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Liu M, Qiu B, Zhang Z, Zheng Y, Yuan J, Li H, Zhang X. Ligand-Enabled C6-Selective C-H Arylation of Pyrrolo[2,3- d] Pyrimidine Derivatives with Pd Catalysts: An Approach to the Synthesis of EGFR Inhibitor AEE-788. J Org Chem 2024. [PMID: 38768046 DOI: 10.1021/acs.joc.4c00667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Herein, we report the Pd(II)-catalyzed direct C-H arylation of pyrrolo[2,3-d]pyrimidine derivatives with aryl iodides, which is enabled by bidentate pyridine-pyridine ligands. A range of aryl iodides proved to be suitable coupling partners affording the desired products in good yields with high levels of C6 selectivity. This protocol features good tolerance of reactive functional groups, mild reaction conditions, and a simple reaction system, which provides an expeditious route to an essential class of 6-arylpyrrolo[2,3-d]pyrimidines frequently found in bioactive compounds, and provides a step-economical access to the second-generation EGFR inhibitor AEE-788.
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Affiliation(s)
- Min Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Baojie Qiu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhuo Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yulong Zheng
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Junyu Yuan
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Hailing Li
- Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Xingxian Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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2
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Acharya A, Yadav M, Nagpure M, Kumaresan S, Guchhait SK. Molecular medicinal insights into scaffold hopping-based drug discovery success. Drug Discov Today 2024; 29:103845. [PMID: 38013043 DOI: 10.1016/j.drudis.2023.103845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
In both academia and the pharmaceutical industry, innovative hypotheses, methodologies and technologies that can shorten the drug research and development, leading to higher success rates, are vital. In this review, we demonstrate how innovative variations of the scaffold-hopping strategy have been used to create new druggable molecular spaces, drugs, clinical candidates, preclinical candidates, and bioactive agents. We also analyze molecular modulations that enabled improvements of the pharmacodynamic (PD), physiochemical, and pharmacokinetic (PK) properties (P3 properties) of the drugs resulting from these scaffold-hopping strategies.
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Affiliation(s)
- Ayan Acharya
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mukul Yadav
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mithilesh Nagpure
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sanathanalaxmi Kumaresan
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India; National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sankar K Guchhait
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India.
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3
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Huang G, Hucek D, Cierpicki T, Grembecka J. Applications of oxetanes in drug discovery and medicinal chemistry. Eur J Med Chem 2023; 261:115802. [PMID: 37713805 DOI: 10.1016/j.ejmech.2023.115802] [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: 07/09/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023]
Abstract
The compact and versatile oxetane motifs have gained significant attention in drug discovery and medicinal chemistry campaigns. This review presents an overview of the diverse applications of oxetanes in clinical and preclinical drug candidates targeting various human diseases, including cancer, viral infections, autoimmune disorders, neurodegenerative conditions, metabolic disorders, and others. Special attention is given to biologically active oxetane-containing compounds and their disease-related targets, such as kinases, epigenetic and non-epigenetic enzymes, and receptors. The review also details the effect of the oxetane motif on important properties, including aqueous solubility, lipophilicity, pKa, P-glycoprotein (P-gp) efflux, metabolic stability, conformational preferences, toxicity profiles (e.g., cytochrome P450 (CYP) suppression and human ether-a-go-go related gene (hERG) inhibition), pharmacokinetic (PK) properties, potency, and target selectivity. We anticipate that this work will provide valuable insights that can drive future discoveries of novel bioactive oxetane-containing small molecules, enabling their effective application in combating a wide range of human diseases.
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Affiliation(s)
- Guang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Devon Hucek
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
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4
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Easaw S, Ezzati S, Coombs CC. SOHO State of the Art Updates and Next Questions: Updates on BTK Inhibitors for the Treatment of Chronic Lymphocytic Leukemia. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2023; 23:697-704. [PMID: 37544810 DOI: 10.1016/j.clml.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
Over the last decade, targeted inhibition of Bruton's tyrosine kinase (BTK) has led to a paradigm shift in the way chronic lymphocytic leukemia (CLL) is managed. BTK inhibitors (BTKi) are broadly classified as covalent BTKI and noncovalent BTKi (cBTKi and ncBTK) Ibrutinib, as the first approved cBTKi, vastly improved outcomes for patients with CLL over prior chemoimmunotherapy regimens. However, long-term use is limited by both intolerance and resistance. The second generation of more selective BTKi were developed to improve tolerability. While these agents have led to an improved safety profile in comparison to Ibrutinib (both acalabrutinib and zanubrutinib), and improved efficacy (zanubrutinib), intolerance occasionally occurs, and resistance remains a challenge. The third generation of BTKi, which noncovalently or reversibly inhibits BTK, has shown promising results in early phase trials and are being evaluated in the phase 3 setting. These drugs could be an effective treatment option in patients with either resistance and intolerance to cBTKi. The most recent development in therapeutic agents targeting BTK is the development of BTK degraders. By removing BTK, as opposed to inhibiting it, these drugs could remain efficacious irrespective of BTK resistance mutations, however clinical data are limited at this time. This review summarizes the evolution and ongoing development of newer BTKi and BTK degraders in the management of CLL, with a focus of future directions in this field, including how emerging clinical data could inform therapeutic sequencing in CLL management.
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Affiliation(s)
| | - Shawyon Ezzati
- California Northstate University College of Medicine, Elk Grove, CA
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5
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Abstract
The oxetane ring is an emergent, underexplored motif in drug discovery that shows attractive properties such as low molecular weight, high polarity, and marked three-dimensionality. Oxetanes have garnered further interest as isosteres of carbonyl groups and as molecular tools to fine-tune physicochemical properties of drug compounds such as pKa, LogD, aqueous solubility, and metabolic clearance. This perspective highlights recent applications of oxetane motifs in drug discovery campaigns (2017-2022), with emphasis on the effect of the oxetane on medicinally relevant properties and on the building blocks used to incorporate the oxetane ring. Based on this analysis, we provide an overview of the potential benefits of appending an oxetane to a drug compound, as well as potential pitfalls, challenges, and future directions.
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Affiliation(s)
- Juan J. Rojas
- Department of Chemistry,
Imperial College London, Molecular Sciences
Research Hub, White City
Campus, Wood Lane, London W12 0BZ, U.K.
| | - James A. Bull
- Department of Chemistry,
Imperial College London, Molecular Sciences
Research Hub, White City
Campus, Wood Lane, London W12 0BZ, U.K.
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6
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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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7
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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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8
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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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9
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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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