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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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Iliev P, Jaworski C, Wängler C, Wängler B, Page BDG, Schirrmacher R, Bailey JJ. Type II & III inhibitors of tropomyosin receptor kinase (Trk): a 2020-2022 patent update. Expert Opin Ther Pat 2024; 34:231-244. [PMID: 38785069 DOI: 10.1080/13543776.2024.2358818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION The Trk family proteins are membrane-bound kinases predominantly expressed in neuronal tissues. Activated by neurotrophins, they regulate critical cellular processes through downstream signaling pathways. Dysregulation of Trk signaling can drive a range of diseases, making the design and study of Trk inhibitors a vital area of research. This review explores recent advances in the development of type II and III Trk inhibitors, with implications for various therapeutic applications. AREAS COVERED Patents covering type II and III inhibitors targeting the Trk family are discussed as a complement of the previous review, Type I inhibitors of tropomyosin receptor kinase (Trk): a 2020-2022 patent update. Relevant patents were identified using the Web of Science database, Google, and Google Patents. EXPERT OPINION While type II and III Trk inhibitor development has advanced more gradually compared to their type I counterparts, they hold significant promise in overcoming resistance mutations and achieving enhanced subtype selectivity - a critical factor in reducing adverse effects associated with pan-Trk inhibition. Recent interdisciplinary endeavors have marked substantial progress in the design of subtype selective Trk inhibitors, with impressive success heralded by the type III inhibitors. Notably, the emergence of mutant-selective Trk inhibitors introduces an intriguing dimension to the field, offering precise treatment possibilities.
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Affiliation(s)
- Petar Iliev
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | | | - Carmen Wängler
- Biomedical Chemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Björn Wängler
- Molecular Imaging and Radiochemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
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Gupta SRR, Ta TM, Khan M, Singh A, Singh IK, Peethambaran B. Identification and validation of a small molecule targeting ROR1 for the treatment of triple negative breast cancer. Front Cell Dev Biol 2023; 11:1243763. [PMID: 37779899 PMCID: PMC10534069 DOI: 10.3389/fcell.2023.1243763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction: Breast cancer is the most common cancer in women, with roughly 10-15% of new cases classified as triple-negative breast cancer (TNBC). Traditional chemotherapies are often toxic to normal cells. Therefore, it is important to discover new anticancer compounds that target TNBC while causing minimal damage to normal cells. Receptor tyrosine kinase-like Orphan Receptor 1 (ROR1) is an oncofetal protein overexpressed in numerous human malignancies, including TNBC. This study investigated potential small molecules targeting ROR1. Methodology: Using AutoDock Vina and Glide, we screened 70,000 chemicals for our investigation. We obtained 10 representative compounds via consensus voting, deleting structural alerts, and clustering. After manual assessment, compounds 2 and 4 were chosen for MD simulation and cell viability experiment. Compound 4 showed promising results in the viability assay, which led us to move further with the apoptosis assay and immunoblotting. Results: Compound 4 (CID1261330) had docking scores of -6.635 and -10.8. It fits into the pocket and shows interactions with GLU64, ASP174, and PHE93. Its RMSD fluctuates around 0.20 nm and forms two stable H-bonds indicating compound 4 stability. It inhibits cell proliferation in MDA-MB-231, HCC1937, and HCC1395 cell lines, with IC50 values of approximately 2 μM to 10 μM, respectively. Compound 4 did not kill non-malignant epithelial breast cells MCF-10A (IC50 > 27 μM). These results were confirmed by the significant number of apoptotic cells in MDA-MB-231 cells (47.6%) but not in MCF-10A cells (7.3%). Immunoblot analysis provided additional support in the same direction. Discussion: These findings collectively suggest that compound 4 has the potential to effectively eliminate TNBC cells while causing minimal harm to normal breast cells. The promising outcomes of this study lay the groundwork for further testing of compound 4 in other malignancies characterized by ROR1 upregulation, serving as a proof-of-concept for its broader applicability.
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Affiliation(s)
- Shradheya R. R. Gupta
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Tram M. Ta
- Department of Biology, Saint Joseph’s University, Philadelphia, PA, United States
| | - Maryam Khan
- Department of Biology, Saint Joseph’s University, Philadelphia, PA, United States
| | - Archana Singh
- Department of Botany, Hans Raj College, University of Delhi, New Delhi, India
| | - Indrakant K. Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, CA, United States
| | - Bela Peethambaran
- Department of Biology, Saint Joseph’s University, Philadelphia, PA, United States
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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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Solid Tumors and Kinase Inhibition: Management and Therapy Efficacy Evolution. Int J Mol Sci 2022; 23:ijms23073830. [PMID: 35409190 PMCID: PMC8998551 DOI: 10.3390/ijms23073830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
The increasing numbers of cancer cases worldwide and the exceedingly high mortality rates of some tumor subtypes raise the question about if the current protocols for cancer management are effective and what has been done to improve upon oncologic patients’ prognoses. The traditional chemo-immunotherapy options for cancer treatment focus on the use of cytotoxic agents that are able to overcome neoplastic clones’ survival mechanisms and induce apoptosis, as well as on the ability to capacitate the host’s immune system to hinder the continuous growth of malignant cells. The need to avert the highly toxic profiles of conventional chemo-immunotherapy and to overcome the emerging cases of tumor multidrug resistance has fueled a growing interest in the field of precision medicine and targeted molecular therapies in the last couple of decades, although relatively new alternatives in oncologic practices, the increased specificity, and the positive clinical outcomes achieved through targeted molecular therapies have already consolidated them as promising prospects for the future of cancer management. In recent years, the development and application of targeted drugs as tyrosine kinase inhibitors have enabled cancer treatment to enter the era of specificity. In addition, the combined use of targeted therapy, immunotherapy, and traditional chemotherapy has innovated the standard treatment for many malignancies, bringing new light to patients with recurrent tumors. This article comprises a series of clinical trials that, in the past 5 years, utilized kinase inhibitors (KIs) as a monotherapy or in combination with other cytotoxic agents to treat patients afflicted with solid tumors. The results, with varying degrees of efficacy, are reported.
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Abstract
With several marketed drugs, allosteric inhibition of kinases has translated to pharmacological effects and clinical benefits comparable to those from orthosteric inhibition. However, despite much effort over more than 20 years, the number of kinase targets associated with FDA-approved allosteric drugs is limited, suggesting the challenges in identifying and validating allosteric inhibitors. Here we review the principles of allosteric inhibition, summarize the discovery of allosteric MEK1/2 and BCR-ABL1 inhibitors, and discuss the approaches to screening and demonstrating the functional activity of allosteric pocket ligands.
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Affiliation(s)
- Yue Pan
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Mary M Mader
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
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van der Westhuizen L, Weisner J, Taher A, Landel I, Quambusch L, Lindemann M, Uhlenbrock N, Müller MP, Green IR, Pelly SC, Rauh D, van Otterlo WAL. Covalent allosteric inhibitors of Akt generated using a click fragment approach. ChemMedChem 2022; 17:e202100776. [PMID: 35170857 PMCID: PMC9311865 DOI: 10.1002/cmdc.202100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/14/2022] [Indexed: 11/30/2022]
Abstract
Akt is a protein kinase that has been implicated in the progression of cancerous tumours. A number of covalent allosteric Akt inhibitors are known, and based on these scaffolds, a small library of novel potential covalent allosteric imidazopyridine‐based inhibitors was designed. The envisaged compounds were synthesised, with click chemistry enabling a modular approach to a number of the target compounds. The binding modes, potencies and antiproliferative activities of these synthesised compounds were explored, thereby furthering the structure activity relationship knowledge of this class of Akt inhibitors. Three novel covalent inhibitors were identified, exhibiting moderate activity against Akt1 and various cancer cell lines, potentially paving the way for future covalent allosteric inhibitors with improved properties.
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Affiliation(s)
| | - Jörn Weisner
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Abu Taher
- Stellenbosch University, Chemistry and Polymer Science, SOUTH AFRICA
| | - Ina Landel
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Lena Quambusch
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Marius Lindemann
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Niklas Uhlenbrock
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Matthias P Müller
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Ivan R Green
- Stellenbosch University, Chemistry and Polymer Science, SOUTH AFRICA
| | | | - Daniel Rauh
- TU Dortmund: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Willem A L van Otterlo
- Stellenbosch University, Department of Chemistry and Polymer Sciences, Department of Chemistry and Polyme, Merriman Street, 7602, Stellenbosch, SOUTH AFRICA
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Kinase Inhibition in Relapsed/Refractory Leukemia and Lymphoma Settings: Recent Prospects into Clinical Investigations. Pharmaceutics 2021; 13:pharmaceutics13101604. [PMID: 34683897 PMCID: PMC8540545 DOI: 10.3390/pharmaceutics13101604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 01/19/2023] Open
Abstract
Cancer is still a major barrier to life expectancy increase worldwide, and hematologic neoplasms represent a relevant percentage of cancer incidence rates. Tumor dependence of continuous proliferative signals mediated through protein kinases overexpression instigated increased strategies of kinase inhibition in the oncologic practice over the last couple decades, and in this review, we focused our discussion on relevant clinical trials of the past five years that investigated kinase inhibitor (KI) usage in patients afflicted with relapsed/refractory (R/R) hematologic malignancies as well as in the pharmacological characteristics of available KIs and the dissertation about traditional chemotherapy treatment approaches and its hindrances. A trend towards investigations on KI usage for the treatment of chronic lymphoid leukemia and acute myeloid leukemia in R/R settings was observed, and it likely reflects the existence of already established treatment protocols for chronic myeloid leukemia and acute lymphoid leukemia patient cohorts. Overall, regimens of KI treatment are clinically manageable, and results are especially effective when allied with tumor genetic profiles, giving rise to encouraging future prospects of an era where chemotherapy-free treatment regimens are a reality for many oncologic patients.
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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Juillet C, Ermolenko L, Boyarskaya D, Baratte B, Josselin B, Nedev H, Bach S, Iorga BI, Bignon J, Ruchaud S, Al-Mourabit A. From Synthetic Simplified Marine Metabolite Analogues to New Selective Allosteric Inhibitor of Aurora B Kinase. J Med Chem 2021; 64:1197-1219. [PMID: 33417773 DOI: 10.1021/acs.jmedchem.0c02064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significant inhibition of Aurora B was achieved by the synthesis of simplified fragments of benzosceptrins and oroidin belonging to the marine pyrrole-2-aminoimidazoles metabolites isolated from sponges. Evaluation of kinase inhibition enabled the discovery of a synthetically accessible rigid acetylenic structural analogue EL-228 (1), whose structure could be optimized into the potent CJ2-150 (37). Here we present the synthesis of new inhibitors of Aurora B kinase, which is an important target for cancer therapy through mitosis regulation. The biologically oriented synthesis yielded several nanomolar inhibitors. The optimized compound CJ2-150 (37) showed a non-ATP competitive allosteric mode of action in a mixed-type inhibition for Aurora B kinase. Molecular docking identified a probable binding mode in the allosteric site "F" and highlighted the key interactions with the protein. We describe the improvement of the inhibitory potency and specificity of the novel scaffold as well as the characterization of the mechanism of action.
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Affiliation(s)
- Charlotte Juillet
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Ludmila Ermolenko
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Dina Boyarskaya
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Blandine Baratte
- Plateforme de Criblage KISSf, Station Biologique de Roscoff, Sorbonne Université, CNRS, FR 2424, Roscoff, 29680, France
| | - Béatrice Josselin
- Plateforme de Criblage KISSf, Station Biologique de Roscoff, Sorbonne Université, CNRS, FR 2424, Roscoff, 29680, France
| | - Hristo Nedev
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Stéphane Bach
- Plateforme de Criblage KISSf, Station Biologique de Roscoff, Sorbonne Université, CNRS, FR 2424, Roscoff, 29680, France.,Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 8227, Roscoff, 29680, France
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Jérôme Bignon
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
| | - Sandrine Ruchaud
- Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 8227, Roscoff, 29680, France
| | - Ali Al-Mourabit
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, Gif-sur-Yvette, 91190, France
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