective inhibitors. The recent progress of drug or lead molecule development made for small GTPases profoundly delineated how modern NMR techniques reshape the field of drug discovery. In this review, we will summarize the progress of structural and dynamic studies of small GTPases, the NMR techniques developed for structure-based drug screening and their applications in early-stage drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guohua Lv
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Jerry Zhang
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Tianqi Lai
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Yushan Yang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Yong Ren
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Chenju Yi
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China; Research Institute of Xi'an Jiaotong University, Zhejiang, Hangzhou, Zhejiang Province 311215, PR China
| | - Yun Huang
- Howard Hughes Medical Institute, Chevy Chase 20815, MD, USA; Department of Physiology & Biophysics, Weill Cornell Medicine, New York 10065, NY, USA.
| | - Chaoni Xiao
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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3
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Damaskinaki FN, Moran LA, Garcia A, Kellam B, Watson SP. Overcoming challenges in developing small molecule inhibitors for GPVI and CLEC-2. Platelets 2021; 32:744-752. [PMID: 33406951 DOI: 10.1080/09537104.2020.1863939] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
GPVI and CLEC-2 have emerged as promising targets for long-term prevention of both arterial thrombosis and thrombo-inflammation with a decreased bleeding risk relative to current drugs. However, while there are potent blocking antibodies of both receptors, their protein nature comes with decreased bioavailability, making formulation for oral medication challenging. Small molecules are able to overcome these limitations, but there are many challenges in developing antagonists of nanomolar potency, which is necessary when considering the structural features that underlie the interaction of CLEC-2 and GPVI with their protein ligands. In this review, we describe current small-molecule inhibitors for both receptors and strategies to overcome such limitations, including considerations when it comes to in silico drug design and the importance of complex compound library selection.
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Affiliation(s)
- Foteini-Nafsika Damaskinaki
- Institute of Cardiovascular Sciences, Level 1 IBR, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK.,Biodiscovery Institute, University Park, University of Nottingham, Nottingham, UK
| | - Luis A Moran
- Institute of Cardiovascular Sciences, Level 1 IBR, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, and Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Angel Garcia
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, and Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Barrie Kellam
- Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK.,Biodiscovery Institute, University Park, University of Nottingham, Nottingham, UK
| | - Steve P Watson
- Institute of Cardiovascular Sciences, Level 1 IBR, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, The Midlands, UK
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4
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Foster H, Wilson C, Philippou H, Foster R. Progress toward a Glycoprotein VI Modulator for the Treatment of Thrombosis. J Med Chem 2020; 63:12213-12242. [PMID: 32463237 DOI: 10.1021/acs.jmedchem.0c00262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pathogenic thrombus formation accounts for the etiology of many serious conditions including myocardial infarction, stroke, deep vein thrombosis, and pulmonary embolism. Despite the development of numerous anticoagulants and antiplatelet agents, the mortality rate associated with these diseases remains high. In recent years, however, significant epidemiological evidence and clinical models have emerged to suggest that modulation of the glycoprotein VI (GPVI) platelet receptor could be harnessed as a novel antiplatelet strategy. As such, many peptidic agents have been described in the past decade, while more recent efforts have focused on the development of small molecule modulators. Herein the rationale for targeting GPVI is summarized and the published GPVI modulators are reviewed, with particular focus on small molecules. A qualitative pharmacophore hypothesis for small molecule ligands at GPVI is also presented.
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Affiliation(s)
- Holly Foster
- School of Chemistry and Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), School of Medicine, University of Leeds, Leeds LS2 9JT, U.K
| | - Clare Wilson
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), School of Medicine, University of Leeds, Leeds LS2 9JT, U.K
| | - Helen Philippou
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), School of Medicine, University of Leeds, Leeds LS2 9JT, U.K
| | - Richard Foster
- School of Chemistry and Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), School of Medicine, University of Leeds, Leeds LS2 9JT, U.K
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5
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Kadavath H, Cabrales Fontela Y, Jaremko M, Jaremko Ł, Overkamp K, Biernat J, Mandelkow E, Zweckstetter M. Der Bindungsmodus eines Tau-Peptids mit Tubulin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Harindranath Kadavath
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Yunior Cabrales Fontela
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Mariusz Jaremko
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
| | - Łukasz Jaremko
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Kerstin Overkamp
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
| | - Jacek Biernat
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- CAESAR Forschungszentrum; Ludwig-Erhard-Allee 2 Bonn Deutschland
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- CAESAR Forschungszentrum; Ludwig-Erhard-Allee 2 Bonn Deutschland
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE); Von-Siebold Straße 3a 37075 Göttingen Deutschland
- Max-Planck-Institut für Biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
- Klinik für Neurologie; Universitätsmedizin Göttingen; Waldweg 33 37073 Göttingen Deutschland
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7
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Kadavath H, Cabrales Fontela Y, Jaremko M, Jaremko Ł, Overkamp K, Biernat J, Mandelkow E, Zweckstetter M. The Binding Mode of a Tau Peptide with Tubulin. Angew Chem Int Ed Engl 2018; 57:3246-3250. [PMID: 29314492 DOI: 10.1002/anie.201712089] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/15/2017] [Indexed: 11/09/2022]
Abstract
The microtubule-associated protein Tau promotes the polymerization of tubulin and modulates the function of microtubules. As a consequence of the dynamic nature of the Tau-tubulin interaction, the structural basis of this complex has remained largely elusive. By using NMR methods optimized for ligand-receptor interactions in combination with site-directed mutagenesis we demonstrate that the flanking domain downstream of the four microtubule-binding repeats of Tau binds competitively to a site on the α-tubulin surface. The binding process is complex, involves partial coupling of different interacting regions, and is modulated by phosphorylation at Y394 and S396. This study strengthens the hypothesis of an intimate relationship between Tau phosphorylation and tubulin binding and highlights the power of the INPHARMA NMR method to characterize the interaction of peptides derived from intrinsically disordered proteins with their molecular partners.
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Affiliation(s)
- Harindranath Kadavath
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Yunior Cabrales Fontela
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariusz Jaremko
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany
| | - Łukasz Jaremko
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kerstin Overkamp
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany
| | - Jacek Biernat
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,CAESAR Research Center, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,CAESAR Research Center, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Strasse 3a, 37075, Goettingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Klinik für Neurologie, Universitätsmedizin Göttingen, Waldweg 33, 37073, Göttingen, Germany
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8
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Ding Y, Hua X, Chen H, Liu F, González-Sapien G, Wang M. Recombinant Peptidomimetic-Nano Luciferase Tracers for Sensitive Single-Step Immunodetection of Small Molecules. Anal Chem 2018; 90:2230-2237. [DOI: 10.1021/acs.analchem.7b04601] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yuan Ding
- College
of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Xiude Hua
- College
of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - He Chen
- College
of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Fengquan Liu
- College
of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
- Institute
of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Gualberto González-Sapien
- Cátedra
de Inmunología, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo 11600, Uruguay
| | - Minghua Wang
- College
of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
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9
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Sugiki T, Furuita K, Fujiwara T, Kojima C. Current NMR Techniques for Structure-Based Drug Discovery. Molecules 2018; 23:molecules23010148. [PMID: 29329228 PMCID: PMC6017608 DOI: 10.3390/molecules23010148] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/28/2017] [Accepted: 01/09/2018] [Indexed: 12/22/2022] Open
Abstract
A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR (19F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
| | | | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
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10
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Bhunia SS, Saxena AK. Molecular modelling studies in explaining the higher GPVI antagonistic activity of the racemic 2-(4-methoxyphenylsulfonyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide than its enantiomers. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:783-799. [PMID: 29135287 DOI: 10.1080/1062936x.2017.1396247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25.3 μM; IC50 R enantiomer = 126.3 μM). In order to explain this, the molecular modelling approaches viz. site map analysis, protein-protein docking and molecular dynamics simulation were carried out, which led to the identification of a second binding site located near the primary antagonist binding site known to bind losartan. The induced fit docking studies for both the enantiomers at the primary and secondary binding sites showed that the S-enantiomer has better interactions at the primary binding site than the R-enantiomer, while the R-enantiomer has better interactions at the secondary site than the S-enantiomer. Hence, the overall interactions of the racemic compound containing equimolar mixture may be higher than any one of the enantiomers and may explain the higher activity than its enantiomers of the racemic compound.
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Affiliation(s)
- S S Bhunia
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
| | - A K Saxena
- a Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
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11
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Helmer D, Schmitz K. Peptides and Peptide Analogs to Inhibit Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:147-83. [PMID: 27236556 DOI: 10.1007/978-3-319-32805-8_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein-protein interactions are governed by relatively few amino acid residues at the binding interface. Peptides derived from these protein regions may serve as mimics of one of the interaction partners in structural studies or as inhibitors to disrupt the respective interaction and investigate its biological consequences. Inhibitory peptides may also be lead structures for drug development if the respective protein-protein interaction is essential for a pathogen or disease mechanism. Binding peptides may be systematically derived from one of the binding partners or found in the screen of combinatorial peptide libraries. Molecular modelling based on structural data helps to refine existing peptides or even design novel binding peptides. This chapter gives an outline of the binding peptide discovery process and subsequent chemical modifications to further enhance affinity and specificity and to increase stability against degradation in vivo. Examples from the past three decades illustrate the great diversity of applications for protein binding peptides and peptide analogs.
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Affiliation(s)
- Dorothea Helmer
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Katja Schmitz
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
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12
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Aguirre C, Cala O, Krimm I. Overview of Probing Protein‐Ligand Interactions Using NMR. ACTA ACUST UNITED AC 2015; 81:17.18.1-17.18.24. [DOI: 10.1002/0471140864.ps1718s81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Olivier Cala
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
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13
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Moriya J, Takeuchi K, Tai K, Arai K, Kobayashi N, Yoneda N, Fukunishi Y, Inoue A, Kihara M, Murakami T, Chiba K, Shimada I. Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6. J Med Chem 2015; 58:5674-83. [PMID: 26132273 DOI: 10.1021/acs.jmedchem.5b00778] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interactions between tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and TNF superfamily receptors (TNFRSFs) are promising targets for rheumatoid arthritis (RA) treatment. However, due to the challenging nature of protein-protein interactions (PPIs), a potent inhibitor that surpasses the affinity of the TRAF6-TNFRSF interactions has not been developed. We developed a small-molecule PPI inhibitor of TRAF6-TNFRSF interactions using NMR and in silico techniques. The most potent compound, TRI4, exhibited an affinity higher than those of TNFRSFs and competitively inhibited a TRAF6-TNFRSF interaction. Structural characterization of the TRAF6-TRI4 complex revealed that TRI4 supplants key interactions in the TRAF6-TNFRSF interfaces. In addition, some TRAF6-TRI4 interactions extend beyond the TRAF6-TNFRSF interfaces and increase the binding affinity. Our successful development of TRI4 provides a new opportunity for RA treatment and implications for structure-guided development of PPI inhibitors.
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Affiliation(s)
- Jun Moriya
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Koh Takeuchi
- ‡Biological Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Kenji Tai
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Kenzo Arai
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Naoki Kobayashi
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Naoki Yoneda
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Yoshifumi Fukunishi
- ‡Biological Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Atsushi Inoue
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Miho Kihara
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Takumi Murakami
- §Pharmacological Evaluation Unit, Tsukuba Division, Sunplanet Co., Ltd., Tokodai 5-11-1, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Kenichi Chiba
- †Eisai Product Creation Systems, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba-shi, Ibaraki 300-2635, Japan
| | - Ichio Shimada
- ∥Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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14
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Mizukoshi Y, Takeuchi K, Arutaki M, Takizawa T, Hanzawa H, Takahashi H, Shimada I. Suppression of problematic compound oligomerization by cosolubilization of nondetergent sulfobetaines. ChemMedChem 2015; 10:736-41. [PMID: 25760302 PMCID: PMC4471626 DOI: 10.1002/cmdc.201500057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 11/24/2022]
Abstract
Numerous small organic compounds exist in equilibrium among monomers, soluble oligomers, and insoluble aggregates in aqueous solution. Compound aggregation is a major reason for false positives in drug screening, and even soluble oligomers can interfere with structural and biochemical analyses. However, an efficient way to manage the equilibrium of aggregation-prone compounds, especially those involved with soluble oligomers, has not been established. In this study, solution NMR spectroscopy was used as a suitable technique to detect compound oligomers in equilibrium, and it was demonstrated that cosolubilization of nondetergent sulfobetaines (NDSBs) can largely suppress compound oligomerization and aggregation by shifting the equilibrium toward the monomers. The rotational correlation time was obtained from the ratio of the selective and nonselective longitudinal NMR relaxation times, which directly and quantitatively reflected the apparent sizes of the compounds in the equilibrium. The rotational correlation time of the aggregation-prone compound SKF86002 (1 mM) was substantially reduced from 0.31 to 0.23 ns by cosolubilization of 100 mM NDSB195. NDSB cosolubilization allowed us to perform successful structural and biochemical experiments with substantially fewer artifacts, which represents a strategy to directly resolve the problematic oligomerization and aggregation of compounds.
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Affiliation(s)
- Yumiko Mizukoshi
- Biomedicinal Information Research Center (BIRC) and Molecular Profiling Research Center (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo 135-0064 (Japan); Japan Biological Informatics Consortium (JBIC), 2-3-26 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
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15
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Pihan E, Delgadillo RF, Tonkin ML, Pugnière M, Lebrun M, Boulanger MJ, Douguet D. Computational and biophysical approaches to protein-protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex. J Comput Aided Mol Des 2015; 29:525-39. [PMID: 25822046 DOI: 10.1007/s10822-015-9842-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/25/2015] [Indexed: 11/30/2022]
Abstract
Invasion of the red blood cell by Plasmodium falciparum parasites requires formation of an electron dense circumferential ring called the Moving Junction (MJ). The MJ is anchored by a high affinity complex of two parasite proteins: Apical Membrane Antigen 1 (PfAMA1) displayed on the surface of the parasite and Rhoptry Neck Protein 2 that is discharged from the parasite and imbedded in the membrane of the host cell. Structural studies of PfAMA1 revealed a conserved hydrophobic groove localized to the apical surface that coordinates RON2 and invasion inhibitory peptides. In the present work, we employed computational and biophysical methods to identify competitive P. falciparum AMA1-RON2 inhibitors with the goal of exploring the 'druggability' of this attractive antimalarial target. A virtual screen followed by molecular docking with the PfAMA1 crystal structure was performed using an eight million compound collection that included commercial molecules, the ChEMBL malaria library and approved drugs. The consensus approach resulted in the selection of inhibitor candidates. We also developed a fluorescence anisotropy assay using a modified inhibitory peptide to experimentally validate the ability of the selected compounds to inhibit the AMA1-RON2 interaction. Among those, we identified one compound that displayed significant inhibition. This study offers interesting clues to improve the throughput and reliability of screening for new drug leads.
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Affiliation(s)
- Emilie Pihan
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis, CNRS, UMR 7275, 660, Route des Lucioles, Sophia Antipolis, 06560, Valbonne, France
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16
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Molecular insights into the interaction between Plasmodium falciparum apical membrane antigen 1 and an invasion-inhibitory peptide. PLoS One 2014; 9:e109674. [PMID: 25343578 PMCID: PMC4208761 DOI: 10.1371/journal.pone.0109674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/03/2014] [Indexed: 11/28/2022] Open
Abstract
Apical membrane antigen 1 (AMA1) of the human malaria parasite Plasmodium falciparum has been implicated in invasion of the host erythrocyte. It interacts with malarial rhoptry neck (RON) proteins in the moving junction that forms between the host cell and the invading parasite. Agents that block this interaction inhibit invasion and may serve as promising leads for anti-malarial drug development. The invasion-inhibitory peptide R1 binds to a hydrophobic cleft on AMA1, which is an attractive target site for small molecules that block parasite invasion. In this work, truncation and mutational analyses show that Phe5-Phe9, Phe12 and Arg15 in R1 are the most important residues for high affinity binding to AMA1. These residues interact with two well-defined binding hot spots on AMA1. Computational solvent mapping reveals that one of these hot spots is suitable for small molecule targeting. We also confirm that R1 in solution binds to AMA1 with 1∶1 stoichiometry and adopts a secondary structure consistent with the major form of R1 observed in the crystal structure of the complex. Our results provide a basis for designing high affinity inhibitors of the AMA1-RON2 interaction.
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17
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Masini T, Pilger J, Kroezen BS, Illarionov B, Lottmann P, Fischer M, Griesinger C, Hirsch AKH. De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy. Chem Sci 2014. [DOI: 10.1039/c4sc00588k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A ligand-based NMR methodology (STI) enabled de novo fragment-based design of inhibitors of the enzyme DXS present in the non-mevalonate pathway in the absence of X-ray co-crystal structures.
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Affiliation(s)
- T. Masini
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - J. Pilger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - B. S. Kroezen
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - B. Illarionov
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - P. Lottmann
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - M. Fischer
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - C. Griesinger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - A. K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
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