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Zhang Y, Zhang Z, Ke D, Pan X, Wang X, Xiao X, Ji C. FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints. J Chem Inf Model 2024; 64:3970-3976. [PMID: 38725251 DOI: 10.1021/acs.jcim.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
Fragment growing is an important ligand design strategy in drug discovery. In this study, we present FragGrow, a web server that facilitates structure-based drug design by fragment growing. FragGrow offers two working modes: one for growing molecules through the direct replacement of hydrogen atoms or substructures and the other for growing via virtual synthesis. FragGrow works by searching for suitable fragments that meet a set of constraints from an indexed 3D fragment database and using them to create new compounds in 3D space. The users can set a range of constraints when searching for their desired fragment, including the fragment's ability to interact with specific protein sites; its size, topology, and physicochemical properties; and the presence of particular heteroatoms and functional groups within the fragment. We hope that FragGrow will serve as a useful tool for medicinal chemists in ligand design. The FragGrow server is freely available to researchers and can be accessed at https://fraggrow.xundrug.cn.
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Affiliation(s)
- Yueqing Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Zhihan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Dongliang Ke
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Xiaolin Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Xingyu Wang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Xudong Xiao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
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2
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Wang L, Zhang Z, Yu D, Yang L, Li L, He Y, Shi J. Recent research of BTK inhibitors: Methods of structural design, pharmacological activities, manmade derivatives and structure-activity relationship. Bioorg Chem 2023; 138:106577. [PMID: 37178649 DOI: 10.1016/j.bioorg.2023.106577] [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: 03/06/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Protein kinases constitute the largest group within the kinase family, and mutations and translocations of protein kinases due to genetic alterations are intimately linked to the pathogenesis of numerous diseases. Bruton's tyrosine kinase (BTK) is a member of the protein kinases and plays a pivotal role in the development and function of B cells. BTK belongs to the tyrosine TEC family. The aberrant activation of BTK is closely associated with the pathogenesis of B-cell lymphoma. Consequently, BTK has always been a critical target for treating hematological malignancies. To date, two generations of small-molecule covalent irreversible BTK inhibitors have been employed to treat malignant B-cell tumors, and have exhibited clinical efficacy in hitherto refractory diseases. However, these drugs are covalent BTK inhibitors, which inevitably lead to drug resistance after prolonged use, resulting in poor tolerance in patients. The third-generation non-covalent BTK inhibitor Pirtobrutinib has obtained approval for marketing in the United States, thereby circumventing drug resistance caused by C481 mutation. Currently, enhancing safety and tolerance constitutes the primary issue in developing novel BTK inhibitors. This article systematically summarizes recently discovered covalent and non-covalent BTK inhibitors and classifies them according to their structures. This article also provides a detailed discussion of binding modes, structural features, pharmacological activities, advantages and limitations of typical compounds within each structure type, providing valuable references and insights for developing safer, more effective and more targeted BTK inhibitors in future studies.
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Affiliation(s)
- Lin Wang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Zhengjie Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Dongke Yu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Liuqing Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Ling Li
- School of Comprehensive Health Management, Xihua University, Chengdu, Sichuan 610039, China.
| | - Yuxin He
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China.
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China.
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3
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Li G, Li J, Tian Y, Zhao Y, Pang X, Yan A. Machine learning-based classification models for non-covalent Bruton's tyrosine kinase inhibitors: predictive ability and interpretability. Mol Divers 2023:10.1007/s11030-023-10696-6. [PMID: 37479824 DOI: 10.1007/s11030-023-10696-6] [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: 05/06/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
In this study, we built classification models using machine learning techniques to predict the bioactivity of non-covalent inhibitors of Bruton's tyrosine kinase (BTK) and to provide interpretable and transparent explanations for these predictions. To achieve this, we gathered data on BTK inhibitors from the Reaxys and ChEMBL databases, removing compounds with covalent bonds and duplicates to obtain a dataset of 3895 inhibitors of non-covalent. These inhibitors were characterized using MACCS fingerprints and Morgan fingerprints, and four traditional machine learning algorithms (decision trees (DT), random forests (RF), support vector machines (SVM), and extreme gradient boosting (XGBoost)) were used to build 16 classification models. In addition, four deep learning models were developed using deep neural networks (DNN). The best model, Model D_4, which was built using XGBoost and MACCS fingerprints, achieved an accuracy of 94.1% and a Matthews correlation coefficient (MCC) of 0.75 on the test set. To provide interpretable explanations, we employed the SHAP method to decompose the predicted values into the contributions of each feature. We also used K-means dimensionality reduction and hierarchical clustering to visualize the clustering effects of molecular structures of the inhibitors. The results of this study were validated using crystal structures, and we found that the interaction between the BTK amino acid residue and the important features of clustered scaffold was consistent with the known properties of the complex crystal structures. Overall, our models demonstrated high predictive ability and a qualitative model can be converted to a quantitative model to some extent by SHAP, making them valuable for guiding the design of new BTK inhibitors with desired activity.
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Affiliation(s)
- Guo Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Jiaxuan Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Yujia Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Yunyang Zhao
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Xiaoyang Pang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China.
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4
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Abstract
An analysis of 156 published clinical candidates from the Journal of Medicinal Chemistry between 2018 and 2021 was conducted to identify lead generation strategies most frequently employed leading to drug candidates. As in a previous publication, the most frequent lead generation strategies resulting in clinical candidates were from known compounds (59%) followed by random screening approaches (21%). The remainder of the approaches included directed screening, fragment screening, DNA-encoded library screening (DEL), and virtual screening. An analysis of similarity was also conducted based on Tanimoto-MCS and revealed most clinical candidates were distant from their original hits; however, most shared a key pharmacophore that translated from hit-to-clinical candidate. An examination of frequency of oxygen, nitrogen, fluorine, chlorine, and sulfur incorporation in clinical candidates was also conducted. The three most similar and least similar hit-to-clinical pairs from random screening were examined to provide perspective on changes that occur that lead to successful clinical candidates.
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Affiliation(s)
- Dean G Brown
- Jnana Therapeutics, One Design Center Pl Suite 19-400, Boston, Massachusetts 02210, United States
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5
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Li K, Wang M, Akoglu M, Pollard AC, Klecker JB, Alfonso P, Corrionero A, Prendiville N, Qu W, Parker MFL, Turkman N, Cohen JA, Tonge PJ. Synthesis and Preclinical Evaluation of a Novel Fluorine-18-Labeled Tracer for Positron Emission Tomography Imaging of Bruton's Tyrosine Kinase. ACS Pharmacol Transl Sci 2023; 6:410-421. [PMID: 36926452 PMCID: PMC10012250 DOI: 10.1021/acsptsci.2c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Indexed: 02/12/2023]
Abstract
Bruton's tyrosine kinase (BTK) is a target for treating B-cell malignancies and autoimmune diseases. To aid in the discovery and development of BTK inhibitors and improve clinical diagnoses, we have developed a positron emission tomography (PET) radiotracer based on a selective BTK inhibitor, remibrutinib. [18F]PTBTK3 is an aromatic, 18F-labeled tracer that was synthesized in 3 steps with a 14.8 ± 2.4% decay-corrected radiochemical yield and ≥99% radiochemical purity. The cellular uptake of [18F]PTBTK3 was blocked up to 97% in JeKo-1 cells using remibrutinib or non-radioactive PTBTK3. [18F]PTBTK3 exhibited renal and hepatobiliary clearance in NOD SCID (non-obese diabetic/severe combined immunodeficiency) mice, and the tumor uptake of [18F]PTBTK3 in BTK-positive JeKo-1 xenografts (1.23 ± 0.30% ID/cc) was significantly greater at 60 min post injection compared to the tumor uptake in BTK-negative U87MG xenografts (0.41 ± 0.11% ID/cc). In the JeKo-1 xenografts, tumor uptake was blocked up to 62% by remibrutinib, indicating the BTK-dependent uptake of [18F]PTBTK3 in tumors.
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Affiliation(s)
- Kaixuan Li
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
| | - Mingqian Wang
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
| | - Melike Akoglu
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
| | - Alyssa C. Pollard
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
| | - John B. Klecker
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
| | - Patricia Alfonso
- Enzymlogic
S.L., QUBE Technology
Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Ana Corrionero
- Enzymlogic
S.L., QUBE Technology
Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Niall Prendiville
- Enzymlogic
S.L., QUBE Technology
Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Wenchao Qu
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
- Department
of Psychiatry, Department of Radiology, Department of Medicine, Stony Brook Cancer
Center, and Facility of Experimental Radiopharmaceutical Manufacturing (FERM), Stony Brook Renaissance School of Medicine, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Matthew F. L. Parker
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
- Department
of Psychiatry, Department of Radiology, Department of Medicine, Stony Brook Cancer
Center, and Facility of Experimental Radiopharmaceutical Manufacturing (FERM), Stony Brook Renaissance School of Medicine, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Nashaat Turkman
- Department
of Psychiatry, Department of Radiology, Department of Medicine, Stony Brook Cancer
Center, and Facility of Experimental Radiopharmaceutical Manufacturing (FERM), Stony Brook Renaissance School of Medicine, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Jules A. Cohen
- Department
of Psychiatry, Department of Radiology, Department of Medicine, Stony Brook Cancer
Center, and Facility of Experimental Radiopharmaceutical Manufacturing (FERM), Stony Brook Renaissance School of Medicine, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Peter J. Tonge
- Center
for Advanced Study of Drug Action and Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony
Brook, New York 11794-3400, United States
- Department
of Psychiatry, Department of Radiology, Department of Medicine, Stony Brook Cancer
Center, and Facility of Experimental Radiopharmaceutical Manufacturing (FERM), Stony Brook Renaissance School of Medicine, Stony
Brook University, Stony
Brook, New York 11794, United States
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6
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Najmi A, Thangavel N, Mohanan AT, Qadri M, Albratty M, Ashraf SE, Saleh SF, Nayeem M, Mohan S. Structural Complementarity of Bruton’s Tyrosine Kinase and Its Inhibitors for Implication in B-Cell Malignancies and Autoimmune Diseases. Pharmaceuticals (Basel) 2023; 16:ph16030400. [PMID: 36986499 PMCID: PMC10051736 DOI: 10.3390/ph16030400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/08/2023] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
Bruton’s tyrosine kinase (BTK) is a critical component in B-cell receptor (BCR) signaling and is also expressed in haematogenic and innate immune cells. Inhibition of BTK hyperactivity is implicated in B-cell malignancies and autoimmune diseases. This review derives the structural complementarity of the BTK-kinase domain and its inhibitors from recent three-dimensional structures of inhibitor-bound BTK in the protein data bank (PDB). Additionally, this review analyzes BTK-mediated effector responses of B-cell development and antibody production. Covalent inhibitors contain an α, β-unsaturated carbonyl moiety that forms a covalent bond with Cys481, stabilizing αC-helix in inactive-out conformation which inhibits Tyr551 autophosphorylation. Asn484, located two carbons far from Cys481, influences the stability of the BTK-transition complex. Non-covalent inhibitors engage the BTK-kinase domain through an induced-fit mechanism independent of Cys481 interaction and bind to Tyr551 in the activation kink resulting in H3 cleft, determining BTK selectivity. Covalent and non-covalent binding to the kinase domain of BTK shall induce conformational changes in other domains; therefore, investigating the whole-length BTK conformation is necessary to comprehend BTK’s autophosphorylation inhibition. Knowledge about the structural complementarity of BTK and its inhibitors supports the optimization of existing drugs and the discovery of drugs for implication in B-cell malignancies and autoimmune diseases.
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Affiliation(s)
- Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Neelaveni Thangavel
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Correspondence: (N.T.); (S.M.)
| | | | - Marwa Qadri
- Department of Pharmacology, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medical Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Safeena Eranhiyil Ashraf
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Safaa Fathy Saleh
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Maryam Nayeem
- Department of Pharmacology, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Syam Mohan
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Fayoum University, Fayoum 63514, Egypt
- Substance Abuse and Research Centre, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- School of Health Sciences, University of Petroleum and Energy Studies, Dehradun 248007, India
- Correspondence: (N.T.); (S.M.)
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7
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Comparison of Intermolecular Interactions of Irreversible and Reversible Inhibitors with Bruton’s Tyrosine Kinase via Molecular Dynamics Simulations. Molecules 2022; 27:molecules27217451. [DOI: 10.3390/molecules27217451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is a key protein from the TEC family and is involved in B-cell lymphoma occurrence and development. Targeting BTK is therefore an effective strategy for B-cell lymphoma treatment. Since previous studies on BTK have been limited to structure-function analyses of static protein structures, the dynamics of conformational change of BTK upon inhibitor binding remain unclear. Here, molecular dynamics simulations were conducted to investigate the molecular mechanisms of association and dissociation of a reversible (ARQ531) and irreversible (ibrutinib) small-molecule inhibitor to/from BTK. The results indicated that the BTK kinase domain was found to be locked in an inactive state through local conformational changes in the DFG motif, and P-, A-, and gatekeeper loops. The binding of the inhibitors drove the outward rotation of the C-helix, resulting in the upfolded state of Trp395 and the formation of the salt bridge of Glu445-Arg544, which maintained the inactive conformation state. Met477 and Glu475 in the hinge region were found to be the key residues for inhibitor binding. These findings can be used to evaluate the inhibitory activity of the pharmacophore and applied to the design of effective BTK inhibitors. In addition, the drug resistance to the irreversible inhibitor Ibrutinib was mainly from the strong interaction of Cys481, which was evidenced by the mutational experiment, and further confirmed by the measurement of rupture force and rupture times from steered molecular dynamics simulation. Our results provide mechanistic insights into resistance against BTK-targeting drugs and the key interaction sites for the development of high-quality BTK inhibitors. The steered dynamics simulation also offers a means to rapidly assess the binding capacity of newly designed inhibitors.
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Xiao M, Zhu M, Wu S, Ma L, Qi L, Ha S, Xiong S, Chen M, Chen D, Luo G, Xiang H. Novel 6-amino-1,3,5-triazine derivatives as potent BTK inhibitors: structure-activity relationship (SAR) analysis and preliminary mechanism investigation. Bioorg Chem 2022; 130:106263. [DOI: 10.1016/j.bioorg.2022.106263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
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9
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Alu A, Lei H, Han X, Wei Y, Wei X. BTK inhibitors in the treatment of hematological malignancies and inflammatory diseases: mechanisms and clinical studies. J Hematol Oncol 2022; 15:138. [PMID: 36183125 PMCID: PMC9526392 DOI: 10.1186/s13045-022-01353-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022] Open
Abstract
Bruton's tyrosine kinase (BTK) is an essential component of multiple signaling pathways that regulate B cell and myeloid cell proliferation, survival, and functions, making it a promising therapeutic target for various B cell malignancies and inflammatory diseases. Five small molecule inhibitors have shown remarkable efficacy and have been approved to treat different types of hematological cancers, including ibrutinib, acalabrutinib, zanubrutinib, tirabrutinib, and orelabrutinib. The first-in-class agent, ibrutinib, has created a new era of chemotherapy-free treatment of B cell malignancies. Ibrutinib is so popular and became the fourth top-selling cancer drug worldwide in 2021. To reduce the off-target effects and overcome the acquired resistance of ibrutinib, significant efforts have been made in developing highly selective second- and third-generation BTK inhibitors and various combination approaches. Over the past few years, BTK inhibitors have also been repurposed for the treatment of inflammatory diseases. Promising data have been obtained from preclinical and early-phase clinical studies. In this review, we summarized current progress in applying BTK inhibitors in the treatment of hematological malignancies and inflammatory disorders, highlighting available results from clinical studies.
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Affiliation(s)
- Aqu Alu
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Lei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xuejiao Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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10
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Kim T, Kim K, Park I, Hong S, Park H. Two-Track Virtual Screening Approach to Identify the Dual Inhibitors of Wild Type and C481S Mutant of Bruton's Tyrosine Kinase. J Chem Inf Model 2022; 62:4500-4511. [PMID: 36001093 DOI: 10.1021/acs.jcim.2c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bruton's tyrosine kinase (BTK) is responsible for the pathogenesis of various autoimmune diseases and chronic lymphocytic leukemia. However, the discovery of efficient medicines has seen limited success due to the constitutively active mutants that acquired the drug resistance. To disclose the dual inhibitors against the wild-type BTK and the problematic drug-resistant C481S mutant, a large chemical library was virtually screened with extensive molecular docking simulations using two target proteins. As a consequence of imposing the configurational restraint to make a hydrogen bond in the hinge region of BTK as well as modifying the ligand dehydration term in the scoring function, a total of 20 dual inhibitors were discovered with the range of the associated IC50 values from 2.5 to 15 μM. All these dual inhibitors revealed the inhibitory activity against the C481S mutant to a comparable extent to that measured for the wild type. Among the new inhibitors, N-(3,5-dimethoxyphenyl)-6,7-dimethoxyquinazolin-4-amine (1) appeared to be most suitable as a starting point of the lead optimization due to the highest biochemical potency against the C481S mutant as well as the lowest molecular weight. To increase the potential of a drug candidate, 1 was modified into 6,7-dimethoxy-N-(pyridin-3-yl)quinazolin-4-amine (12) via chemical synthesis so as to possess better physicochemical properties without loss of the biochemical potency. 12 is suggested as a new effective molecular core from which numerous druggable dual inhibitors of the wild-type BTK and the C481S mutant would be derivatized.
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Affiliation(s)
- Taeho Kim
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Inyoung Park
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
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11
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Design, synthesis, and biological evaluation of pyrrolopyrimidine derivatives as novel Bruton's tyrosine kinase (BTK) inhibitors. Eur J Med Chem 2022; 241:114611. [DOI: 10.1016/j.ejmech.2022.114611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 11/22/2022]
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12
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Bruton's Kinase Inhibitors for the Treatment of Immunological Diseases: Current Status and Perspectives. J Clin Med 2022; 11:jcm11102807. [PMID: 35628931 PMCID: PMC9145705 DOI: 10.3390/jcm11102807] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
The use of Bruton’s tyrosine kinase (BTK) inhibitors has changed the management of patients with B-cell lymphoid malignancies. BTK is an important molecule that interconnects B-cell antigen receptor (BCR) signaling. BTK inhibitors (BTKis) are classified into three categories, namely covalent irreversible inhibitors, covalent reversible inhibitors, and non-covalent reversible inhibitors. Ibrutinib is the first covalent, irreversible BTK inhibitor approved in 2013 as a breakthrough therapy for chronic lymphocytic leukemia patients. Subsequently, two other covalent, irreversible, second-generation BTKis, acalabrutinib and zanubrutinib, have been developed for lymphoid malignancies to reduce the ibrutinib-mediated adverse effects. More recently, irreversible and reversible BTKis have been under development for immune-mediated diseases, including autoimmune hemolytic anemia, immune thrombocytopenia, multiple sclerosis, pemphigus vulgaris, atopic dermatitis, rheumatoid arthritis, systemic lupus erythematosus, Sjögren’s disease, and chronic spontaneous urticaria, among others. This review article summarizes the preclinical and clinical evidence supporting the role of BTKis in various autoimmune, allergic, and inflammatory conditions.
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13
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Hopkins BT, Bame E, Bajrami B, Black C, Bohnert T, Boiselle C, Burdette D, Burns JC, Delva L, Donaldson D, Grater R, Gu C, Hoemberger M, Johnson J, Kapadnis S, King K, Lulla M, Ma B, Marx I, Magee T, Meissner R, Metrick CM, Mingueneau M, Murugan P, Otipoby KL, Polack E, Poreci U, Prince R, Roach AM, Rowbottom C, Santoro JC, Schroeder P, Tang H, Tien E, Zhang F, Lyssikatos J. Discovery and Preclinical Characterization of BIIB091, a Reversible, Selective BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2022; 65:1206-1224. [PMID: 34734694 DOI: 10.1021/acs.jmedchem.1c00926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple Sclerosis is a chronic autoimmune neurodegenerative disorder of the central nervous system (CNS) that is characterized by inflammation, demyelination, and axonal injury leading to permeant disability. In the early stage of MS, inflammation is the primary driver of the disease progression. There remains an unmet need to develop high efficacy therapies with superior safety profiles to prevent the inflammation processes leading to disability. Herein, we describe the discovery of BIIB091, a structurally distinct orthosteric ATP competitive, reversible inhibitor that binds the BTK protein in a DFG-in confirmation designed to sequester Tyr-551, an important phosphorylation site on BTK, into an inactive conformation with excellent affinity. Preclinical studies demonstrated BIB091 to be a high potency molecule with good drug-like properties and a safety/tolerability profile suitable for clinical development as a highly selective, reversible BTKi for treating autoimmune diseases such as MS.
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Affiliation(s)
- Brian T Hopkins
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eris Bame
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Cheryl Black
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tonika Bohnert
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Carrie Boiselle
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Doug Burdette
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Jeremy C Burns
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Luisette Delva
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Douglas Donaldson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Richard Grater
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chungang Gu
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Josh Johnson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Sudarshan Kapadnis
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kris King
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Mukesh Lulla
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Isaac Marx
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robert Meissner
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kevin L Otipoby
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Evelyne Polack
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Urjana Poreci
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robin Prince
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Allie M Roach
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chris Rowbottom
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph C Santoro
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Patricia Schroeder
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eric Tien
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Fengmei Zhang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph Lyssikatos
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
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14
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Optimization of a novel piperazinone series as potent selective peripheral covalent BTK inhibitors. Bioorg Med Chem Lett 2022; 60:128549. [PMID: 35041943 DOI: 10.1016/j.bmcl.2022.128549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 11/23/2022]
Abstract
BTK is a tyrosine kinase playing an important role in B cell and myeloid cell functions through B cell receptor (BCR) signaling and Fc receptor (FcR) signaling. Selective inhibition of BTK has the potential to provide therapeutical benefits to patients suffering from autoimmune diseases. Here we report the design, optimization, and characterization of novel potent and highly selective covalent BTK inhibitors. Starting from a piperazinone hit derived from a selective reversible inhibitor, we solved the whole blood cellular potency issue by introducing an electrophilic warhead to reach Cys481. This design led to a covalent irreversible BTK inhibitor series with excellent kinase selectivity as well as excellent CD69 cellular potency. Optimization of metabolic stability led to representative compound like 42, which demonstrated strong cellular potency based on BTK target occupancy and the inhibition of B-cell proliferation as readouts of proximal and distal functional activity.
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15
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Bruton's Tyrosine Kinase Inhibitors in Multiple Sclerosis: Pioneering the Path Towards Treatment of Progression? CNS Drugs 2022; 36:1019-1030. [PMID: 36178589 PMCID: PMC9550714 DOI: 10.1007/s40263-022-00951-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2022] [Indexed: 11/03/2022]
Abstract
In multiple sclerosis (MS) persisting disability can derive from acute relapses or, alternatively, from slow and steady deterioration, termed chronic progression. Emerging data suggest that the latter process occurs largely independent from relapse activity or development of new central nervous system (CNS) inflammatory lesions. Pathophysiologically, acute relapses develop as a consequence of de novo CNS infiltration of immune cells, while MS progression appears to be driven by a CNS-trapped inflammatory circuit between CNS-established hematopoietic cells as well as CNS-resident cells, such as microglia, astrocytes, and oligodendrocytes. Within the last decades, powerful therapies have been developed to control relapse activity in MS. All of these agents were primarily designed to systemically target the peripheral immune system and/or to prevent CNS infiltration of immune cells. Based on the above described dichotomy of MS pathophysiology, it is understandable that these agents only exert minor effects on progression and that novel targets within the CNS have to be utilized to control MS progression independent of relapse activity. In this regard, one promising strategy may be the inhibition of the enzyme Bruton's tyrosine kinase (BTK), which is centrally involved in the activation of B cells as well as myeloid cells, such as macrophages and microglia. In this review, we discuss where and to what extent BTK is involved in the immunological and molecular cascades driving MS progression. We furthermore summarize all mechanistic, preclinical, and clinical data on the various BTK inhibitors (evobrutinib, tolebrutinib, fenebrutinib, remibrutinib, orelabrutinib, BIIB091) that are currently in development for treatment of MS, with a particular focus on the potential ability of either drug to control MS progression.
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16
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Dou D, Sha W, Diao Y, Su R, Qiao Y, Yu Z, Zhao Z, Li H, Chen Z, Xu Y. Discovery of pyrido[3,4-b]indol-1-one derivatives as novel non-covalent Bruton's tyrosine kinase (BTK) inhibitors. Bioorg Chem 2021; 119:105541. [PMID: 34910982 DOI: 10.1016/j.bioorg.2021.105541] [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: 09/15/2021] [Revised: 11/02/2021] [Accepted: 12/02/2021] [Indexed: 11/02/2022]
Abstract
Bruton's tyrosine kinase (BTK) is an attractive target for the treatment of malignancy and inflammatory/autoimmune diseases. Most of the covalent BTK inhibitors would induce off-target side effects and drug resistance. To improve the drug safety of BTK inhibitors, non-covalent inhibitors have attracted more and more attention. We designed a series of novel pyrido[3,4-b]indol-1-one derivatives (N-A and N-B) via scaffold hopping from CGI-1746. The structure-activity relationship (SAR) of the newly-synthesized compounds was explored. The results showed that compounds 12 and 18 exhibited potent enzymatic potency against BTK with IC50 values of 0.22 μM and 0.19 μM, respectively. In lymphoma cell lines U-937 cells and Ramos cells, compounds 12 and 18 displayed comparative antiproliferative activity with Ibrutinib. Moreover, compound 12 induced G1-phase cell cycle arrest and apoptosis in U-937 cells. And it could effectively inhibit tumor growth in U-937 xenograft mouse model (TGI = 41.90% at 50 mg/kg). In all, the new pyrido[3,4-b]indol-1-one derivatives have the antitumor potency by BTK inhibition and were worthy of further exploration.
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Affiliation(s)
- Dou Dou
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Wenjie Sha
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Rongrong Su
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Yunjin Qiao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Zhixiao Yu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China.
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China.
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China.
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17
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Ma C, Li Q, Zhao M, Fan G, Zhao J, Zhang D, Yang S, Zhang S, Gao D, Mao L, Zhu L, Li W, Xu G, Jiang Y, Ding Q. Discovery of 1-Amino-1 H-imidazole-5-carboxamide Derivatives as Highly Selective, Covalent Bruton's Tyrosine Kinase (BTK) Inhibitors. J Med Chem 2021; 64:16242-16270. [PMID: 34672559 DOI: 10.1021/acs.jmedchem.1c01559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bruton's tyrosine kinase (BTK) inhibitors suppressing the aberrant activation of BTK have led to a paradigm shift in the therapy of B-cell malignancies. However, there is an urgent need to discover more selective covalent BTK inhibitors owing to the off-target adverse effects of the approved inhibitor, ibrutinib. Herein, we disclose the discovery and preliminary activity studies of novel BTK inhibitors carrying 1-amino-1H-imidazole-5-carboxamide as a hinge binder. The most potent BTK inhibitor 26 demonstrates impressive selectivity, favorable pharmacokinetic properties, and robust antitumor efficacy in vivo, which indicates its potential as a novel therapeutic option for B-cell lymphomas. Importantly, to the best of our knowledge, this is the first example of a 1-amino-1H-imidazole-5-carboxamide scaffold used as the hinge binder of kinase inhibitors, which will largely expand the chemical diversity of kinase inhibitors.
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Affiliation(s)
- Chunhua Ma
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Qingyun Li
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Minghao Zhao
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Goujie Fan
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Jie Zhao
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Dandan Zhang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Shouning Yang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Shuting Zhang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Longfei Mao
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China.,Henan Zhiwei Biomedicine Co., Ltd., Xinxiang, Henan 453007, China
| | - Liang Zhu
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Wei Li
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China.,Henan Zhiwei Biomedicine Co., Ltd., Xinxiang, Henan 453007, China
| | - Guiqing Xu
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yuqin Jiang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Qingjie Ding
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Engineering Research Centre of Chiral Hydroxyl Pharmaceutical, Henan Engineering Laboratory of Chemical Pharmaceutical and Biomedical Materials, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
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18
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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19
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Recent Advances in BTK Inhibitors for the Treatment of Inflammatory and Autoimmune Diseases. Molecules 2021; 26:molecules26164907. [PMID: 34443496 PMCID: PMC8399599 DOI: 10.3390/molecules26164907] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) plays a crucial role in B-cell receptor and Fc receptor signaling pathways. BTK is also involved in the regulation of Toll-like receptors and chemokine receptors. Given the central role of BTK in immunity, BTK inhibition represents a promising therapeutic approach for the treatment of inflammatory and autoimmune diseases. Great efforts have been made in developing BTK inhibitors for potential clinical applications in inflammatory and autoimmune diseases. This review covers the recent development of BTK inhibitors at preclinical and clinical stages in treating these diseases. Individual examples of three types of inhibitors, namely covalent irreversible inhibitors, covalent reversible inhibitors, and non-covalent reversible inhibitors, are discussed with a focus on their structure, bioactivity and selectivity. Contrary to expectations, reversible BTK inhibitors have not yielded a significant breakthrough so far. The development of covalent, irreversible BTK inhibitors has progressed more rapidly. Many candidates entered different stages of clinical trials; tolebrutinib and evobrutinib are undergoing phase 3 clinical evaluation. Rilzabrutinib, a covalent reversible BTK inhibitor, is now in phase 3 clinical trials and also offers a promising future. An analysis of the protein–inhibitor interactions based on published co-crystal structures provides useful clues for the rational design of safe and effective small-molecule BTK inhibitors.
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20
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Btk Inhibitors: A Medicinal Chemistry and Drug Delivery Perspective. Int J Mol Sci 2021; 22:ijms22147641. [PMID: 34299259 PMCID: PMC8303217 DOI: 10.3390/ijms22147641] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
In the past few years, Bruton’s tyrosine Kinase (Btk) has emerged as new target in medicinal chemistry. Since approval of ibrutinib in 2013 for treatment of different hematological cancers (as leukemias and lymphomas), two other irreversible Btk inhibitors have been launched on the market. In the attempt to overcome irreversible Btk inhibitor limitations, reversible compounds have been developed and are currently under evaluation. In recent years, many Btk inhibitors have been patented and reported in the literature. In this review, we summarized the (ir)reversible Btk inhibitors recently developed and studied clinical trials and preclinical investigations for malignancies, chronic inflammation conditions and SARS-CoV-2 infection, covering advances in the field of medicinal chemistry. Furthermore, the nanoformulations studied to increase ibrutinib bioavailability are reported.
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21
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Hopkins BT, Bame E, Bell N, Bohnert T, Bowden-Verhoek JK, Bui M, Cancilla MT, Conlon P, Cullen P, Erlanson DA, Fan J, Fuchs-Knotts T, Hansen S, Heumann S, Jenkins TJ, Gua C, Liu Y, Liu Y, Lulla M, Marcotte D, Marx I, McDowell B, Mertsching E, Negrou E, Romanowski MJ, Scott D, Silvian L, Yang W, Zhong M. Utilizing structure based drug design and metabolic soft spot identification to optimize the in vitro potency and in vivo pharmacokinetic properties leading to the discovery of novel reversible Bruton's tyrosine kinase inhibitors. Bioorg Med Chem 2021; 44:116275. [PMID: 34314938 DOI: 10.1016/j.bmc.2021.116275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
Bruton's tyrosine kinase (BTK) is an essential node on the BCR signaling in B cells, which are clinically validated to play a critical role in B-cell lymphomas and various auto-immune diseases such as Multiple Sclerosis (MS), Pemphigus, and rheumatoid arthritis (RA). Although non-selective irreversible BTK inhibitors have been approved for oncology, due to the emergence of drug resistance in B-cell lymphoma associated with covalent inhibitor, there an unmet medical need to identify reversible, selective, potent BTK inhibitor as viable therapeutics for patients. Herein, we describe the identification of Hits and subsequence optimization to improve the physicochemical properties, potency and kinome selectivity leading to the discovery of a novel class of BTK inhibitors. Utilizing Met ID and structure base design inhibitors were synthesized with increased in vivo metabolic stability and oral exposure in rodents suitable for advancing to lead optimization.
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Affiliation(s)
| | - Eris Bame
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Noah Bell
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Tonika Bohnert
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | | | - Minna Bui
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Mark T Cancilla
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Patrick Conlon
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Patrick Cullen
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Junfa Fan
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Tarra Fuchs-Knotts
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Stig Hansen
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Stacey Heumann
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | - Chuck Gua
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Ying Liu
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - YuTing Liu
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Mukush Lulla
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | | | - Isaac Marx
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Bob McDowell
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | - Ella Negrou
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Michael J Romanowski
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Daniel Scott
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Laura Silvian
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Wenjin Yang
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Min Zhong
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
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22
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Bame E, Tang H, Burns JC, Arefayene M, Michelsen K, Ma B, Marx I, Prince R, Roach AM, Poreci U, Donaldson D, Cullen P, Casey F, Zhu J, Carlile TM, Sangurdekar D, Zhang B, Trapa P, Santoro J, Muragan P, Pellerin A, Rubino S, Gianni D, Bajrami B, Peng X, Coppell A, Riester K, Belachew S, Mehta D, Palte M, Hopkins BT, Scaramozza M, Franchimont N, Mingueneau M. Next-generation Bruton's tyrosine kinase inhibitor BIIB091 selectively and potently inhibits B cell and Fc receptor signaling and downstream functions in B cells and myeloid cells. Clin Transl Immunology 2021; 10:e1295. [PMID: 34141433 PMCID: PMC8204096 DOI: 10.1002/cti2.1295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Objectives Bruton's tyrosine kinase (BTK) plays a non-redundant signaling role downstream of the B-cell receptor (BCR) in B cells and the receptors for the Fc region of immunoglobulins (FcR) in myeloid cells. Here, we characterise BIIB091, a novel, potent, selective and reversible small-molecule inhibitor of BTK. Methods BIIB091 was evaluated in vitro and in vivo in preclinical models and in phase 1 clinical trial. Results In vitro, BIIB091 potently inhibited BTK-dependent proximal signaling and distal functional responses in both B cells and myeloid cells with IC50s ranging from 3 to 106 nm, including antigen presentation to T cells, a key mechanism of action thought to be underlying the efficacy of B cell-targeted therapeutics in multiple sclerosis. BIIB091 effectively sequestered tyrosine 551 in the kinase pocket by forming long-lived complexes with BTK with t 1/2 of more than 40 min, thereby preventing its phosphorylation by upstream kinases. As a key differentiating feature of BIIB091, this property explains the very potent whole blood IC50s of 87 and 106 nm observed with stimulated B cells and myeloid cells, respectively. In vivo, BIIB091 blocked B-cell activation, antibody production and germinal center differentiation. In phase 1 healthy volunteer trial, BIIB091 inhibited naïve and unswitched memory B-cell activation, with an in vivo IC50 of 55 nm and without significant impact on lymphoid or myeloid cell survival after 14 days of dosing. Conclusion Pharmacodynamic results obtained in preclinical and early clinical settings support the advancement of BIIB091 in phase 2 clinical trials.
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Affiliation(s)
- Eris Bame
- Clinical Sciences Biogen Cambridge MA USA
| | - Hao Tang
- Biogen Research Biogen Cambridge MA USA
| | | | | | - Klaus Michelsen
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA.,Present address: Relay Therapeutics Cambridge MA USA
| | - Bin Ma
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Isaac Marx
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Robin Prince
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Allie M Roach
- Biogen Research Biogen Cambridge MA USA.,Present address: Gilead Sciences Seattle WA USA
| | - Urjana Poreci
- Clinical Sciences Biogen Cambridge MA USA.,Present address: Pandion Therapeutics Watertown MA USA
| | - Douglas Donaldson
- Clinical Sciences Biogen Cambridge MA USA.,Present address: Giner Labs Newton MA USA
| | | | | | - Jing Zhu
- Biogen Research Biogen Cambridge MA USA
| | | | - Dipen Sangurdekar
- Biogen Research Biogen Cambridge MA USA.,Present address: Takeda Cambridge MA USA
| | | | - Patrick Trapa
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Joseph Santoro
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Param Muragan
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | | | | | - Davide Gianni
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Bekim Bajrami
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
| | - Xiaomei Peng
- Global Safety and Regulatory Sciences Biogen Cambridge MA USA
| | | | | | | | - Devangi Mehta
- Clinical Sciences Biogen Cambridge MA USA.,Present address: Immunologix Laboratories Cambridge MA USA
| | - Mike Palte
- MS Development Unit Biogen Cambridge MA USA
| | - Brian T Hopkins
- Biotherapeutics and Medicinal Sciences Biogen Cambridge MA USA
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23
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Qiu H, Ali Z, Bender A, Caldwell R, Chen YY, Fang Z, Gardberg A, Glaser N, Goettsche A, Goutopoulos A, Grenningloh R, Hanschke B, Head J, Johnson T, Jones C, Jones R, Kulkarni S, Maurer C, Morandi F, Neagu C, Poetzsch S, Potnick J, Schmidt R, Roe K, Viacava Follis A, Wing C, Zhu X, Sherer B. Discovery of potent and selective reversible Bruton's tyrosine kinase inhibitors. Bioorg Med Chem 2021; 40:116163. [PMID: 33932711 DOI: 10.1016/j.bmc.2021.116163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/06/2021] [Accepted: 04/11/2021] [Indexed: 11/29/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase member of the TEC family of tyrosine kinases. Pre-clinical and clinical data have shown that targeting BTK can be used for the treatment for B-cell disorders. Here we disclose the discovery of a novel imidazo[4,5-b]pyridine series of potent, selective reversible BTK inhibitors through a rational design approach. From a starting hit molecule 1, medicinal chemistry optimization led to the development of a lead compound 30, which exhibited 58 nM BTK inhibitory potency in human whole blood and high kinome selectivity. Additionally, the compound demonstrated favorable pharmacokinetics (PK), and showed potent dose-dependent efficacy in a rat CIA model.
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Affiliation(s)
- Hui Qiu
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1).
| | - Zahid Ali
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Andrew Bender
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Richard Caldwell
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Yi-Ying Chen
- Stoke Therapeutics, 45 Wiggins Ave, Bedford, MA 01730, USA
| | - Zhizhou Fang
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Anna Gardberg
- Constellation Pharmaceuticals, 215 First St #200, Cambridge, MA 02142, USA
| | - Nina Glaser
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Anja Goettsche
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Andreas Goutopoulos
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Roland Grenningloh
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Bettina Hanschke
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Jared Head
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Theresa Johnson
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Christopher Jones
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Reinaldo Jones
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Shashank Kulkarni
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Christine Maurer
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Federica Morandi
- Roche Pharma Research and Early Development, Grenzacherstrasse 124, Basel, Basel-Stadt, CH 4070, Switzerland
| | - Constantin Neagu
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Sven Poetzsch
- Merck KGaA, Frankfurter Strasse 250, Darmstadt, Hessen, DE 64293, Germany
| | - Justin Potnick
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Ralf Schmidt
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Katherine Roe
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Ariele Viacava Follis
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Carolyn Wing
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Xiaohua Zhu
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
| | - Brian Sherer
- EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA 01821, USA(1)
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