1
|
Jin X, Ding N, Guo HY, Hu Q. Macrocyclic-based strategy in drug design: From lab to the clinic. Eur J Med Chem 2024; 277:116733. [PMID: 39098132 DOI: 10.1016/j.ejmech.2024.116733] [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: 07/05/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.
Collapse
Affiliation(s)
- Xin Jin
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ning Ding
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hong-Yu Guo
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
| |
Collapse
|
2
|
Gerninghaus J, Zhubi R, Krämer A, Karim M, Tran DHN, Joerger AC, Schreiber C, Berger LM, Berger BT, Ehret TAL, Elson L, Lenz C, Saxena K, Müller S, Einav S, Knapp S, Hanke T. Back-Pocket Optimization of 2-Aminopyrimidine-Based Macrocycles Leads to Potent EPHA2/GAK Kinase Inhibitors. J Med Chem 2024. [PMID: 39028937 DOI: 10.1021/acs.jmedchem.4c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
Macrocyclization of acyclic compounds is a powerful strategy for improving inhibitor potency and selectivity. Here we have optimized 2-aminopyrimidine-based macrocycles to use these compounds as chemical tools for the ephrin kinase family. Starting with a promiscuous macrocyclic inhibitor, 6, we performed a structure-guided activity relationship and selectivity study using a panel of over 100 kinases. The crystal structure of EPHA2 in complex with the developed macrocycle 23 provided a basis for further optimization by specifically targeting the back pocket, resulting in compound 55, a potent inhibitor of EPHA2/A4 and GAK. Subsequent front-pocket derivatization resulted in an interesting in cellulo selectivity profile, favoring EPHA4 over the other ephrin receptor kinase family members. The dual EPHA2/A4 and GAK inhibitor 55 prevented dengue virus infection of Huh7 liver cells. However, further investigations are needed to determine whether this was a compound-specific effect or target-related.
Collapse
Affiliation(s)
- Joshua Gerninghaus
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Rezart Zhubi
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Do Hoang Nhu Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Christian Schreiber
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Theresa A L Ehret
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Christopher Lenz
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Krishna Saxena
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, California 94158, United States
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| |
Collapse
|
3
|
Zhang H, Xie F, Yuan XY, Dai XT, Tian YF, Sun MM, Yu SQ, Cai JY, Sun B, Zhang WC, Shan CL. Discovery of a nitroaromatic nannocystin with potent in vivo anticancer activity against colorectal cancer by targeting AKT1. Acta Pharmacol Sin 2024; 45:1044-1059. [PMID: 38326625 PMCID: PMC11053100 DOI: 10.1038/s41401-024-01231-w] [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: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
The development of targeted chemotherapeutic agents against colorectal cancer (CRC), one of the most common cancers with a high mortality rate, is in a constant need. Nannocystins are a family of myxobacterial secondary metabolites featuring a 21-membered depsipeptide ring. The in vitro anti-CRC activity of natural and synthetic nannocystins was well documented, but little is known about their in vivo efficacy and if positive, the underlying mechanism of action. In this study we synthesized a nitroaromatic nannocystin through improved preparation of a key fragment, and characterized its in vitro activity and in vivo efficacy against CRC. We first described the total synthesis of compounds 2-4 featuring Heck macrocyclization to forge their 21-membered macrocycle. In a panel of 7 cancer cell lines from different tissues, compound 4 inhibited the cell viability with IC values of 1-6 nM. In particular, compound 4 (1, 2, 4 nM) inhibited the proliferation of CRC cell lines (HCT8, HCT116 and LoVo) in both concentration and time dependent manners. Furthermore, compound 4 concentration-dependently inhibited the colony formation and migration of CRC cell lines. Moreover, compound 4 induced cell cycle arrest at sub-G1 phase, apoptosis and cellular senescence in CRC cell lines. In three patient-derived CRC organoids, compound 4 inhibited the PDO with IC values of 3.68, 28.93 and 11.81 nM, respectively. In a patient-derived xenograft mouse model, injection of compound 4 (4, 8 mg/kg, i.p.) every other day for 12 times dose-dependently inhibited the tumor growth without significant change in body weight. We conducted RNA-sequencing, molecular docking and cellular thermal shift assay to elucidate the anti-CRC mechanisms of compound 4, and revealed that it exerted its anti-CRC effect at least in part by targeting AKT1.
Collapse
Affiliation(s)
- Han Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Fei Xie
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Xiao-Ya Yuan
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Xin-Tong Dai
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Yun-Feng Tian
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Ming-Ming Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Si-Qi Yu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Jia-You Cai
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Bin Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Wei-Cheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China.
| | - Chang-Liang Shan
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China.
| |
Collapse
|
4
|
Niu P, Tao Y, Lin G, Xu H, Meng Q, Yang K, Huang W, Song M, Ding K, Ma D, Fan M. Design and Synthesis of Novel Macrocyclic Derivatives as Potent and Selective Cyclin-Dependent Kinase 7 Inhibitors. J Med Chem 2024; 67:6099-6118. [PMID: 38586950 DOI: 10.1021/acs.jmedchem.3c01832] [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: 04/09/2024]
Abstract
The duality of function (cell cycle regulation and gene transcription) of cyclin-dependent kinase 7 (CDK7) makes it an attractive oncology target and the discovery of CDK7 inhibitors has been a long-term pursuit by academia and pharmaceutical companies. However, achieving selective leading compounds is still difficult owing to the similarities among the ATP binding pocket. Herein, we detail the design and synthesis of a series of macrocyclic derivatives with pyrazolo[1,5-a]-1,3,5-triazine core structure as potent and selective CDK7 inhibitors. The diverse manners of macrocyclization led to distinguished selectivity profiles of the CDK family. Molecular dynamics (MD) simulation explained the binding difference between 15- and 16-membered macrocyclic compounds. Further optimization generated compound 37 exhibiting good CDK7 inhibitory activity and high selectivity over other CDKs. This work clearly demonstrated macrocyclization is a versatile method to finely tune the selectivity profile of small molecules and MD simulation can be a valuable tool in prioritizing designs of the macrocycle.
Collapse
Affiliation(s)
- Pengpeng Niu
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Yanxin Tao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Guohao Lin
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Huiqi Xu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Qingyuan Meng
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kang Yang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Weixue Huang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Meiru Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Ke Ding
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Dawei Ma
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 20032, China
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
5
|
Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [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: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
Collapse
Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
6
|
Hekking KFW, Maroto S, van Kekem K, Haasjes FS, Slootweg JC, Oude Alink PGB, Dirks R, Sardana M, Bolster MG, Kuijpers B, Smith D, Doodeman R, Scheepstra M, Zech B, Mulvihill M, Renzetti LM, Babiss L, Centrella PA, Clark MA, Cuozzo JW, Guié MA, Sigel E, Habeshian S, Hupp CD, Liu J, Thomson HA, Zhang Y, Keefe AD, Müller G, Gremmen S. Development of Potent Mcl-1 Inhibitors: Structural Investigations on Macrocycles Originating from a DNA-Encoded Chemical Library Screen. J Med Chem 2024; 67:3039-3065. [PMID: 38306405 DOI: 10.1021/acs.jmedchem.3c02206] [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: 02/04/2024]
Abstract
Evasion of apoptosis is critical for the development and growth of tumors. The pro-survival protein myeloid cell leukemia 1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family, associated with tumor aggressiveness, poor survival, and drug resistance. Development of Mcl-1 inhibitors implies blocking of protein-protein interactions, generally requiring a lengthy optimization process of large, complex molecules. Herein, we describe the use of DNA-encoded chemical library synthesis and screening to directly generate complex, yet conformationally privileged macrocyclic hits that serve as Mcl-1 inhibitors. By applying a conceptual combination of conformational analysis and structure-based design in combination with a robust synthetic platform allowing rapid analoging, we optimized in vitro potency of a lead series into the low nanomolar regime. Additionally, we demonstrate fine-tuning of the physicochemical properties of the macrocyclic compounds, resulting in the identification of lead candidates 57/59 with a balanced profile, which are suitable for future development toward therapeutic use.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ron Dirks
- Symeres, 6546BB Nijmegen, The Netherlands
| | | | | | | | | | | | | | - Birgit Zech
- X-Rx, Inc., New York, New York 10016, United States
| | | | | | - Lee Babiss
- X-Rx, Inc., New York, New York 10016, United States
| | | | | | - John W Cuozzo
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | - Eric Sigel
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | | | - Julie Liu
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | - Ying Zhang
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | | | | |
Collapse
|
7
|
Acharya B, Saha D, Armstrong D, Jabali B, Hanafi M, Herrera-Rueda A, Lakkaniga NR, Frett B. Kinase inhibitor macrocycles: a perspective on limiting conformational flexibility when targeting the kinome with small molecules. RSC Med Chem 2024; 15:399-415. [PMID: 38389874 PMCID: PMC10880908 DOI: 10.1039/d3md00457k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/10/2023] [Indexed: 02/24/2024] Open
Abstract
Methods utilized for drug discovery and development within the kinome have rapidly evolved since the approval of imatinib, the first small molecule kinase inhibitor. Macrocycles have received increasing interest as a technique to improve kinase inhibitor drug properties evident by the FDA approvals of lorlatinib, pacritinib, and repotrectinib. Compared to their acyclic counterparts, macrocycles can possess improved pharmacodynamic and pharmacokinetic properties. This review highlights clinical success stories when implementing macrocycles in kinase-based drug discovery and showcases that macrocyclization is a clinically validated drug discovery strategy when targeting the kinome.
Collapse
Affiliation(s)
- Baku Acharya
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Conrad Prebys Centre for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA
| | - Daniel Armstrong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Baha'a Jabali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Maha Hanafi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University Cairo 11526 Egypt
| | - Alan Herrera-Rueda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Sun JG, Nie P, Herdewijn P, Li XJ. Exploring the synthetic approaches and clinical prowess of established macrocyclic pharmaceuticals. Eur J Med Chem 2024; 264:116051. [PMID: 38104377 DOI: 10.1016/j.ejmech.2023.116051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Macrocyclic compounds, characterized by cyclic structures, often originate from either modified forms of unicyclic canonical molecules or natural products. Within the field of medicinal chemistry, there has been a growing fascination with drug-like macrocycles in recent years, primarily due to compelling evidence indicating that macrocyclization can significantly influence both the biological and physiochemical properties, as well as the selectivity, when compared to their acyclic counterparts. The approval of contemporary pharmaceutical agents like Lorlatinib underscore the notable clinical relevance of drug-like macrocycles. Nonetheless, the synthesis of these drug-like macrocycles poses substantial challenges, primarily stemming from the complexity of ring-closing reactions, which are inherently dependent on the size and geometry of the bridging linker, impacting overall yields. Nevertheless, macrocycles offer a promising avenue for expanding the synthetic toolkit in medicinal chemistry, enabling the creation of bioactive compounds. To shed light on the subject, we delve into the clinical prowess of established macrocyclic drugs, spanning various therapeutic areas, including oncology, and infectious diseases. Case studies of clinically approved macrocyclic agents illustrate their profound impact on patient care and disease management. As we embark on this journey through the world of macrocyclic pharmaceuticals, we aim to provide a comprehensive overview of their synthesis and clinical applications, shedding light on the pivotal role they play in modern medicine.
Collapse
Affiliation(s)
- Jian-Gang Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Peng Nie
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Xiao-Jing Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
| |
Collapse
|
10
|
Amrhein JA, Berger LM, Balourdas DI, Joerger AC, Menge A, Krämer A, Frischkorn JM, Berger BT, Elson L, Kaiser A, Schubert-Zsilavecz M, Müller S, Knapp S, Hanke T. Synthesis of Pyrazole-Based Macrocycles Leads to a Highly Selective Inhibitor for MST3. J Med Chem 2024; 67:674-690. [PMID: 38126712 DOI: 10.1021/acs.jmedchem.3c01980] [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: 12/23/2023]
Abstract
MST1, MST2, MST3, MST4, and YSK1 are conserved members of the mammalian sterile 20-like serine/threonine (MST) family that regulate cellular functions such as proliferation and migration. The MST3 isozyme plays a role in regulating cell growth and apoptosis, and its dysregulation has been linked to high-grade tumors. To date, there are no isoform-selective inhibitors that could be used for validating the role of MST3 in tumorigenesis. We designed a series of 3-aminopyrazole-based macrocycles based on the structure of a promiscuous inhibitor. By varying the moieties targeting the solvent-exposed region and optimizing the linker, macrocycle JA310 (21c) was synthesized. JA310 exhibited high cellular potency for MST3 (EC50 = 106 nM) and excellent kinome-wide selectivity. The crystal structure of the MST3-JA310 complex provided intriguing insights into the binding mode, which is associated with large-scale structural rearrangements. In summary, JA310 demonstrates the utility of macrocyclization for the design of highly selective inhibitors and presents the first chemical probe for MST3.
Collapse
Affiliation(s)
- Jennifer Alisa Amrhein
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena Marie Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz 69120 Heidelberg, Germany
| | - Julia Marie Frischkorn
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz 69120 Heidelberg, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| |
Collapse
|
11
|
Fabbri L, Di Federico A, Astore M, Marchiori V, Rejtano A, Seminerio R, Gelsomino F, De Giglio A. From Development to Place in Therapy of Lorlatinib for the Treatment of ALK and ROS1 Rearranged Non-Small Cell Lung Cancer (NSCLC). Diagnostics (Basel) 2023; 14:48. [PMID: 38201357 PMCID: PMC10804309 DOI: 10.3390/diagnostics14010048] [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: 11/15/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Following the results of the CROWN phase III trial, the third-generation macrocyclic ALK inhibitor lorlatinib has been introduced as a salvage option after the failure of a first-line TKI in ALK-rearranged NSCLC, while its precise role in the therapeutic algorithm of ROS1 positive disease is still to be completely defined. The ability to overcome acquired resistance to prior generation TKIs (alectinib, brigatinib, ceritinib, and crizotinib) and the high intracranial activity in brain metastatic disease thanks to increased blood-brain barrier penetration are the reasons for the growing popularity and interest in this molecule. Nevertheless, the major vulnerability of this drug resides in a peculiar profile of related collateral events, with neurological impairment being the most conflicting and debated clinical issue. The cognitive safety concern, the susceptibility to heterogeneous resistance pathways, and the absence of a valid alternative in the second line are strongly jeopardizing a potential paradigm shift in this oncogene-addicted disease. So, when prescribing lorlatinib, clinicians must face two diametrically opposed characteristics: a great therapeutic potential without the intrinsic limitations of its precursor TKIs, a cytotoxic activity threatened by suboptimal tolerability, and the unavoidable onset of resistance mechanisms we cannot properly manage yet. In this paper, we give a critical point of view on the stepwise introduction of this promising drug into clinical practice, starting from its innovative molecular and biochemical properties to intriguing future developments, without forgetting its weaknesses.
Collapse
Affiliation(s)
- Laura Fabbri
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
| | - Alessandro Di Federico
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, 40138 Bologna, Italy;
| | - Martina Astore
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
| | - Virginia Marchiori
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
| | - Agnese Rejtano
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
| | - Renata Seminerio
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
| | - Francesco Gelsomino
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, 40138 Bologna, Italy;
| | - Andrea De Giglio
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (L.F.); (A.D.F.); (M.A.); (V.M.); (A.R.); (R.S.)
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, 40138 Bologna, Italy;
| |
Collapse
|
12
|
Chao Y, Subramaniam M, Namitharan K, Zhu Y, Koolma V, Hao Z, Li S, Wang Y, Hudoynazarov I, Miloserdov FM, Zuilhof H. Synthesis of Large Macrocycles with Chiral Sulfur Centers via Enantiospecific SuFEx and SuPhenEx Click Reactions. J Org Chem 2023; 88:15658-15665. [PMID: 37903243 PMCID: PMC10660663 DOI: 10.1021/acs.joc.3c01656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 11/01/2023]
Abstract
Here we report the first asymmetric synthesis of large chiral macrocycles with chiral sulfur atoms. Building on stereospecific SuFEx and SuPhenEx click chemistries, this approach utilizes disulfonimidoyl fluorides and disulfonimidoyl p-nitrophenolates─which are efficient building blocks with two chiral sulfur centers, and diphenols to efficiently form novel S-O bonds. Characteristic results include the enantiospecific one-step synthesis of rings consisting of 21-58 members and characterization of both enantiomers (R,R and S,S) by e.g. X-ray crystallography.
Collapse
Affiliation(s)
- Yang Chao
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Muthusamy Subramaniam
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Kayambu Namitharan
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Yumei Zhu
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Victor Koolma
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Zitong Hao
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Shikang Li
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Yaxin Wang
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Ilyos Hudoynazarov
- Division
of Organic Synthesis and Applied Chemistry, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Fedor M. Miloserdov
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Han Zuilhof
- School
of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| |
Collapse
|
13
|
Brady PB, Sorensen BK, Risi RM, Curtin ML, Mantei RA, Florjancic AS, Mastracchio A, Ji C, Kunzer AR, Lai C, Storer GE, Chan VS, Henry RF, Souers AJ, Michaelides MR, Judd AS, Hansen TM. Enabling, Decagram-Scale Synthesis of Macrocyclic MCL-1 Inhibitor ABBV-467. J Org Chem 2023; 88:15562-15568. [PMID: 37909857 DOI: 10.1021/acs.joc.3c00939] [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: 11/03/2023]
Abstract
ABBV-467 is a highly potent and selective MCL-1 inhibitor that was advanced to a phase I clinical trial for the treatment of multiple myeloma. Due to its large size and structural complexity, ABBV-467 is a challenging synthetic target. Herein, we describe the synthesis of ABBV-467 on a decagram scale, which enabled preclinical characterization. The strategy is convergent and stereoselective, featuring a hindered biaryl cross coupling, enantioselective hydrogenation, and conformationally preorganized macrocyclization by C-O bond formation as key steps.
Collapse
Affiliation(s)
- Patrick B Brady
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Bryan K Sorensen
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Roberto M Risi
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Michael L Curtin
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Robert A Mantei
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Alan S Florjancic
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Anthony Mastracchio
- Global Medicinal Chemistry, Small Molecule Therapeutic and Platform Technologies, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Cheng Ji
- Global Medicinal Chemistry, Small Molecule Therapeutic and Platform Technologies, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Aaron R Kunzer
- Global Medicinal Chemistry, Small Molecule Therapeutic and Platform Technologies, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Chunqiu Lai
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Gregory E Storer
- Center of Catalysis, Process Research and Development, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Vincent S Chan
- Center of Catalysis, Process Research and Development, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Rodger F Henry
- Analytical Sciences, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Andrew J Souers
- Oncology Discovery, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | | | - Andrew S Judd
- Global Medicinal Chemistry, Small Molecule Therapeutic and Platform Technologies, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - T Matthew Hansen
- Centralized Organic Synthesis Group, Small Molecule Therapeutic and Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| |
Collapse
|
14
|
Yang Z, Liu Z, Xu C, Xu J, Liu T, He H, Li L, Ren Y, Chen J. Discovery of novel resorcinol biphenyl ether-based macrocyclic small molecules as PD-1/PD-L1 inhibitors with favorable pharmacokinetics for cancer immunotherapy. Bioorg Chem 2023; 139:106740. [PMID: 37478546 DOI: 10.1016/j.bioorg.2023.106740] [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: 06/07/2023] [Revised: 07/08/2023] [Accepted: 07/16/2023] [Indexed: 07/23/2023]
Abstract
Programmed death protein 1 (PD-1)/programmed death protein ligand 1 (PD-L1) is one of the most promising immune checkpoints (ICs) in tumor immunology and has been actively pursued as a target for anticancer drug discovery. Based on our previous research in small molecule PD-1/PD-L1 modulators, we designed and synthesized a series of resorcinol biphenyl ether-bearing macrocyclic compounds and evaluated their anti-PD-1/PD-L1 activities. Among them, compound 8d exhibited the highest inhibitory activity against PD-1/PD-L1 interaction with IC50 of 259.7 nM in the homogenous time-resolved fluorescence (HTRF) assay. In addition, 8d displayed in vitro immunomodulatory effects by promoting HepG2 cell death in a HepG2/Jurkat cell co-culture model. Furthermore, 8d effectively inhibited tumor growth (TGI = 74.6% at 40 mg/kg) in a melanoma tumor model in mice without causing obvious toxicity. Moreover, 8d exhibited favorable pharmacokinetics [e.g. high stability, reasonable half-life, and good oral bioavailability (F = 21.5%)]. Finally, molecular modeling studies showed that 8d bound to PD-L1 with high affinity. These results suggest that 8d may serve as a starting point for further development of macrocyclic small molecule-based PD-1/PD-L1 inhibitors for cancer treatment.
Collapse
Affiliation(s)
- Zichao Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ziqing Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chenglong Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianwei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ting Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haiqi He
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ling Li
- The Eighth Affiliated Hospital, Sun Yat sen University, Shenzhen 518033, China
| | - Yichang Ren
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
15
|
Tosh D, Fisher CL, Salmaso V, Wan TC, Campbell RG, Chen E, Gao ZG, Auchampach JA, Jacobson KA. First Potent Macrocyclic A 3 Adenosine Receptor Agonists Reveal G-Protein and β-Arrestin2 Signaling Preferences. ACS Pharmacol Transl Sci 2023; 6:1288-1305. [PMID: 37705595 PMCID: PMC10496144 DOI: 10.1021/acsptsci.3c00126] [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: 06/21/2023] [Indexed: 09/15/2023]
Abstract
(N)-Methanocarba adenosine derivatives (A3 adenosine receptor (AR) agonists containing bicyclo[3.1.0]hexane replacing furanose) were chain-extended at N6 and C2 positions with terminal alkenes for ring closure. The resulting macrocycles of 17-20 atoms retained affinity, indicating a spatially proximal orientation of these receptor-bound chains, consistent with molecular modeling of 12. C2-Arylethynyl-linked macrocycle 19 was more A3AR-selective than 2-ether-linked macrocycle 12 (both 5'-methylamides, human (h) A3AR affinities (Ki): 22.1 and 25.8 nM, respectively), with lower mouse A3AR affinities. Functional hA3AR comparison of two sets of open/closed analogues in β-arrestin2 and Gi/o protein assays showed certain signaling preferences divergent from reference agonist Cl-IB-MECA 1. The potencies of 1 at all three Gαi isoforms were slightly less than its hA3AR binding affinity (Ki: 1.4 nM), while the Gαi1 and Gαi2 potencies of macrocycle 12 were roughly an order of magnitude higher than its radioligand binding affinity. Gαi2-coupling was enhanced in macrocycle 12 (EC50 2.56 nM, ∼40% greater maximal efficacy than 1). Di-O-allyl precursor 18 cyclized to form 19, increasing the Gαi1 potency by 7.5-fold. The macrocycles 12 and 19 and their open precursors 11 and 18 potently stimulated β-arrestin2 recruitment, with EC50 values (nM) of 5.17, 4.36, 1.30, and 4.35, respectively, and with nearly 50% greater efficacy compared to 1. This example of macrocyclization altering the coupling pathways of small-molecule (nonpeptide) GPCR agonists is the first for potent and selective macrocyclic AR agonists. These initial macrocyclic derivatives can serve as a guide for the future design of macrocyclic AR agonists displaying unanticipated pharmacology.
Collapse
Affiliation(s)
- Dilip
K. Tosh
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Courtney L. Fisher
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Veronica Salmaso
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
- Molecular
Modeling Section, Department of Pharmaceutical and Pharmacological
Sciences, University of Padua, Padua 35131, Italy
| | - Tina C. Wan
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Ryan G. Campbell
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Eric Chen
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| |
Collapse
|
16
|
Fragkiadakis M, Anastasiou PK, Zingiridis M, Triantafyllou-Rundell ME, Reyes Romero A, Stoumpos CC, Neochoritis CG. Instant Macrocyclizations via Multicomponent Reactions. J Org Chem 2023; 88:12709-12715. [PMID: 37596972 DOI: 10.1021/acs.joc.3c01379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Macrocycles fascinate chemists due to both their structure and their applications. However, we still lack efficient and sustainable synthetic methods, giving us straightforward access to them. Herein, a rapid macrocyclization utilizing a two-step, one-pot approach based on orthogonal multicomponent reaction (MCR) tactics is introduced. This synthetic protocol, which is based on Ugi and Groebke-Blackburn-Bienaymé reactions with isocyanides tethered to alkyl tosylates, yields medium sized macrocycles that are otherwise difficult to achieve. Single crystal structures reveal conformational reorganization via intramolecular hydrogen bonding, and modeling studies profile the synthesized libraries.
Collapse
Affiliation(s)
| | | | - Marios Zingiridis
- Department of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | | | - Atilio Reyes Romero
- Genetic Intelligence Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, P.O. Box 24144, New York, New York 10065, United States
| | - Constantinos C Stoumpos
- Department of Materials Science & Technology, University of Crete, Voutes, 70013 Heraklion, Greece
| | | |
Collapse
|
17
|
Zhao Z, Bourne PE. Rigid Scaffolds Are Promising for Designing Macrocyclic Kinase Inhibitors. ACS Pharmacol Transl Sci 2023; 6:1182-1191. [PMID: 37588756 PMCID: PMC10425998 DOI: 10.1021/acsptsci.3c00078] [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: 04/12/2023] [Indexed: 08/18/2023]
Abstract
Macrocyclic kinase inhibitors (MKIs) are gaining attention due to their favorable selectivity and potential to overcome drug resistance, yet they remain challenging to design because of their novel structures. To facilitate the design and discovery of MKIs, we investigate MKI rational design starting from initial acyclic compounds by performing microsecond-scale atomistic simulations for multiple MKIs, constructing an MKI database, and analyzing MKIs using hierarchical cluster analysis. Our studies demonstrate that the binding modes of MKIs are like those of their corresponding acyclic counterparts against the same kinase targets. Importantly, within the respective binding sites, the MKI scaffolds retain the same conformations as their corresponding acyclic counterparts, demonstrating the rigidity of scaffolds before and after molecular cyclization. The MKI database includes 641 nanomole-level MKIs from 56 human kinases elucidating the features of rigid scaffolds and the core structures of MKIs. Collectively these results and resources can facilitate MKI development.
Collapse
Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
18
|
Bhujbal SP, Hah JM. An Intriguing Purview on the Design of Macrocyclic Inhibitors for Unexplored Protein Kinases through Their Binding Site Comparison. Pharmaceuticals (Basel) 2023; 16:1009. [PMID: 37513921 PMCID: PMC10386424 DOI: 10.3390/ph16071009] [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: 06/07/2023] [Revised: 07/02/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Kinases play an important role in regulating various intracellular signaling pathways that control cell proliferation, differentiation, survival, and other cellular processes, and their deregulation causes more than 400 diseases. Consequently, macrocyclization can be considered a noteworthy approach to developing new therapeutic agents for human diseases. Macrocyclization has emerged as an effective drug discovery strategy over the past decade to improve target selectivity and potency of small molecules. Small compounds with linear structures upon macrocyclization can lead to changes in their physicochemical and biological properties by firmly reducing conformational flexibility. A number of distinct protein kinases exhibit similar binding sites. Comparison of protein binding sites provides crucial insights for drug discovery and development. Binding site similarities are helpful in understanding polypharmacology, identifying potential off-targets, and repurposing known drugs. In this review, we focused on comparing the binding sites of those kinases for which macrocyclic inhibitors are available/studied so far. Furthermore, we calculated the volume of the binding site pocket for each targeted kinase and then compared it with the binding site pocket of the kinase for which only acyclic inhibitors were designed to date. Our review and analysis of several explored kinases might be useful in targeting new protein kinases for macrocyclic drug discovery.
Collapse
Affiliation(s)
- Swapnil P Bhujbal
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jung-Mi Hah
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| |
Collapse
|
19
|
Amrhein J, Wang G, Berger BT, Berger LM, Kalampaliki AD, Krämer A, Knapp S, Hanke T. Design and Synthesis of Pyrazole-Based Macrocyclic Kinase Inhibitors Targeting BMPR2. ACS Med Chem Lett 2023; 14:833-840. [PMID: 37312836 PMCID: PMC10258821 DOI: 10.1021/acsmedchemlett.3c00127] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
Bone morphogenetic protein (BMP) signaling is mediated by transmembrane protein kinases that form heterotetramers consisting of type-I and type-II receptors. Upon BMP binding, the constitutively active type-II receptors activate specific type-I receptors by transphosphorylation, resulting in the phosphorylation of SMAD effector proteins. Drug discovery in the receptor tyrosine kinase-like (TKL) family has largely focused on type-I receptors, with few inhibitors that have been published targeting type-II receptors. BMPR2 is involved in several diseases, most notably pulmonary arterial hypertension, but also contributes to Alzheimer's disease and cancer. Here, we report that macrocyclization of the promiscuous inhibitor 1, based on a 3-amino-1H-pyrazole hinge binding moiety, led to a selective and potent BMPR2 inhibitor 8a.
Collapse
Affiliation(s)
- Jennifer
A. Amrhein
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Guiqun Wang
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Lena M. Berger
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Amalia D. Kalampaliki
- Department
of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Andreas Krämer
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Stefan Knapp
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
- German
Cancer Consortium (DKTK), German Cancer
Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Thomas Hanke
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang
Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Structure
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| |
Collapse
|
20
|
Chai J, Arico-Muendel CC, Ding Y, Pollastri MP, Scott S, Mantell MA, Yao G. Synthesis of a DNA-Encoded Macrocyclic Library Utilizing Intramolecular Benzimidazole Formation. Bioconjug Chem 2023. [PMID: 37216465 DOI: 10.1021/acs.bioconjchem.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Macrocycles occupy chemical space "beyond the rule of five". They bridge traditional bioactive small molecule drugs and macromolecules and have the potential to modulate challenging targets such as PPI or proteases. Here we report an on-DNA macrocyclization reaction utilizing intramolecular benzimidazole formation. A 129-million-member macrocyclic library composed of a privileged benzimidazole core, a dipeptide sequence (natural or non-natural), and linkers of varying length and flexibility was designed and synthesized.
Collapse
Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Christopher C Arico-Muendel
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Michael P Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sarah Scott
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Mark A Mantell
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Gang Yao
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| |
Collapse
|
21
|
Hu J, Zhang D, Tian K, Ren C, Li H, Lin C, Huang X, Liu J, Mao W, Zhang J. Small-molecule LRRK2 inhibitors for PD therapy: Current achievements and future perspectives. Eur J Med Chem 2023; 256:115475. [PMID: 37201428 DOI: 10.1016/j.ejmech.2023.115475] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that orchestrates a diverse array of cellular processes, including vesicle transport, autophagy, lysosome degradation, neurotransmission, and mitochondrial activity. Hyperactivation of LRRK2 triggers vesicle transport dysfunction, neuroinflammation, accumulation of α-synuclein, mitochondrial dysfunction, and the loss of cilia, ultimately leading to Parkinson's disease (PD). Therefore, targeting LRRK2 protein is a promising therapeutic strategy for PD. The clinical translation of LRRK2 inhibitors was historically impeded by issues surrounding tissue specificity. Recent studies have identified LRRK2 inhibitors that have no effect on peripheral tissues. Currently, there are four small-molecule LRRK2 inhibitors undergoing clinical trials. This review provides a summary of the structure and biological functions of LRRK2, along with an overview of the binding modes and structure-activity relationships (SARs) of small-molecule inhibitors targeting LRRK2. It offers valuable references for developing novel drugs targeting LRRK2.
Collapse
Affiliation(s)
- Jiarui Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changyu Ren
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Heng Li
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoli Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wuyu Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
22
|
Cai J, Sun B, Yu S, Zhang H, Zhang W. Heck Macrocyclization in Forging Non-Natural Large Rings including Macrocyclic Drugs. Int J Mol Sci 2023; 24:ijms24098252. [PMID: 37175956 PMCID: PMC10179193 DOI: 10.3390/ijms24098252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The intramolecular Heck reaction is a well-established strategy for natural product total synthesis. When constructing large rings, this reaction is also referred to as Heck macrocyclization, which has proved a viable avenue to access diverse naturally occurring macrocycles. Less noticed but likewise valuable, it has created novel macrocycles of non-natural origin that neither serve as nor derive from natural products. This review presents a systematic account of the title reaction in forging this non-natural subset of large rings, thereby addressing a topic rarely covered in the literature. Walking through two complementary sections, namely (1) drug discovery research and (2) synthetic methodology development, it demonstrates that beyond the well-known domain of natural product synthesis, Heck macrocyclization also plays a remarkable role in forming synthetic macrocycles, in particular macrocyclic drugs.
Collapse
Affiliation(s)
- Jiayou Cai
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Bin Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Siqi Yu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Han Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| | - Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
| |
Collapse
|
23
|
Parate S, Kumar V, Hong JC, Lee KW. Investigation of Macrocyclic mTOR Modulators of Rapamycin Binding Site via Pharmacoinformatics Approaches. Comput Biol Chem 2023; 104:107875. [PMID: 37148678 DOI: 10.1016/j.compbiolchem.2023.107875] [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: 07/25/2022] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/08/2023]
Abstract
The PI3K/Akt/mTOR is an essential intracellular signaling pathway in which the serine/threonine mTOR kinase portrays a major role in cell growth, proliferation and survival. The mTOR kinase is frequently dysregulated in a broad spectrum of cancers, thus making it a potential target. Rapamycin and its analogs (rapalogs) allosterically inhibit mTOR, thereby dodging the deleterious effects prompted by ATP-competitive mTOR inhibitors. However, the available mTOR allosteric site inhibitors exhibit low oral bioavailability and suboptimal solubility. Bearing in mind this narrow therapeutic window of the current allosteric mTOR inhibitors, an in silico study was designed in search of new macrocyclic inhibitors. The macrocycles from the ChemBridge database (12,677 molecules) were filtered for their drug-likeness properties and the procured compounds were subjected for molecular docking within the binding cleft between FKBP25 and FRB domains of mTOR. The docking analysis resulted with 15 macrocycles displaying higher scores than the selective mTOR allosteric site inhibitor, DL001. The docked complexes were refined by subsequent molecular dynamics simulations for a period of 100 ns. Successive binding free energy computation revealed a total of 7 macrocyclic compounds (HITS) demonstrating better binding affinity than DL001, towards mTOR. The consequent assessment of pharmacokinetic properties resulted in HITS with similar or better properties than the selective inhibitor, DL001. The HITS from this investigation could act as effective mTOR allosteric site inhibitors and serve as macrocyclic scaffolds for developing compounds targeting the dysregulated mTOR.
Collapse
Affiliation(s)
- Shraddha Parate
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea; Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden.
| | - Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea.
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea.
| |
Collapse
|
24
|
Xie Z, Meng Z, Yang X, Duan Y, Wang Q, Liao C. Factor XIa Inhibitors in Anticoagulation Therapy: Recent Advances and Perspectives. J Med Chem 2023; 66:5332-5363. [PMID: 37037122 DOI: 10.1021/acs.jmedchem.2c02130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Factor XIa (FXIa) in the intrinsic pathway of the coagulation process has been proven to be an effective and safe target for anticoagulant discovery with limited or no bleeding. Numerous small-molecule FXIa inhibitors (SMFIs) with various scaffolds have been identified in the early stages of drug discovery. They have served as the foundation for the recent discovery of additional promising SMFIs with improved potency, selectivity, and pharmacokinetic profiles, some of which have entered clinical trials for the treatment of thrombosis. After reviewing the coagulation process and structure of FXIa, this perspective discusses the rational or structure-based design, discovery, structure-activity relationships, and development of SMFIs disclosed in recent years. Strategies for identifying more selective and druggable SMFIs are provided, paving the way for the design and discovery of more useful SMFIs for anticoagulation therapy.
Collapse
Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Zhiwei Meng
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Qin Wang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, P. R. China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| |
Collapse
|
25
|
Song B, Guo X, Yang L, Yu H, Zong X, Liu X, Wang H, Xu Z, Lin Z, Yang W. Rhodium(III)-Catalyzed C-H/O 2 Dual Activation and Macrocyclization: Synthesis and Evaluation of Pyrido[2,1-a]isoindole Grafted Macrocyclic Inhibitors for Influenza H1N1. Angew Chem Int Ed Engl 2023; 62:e202218886. [PMID: 36788706 DOI: 10.1002/anie.202218886] [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: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The development of environment-friendly, step economic couplings to generate structurally diverse macrocyclic compounds is highly desirable but poses a marked challenge. Inspired by the C-H oxidation mechanism of cytochromes P450, an unprecedented and practical RhIII -catalyzed acylmethylation macrocyclization via C-H/O2 dual activation has been developed by us. The process of macrocyclization is facilitated by a synergic coordination from pyridine and ester group. Interestingly, the reaction mode derives from a three-component coupling which differs from established olefination and alkylation paths. Density functional theory (DFT) calculations and control experiments revealed the mechanism of this unique C-H/O2 dual activation. The newly achieved acylmethylation macrocyclic products and their derivatives showed a potent anti-H1N1 bioactivity, which may provide an opportunity for the discovery of novel anti-H1N1 macrocyclic leading compounds.
Collapse
Affiliation(s)
- Bichao Song
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueying Guo
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong, China
| | - Li Yang
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyue Yu
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlei Zong
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Xiujuan Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Hao Wang
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongliang Xu
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenyang Lin
- Department of Chemistry, The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong, China
| | - Weibo Yang
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210000, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| |
Collapse
|
26
|
Clément DA, Gelin M, Leseigneur C, Huteau V, Mondange L, Pons JL, Dussurget O, Lionne C, Labesse G, Pochet S. Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria. Eur J Med Chem 2023; 246:114941. [PMID: 36455355 DOI: 10.1016/j.ejmech.2022.114941] [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: 10/11/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Nicotinamide adenine dinucleotide kinases (NAD kinases) are essential and ubiquitous enzymes involved in the production of NADP(H) which is an essential cofactor in many metabolic pathways. Targeting NAD kinase (NADK), a rate limiting enzyme of NADP biosynthesis pathway, represents a new promising approach to treat bacterial infections. Previously, we have produced the first NADK inhibitor active against staphylococcal infection. From this linear di-adenosine derivative, namely NKI1, we designed macrocyclic analogues. Here, we describe the synthesis and evaluation of an original series of cyclic diadenosine derivatives as NADK inhibitors of two pathogenic bacteria, Listeria monocytogenes and Staphylococcus aureus. The nature and length of the link between the two adenosine units were examined leading to sub-micromolar inhibitors of NADK1 from L. monocytogenes, including its most potent in vitro inhibitor reported so far (with a 300-fold improvement compared to NKI1).
Collapse
Affiliation(s)
- David A Clément
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Clarisse Leseigneur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Valérie Huteau
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France
| | - Lou Mondange
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Jean-Luc Pons
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, F-75015, Paris, France
| | - Corinne Lionne
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), CNRS UMR5048, INSERM U1054, Université de Montpellier, 34090, Montpellier, France.
| | - Sylvie Pochet
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie et Biocatalyse, F-75015, Paris, France.
| |
Collapse
|
27
|
Amrhein JA, Beyett TS, Feng WW, Krämer A, Weckesser J, Schaeffner IK, Rana JK, Jänne PA, Eck MJ, Knapp S, Hanke T. Macrocyclization of Quinazoline-Based EGFR Inhibitors Leads to Exclusive Mutant Selectivity for EGFR L858R and Del19. J Med Chem 2022; 65:15679-15697. [PMID: 36384036 PMCID: PMC10410606 DOI: 10.1021/acs.jmedchem.2c01041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Activating mutations in the epidermal growth factor receptor (EGFR) are frequent oncogenic drivers of non-small-cell lung cancer (NSCLC). The most frequent alterations in EGFR are short in-frame deletions in exon 19 (Del19) and the missense mutation L858R, which both lead to increased activity and sensitization of NSCLC to EGFR inhibition. The first approved EGFR inhibitors used for first-line treatment of NSCLC, gefitinib and erlotinib, are quinazoline-based. However, both inhibitors have several known off-targets, and they also potently inhibit wild-type (WT) EGFR, resulting in side effects. Here, we applied a macrocyclic strategy on a quinazoline-based scaffold as a proof-of-concept study with the goal of increasing kinome-wide selectivity of this privileged inhibitor scaffold. Kinome-wide screens and SAR studies yielded 3f, a potent inhibitor for the most common EGFR mutation (EGFR Del19: 119 nM) with selectivity against the WT receptor (EGFR: >10 μM) and the kinome.
Collapse
Affiliation(s)
- Jennifer A. Amrhein
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| | - Tyler S. Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - William W. Feng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Department of Medical Oncology, Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| | - Janik Weckesser
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| | - Ilse K. Schaeffner
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jaimin K. Rana
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Pasi A. Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Department of Medical Oncology, Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Michael J. Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Max-von-Laue-Straße 9, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, 60438 Frankfurt, Germany
| |
Collapse
|
28
|
Design, synthesis and biological evaluation of novel macrocyclic derivatives bearing aniline pyrimidine scaffolds as EGFR-TKIs. Bioorg Med Chem Lett 2022; 75:128970. [PMID: 36064123 DOI: 10.1016/j.bmcl.2022.128970] [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: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022]
Abstract
Based on EGFR-TKI Osimertinib as lead compound, a series of novel macrocyclic derivatives bearing aniline pyrimidine scaffolds were designed and synthesized by macrocyclization. Their structures were identified by 1H NMR, 13C NMR, 19F NMR and HRMS. The pharmacological activities of the target compounds were tested and the preliminary structure-activity relationship was discussed. Among them, 17-membered ring compound H1 displayed the best inhibitory activities against EGFRL858R/T790M and EGFRd746-750/T790M with IC50 value of 2.92 nM and 0.34 nM, respectively. Exhilaratingly, 17-membered ring compound H7 possessed the most potent antiproliferative activity against BaF3-EGFRdel19/T790M cell lines (IC50 = 0.035 µm), which rivaled that of Osimertinib (IC50 = 0.033 µm).
Collapse
|
29
|
Diamanti E, Méndez M, Ross T, Kuttruff CA, Lefranc J, Klingler FM, von Nussbaum F, Jung M, Gehringer M. Frontiers in Medicinal Chemistry 2022 Goes Virtual. ChemMedChem 2022; 17:e202200419. [PMID: 36198574 DOI: 10.1002/cmdc.202200419] [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: 07/30/2022] [Indexed: 11/09/2022]
Abstract
The Frontiers in Medicinal Chemistry (FiMC) meeting, which represents the largest international medicinal chemistry conference in Germany, took place from March 14th to 16th 2022 in a fully virtual format. Organized by the Division of Medicinal Chemistry of the German Chemical Society (GDCh) together with the Division of Pharmaceutical & Medicinal Chemistry of the German Pharmaceutical Society (DPhG) and a "local" organization committee from the University of Freiburg headed by Manfred Jung, the meeting brought together 271 participants from around 20 countries. The program included 33 lectures by leading scientists from industry and academia as well as early career investigators. 67 posters were presented in two poster sessions and with over 20.000 poster abstract downloads. The general organization and the time-shift function were very much appreciated as demonstrated by almost 600 on-demand contents retrieved. The online format fitted perfectly to bring together medicinal chemists from academia and industry across the globe.
Collapse
Affiliation(s)
- Eleonora Diamanti
- HIPS - Helmholtz-Institut für Pharmazeutische Forschung Saarland, Campus E8 1, 66123, Saarbrücken, Germany
| | - María Méndez
- Sanofi R&D, Integrated Drug Discovery, Industriepark Höchst, Blg. G838, 65926, Frankfurt am Main, Germany
| | - Tatjana Ross
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Christian A Kuttruff
- Boehringer Ingelheim International GmbH, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
| | - Julien Lefranc
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | | | - Franz von Nussbaum
- NUVISAN Innovation Campus Berlin, NUVISAN ICB GmbH, Muellerstr. 178, 13353, Berlin, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg im Breisgau, Germany
| | - Matthias Gehringer
- University of Tübingen, Institute of Pharmaceutical Sciences, Pharmaceutical/Medicinal Chemistry Department, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| |
Collapse
|
30
|
Kurz CG, Preuss F, Tjaden A, Cusack M, Amrhein JA, Chatterjee D, Mathea S, Berger LM, Berger BT, Krämer A, Weller M, Weiss T, Müller S, Knapp S, Hanke T. Illuminating the Dark: Highly Selective Inhibition of Serine/Threonine Kinase 17A with Pyrazolo[1,5- a]pyrimidine-Based Macrocycles. J Med Chem 2022; 65:7799-7817. [PMID: 35608370 DOI: 10.1021/acs.jmedchem.2c00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serine/threonine kinase 17A (death-associated protein kinase-related apoptosis-inducing protein kinase 1─DRAK1) is a part of the death-associated protein kinase (DAPK) family and belongs to the so-called dark kinome. Thus, the current state of knowledge of the cellular function of DRAK1 and its involvement in pathophysiological processes is very limited. Recently, DRAK1 has been implicated in tumorigenesis of glioblastoma multiforme (GBM) and other cancers, but no selective inhibitors of DRAK1 are available yet. To this end, we optimized a pyrazolo[1,5-a]pyrimidine-based macrocyclic scaffold. Structure-guided optimization of this macrocyclic scaffold led to the development of CK156 (34), which displayed high in vitro potency (KD = 21 nM) and selectivity in kinomewide screens. Crystal structures demonstrated that CK156 (34) acts as a type I inhibitor. However, contrary to studies using genetic knockdown of DRAK1, we have seen the inhibition of cell growth of glioma cells in 2D and 3D culture only at low micromolar concentrations.
Collapse
Affiliation(s)
- Christian G Kurz
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Franziska Preuss
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Martin Cusack
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Jennifer Alisa Amrhein
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Deep Chatterjee
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Lena Marie Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Straße 42-44, Frankfurt 60596, Germany
| | - Michael Weller
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Tobias Weiss
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt 60438, Germany.,Structural Genomics Consortium, Buchman Institute for Molecular Life Science (BMLS), Max-von-Laue-Straße 15, Frankfurt 60438, Germany
| |
Collapse
|
31
|
Development of small macrocyclic kinase inhibitors. Future Med Chem 2022; 14:389-391. [PMID: 35029506 DOI: 10.4155/fmc-2021-0342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
32
|
Zheng S, Smit W, Spannenberg A, Tin S, de Vries JG. Synthesis of α-Keto Aldehydes via Selective Cu(I)-catalyzed Oxidation of α-Hydroxy Ketones. Chem Commun (Camb) 2022; 58:4639-4642. [DOI: 10.1039/d2cc00773h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient approach to synthesize α-keto aldehydes was established through selective oxidation of α-hydroxy ketones catalyzed by Cu(I) using oxygen as oxidant. A wide array of α-keto aldehydes was prepared...
Collapse
|
33
|
Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
Collapse
Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
| |
Collapse
|
34
|
Smith AN, Blackwell DJ, Knollmann BC, Johnston JN. Ring Size as an Independent Variable in Cyclooligomeric Depsipeptide Antiarrhythmic Activity. ACS Med Chem Lett 2021; 12:1942-1947. [PMID: 34917258 DOI: 10.1021/acsmedchemlett.1c00508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Hit-to-lead studies employ a variety of strategies to optimize binding to a target of interest. When a structure for the target is available, hypothesis-driven structure-activity relationships (SAR) are a powerful strategy for refining the pharmacophore to achieve robust binding and selectivity characteristics necessary to identify a lead compound. Recrafting the three-dimensional space occupied by a small molecule, optimization of hydrogen bond contacts, and enhancing local attractive interactions are traditional approaches in medicinal chemistry. Ring size, however, is rarely able to be leveraged as an independent variable because most hits lack the symmetry required for such a study. Our discovery that the cyclic oligomeric depsipeptide ent-verticilide inhibits mammalian cardiac ryanodine receptor calcium release channels with submicromolar potency provided an opportunity to explore ring size as a variable, independent of other structural or functional group changes. We report here that ring size can be a critical independent variable, suggesting that modest conformational changes alone can dramatically affect potency.
Collapse
Affiliation(s)
- Abigail N. Smith
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| | - Bjorn C. Knollmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| | - Jeffrey N. Johnston
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
35
|
Chirality-matched catalyst-controlled macrocyclization reactions. Proc Natl Acad Sci U S A 2021; 118:2113122118. [PMID: 34599107 DOI: 10.1073/pnas.2113122118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 11/18/2022] Open
Abstract
Macrocycles, formally defined as compounds that contain a ring with 12 or more atoms, continue to attract great interest due to their important applications in physical, pharmacological, and environmental sciences. In syntheses of macrocyclic compounds, promoting intramolecular over intermolecular reactions in the ring-closing step is often a key challenge. Furthermore, syntheses of macrocycles with stereogenic elements confer an additional challenge, while access to such macrocycles are of great interest. Herein, we report the remarkable effect peptide-based catalysts can have in promoting efficient macrocyclization reactions. We show that the chirality of the catalyst is essential for promoting favorable, matched transition-state relationships that favor macrocyclization of substrates with preexisting stereogenic elements; curiously, the chirality of the catalyst is essential for successful reactions, even though no new static (i.e., not "dynamic") stereogenic elements are created. Control experiments involving either achiral variants of the catalyst or the enantiomeric form of the catalyst fail to deliver the macrocycles in significant quantity in head-to-head comparisons. The generality of the phenomenon, demonstrated here with a number of substrates, stimulates analogies to enzymatic catalysts that produce naturally occurring macrocycles, presumably through related, catalyst-defined peripheral interactions with their acyclic substrates.
Collapse
|