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Gadiya Y, Shetty S, Hofmann-Apitius M, Gribbon P, Zaliani A. Exploring SureChEMBL from a drug discovery perspective. Sci Data 2024; 11:507. [PMID: 38755219 PMCID: PMC11099139 DOI: 10.1038/s41597-024-03371-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
In the pharmaceutical industry, the patent protection of drugs and medicines is accorded importance because of the high costs involved in the development of novel drugs. Over the years, researchers have analyzed patent documents to identify freedom-to-operate spaces for novel drug candidates. To assist this, several well-established public patent document data repositories have enabled automated methodologies for extracting information on therapeutic agents. In this study, we delve into one such publicly available patent database, SureChEMBL, which catalogues patent documents related to life sciences. Our exploration begins by identifying patent compounds across public chemical data resources, followed by pinpointing sections in patent documents where the chemical annotations were found. Next, we exhibit the potential of compounds to serve as drug candidates by evaluating their conformity to drug-likeness criteria. Lastly, we examine the drug development stage reported for these compounds to understand their clinical success. In summary, our investigation aims at providing a comprehensive overview of the patent compounds catalogued in SureChEMBL, assessing their relevance to pharmaceutical drug discovery.
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Affiliation(s)
- Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany.
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany.
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53113, Bonn, Germany.
| | - Simran Shetty
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
- Hamburg University of Applied Sciences (HAW), 20099, Hamburg, Germany
| | - Martin Hofmann-Apitius
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53113, Bonn, Germany
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
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2
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Zheng X, Chen Z, Guo M, Liang H, Song X, Liu Y, Liao Z, Zhang Y, Guo J, Zhou Y, Zhang ZM, Tu Z, Zhang Y, Chen Y, Zhang Z, Lu X. Structure-Based Optimization of Pyrazinamide-Containing Macrocyclic Derivatives as Fms-like Tyrosine Kinase 3 (FLT3) Inhibitors to Overcome Clinical Mutations. ACS Pharmacol Transl Sci 2024; 7:1485-1506. [PMID: 38751627 PMCID: PMC11092118 DOI: 10.1021/acsptsci.4c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Secondary mutations in Fms-like tyrosine kinase 3-tyrosine kinase domain (FLT3-TKD) (e.g., D835Y and F691L) have become a major on-target resistance mechanism of FLT3 inhibitors, which present a significant clinical challenge. To date, no effective drugs have been approved to simultaneously overcome clinical resistance caused by these two mutants. Thus, a series of pyrazinamide macrocyclic compounds were first designed and evaluated to overcome the secondary mutations of FLT3. The representative 8v exhibited potent inhibitory activities against FLT3D835Y and FLT3D835Y/F691L with IC50 values of 1.5 and 9.7 nM, respectively. 8v also strongly suppressed the proliferation against Ba/F3 cells transfected with FLT3-ITD, FLT3-ITD-D835Y, FLT3-ITD-F691L, FLT3-ITD-D835Y-F691L, and MV4-11 acute myeloid leukemia (AML) cell lines with IC50 values of 12.2, 10.5, 24.6, 16.9, and 6.8 nM, respectively. Furthermore, 8v demonstrated ideal anticancer efficacy in a Ba/F3-FLT3-ITD-D835Y xenograft model. The results suggested that 8v can serve as a promising macrocycle-based FLT3 inhibitor for the treatment of AML.
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Affiliation(s)
- Xuan Zheng
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhiwen Chen
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ming Guo
- Department
of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local
Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hong Liang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yiling Liu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhenling Liao
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yan Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jing Guo
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhi-min Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhengchao Tu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ye Zhang
- Guangxi
Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China
| | - Yongheng Chen
- Department
of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local
Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhang Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaoyun Lu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
- Department
of Hematology, Guangdong Second Provincial General Hospital, Jinan University, Guangzhou 510632, China
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3
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Naufal M, Hermawati E, Syah YM, Hidayat AT, Hidayat IW, Al-Anshori J. Structure-Activity Relationship Study and Design Strategies of Hydantoin, Thiazolidinedione, and Rhodanine-Based Kinase Inhibitors: A Two-Decade Review. ACS OMEGA 2024; 9:4186-4209. [PMID: 38313530 PMCID: PMC10832052 DOI: 10.1021/acsomega.3c04749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 02/06/2024]
Abstract
Cancer is one of the most prominent causes of the rapidly growing mortality numbers worldwide. Cancer originates from normal cells that have acquired the capability to alter their molecular, biochemical, and cellular traits. The alteration of cell signaling enzymes, such as kinases, can initiate and amplify cancer progression. As a curative method, the targeted therapy utilized small molecules' capability to inhibit kinase's cellular function. This review provides a brief history (1999-2023) of Small Molecule Kinase Inhibitors (SMKIs) discovery with their molecular perspective. Furthermore, this current review also addresses the application and the development of hydantoin, thiazolidinedione, and rhodanine-based derivatives as kinase inhibitors toward several subclasses (EGFR, PI3K, VEGFR, Pim, c-Met, CDK, IGFR, and ERK) accompanied by their structure-activity relationship study and their molecular interactions. The present work summarizes and compiles all the important structural information essential for developing hydantoin, thiazolidinedione, and rhodanine-based kinase inhibitors to improve their potency in the future.
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Affiliation(s)
- Muhammad Naufal
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Elvira Hermawati
- Department
of Chemistry, Bandung Institute of Technology, Jalan Ganesha Nomor 10, Bandung, Jawa Barat 40132, Indonesia
| | - Yana Maolana Syah
- Department
of Chemistry, Bandung Institute of Technology, Jalan Ganesha Nomor 10, Bandung, Jawa Barat 40132, Indonesia
| | - Ace Tatang Hidayat
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Ika Wiani Hidayat
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
| | - Jamaludin Al-Anshori
- Department
of Chemistry, Padjadjaran University, Jalan Raya Bandung-Sumedang Km.
21, Jatinangor, Sumedang 45363, Indonesia
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