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Long L, Zhang H, Zhou Z, Duan L, Fan D, Wang R, Xu S, Qiao D, Zhu W. Pyrrole-containing hybrids as potential anticancer agents: An insight into current developments and structure-activity relationships. Eur J Med Chem 2024; 273:116470. [PMID: 38762915 DOI: 10.1016/j.ejmech.2024.116470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Cancer poses a significant threat to human health. Therefore, it is urgent to develop potent anti-cancer drugs with excellent inhibitory activity and no toxic side effects. Pyrrole and its derivatives are privileged heterocyclic compounds with significant diverse pharmacological effects. These compounds can target various aspects of cancer cells and have been applied in clinical settings or are undergoing clinical trials. As a result, pyrrole has emerged as a promising drug scaffold and has been further probed to get novel entities for the treatment of cancer. This article reviews recent research progress on anti-cancer drugs containing pyrrole. It focuses on the mechanism of action, biological activity, and structure-activity relationships of pyrrole derivatives, aiming to assist in designing and synthesizing innovative pyrrole-based anti-cancer compounds.
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Affiliation(s)
- Li Long
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Han Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - ZhiHui Zhou
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Lei Duan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Dang Fan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Ran Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Dan Qiao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi, 330013, China.
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2
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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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3
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Vandeveer GH, Arduini RM, Baker DP, Barry K, Bohnert T, Bowden-Verhoek JK, Conlon P, Cullen PF, Guan B, Jenkins TJ, Liao SY, Lin L, Liu YT, Marcotte D, Mertsching E, Metrick CM, Negrou E, Powell N, Scott D, Silvian LF, Hopkins BT. Discovery of structural diverse reversible BTK inhibitors utilized to develop a novel in vivo CD69 and CD86 PK/PD mouse model. Bioorg Med Chem Lett 2023; 80:129108. [PMID: 36538993 DOI: 10.1016/j.bmcl.2022.129108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 11/27/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
For the past two decades, BTK a tyrosine kinase and member of the Tec family has been a drug target of significant interest due to its potential to selectively treat various B cell-mediated diseases such as CLL, MCL, RA, and MS. Owning to the challenges encountered in identifying drug candidates exhibiting the potency block B cell activation via BTK inhibition, the pharmaceutical industry has relied on the use of covalent/irreversible inhibitors to address this unmet medical need. Herein, we describe a medicinal chemistry campaign to identify structurally diverse reversible BTK inhibitors originating from HITS identified using a fragment base screen. The leads were optimized to improve the potency and in vivo ADME properties resulting in a structurally distinct chemical series used to develop and validate a novel in vivo CD69 and CD86 PD assay in rodents.
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Affiliation(s)
| | | | | | - Kevin Barry
- Medicinal Chemistry, Cambridge, MA 02142, USA
| | - Tonika Bohnert
- Drug Metabolism & Pharmacokinetics, Cambridge, MA 02142, USA
| | | | | | | | - Bing Guan
- Medicinal Chemistry, Cambridge, MA 02142, USA
| | | | - Shu-Yu Liao
- Biophysics and Structural Biology, Cambridge, MA 02142, USA
| | - Lin Lin
- Technical development, Cambridge, MA 02142, USA
| | | | | | | | | | - Ella Negrou
- Immunology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Noel Powell
- Medicinal Chemistry, Cambridge, MA 02142, USA
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4
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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5
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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Ullah H, Zhang B, Sharma NK, McCrea PD, Srivastava Y. In-silico probing of AML related RUNX1 cancer-associated missense mutations: Predicted relationships to DNA binding and drug interactions. Front Mol Biosci 2022; 9:981020. [PMID: 36090034 PMCID: PMC9454315 DOI: 10.3389/fmolb.2022.981020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
The molecular consequences of cancer associated mutations in Acute myeloid leukemia (AML) linked factors are not very well understood. Here, we interrogated the COSMIC database for missense mutations associated with the RUNX1 protein, that is frequently mis-regulated in AML, where we sought to identify recurrently mutated positions at the DNA-interacting interface. Indeed, six of the mutated residues, out of a total 417 residues examined within the DNA binding domain, evidenced reduced DNA association in in silico predictions. Further, given the prominence of RUNX1’s compromised function in AML, we asked the question if the mutations themselves might alter RUNX1’s interaction (off-target) with known FDA-approved drug molecules, including three currently used in treating AML. We identified several AML-associated mutations in RUNX1 that were calculated to enhance RUNX1’s interaction with specific drugs. Specifically, we retrieved data from the COSMIC database for cancer-associated mutations of RUNX1 by using R package “data.table” and “ggplot2” modules. In the presence of DNA and/or drug, we used docking scores and energetics of the complexes as tools to evaluate predicted interaction strengths with RUNX1. For example, we performed predictions of drug binding pockets involving Enasidenib, Giltertinib, and Midostaurin (AML associated), as well as ten different published cancer associated drug compounds. Docking of wild type RUNX1 with these 13 different cancer-associated drugs indicates that wild-type RUNX1 has a lower efficiency of binding while RUNX1 mutants R142K, D171N, R174Q, P176H, and R177Q suggested higher affinity of drug association. Literature evidence support our prediction and suggests the mutation R174Q affects RUNX1 DNA binding and could lead to compromised function. We conclude that specific RUNX1 mutations that lessen DNA binding facilitate the binding of a number of tested drug molecules. Further, we propose that molecular modeling and docking studies for RUNX1 in the presence of DNA and/or drugs enables evaluation of the potential impact of RUNX1 cancer associated mutations in AML.
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Affiliation(s)
- Hanif Ullah
- Guangxi Key Laboratory for Genomics and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baoyun Zhang
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Tonk, Rajasthan, India
| | - Pierre D. McCrea
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yogesh Srivastava
- University of Chinese Academy of Sciences, Beijing, China
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Genome Regulation Laboratory; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Yogesh Srivastava,
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7
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Allosteric inhibition of LRRK2, where are we now. Biochem Soc Trans 2021; 48:2185-2194. [PMID: 33079169 PMCID: PMC7609032 DOI: 10.1042/bst20200424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. In recent years, it has been shown that leucine-rich repeat kinase 2 (LRRK2) has a crucial function in both familial and sporadic forms of PD. LRRK2 pathogenic mutations are thought to result in an increase in LRRK2 kinase activity. Thus, inhibiting LRRK2 kinase activity has become a main therapeutic target. Many compounds capable of inhibiting LRRK2 kinase activity with high selectivity and brain availability have been described. However, the safety of long-term use of these ATP-competitive LRRK2 kinase inhibitors has been challenged by several studies. Therefore, alternative ways of targeting LRRK2 activity will have a great benefit. In this review, we discuss the recent progress in the development of allosteric inhibitors of LRRK2, mainly via interfering with GTPase activity, and propose potential new intra and interprotein interactions targets that can lead to open doors toward new therapeutics.
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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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9
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Liu J, Chen C, Wang D, Zhang J, Zhang T. Emerging small-molecule inhibitors of the Bruton's tyrosine kinase (BTK): Current development. Eur J Med Chem 2021; 217:113329. [PMID: 33740548 DOI: 10.1016/j.ejmech.2021.113329] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/12/2021] [Accepted: 02/21/2021] [Indexed: 12/29/2022]
Abstract
Therapy based on Bruton's tyrosine kinase (BTK) inhibitors one of the major treatment options currently recommended for lymphoma patients. The first generation of BTK inhibitor, Ibrutinib, achieved remarkable progress in the treatment of B-cell malignancies, but still has problems with drug-resistance or off-target induced serious side effects. Therefore, numerous new BTK inhibitors were developed to address this unmet medical need. In parallel, the effect of BTK inhibitors against immune-related diseases has been evaluated in clinical trials. This review summarizes recent progress in the research and development of BTK inhibitors, with a focus on structural characteristics and structure-activity relationships. The structure-refinement process of representative pharmacophores as well as their effects on binding affinity, biological activity and pharmacokinetics profiles were analyzed. The advantages and disadvantages of reversible/irreversible BTK inhibitors and their potential implications were discussed to provide a reference for the rational design and development of novel potent BTK inhibitors.
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Affiliation(s)
- Jiakuo Liu
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China
| | - Chengjuan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China
| | - Jie Zhang
- Pharmaceutical Department, PLA Strategic Support Force Medical Center, No.9 Anxiangbeili Road, Chaoyang District, Beijing, 100101, PR China.
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100050, PR China.
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10
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Jahnke W, Erlanson DA, de Esch IJP, Johnson CN, Mortenson PN, Ochi Y, Urushima T. Fragment-to-Lead Medicinal Chemistry Publications in 2019. J Med Chem 2020; 63:15494-15507. [PMID: 33226222 DOI: 10.1021/acs.jmedchem.0c01608] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fragment-based drug discovery (FBDD) has grown and matured to a point where it is valuable to keep track of its extent and details of application. This Perspective summarizes successful fragment-to-lead stories published in 2019. It is the fifth in a series that started with literature published in 2015. The analysis of screening methods, optimization strategies, and molecular properties of hits and leads are presented in the hope of informing best practices for FBDD. Moreover, FBDD is constantly evolving, and the latest technologies and emerging trends are summarized. These include covalent FBDD, FBDD for the stabilization of proteins or protein-protein interactions, FBDD for enzyme activators, new screening technologies, and advances in library design and chemical synthesis.
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Affiliation(s)
- Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States of America
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yuji Ochi
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Tatsuya Urushima
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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11
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Ma B, Bohnert T, Otipoby KL, Tien E, Arefayene M, Bai J, Bajrami B, Bame E, Chan TR, Humora M, MacPhee JM, Marcotte D, Mehta D, Metrick CM, Moniz G, Polack E, Poreci U, Prefontaine A, Sheikh S, Schroeder P, Smirnakis K, Zhang L, Zheng F, Hopkins BT. Discovery of BIIB068: A Selective, Potent, Reversible Bruton's Tyrosine Kinase Inhibitor as an Orally Efficacious Agent for Autoimmune Diseases. J Med Chem 2020; 63:12526-12541. [PMID: 32696648 DOI: 10.1021/acs.jmedchem.0c00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autoreactive B cell-derived antibodies form immune complexes that likely play a pathogenic role in autoimmune diseases. In systemic lupus erythematosus (SLE), these antibodies bind Fc receptors on myeloid cells and induce proinflammatory cytokine production by monocytes and NETosis by neutrophils. Bruton's tyrosine kinase (BTK) is a non-receptor tyrosine kinase that signals downstream of Fc receptors and plays a transduction role in antibody expression following B cell activation. Given the roles of BTK in both the production and sensing of autoreactive antibodies, inhibitors of BTK kinase activity may provide therapeutic value to patients suffering from autoantibody-driven immune disorders. Starting from an in-house proprietary screening hit followed by structure-based rational design, we have identified a potent, reversible BTK inhibitor, BIIB068 (1), which demonstrated good kinome selectivity with good overall drug-like properties for oral dosing, was well tolerated across preclinical species at pharmacologically relevant doses with good ADME properties, and achieved >90% inhibition of BTK phosphorylation (pBTK) in humans.
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Affiliation(s)
- Bin Ma
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tonika Bohnert
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kevin L Otipoby
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Eric Tien
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Million Arefayene
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Judy Bai
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Eris Bame
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Timothy R Chan
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Humora
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J Michael MacPhee
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas Marcotte
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Devangi Mehta
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - George Moniz
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Evelyne Polack
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Urjana Poreci
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Annick Prefontaine
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Sarah Sheikh
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Patricia Schroeder
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Karen Smirnakis
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Lei Zhang
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Fengmei Zheng
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T Hopkins
- Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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12
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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Zhai Z, Li R, Bai X, Ning X, Lin Z, Zhao X, Jin Y, Yin Y. Design, synthesis and biological evaluation of novel dithiocarbamate-substituted diphenylaminopyrimidine derivatives as BTK inhibitors. Bioorg Med Chem 2019; 27:4124-4142. [DOI: 10.1016/j.bmc.2019.07.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/21/2019] [Accepted: 07/26/2019] [Indexed: 02/08/2023]
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