1
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Inoue M, Nagamori H, Morita T, Kobayashi S, Suzawa K, Kitao Y, Saito T, Kawahara I, Orita T, Akai S, Adachi T, Motomura T. Design and synthesis of novel fluorene derivatives as inhibitors of pyruvate dehydrogenase kinase. Bioorg Med Chem Lett 2024; 109:129839. [PMID: 38844173 DOI: 10.1016/j.bmcl.2024.129839] [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: 03/26/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
Activation of pyruvate dehydrogenase (PDH) by inhibition of pyruvate dehydrogenase kinase (PDHK) has the potential for the treatment of diabetes mellitus and its complications, caused by the malfunction of the glycolytic system and glucose oxidation. In this paper, we describe the identification of novel PDHK inhibitors with a fluorene structure. High-throughput screening using our in-house library provided compound 6 as a weak inhibitor that occupied the allosteric lipoyl group binding site in PDHK2. Structure-based drug design (SBDD) while addressing physicochemical properties succeeded in boosting inhibitory activity approximately 700-fold. Thus obtained compound 32 showed favorable pharmacokinetics profiles supported by high membrane permeability and metabolic stability, and exhibited activation of PDH in rat livers and a glucose lowering effect in Zucker fatty rats.
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Affiliation(s)
- Masafumi Inoue
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
| | - Hironobu Nagamori
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Morita
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Satoru Kobayashi
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Koichi Suzawa
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yuki Kitao
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tomoyuki Saito
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Iichiro Kawahara
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takuya Orita
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Shota Akai
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takahisa Motomura
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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2
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [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: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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3
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Bhujbal SP, Jun J, Park H, Moon J, Min K, Hah JM. Gaining Insights into Key Structural Hotspots within the Allosteric Binding Pockets of Protein Kinases. Int J Mol Sci 2024; 25:4725. [PMID: 38731943 PMCID: PMC11084947 DOI: 10.3390/ijms25094725] [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: 03/08/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Protein kinases are essential regulators of cell function and represent one of the largest and most diverse protein families. They are particularly influential in signal transduction and coordinating complex processes like the cell cycle. Out of the 518 human protein kinases identified, 478 are part of a single superfamily sharing catalytic domains that are related in sequence. The dysregulation of protein kinases due to certain mutations has been associated with various diseases, including cancer. Although most of the protein kinase inhibitors identified as type I or type II primarily target the ATP-binding pockets of kinases, the structural and sequential resemblances among these pockets pose a significant challenge for selective inhibition. Therefore, targeting allosteric pockets that are beside highly conserved ATP pockets has emerged as a promising strategy to prevail current limitations, such as poor selectivity and drug resistance. In this article, we compared the binding pockets of various protein kinases for which allosteric (type III) inhibitors have already been developed. Additionally, understanding the structure and shape of existing ligands could aid in identifying key interaction sites within the allosteric pockets of kinases. This comprehensive review aims to facilitate the design of more effective and selective allosteric inhibitors.
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Affiliation(s)
- Swapnil P. Bhujbal
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Joonhong Jun
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Haebeen Park
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jihyun Moon
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Kyungbae Min
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jung-Mi Hah
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea; (S.P.B.); (J.J.); (H.P.); (J.M.); (K.M.)
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
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4
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Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [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: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
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Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Charalampidou A, Nehls T, Meyners C, Gandhesiri S, Pomplun S, Pentelute BL, Lermyte F, Hausch F. Automated Flow Peptide Synthesis Enables Engineering of Proteins with Stabilized Transient Binding Pockets. ACS CENTRAL SCIENCE 2024; 10:649-657. [PMID: 38559286 PMCID: PMC10979424 DOI: 10.1021/acscentsci.3c01283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024]
Abstract
Engineering at the amino acid level is key to enhancing the properties of existing proteins in a desired manner. So far, protein engineering has been dominated by genetic approaches, which have been extremely powerful but only allow for minimal variations beyond the canonical amino acids. Chemical peptide synthesis allows the unrestricted incorporation of a vast set of unnatural amino acids with much broader functionalities, including the incorporation of post-translational modifications or labels. Here we demonstrate the potential of chemical synthesis to generate proteins in a specific conformation, which would have been unattainable by recombinant protein expression. We use recently established rapid automated flow peptide synthesis combined with solid-phase late-stage modifications to rapidly generate a set of FK506-binding protein 51 constructs bearing defined intramolecular lactam bridges. This trapped an otherwise rarely populated transient pocket-as confirmed by crystal structures-which led to an up to 39-fold improved binding affinity for conformation-selective ligands and represents a unique system for the development of ligands for this rare conformation. Overall, our results show how rapid automated flow peptide synthesis can be applied to precision protein engineering.
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Affiliation(s)
- Anna Charalampidou
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Thomas Nehls
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Satish Gandhesiri
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sebastian Pomplun
- Leiden
Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frederik Lermyte
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
| | - Felix Hausch
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
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6
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Liu M, Zhang J, Li X, Wang Y. Research progress of DDR1 inhibitors in the treatment of multiple human diseases. Eur J Med Chem 2024; 268:116291. [PMID: 38452728 DOI: 10.1016/j.ejmech.2024.116291] [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: 12/03/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Discoidin domain receptor 1 (DDR1) is a collagen-activated receptor tyrosine kinase (RTK) and plays pivotal roles in regulating cellular functions such as proliferation, differentiation, invasion, migration, and matrix remodeling. DDR1 is involved in the occurrence and progression of many human diseases, including cancer, fibrosis, and inflammation. Therefore, DDR1 represents a highly promising therapeutic target. Although no selective small-molecule inhibitors have reached clinical trials to date, many molecules have shown therapeutic effects in preclinical studies. For example, BK40143 has demonstrated significant promise in the therapy of neurodegenerative diseases. In this context, our perspective aims to provide an in-depth exploration of DDR1, encompassing its structure characteristics, biological functions, and disease relevance. Furthermore, we emphasize the importance of understanding the structure-activity relationship of DDR1 inhibitors and highlight the unique advantages of dual-target or multitarget inhibitors. We anticipate offering valuable insights into the development of more efficacious DDR1-targeted drugs.
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Affiliation(s)
- Mengying Liu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Neuro-system and Multimorbidity Laboratory, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Jifa Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Neuro-system and Multimorbidity Laboratory, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Xiaoxue Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, Neuro-system and Multimorbidity Laboratory, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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7
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Maddeboina K, Yada B, Kumari S, McHale C, Pal D, Durden DL. Recent advances in multitarget-directed ligands via in silico drug discovery. Drug Discov Today 2024; 29:103904. [PMID: 38280625 DOI: 10.1016/j.drudis.2024.103904] [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: 09/21/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
To combat multifactorial refractory diseases, such as cancer, cardiovascular, and neurodegenerative diseases, multitarget drugs have become an emerging area of research aimed at 'synthetic lethality' (SL) relationships associated with drug-resistance mechanisms. In this review, we discuss the in silico design of dual and triple-targeted ligands, strategies by which specific 'warhead' groups are incorporated into a parent compound or scaffold with primary inhibitory activity against one target to develop one small molecule that inhibits two or three molecular targets in an effort to increase potency against multifactorial diseases. We also discuss the analytical exploration of structure-activity relationships (SARs), physicochemical properties, polypharmacology, scaffold feature extraction of US Food and Drug Administration (FDA)-approved multikinase inhibitors (MKIs), and updates regarding the clinical status of dual-targeted chemotypes.
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Affiliation(s)
- Krishnaiah Maddeboina
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
| | - Bharath Yada
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Shikha Kumari
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Cody McHale
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Dhananjaya Pal
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Donald L Durden
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
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8
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Tee WV, Berezovsky IN. Allosteric drugs: New principles and design approaches. Curr Opin Struct Biol 2024; 84:102758. [PMID: 38171188 DOI: 10.1016/j.sbi.2023.102758] [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: 09/29/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Focusing on an important biomedical implication of allostery - design of allosteric drugs, we describe characteristics of allosteric sites, effectors, and their modes of actions distinguishing them from the orthosteric counterparts and calling for new principles and protocols in the quests for allosteric drugs. We show the importance of considering both binding affinity and allosteric signaling in establishing the structure-activity relationships (SARs) toward design of allosteric effectors, arguing that pairs of allosteric sites and their effector ligands - the site-effector pairs - should be generated and adjusted simultaneously in the framework of what we call directed design protocol. Key ideas and approaches for designing allosteric effectors including reverse perturbation, targeted and agnostic analysis are also discussed here. Several promising computational approaches are highlighted, along with the need for and potential advantages of utilizing generative models to facilitate discovery/design of new allosteric drugs.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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9
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Pasquale EB. Eph receptors and ephrins in cancer progression. Nat Rev Cancer 2024; 24:5-27. [PMID: 37996538 PMCID: PMC11015936 DOI: 10.1038/s41568-023-00634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
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Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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10
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Zhou M, Boulos JC, Klauck SM, Efferth T. The cardiac glycoside ZINC253504760 induces parthanatos-type cell death and G2/M arrest via downregulation of MEK1/2 phosphorylation in leukemia cells. Cell Biol Toxicol 2023; 39:2971-2997. [PMID: 37322258 PMCID: PMC10693532 DOI: 10.1007/s10565-023-09813-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Overcoming multidrug resistance (MDR) represents a major obstacle in cancer chemotherapy. Cardiac glycosides (CGs) are efficient in the treatment of heart failure and recently emerged in a new role in the treatment of cancer. ZINC253504760, a synthetic cardenolide that is structurally similar to well-known GCs, digitoxin and digoxin, has not been investigated yet. This study aims to investigate the cytotoxicity of ZINC253504760 on MDR cell lines and its molecular mode of action for cancer treatment. Four drug-resistant cell lines (P-glycoprotein-, ABCB5-, and EGFR-overexpressing cells, and TP53-knockout cells) did not show cross-resistance to ZINC253504760 except BCRP-overexpressing cells. Transcriptomic profiling indicated that cell death and survival as well as cell cycle (G2/M damage) were the top cellular functions affected by ZINC253504760 in CCRF-CEM cells, while CDK1 was linked with the downregulation of MEK and ERK. With flow cytometry, ZINC253504760 induced G2/M phase arrest. Interestingly, ZINC253504760 induced a novel state-of-the-art mode of cell death (parthanatos) through PARP and PAR overexpression as shown by western blotting, apoptosis-inducing factor (AIF) translocation by immunofluorescence, DNA damage by comet assay, and mitochondrial membrane potential collapse by flow cytometry. These results were ROS-independent. Furthermore, ZINC253504760 is an ATP-competitive MEK inhibitor evidenced by its interaction with the MEK phosphorylation site as shown by molecular docking in silico and binding to recombinant MEK by microscale thermophoresis in vitro. To the best of our knowledge, this is the first time to describe a cardenolide that induces parthanatos in leukemia cells, which may help to improve efforts to overcome drug resistance in cancer. A cardiac glycoside compound ZINC253504760 displayed cytotoxicity against different multidrug-resistant cell lines. ZINC253504760 exhibited cytotoxicity in CCRF-CEM leukemia cells by predominantly inducing a new mode of cell death (parthanatos). ZINC253504760 downregulated MEK1/2 phosphorylation and further affected ERK activation, which induced G2/M phase arrest.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Joelle C Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Sabine M Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Disease (NCT), 69120, Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128, Mainz, Germany.
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11
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Raza SHA, Zhong R, Yu X, Zhao G, Wei X, Lei H. Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application. Mol Biotechnol 2023:10.1007/s12033-023-00951-4. [PMID: 37957479 DOI: 10.1007/s12033-023-00951-4] [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: 07/14/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Allostery is an intriguing phenomenon wherein the binding activity of a biological macromolecule is modulated via non-canonical binding site, resulting in synchronized functional changes. The mechanics underlying allostery are relatively complex and this review is focused on common methodologies used to study allostery, such as X-ray crystallography, NMR spectroscopy, and HDXMS. Different methodological approaches are used to generate data in different scenarios. For example, X-ray crystallography provides high-resolution structural information, NMR spectroscopy offers dynamic insights into allosteric interactions in solution, and HDXMS provides information on protein dynamics. The residue transition state (RTS) approach has emerged as a critical tool in understanding the energetics and conformational changes associated with allosteric regulation. Allostery has significant implications in drug discovery, gene transcription, disease diagnosis, and enzyme catalysis. Enzymes' catalytic activity can be modulated by allosteric regulation, offering opportunities to develop novel therapeutic alternatives. Understanding allosteric mechanisms associated with infectious organisms like SARS-CoV and bacterial pathogens can aid in the development of new antiviral drugs and antibiotics. Allosteric mechanisms are crucial in the regulation of a variety of signal transduction and cell metabolism pathways, which in turn govern various cellular processes. Despite progress, challenges remain in identifying allosteric sites and characterizing their contribution to a variety of biological processes. Increased understanding of these mechanisms can help develop allosteric systems specifically designed to modulate key biological mechanisms, providing novel opportunities for the development of targeted therapeutics. Therefore, the current review aims to summarize common methodologies that are used to further our understanding of allosteric mechanisms. In conclusion, this review provides insights into the methodologies used for the study of allostery, its applications in in silico modeling, the mechanisms underlying antibody allostery, and the ongoing challenges and prospects in advancing our comprehension of this intriguing phenomenon.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruimin Zhong
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoting Yu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Zhao
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoqun Wei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- Licheng Detection and Certification Group Co., Ltd., Zhongshan, 528403, Guangdong, China.
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12
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Xu L, Zhuang C. Profiling of small-molecule necroptosis inhibitors based on the subpockets of kinase-ligand interactions. Med Res Rev 2023; 43:1974-2024. [PMID: 37119044 DOI: 10.1002/med.21968] [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: 08/01/2022] [Revised: 03/13/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Necroptosis is a highly regulated cell death (RCD) form in various inflammatory diseases. Receptor-interacting protein kinase 1 (RIPK1) and RIPK3 are involved in the pathway. Targeting the kinase domains of RIPK1 and/or 3 is a drug design strategy for related diseases. It is generally accepted that essential reoccurring features are observed across the human kinase domains, including RIPK1 and RIPK3. They present common N- and C-terminal domains that are built up mostly by α-helices and β-sheets, respectively. The current RIPK1/3 kinase inhibitors mainly interact with the kinase catalytic cleft. This article aims to present an in-depth profiling for ligand-kinase interactions in the crucial cleft areas by carefully aligning the kinase-ligand cocrystal complexes or molecular docking models. The similarity and differential structural segments of ligands are systematically evaluated. New insights on the adaption of the conserved and selective kinase domains to the diversity of chemical scaffolds are also provided. In a word, our analysis can provide a better structural requirement for RIPK1 and RIPK3 inhibition and a guide for inhibitor discovery and optimization of their potency and selectivity.
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Affiliation(s)
- Lijuan Xu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- School of Pharmacy, Ningxia Medical University, Yinchuan, China
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13
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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14
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Faber EB, Sun L, Tang J, Roberts E, Ganeshkumar S, Wang N, Rasmussen D, Majumdar A, Hirsch LE, John K, Yang A, Khalid H, Hawkinson JE, Levinson NM, Chennathukuzhi V, Harki DA, Schönbrunn E, Georg GI. Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding. Nat Commun 2023; 14:3213. [PMID: 37270540 PMCID: PMC10239507 DOI: 10.1038/s41467-023-38732-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 05/12/2023] [Indexed: 06/05/2023] Open
Abstract
Compared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception. However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs. In this paper, we describe the development and mechanism of action of type III inhibitors that bind CDK2 with nanomolar affinity. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as contraceptive agents is seen by incubation with spermatocyte chromosome spreads from mouse testicular explants, where they recapitulate Cdk2-/- and Spdya-/- phenotypes.
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Affiliation(s)
- Erik B Faber
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Medical Scientist Training Program, University of Minnesota Medical School-Twin Cities, Minneapolis, MN, USA
| | - Luxin Sun
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Jian Tang
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Emily Roberts
- Department of Molecular and Integrative Physiology, Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sornakala Ganeshkumar
- Department of Molecular and Integrative Physiology, Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Nan Wang
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Damien Rasmussen
- Department of Pharmacology, University of Minnesota Medical School-Twin Cities, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota Medical School-Twin Cities, Minneapolis, MN, USA
| | - Abir Majumdar
- Department of Pharmacology, University of Minnesota Medical School-Twin Cities, Minneapolis, MN, USA
| | - Laura E Hirsch
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Kristen John
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - An Yang
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Hira Khalid
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Jon E Hawkinson
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Nicholas M Levinson
- Department of Pharmacology, University of Minnesota Medical School-Twin Cities, Minneapolis, MN, USA
| | - Vargheese Chennathukuzhi
- Department of Molecular and Integrative Physiology, Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Gunda I Georg
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA.
- Institute for Therapeutics Discovery and Development, University of Minnesota College of Pharmacy-Twin Cities, Minneapolis, MN, USA.
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15
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Luo ML, Zhao Q, He XH, Xie X, Zhu HP, You FM, Peng C, Zhan G, Huang W. Research progress of indole-fused derivatives as allosteric modulators: Opportunities for drug development. Biomed Pharmacother 2023; 162:114574. [PMID: 36996677 DOI: 10.1016/j.biopha.2023.114574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Allosteric modulation is a direct and effective method for regulating the function of biological macromolecules, which play vital roles in various cellular activities. Unlike orthosteric modulators, allosteric modulators bind to sites distant from the protein's orthosteric/active site and can have specific effects on the protein's function or activity without competing with endogenous ligands. Compared to traditional orthosteric modulators, allosteric modulators offer several advantages, including reduced side effects, greater specificity, and lower toxicity, making them a promising strategy for developing novel drugs. Indole-fused architectures are widely distributed in natural products and bioactive drug leads, displaying diverse biological activities that attract the interest of both chemists and biologists in drug discovery. Currently, an increasing number of indole-fused compounds have exhibited potent activities in allosteric modulation. In this review, we provide a brief summary of examples of allosteric modulators based on the indole-fused complex architecture, highlighting the strategies for drug design/discovery and the structure-activity relationships of allosteric modulators from the perspective of medicinal chemistry.
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16
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Elrayess R, Elgawish MS, Nafie MS, Ghareb N, Yassen ASA. 2‐Phenylquinazolin‐4(3
H
)‐one scaffold as newly designed, synthesized VEGFR‐2 allosteric inhibitors with potent cytotoxicity through apoptosis. Arch Pharm (Weinheim) 2023:e2200654. [DOI: 10.1002/ardp.202200654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Affiliation(s)
- Ranza Elrayess
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Mohamed S. Elgawish
- Medicinal Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Mohamed S. Nafie
- Chemistry Department (Biochemistry program), Faculty of Science Suez Canal University Ismailia Egypt
| | - Nagat Ghareb
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Asmaa S. A. Yassen
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
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17
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Zhang Q, Cao J, Zhang Y, Bi Z, Feng Q, Yu L, Li L. Design, synthesis and evaluation of antitumor activity of selective PRMT6 inhibitors. Eur J Med Chem 2023; 247:115032. [PMID: 36566712 DOI: 10.1016/j.ejmech.2022.115032] [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: 09/07/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
PRMT6 is a member of the protein arginine methyltransferase family, which is involved in a variety of physiological processes and plays an important role in the occurrence and development of tumors. Due to the high homology of type Ⅰ PRMTs and the two close binding sites of the SAM pocket and the substrate pocket, selective PRMT6 inhibitors have rarely been reported. In this study, a series of (5-phenylpyridin-3-yl)methanamine derivatives were designed and synthesized, which could form hydrogen bonding interactions with the unique Glu49 of PRMT6, thereby improving the selectivity of the compounds for PRMT6. Among them, a25 had the best activity and selectivity, with more than 25-fold selectivity for PRMT1/8 and more than 50-fold selectivity for PRMT3/4/5/7, which was superior to these reported SAM competitive and substrate competitive PRMT6 inhibitors. Importantly, a25 could significantly inhibit the proliferation of various tumor cells and effectively induce apoptosis of cancer cells. Our data clarified that a25 is a promising selective PRMT6 inhibitor for cancer therapy which is worthy of further evaluation.
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Affiliation(s)
- Qiangsheng Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for Biotherapy, 17#3rd Section, Ren Min South Road, Chengdu, 610041, PR China
| | - Jiaying Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for Biotherapy, 17#3rd Section, Ren Min South Road, Chengdu, 610041, PR China
| | - Yiqian Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for Biotherapy, 17#3rd Section, Ren Min South Road, Chengdu, 610041, PR China
| | - Zhenfei Bi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for Biotherapy, 17#3rd Section, Ren Min South Road, Chengdu, 610041, PR China
| | - Qiang Feng
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, 611130, PR China
| | - Luoting Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Collaborative Innovation Center for Biotherapy, 17#3rd Section, Ren Min South Road, Chengdu, 610041, PR China
| | - Lu Li
- NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Laboratory of Clinical Pharmacology, GCP Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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18
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Dimitrova YN, Gutierrez JA, Huard K. It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes. RSC Med Chem 2023; 14:22-46. [PMID: 36760737 PMCID: PMC9890894 DOI: 10.1039/d2md00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.
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Affiliation(s)
| | | | - Kim Huard
- Genentech 1 DNA Way South San Francisco CA 94080 USA
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19
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Yuan J, Huang X, Gu J, Yuan Y, Liu Z, Zou H, Bian J. Honokiol reduces cadmium-induced oxidative injury and endosomal/lysosomal vacuolation via protecting mitochondrial function in quail (Coturnix japonica) liver tissues. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159626. [PMID: 36280083 DOI: 10.1016/j.scitotenv.2022.159626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Cadmium (Cd) pollution in environment is toxic to birds. This study aimed to assess antagonistic effect of honokiol (HNK) on Cd-induced quail (Coturnix japonica) liver tissue damage and Cd-induced vacuolation in hepatocytes. We found that HNK alleviated Cd-induced liver pathological damage marked by elevated serum liver biochemical indicators, disordered antioxidant levels and trace elements in quails. HNK reduced Cd-induced liver cell apoptosis as assessed by western blotting and TUNEL staining. The ultrastructure of hepatocytes under transmission electron microscope revealed that Cd induced mitochondrial damage in addition to abnormal enlargement and increased vacuolar structure of cells. Mitochondrial damage and vacuolization were reduced in the HNK + Cd group. Cd induced an increase in the levels of endosomal/lysosomal-related genes, while HNK treatment reversed this effect. Finally, we demonstrated that vacuolation in buffalo rat liver 3A (BRL 3A) cells occurred primarily due to Cd-induced oxidative stress damage that reduces mitochondrial ATP content and indirectly led to dysfunction of ATP-dependent lipid kinase PIKfyve complex. In summary, we are the first to report that Cd induces abnormal enlargement of endosome/lysosomes in quail liver cells and HNK alleviated this phenomenon by reducing mitochondrial damage and increasing intracellular ATP level. This study demonstrated the toxic effect of Cd pollution on birds and how HNK mitigated these effect at the cellular level. Overall, more research on Cd pollution and HNK use in animal husbandry is warranted.
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Affiliation(s)
- Junzhao Yuan
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xiaoqian Huang
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China
| | - Jianhong Gu
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China
| | - Yan Yuan
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China
| | - Zongping Liu
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China
| | - Hui Zou
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China
| | - Jianchun Bian
- College of Veterinary Medicine, Yangzhou University, 12 Wenhui East Road, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China.
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20
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Teng M, Young DW, Tan Z. The Pursuit of Enzyme Activation: A Snapshot of the Gold Rush. J Med Chem 2022; 65:14289-14304. [PMID: 36265019 DOI: 10.1021/acs.jmedchem.2c01291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A range of enzymes drive human physiology, and their activities are tightly regulated through numerous signaling pathways. Depending on the context, these pathways may activate or inhibit an enzyme as a way to ensure proper execution of cellular functions. From a drug discovery and development perspective, pharmacological inhibition of enzymes has been a focus of interest, as many diseases are associated with the upregulation of enzyme function. On the other hand, however, pharmacological activation of enzymes such as kinases and phosphatases has been of increasing interest. In this review, we discuss seven case studies that highlight pharmacological activation strategy, describe the binding modes and pharmacology of the activators, and comment on how this on-demand activation strategy complements the commonly pursued inhibition strategy, thus jointly enabling bidirectional modulation of specific target of interest. Going forward, we expect activators to play important roles as chemical probes and drug leads.
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Affiliation(s)
- Mingxing Teng
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Damian W Young
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States
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21
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Obst-Sander U, Ricci A, Kuhn B, Friess T, Koldewey P, Kuglstatter A, Hewings D, Goergler A, Steiner S, Rueher D, Imhoff MP, Raschetti N, Marty HP, Dietzig A, Rynn C, Ehler A, Burger D, Kornacker M, Schaffland JP, Herting F, Pao W, Bischoff JR, Martoglio B, Alice Nagel Y, Jaeschke G. Discovery of Novel Allosteric EGFR L858R Inhibitors for the Treatment of Non-Small-Cell Lung Cancer as a Single Agent or in Combination with Osimertinib. J Med Chem 2022; 65:13052-13073. [PMID: 36178776 DOI: 10.1021/acs.jmedchem.2c00893] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Addressing resistance to third-generation EGFR TKIs such as osimertinib via the EGFRC797S mutation remains a highly unmet need in EGFR-driven non-small-cell lung cancer (NSCLC). Herein, we present the discovery of the allosteric EGFR inhibitor 57, a novel fourth-generation inhibitor to overcome EGFRC797S-mediated resistance in patients harboring the activating EGFRL858R mutation. 57 exhibits an improved potency compared to previous allosteric EGFR inhibitors. To our knowledge, 57 is the first allosteric EGFR inhibitor that demonstrates robust tumor regression in a mutant EGFRL858R/C797S tumor model. Additionally, 57 is active in an H1975 EGFRL858R/T790M NSCLC xenograft model and shows superior efficacy in combination with osimertinib compared to the single agents. Our data highlight the potential of 57 as a single agent against EGFRL858R/C797S and EGFRL858R/T790M/C797S and as combination therapy for EGFRL858R- and EGFRL858R/T790M-driven NSCLC.
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Affiliation(s)
- Ulrike Obst-Sander
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Antonio Ricci
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Thomas Friess
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg82377, Germany
| | - Philipp Koldewey
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - David Hewings
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Annick Goergler
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Sandra Steiner
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Daniel Rueher
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Marie-Paule Imhoff
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Noemi Raschetti
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Hans-Peter Marty
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Aline Dietzig
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Caroline Rynn
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Andreas Ehler
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Dominique Burger
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Martin Kornacker
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Clinical Development Oncology, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Jeannine Petrig Schaffland
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Frank Herting
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg82377, Germany
| | - William Pao
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - James R Bischoff
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Bruno Martoglio
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Yvonne Alice Nagel
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Georg Jaeschke
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
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22
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Leit S, Greenwood JR, Mondal S, Carriero S, Dahlgren M, Harriman GC, Kennedy-Smith JJ, Kapeller R, Lawson JP, Romero DL, Toms AV, Shelley M, Wester RT, Westlin W, McElwee JJ, Miao W, Edmondson SD, Masse CE. Potent and selective TYK2-JH1 inhibitors highly efficacious in rodent model of psoriasis. Bioorg Med Chem Lett 2022; 73:128891. [PMID: 35842205 DOI: 10.1016/j.bmcl.2022.128891] [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: 05/16/2022] [Revised: 07/02/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022]
Abstract
TYK2 is a member of the JAK family of kinases and a key mediator of IL-12, IL-23, and type I interferon signaling. These cytokines have been implicated in the pathogenesis of multiple inflammatory and autoimmune diseases such as psoriasis, rheumatoid arthritis, lupus, and inflammatory bowel diseases. Supported by compelling data from human genetic association studies, TYK2 inhibition is an attractive therapeutic strategy for these diseases. Herein, we report the discovery of a series of highly selective catalytic site TYK2 inhibitors designed using FEP+ and structurally enabled design starting from a virtual screen hit. We highlight the structure-based optimization to identify a lead candidate 30, a potent cellular TYK2 inhibitor with excellent selectivity, pharmacokinetic properties, and in vivo efficacy in a mouse psoriasis model.
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Affiliation(s)
- Silvana Leit
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States.
| | | | - Sayan Mondal
- Schrodinger, Inc., 1540 Broadway, New York, NY 10036, United States
| | - Samantha Carriero
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Markus Dahlgren
- Schrodinger, Inc., 1540 Broadway, New York, NY 10036, United States
| | | | | | - Rosana Kapeller
- Schrodinger, Inc., 1540 Broadway, New York, NY 10036, United States
| | - Jon P Lawson
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Donna L Romero
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Angela V Toms
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Mee Shelley
- Schrodinger, Inc., 1540 Broadway, New York, NY 10036, United States
| | - Ronald T Wester
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - William Westlin
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Joshua J McElwee
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Wenyan Miao
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Scott D Edmondson
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
| | - Craig E Masse
- Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States
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