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Fujiwara D, Mihara K, Takayama R, Nakamura Y, Ueda M, Tsumuraya T, Fujii I. Chemical Modification of Phage-Displayed Helix-Loop-Helix Peptides to Construct Kinase-Focused Libraries. Chembiochem 2021; 22:3406-3409. [PMID: 34605137 PMCID: PMC9297947 DOI: 10.1002/cbic.202100450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Indexed: 11/11/2022]
Abstract
Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target‐focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase‐focused library by chemically modifying helix‐loop‐helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip‐3 retained the α‐helical structure and bound to AurA with a KD value of 13.7 μM. Bip‐3 and the adenosine‐tethered peptide Bip‐3‐Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip‐3‐Adc bivalently inhibited AurA. In addition, the selectivity of Bip‐3‐Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase‐focused library of phage‐displayed HLH peptides.
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kousuke Mihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryo Takayama
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Yusuke Nakamura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Mitsuhiro Ueda
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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2
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Lee S, Kim J, Jo J, Chang JW, Sim J, Yun H. Recent advances in development of hetero-bivalent kinase inhibitors. Eur J Med Chem 2021; 216:113318. [PMID: 33730624 DOI: 10.1016/j.ejmech.2021.113318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Identifying a pharmacological agent that targets only one of more than 500 kinases present in humans is an important challenge. One potential solution to this problem is the development of bivalent kinase inhibitors, which consist of two connected fragments, each bind to a dissimilar binding site of the bisubstrate enzyme. The main advantage of bivalent (type V) kinase inhibitors is generating more interactions with target enzymes that can enhance the molecules' selectivity and affinity compared to single-site inhibitors. Earlier type V inhibitors were not suitable for the cellular environment and were mostly used in in vitro studies. However, recently developed bivalent compounds have high kinase affinity, high biological and chemical stability in vivo. This review summarized the hetero-bivalent kinase inhibitors described in the literature from 2014 to the present. We attempted to classify the molecules by serine/threonine and tyrosine kinase inhibitors, and then each target kinase and its hetero-bivalent inhibitor was assessed in depth. In addition, we discussed the analysis of advantages, limitations, and perspectives of bivalent kinase inhibitors compared with the monovalent kinase inhibitors.
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Affiliation(s)
- Seungbeom Lee
- College of Pharmacy, CHA University, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jae Won Chang
- Department of Pharmacology & Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Hematology & Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA; Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jaehoon Sim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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3
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Jiang Y, Chen G, Li XM, Liu S, Tian G, Li Y, Li X, Li H, Li XD. Selective Targeting of AF9 YEATS Domain by Cyclopeptide Inhibitors with Preorganized Conformation. J Am Chem Soc 2020; 142:21450-21459. [DOI: 10.1021/jacs.0c10324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yixiang Jiang
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Guochao Chen
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Meng Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Sha Liu
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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4
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Pietsch M, Viht K, Schnitzler A, Ekambaram R, Steinkrüger M, Enkvist E, Nienberg C, Nickelsen A, Lauwers M, Jose J, Uri A, Niefind K. Unexpected CK2β-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Bioorg Chem 2020; 96:103608. [PMID: 32058103 DOI: 10.1016/j.bioorg.2020.103608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/11/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023]
Abstract
Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2α) attached to a homodimer of regulatory subunits (CK2β), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (Ki = 84 pM). In a crystal structure of ARC-3140 in complex with CK2α, three copies of the inhibitor are visible, one of them at the CK2β interface of CK2α. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2α/CK2β interaction. A structural inspection revealed that ARC-3140, unlike CK2β antagonists described so far, interferes with both sub-interfaces of the bipartite CK2α/CK2β interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2α2β2 holoenzyme.
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Affiliation(s)
- Markus Pietsch
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Alexander Schnitzler
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Ramesh Ekambaram
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Michaela Steinkrüger
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Christian Nienberg
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Miriam Lauwers
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
| | - Karsten Niefind
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany.
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5
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Patel KD, De Zoysa GH, Kanamala M, Patel K, Pilkington LI, Barker D, Reynisson J, Wu Z, Sarojini V. Novel Cell-Penetrating Peptide Conjugated Proteasome Inhibitors: Anticancer and Antifungal Investigations. J Med Chem 2019; 63:334-348. [DOI: 10.1021/acs.jmedchem.9b01694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kamal D. Patel
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Gayan Heruka De Zoysa
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Manju Kanamala
- School of Pharmacy, University of Auckland, Auckland 1142, New Zealand
| | - Krunal Patel
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Lisa I. Pilkington
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - David Barker
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Zimei Wu
- School of Pharmacy, University of Auckland, Auckland 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science, University of Auckland, Auckland 1142, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
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6
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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7
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Wang C, Xu P, Zhang L, Huang J, Zhu K, Luo C. Current Strategies and Applications for Precision Drug Design. Front Pharmacol 2018; 9:787. [PMID: 30072901 PMCID: PMC6060444 DOI: 10.3389/fphar.2018.00787] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/28/2018] [Indexed: 12/23/2022] Open
Abstract
Since Human Genome Project (HGP) revealed the heterogeneity of individuals, precision medicine that proposes the customized healthcare has become an intractable and hot research. Meanwhile, as the Precision Medicine Initiative launched, precision drug design which aims at maximizing therapeutic effects while minimizing undesired side effects for an individual patient has entered a new stage. One of the key strategies of precision drug design is target based drug design. Once a key pathogenic target is identified, rational drug design which constitutes the major part of precision drug design can be performed. Examples of rational drug design on novel druggable targets and protein-protein interaction surfaces are summarized in this review. Besides, various kinds of computational modeling and simulation approaches increasingly benefit for the drug discovery progress. Molecular dynamic simulation, drug target prediction and in silico clinical trials are discussed. Moreover, due to the powerful ability in handling high-dimensional data and complex system, deep learning has efficiently promoted the applications of artificial intelligence in drug discovery and design. In this review, deep learning methods that tailor to precision drug design are carefully discussed. When a drug molecule is discovered, the development of specific targeted drug delivery system becomes another key aspect of precision drug design. Therefore, state-of-the-art techniques of drug delivery system including antibody-drug conjugates (ADCs), and ligand-targeted conjugates are also included in this review.
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Affiliation(s)
- Chen Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Pan Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Luyu Zhang
- School of Pharmacy, Fudan University, Shanghai, China
| | - Jing Huang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Kongkai Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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8
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Zhan P, Itoh Y, Suzuki T, Liu X. Strategies for the Discovery of Target-Specific or Isoform-Selective Modulators. J Med Chem 2015; 58:7611-33. [PMID: 26086931 DOI: 10.1021/acs.jmedchem.5b00229] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peng Zhan
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry
of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Yukihiro Itoh
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto 606-0823, Japan
| | - Takayoshi Suzuki
- Graduate
School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Xinyong Liu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry
of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
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10
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Kriisa M, Sinijärv H, Vaasa A, Enkvist E, Kostenko S, Moens U, Uri A. Inhibition of CREB Phosphorylation by Conjugates of Adenosine Analogues and Arginine-Rich Peptides, Inhibitors of PKA Catalytic Subunit. Chembiochem 2014; 16:312-9. [DOI: 10.1002/cbic.201402526] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/05/2023]
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11
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Gower CM, Chang MEK, Maly DJ. Bivalent inhibitors of protein kinases. Crit Rev Biochem Mol Biol 2014; 49:102-15. [PMID: 24564382 DOI: 10.3109/10409238.2013.875513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein kinases are key players in a large number of cellular signaling pathways. Dysregulated kinase activity has been implicated in a number of diseases, and members of this enzyme family are of therapeutic interest. However, due to the fact that most inhibitors interact with the highly conserved ATP-binding sites of kinases, it is a significant challenge to develop pharmacological agents that target only one of the greater than 500 kinases present in humans. A potential solution to this problem is the development of bisubstrate and bivalent kinase inhibitors, in which an active site-directed moiety is tethered to another ligand that targets a location outside of the ATP-binding cleft. Because kinase signaling specificity is modulated by regions outside of the ATP-binding site, strategies that exploit these interactions have the potential to provide reagents with high target selectivity. This review highlights examples of kinase interaction sites that can potentially be exploited by bisubstrate and bivalent inhibitors. Furthermore, an overview of efforts to target these interactions with bisubstrate and bivalent inhibitors is provided. Finally, several examples of the successful application of these reagents in a cellular setting are described.
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Affiliation(s)
- Carrie M Gower
- Department of Chemistry, University of Washington , Seattle, WA , USA
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12
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van Ameijde J, Zwiebel AP, Ruijtenbeek R, Liskamp RM. Azide–alkyne cycloaddition affording enzymatically tunable bisubstrate based inhibitors of histone acetyltransferase PCAF. Bioorg Med Chem Lett 2014; 24:113-6. [DOI: 10.1016/j.bmcl.2013.11.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 11/28/2022]
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