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Faris A, Ibrahim IM, Hadni H, Elhallaoui M. High-throughput virtual screening of phenylpyrimidine derivatives as selective JAK3 antagonists using computational methods. J Biomol Struct Dyn 2024; 42:7574-7599. [PMID: 37539779 DOI: 10.1080/07391102.2023.2240413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
In this study, we used phenylpyrimidine derivatives with known biological activity against JAK3, a critical tyrosine kinase enzyme involved in signaling pathways, to find similar compounds as potential treatments for rheumatoid arthritis. These inhibitors inhibited JAK3 activity by forming a covalent bond with the Cys909 residue, which resulted in a strong inhibitory effect. Phenylpyrimidine is considered a promising therapeutic target. For pharmacophore modeling, 39 phenylpyrimidine derivatives with high pIC50 (Exp) values were chosen. The best pharmacophore model produced 28 molecules, and the five-point common pharmacophore hypothesis from P HASE (DHRRR_1) revealed the requirement for a hydrogen bond donor feature, a hydrophobic group feature, and three aromatic ring features for further design. The validation of the pharmacophore model phase was performed through 3D-QSAR using partial least squares (P LS). The 3D-QSAR study produced two successful models, an atom-based model (R2 = 0.95; Q2 = 0.67) and a field-based model (R2 = 0.93; Q2 = 0.76), which were used to predict the biological activity of new compounds. The pharmacophore model successfully distinguished between active and inactive medications, discovered potential JAK3 inhibitors, and demonstrated validity with a ROC of 0. 77. ADME-Tox was used to eliminate compounds that might have adverse effects. The best pharmacokinetics and affinity derivatives were selected for covalent docking. A molecular dynamics simulation of the selected molecules and the protein complex was performed to confirm the stability of the interaction with JAK3, whereas MM/GBSA simulations further confirmed their binding affinity. By using the principle of retrosynthesis, we were able to map out a pathway for synthesizing these potential drug candidates. This study has the potential to offer valuable and practical insights for optimizing novel derivatives of phenylpyrimidine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Hanine Hadni
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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2
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Qiu G, Yu L, Jia L, Cai Y, Chen Y, Jin J, Xu L, Zhu J. Identification of novel covalent JAK3 inhibitors through consensus scoring virtual screening: integration of common feature pharmacophore and covalent docking. Mol Divers 2024:10.1007/s11030-024-10918-5. [PMID: 39009908 DOI: 10.1007/s11030-024-10918-5] [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: 05/06/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Accumulated research strongly indicates that Janus kinase 3 (JAK3) is intricately involved in the initiation and advancement of a diverse range of human diseases, underscoring JAK3 as a promising target for therapeutic intervention. However, JAK3 shows significant homology with other JAK family isoforms, posing substantial challenges in the development of JAK3 inhibitors. To address these limitations, one strategy is to design selective covalent JAK3 inhibitors. Therefore, this study introduces a virtual screening approach that combines common feature pharmacophore modeling, covalent docking, and consensus scoring to identify novel inhibitors for JAK3. First, common feature pharmacophore models were constructed based on a selection of representative covalent JAK3 inhibitors. The optimal qualitative pharmacophore model proved highly effective in distinguishing active and inactive compounds. Second, 14 crystal structures of the JAK3-covalent inhibitor complex were chosen for the covalent docking studies. Following validation of the screening performance, 5TTU was identified as the most suitable candidate for screening potential JAK3 inhibitors due to its higher predictive accuracy. Finally, a virtual screening protocol based on consensus scoring was conducted, integrating pharmacophore mapping and covalent docking. This approach resulted in the discovery of multiple compounds with notable potential as effective JAK3 inhibitors. We hope that the developed virtual screening strategy will provide valuable guidance in the discovery of novel covalent JAK3 inhibitors.
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Affiliation(s)
- Genhong Qiu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Li Yu
- School of Inspection and Testing Certification, Changzhou Vocational Institute of Engineering, Changzhou, 213164, Jiangsu, China
| | - Lei Jia
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yanfei Cai
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yun Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jian Jin
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Jingyu Zhu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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Lv Y, Mi P, Babon JJ, Fan G, Qi J, Cao L, Lang J, Zhang J, Wang F, Kobe B. Small molecule drug discovery targeting the JAK-STAT pathway. Pharmacol Res 2024; 204:107217. [PMID: 38777110 DOI: 10.1016/j.phrs.2024.107217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
The Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway functions as a central hub for transmitting signals from more than 50 cytokines, playing a pivotal role in maintaining hematopoiesis, immune balance, and tissue homeostasis. Dysregulation of this pathway has been implicated in various diseases, including immunodeficiency, autoimmune conditions, hematological disorders, and certain cancers. Proteins within this pathway have emerged as effective therapeutic targets for managing these conditions, with various approaches developed to modulate key nodes in the signaling process, spanning from receptor engagement to transcription factor activation. Following the success of JAK inhibitors such as tofacitinib for RA treatment and ruxolitinib for managing primary myelofibrosis, the pharmaceutical industry has obtained approvals for over 10 small molecule drugs targeting the JAK-STAT pathway and many more are at various stages of clinical trials. In this review, we consolidate key strategies employed in drug discovery efforts targeting this pathway, with the aim of contributing to the collective understanding of small molecule interventions in the context of JAK-STAT signaling. We aspire that our endeavors will contribute to advancing the development of innovative and efficacious treatments for a range of diseases linked to this pathway dysregulation.
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Affiliation(s)
- You Lv
- Center for Molecular Biosciences and Non-Communicable Diseases Research, Xi'an University of Science and Technology, Xi'an, Shaanxi 710054, China; Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi 710026, China
| | - Pengbing Mi
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Guohuang Fan
- Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Longxing Cao
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Jiajia Lang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jin Zhang
- Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi 710026, China
| | - Faming Wang
- Center for Molecular Biosciences and Non-Communicable Diseases Research, Xi'an University of Science and Technology, Xi'an, Shaanxi 710054, China.
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia.
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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Ahmad F, Sachdeva P, Sachdeva B, Singh G, Soni H, Tandon S, Rafeeq MM, Alam MZ, Baeissa HM, Khalid M. Dioxinodehydroeckol: A Potential Neuroprotective Marine Compound Identified by In Silico Screening for the Treatment and Management of Multiple Brain Disorders. Mol Biotechnol 2024; 66:663-686. [PMID: 36513873 DOI: 10.1007/s12033-022-00629-3] [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: 06/07/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Glioblastoma multiforme (GBM), Amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD) are some of the most prevalent neurodegenerative disorders in humans. Even after a variety of advanced therapies, prognosis of all these disorders is not favorable, with survival rates of 14-20 months only. To further improve the prognosis of these disorders, it is imperative to discover new compounds which will target effector proteins involved in these disorders. In this study, we have focused on in silico screening of marine compounds against multiple target proteins involved in AD, GBM, ALS, and PD. Fifty marine-origin compounds were selected from literature, out of which, thirty compounds passed ADMET parameters. Ligand docking was performed after ADMET analysis for AD, GBM, ALS, and PD-associated proteins in which four protein targets Keap1, Ephrin A2, JAK3 Kinase domain, and METTL3-METTL14 N6-methyladenosine methyltransferase (MTA70) were found to be binding strongly with the screened compound Dioxinodehydroeckol (DHE). Molecular dynamics simulations were performed at 100 ns with triplicate runs to validate the docking score and assess the dynamics of DHE interactions with each target protein. The results indicated Dioxinodehydroeckol, a novel marine compound, to be a putative inhibitor among all the screened molecules, which might be effective against multiple target proteins involved in neurological disorders, requiring further in vitro and in vivo validations.
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Affiliation(s)
- Faizan Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard University, Delhi, India.
| | - Punya Sachdeva
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, Uttar Pradesh, India
| | - Bhuvi Sachdeva
- Department of Physics and Astrophysics, University of Delhi, Delhi, India
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, CCRAS, Ministry of AYUSH, Jhansi, India
- Kusuma School of Biological Sciences, India Institute of Technology, Delhi, India
| | - Hemant Soni
- Section of Microbiology, Central Ayurveda Research Institute, CCRAS, Ministry of AYUSH, Jhansi, India
| | - Smriti Tandon
- Section of Microbiology, Central Ayurveda Research Institute, CCRAS, Ministry of AYUSH, Jhansi, India
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Mohammad Zubair Alam
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanadi M Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj, 11942, Saudi Arabia
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Faris A, Cacciatore I, Alnajjar R, Hanine H, Aouidate A, Mothana RA, Alanzi AR, Elhallaoui M. Revealing innovative JAK1 and JAK3 inhibitors: a comprehensive study utilizing QSAR, 3D-Pharmacophore screening, molecular docking, molecular dynamics, and MM/GBSA analyses. Front Mol Biosci 2024; 11:1348277. [PMID: 38516192 PMCID: PMC10956358 DOI: 10.3389/fmolb.2024.1348277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
The heterocycle compounds, with their diverse functionalities, are particularly effective in inhibiting Janus kinases (JAKs). Therefore, it is crucial to identify the correlation between their complex structures and biological activities for the development of new drugs for the treatment of rheumatoid arthritis (RA) and cancer. In this study, a diverse set of 28 heterocyclic compounds selective for JAK1 and JAK3 was employed to construct quantitative structure-activity relationship (QSAR) models using multiple linear regression (MLR). Artificial neural network (ANN) models were employed in the development of QSAR models. The robustness and stability of the models were assessed through internal and external methodologies, including the domain of applicability (DoA). The molecular descriptors incorporated into the model exhibited a satisfactory correlation with the receptor-ligand complex structures of JAKs observed in X-ray crystallography, making the model interpretable and predictive. Furthermore, pharmacophore models ADRRR and ADHRR were designed for each JAK1 and JAK3, proving effective in discriminating between active compounds and decoys. Both models demonstrated good performance in identifying new compounds, with an ROC of 0.83 for the ADRRR model and an ROC of 0.75 for the ADHRR model. Using a pharmacophore model, the most promising compounds were selected based on their strong affinity compared to the most active compounds in the studied series each JAK1 and JAK3. Notably, the pharmacokinetic, physicochemical properties, and biological activities of the selected compounds (As compounds ZINC79189223 and ZINC66252348) were found to be consistent with their therapeutic effects in RA, owing to their non-toxic, cholinergic nature, absence of P-glycoprotein, high gastrointestinal absorption, and ability to penetrate the blood-brain barrier. Furthermore, ADMET properties were assessed, and molecular dynamics and MM/GBSA analysis revealed stability in these molecules.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ivana Cacciatore
- Department of Pharmacy, University ‘G. d’Annunzio’ of Chieti-Pescara, Chieti, Italy
| | - Radwan Alnajjar
- CADD Unit, PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi, Libya
| | - Hadni Hanine
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Adnane Aouidate
- School of Applied Sciences of Ait Melloul, Ibn Zohr University, Fez, Morocco
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah R. Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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7
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Cheke RS, Kharkar PS. Covalent inhibitors: An ambitious approach for the discovery of newer oncotherapeutics. Drug Dev Res 2024; 85:e22132. [PMID: 38054744 DOI: 10.1002/ddr.22132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/04/2023] [Accepted: 10/29/2023] [Indexed: 12/07/2023]
Abstract
Covalent inhibitors have been used to treat several diseases for over a century. However, strategic approaches for the rational design of covalent drugs have taken a definitive shape in recent times. Since the first appearance of covalent inhibitors in the late 18th century, the field has grown tremendously and around 30% of marketed drugs are covalent inhibitors especially, for oncology indications. However, the off-target toxicity and safety concerns can be significant issues related to the covalent drugs. Covalent kinase inhibitor (CKI) targeted oncotherapeutics has advanced dramatically over the last two decades since the discovery of afatinib (Gilotrif®), an EGFR inhibitor. Since then, US FDA has approved 10 CKIs for diverse cancer targets. The present review broadly summarizes the ongoing development in the discovery of newer CKIs from 2016 till the end of 2022. We believe that these efforts will assist the modern medicinal chemist actively working in the field of CKI discovery for varied indications.
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Affiliation(s)
- Rameshwar S Cheke
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
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8
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Ryabukhin SV, Bondarenko DV, Trofymchuk SA, Lega DA, Volochnyuk DM. Aza-Heterocyclic Building Blocks with In-Ring CF 2 -Fragment. CHEM REC 2024; 24:e202300283. [PMID: 37873869 DOI: 10.1002/tcr.202300283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Modern organic chemistry is a titan supporting and reinforcing pharmaceutical, agricultural, food and material science products. Over the past decades, the organic compounds market has been evolving to meet all the research demands. In this regard, medicinal chemistry is especially dependent on available chemical space as subtle tuning of the molecule structure is required to create a drug with relevant physicochemical properties and a remarkable activity profile. The recent rapid evolution of synthetic methodology to deploy fluorine has brought fluorinated compounds to the spotlight of MedChem community. And now unique properties of fluorine still keep fascinating more and more as its justified installation into a molecular framework has a beneficial impact on membrane permeability, lipophilicity, metabolic stability, pharmacokinetic properties, conformation, pKa , etc. The backward influence of medicinal chemistry on organic synthesis has also changed the landscape of the latter towards new fluorinated topologies as well. Such complex relationships create a flexible and ever-changing ecosystem. Given that MedChem investigations strongly lean on the ability to reach suitable building blocks and the existence of reliable synthetic methods in this review we collected advances in the chemistry of respectful, but still enigmatic gem-difluorinated aza-heterocyclic building blocks.
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Affiliation(s)
- S V Ryabukhin
- Enamine Ltd., 78 Winston Churchill str., 02094, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska str., 01033, Kyiv, Ukraine
- Institute of Organic Chemistry of the, National Academy of Sciences of Ukraine, 5 Akademik Kukhar str., 02094, Kyiv, Ukraine
| | - D V Bondarenko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska str., 01033, Kyiv, Ukraine
| | - S A Trofymchuk
- Enamine Ltd., 78 Winston Churchill str., 02094, Kyiv, Ukraine
- Institute of Organic Chemistry of the, National Academy of Sciences of Ukraine, 5 Akademik Kukhar str., 02094, Kyiv, Ukraine
| | - D A Lega
- Enamine Ltd., 78 Winston Churchill str., 02094, Kyiv, Ukraine
- National University of Pharmacy of the Ministry of Health of Ukraine, 53 Pushkinska str., 61002, Kharkiv, Ukraine
| | - D M Volochnyuk
- Enamine Ltd., 78 Winston Churchill str., 02094, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska str., 01033, Kyiv, Ukraine
- Institute of Organic Chemistry of the, National Academy of Sciences of Ukraine, 5 Akademik Kukhar str., 02094, Kyiv, Ukraine
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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Zheng Y, Li J, Qi C, Wu W, Jiang H. Rapid assembly of structurally diverse cyanamides and disulfanes via base-mediated aminoalkylation of aryl thiourea. RSC Adv 2023; 13:33047-33052. [PMID: 37954416 PMCID: PMC10632727 DOI: 10.1039/d3ra06051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
A general method for the preparation of cyanamides and disulfanes from aryl thiourea and halide through a base-mediated strategy is described. Mercaptan and N-aryl cyanamide are the key intermediates in the reaction. The current method is convenient, eco-friendly, and has high yields for the synthesis of substituted cyanamide and functional disulfanes in a one-pot procedure from readily available starting materials.
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Affiliation(s)
- Yongpeng Zheng
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 P. R. China
| | - Jianxiao Li
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 P. R. China
| | - Chaorong Qi
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 P. R. China
| | - Wanqing Wu
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 P. R. China
| | - Huanfeng Jiang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 P. R. China
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Faris A, Cacciatore I, Ibrahim IM, Al Mughram MH, Hadni H, Tabti K, Elhallaoui M. In silico computational drug discovery: a Monte Carlo approach for developing a novel JAK3 inhibitors. J Biomol Struct Dyn 2023:1-23. [PMID: 37861428 DOI: 10.1080/07391102.2023.2270709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023]
Abstract
Inhibition of Janus kinase 3 (JAK3), a member of the JAK family of tyrosine kinases, remains an essential area of research for developing treatments for autoimmune diseases, particularly cancer and rheumatoid arthritis. The recent discovery of a new JAK3 protein, PDB ID: 4Z16, offers exciting possibilities for developing inhibitors capable of forming a covalent bond with the Cys909 residue, thereby contributing to JAK3 inhibition. A powerful prediction model was constructed and validated using Monte Carlo methods, employing various internal and external techniques. This approach resulted in the prediction of eleven new molecules, which were subsequently filtered to identify six compounds exhibiting potent pIC50 values. These candidates were then subjected to ADMET analysis, molecular docking (including reversible-reversible docking with tofacitinib, an FDA-approved drug, and reversible-irreversible docking for the newly designed compounds), molecular dynamics (MD) analysis for 300 ns, and calculation of free binding energy. The results suggested that these compounds hold promise as JAK3 inhibitors. In summary, the new compounds have exhibited favorable outcomes compared to other compounds across various modeling approaches. The collective findings from these investigations provide valuable insights into the potential therapeutic applications of covalent JAK3 inhibitors, offering a promising direction for the development of novel treatments for autoimmune disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ivana Cacciatore
- Department of Pharmacy, University 'G. d'Annunzio' of Chieti-Pescara, Italy
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohammed H Al Mughram
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Hanine Hadni
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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12
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Xu WY, Xu ZY, Zhang ZK, Gong TJ, Fu Y. Tunable Synthesis of Monofluoroalkenes and Gem-Difluoroalkenes via Solvent-Controlled Rhodium-Catalyzed Arylation of 1-Bromo-2,2-difluoroethylene. Angew Chem Int Ed Engl 2023; 62:e202310125. [PMID: 37589202 DOI: 10.1002/anie.202310125] [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: 07/16/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Divergent synthesis of fluorine-containing scaffolds starting from a suite of raw materials is an intriguing topic. Herein, we report the solvent-controlled rhodium-catalyzed tunable arylation of 1-bromo-2,2-difluoroethylene. The selection of the reaction solvents provides switchable defluorinated or debrominated arylation from readily available feedstock resources (both arylboronic acids/esters and 1-bromo-2,2-difluoroethylene are commercially available). This switch is feasible because of the difference in coordination ability between the solvent (CH2 Cl2 or CH3 CN) and the rhodium center, resulting in different olefin insertion. This protocol allows the convenient synthesis of monofluoroalkenes and gem-difluoroalkenes, both of which are important scaffolds in the fields of medicine and materials. Moreover, this newly developed solvent-regulated reaction system can be applied to the site-selective dechlorinated arylation of trichloroethylene. Overall, this study provides a useful strategy for the divergent synthesis of fluorine-containing scaffolds and provides insight into the importance of solvent selection in catalytic reactions.
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Affiliation(s)
- Wen-Yan Xu
- Key Laboratory of Precision and Intelligent Chemistry, iChEM, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, 230026, Hefei, China
| | - Zhe-Yuan Xu
- Key Laboratory of Precision and Intelligent Chemistry, iChEM, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, 230026, Hefei, China
| | - Ze-Kuan Zhang
- Key Laboratory of Precision and Intelligent Chemistry, iChEM, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, 230026, Hefei, China
| | - Tian-Jun Gong
- Key Laboratory of Precision and Intelligent Chemistry, iChEM, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, 230026, Hefei, China
| | - Yao Fu
- Key Laboratory of Precision and Intelligent Chemistry, iChEM, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, 230026, Hefei, China
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13
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Abdoli M, Krasniqi V, Bonardi A, Gütschow M, Supuran CT, Žalubovskis R. 4-Cyanamido-substituted benzenesulfonamides act as dual carbonic anhydrase and cathepsin inhibitors. Bioorg Chem 2023; 139:106725. [PMID: 37442043 DOI: 10.1016/j.bioorg.2023.106725] [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: 05/17/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]
Abstract
A set of novel N-cyano-N-substituted 4-aminobenzenesulfonamide derivatives were synthesized and investigated for their inhibitory activity against four cytosolic carbonic anhydrase (CA, EC 4.2.1.1) isoforms (hCA I, II, VII and XIII) and two cathepsins (S and B). N-alkyl/benzyl-substituted derivatives were revealed to be very potent inhibitors against brain-associated hCA VII, but inactive against both cathepsins. On the other hand, N-acyl-substituted derivatives displayed significant inhibitory activities against cathepsin S, but only moderate to poor inhibitory potency against hCA VII. Both hCA VII and cathepsin S have recently been validated as therapeutic targets in neuropathic pain. This study provided an excellent starting point for further structural optimization of this class of bifunctional compounds to enhance their inhibitory activity and selectivity against hCA VII and cathepsin S and to achieve new compounds with an attractive dual mechanism of action as anti-neuropathic agents.
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Affiliation(s)
- Morteza Abdoli
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
| | - Vesa Krasniqi
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Alessandro Bonardi
- Neurofarba Department, Universita Degli Studi di Firenze, Florence, Italy
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry University of Bonn, An der Immenburg 4, 53121 Bonn, Germany.
| | - Claudiu T Supuran
- Neurofarba Department, Universita Degli Studi di Firenze, Florence, Italy.
| | - Raivis Žalubovskis
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia; Latvian Institute of Organic Synthesis, Riga, Latvia.
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14
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Mishra A, Cong X, Nishiura M, Hou Z. Enantioselective Synthesis of 1-Aminoindanes via [3 + 2] Annulation of Aldimines with Alkenes by Scandium-Catalyzed C-H Activation. J Am Chem Soc 2023; 145:17468-17477. [PMID: 37504799 DOI: 10.1021/jacs.3c06482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Multisubstituted chiral 1-aminoindanes are important components in many pharmaceuticals and bioactive molecules. Therefore, the development of efficient and selective methods for the synthesis of chiral 1-aminoindanes is of great interest and importance. In principle, the asymmetric [3 + 2] annulation of aldimines with alkenes through C-H activation is the most atom-efficient and straightforward route for the construction of chiral 1-aminoindanes, but such a transformation has remained undeveloped to date probably due to the lack of suitable catalysts. Herein, we report for the first time the enantioselective [3 + 2] annulation of a wide range of aromatic aldimines and alkenes via ortho-C(sp2)-H activation by chiral half-sandwich scandium catalysts, which provides a straightforward route for the synthesis of multisubstituted chiral 1-aminoindanes. This protocol features 100% atom-efficiency, broad functional group compatibility, and high regio-, diastereo-, and enantioselectivity (up to >19:1 dr and 99:1 er). Remarkably, by fine-tuning the sterics of the chiral ligand around the catalyst metal center, the diastereodivergent asymmetric [3 + 2] annulation of aldimines and styrenes has been achieved with a high level of diastereo- and enantioselectivity, offering an efficient method for the synthesis of both the trans and cis diastereomers of a novel class of chiral 1-aminoindane derivatives containing two contiguous stereocenters from the same set of starting materials. Moreover, the asymmetric [3 + 2] annulation of aldimines with aliphatic α-olefins, norbornene, and 1,3-dienes has also been achieved.
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Affiliation(s)
- Aniket Mishra
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Xuefeng Cong
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Masayoshi Nishiura
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Zhaomin Hou
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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15
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Hartung IV, Rudolph J, Mader MM, Mulder MPC, Workman P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J Med Chem 2023; 66:9297-9312. [PMID: 37403870 PMCID: PMC10388296 DOI: 10.1021/acs.jmedchem.3c00550] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 07/06/2023]
Abstract
Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Molecules with such modes of action have a large potential not only as drugs but also as chemical probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-molecule probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and molecular glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compounds.
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Affiliation(s)
- Ingo V. Hartung
- Medicinal
Chemistry, Global Research & Development, Merck Healthcare KGaA, 64293 Darmstadt, Germany
| | - Joachim Rudolph
- Discovery
Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Mary M. Mader
- Molecular
Innovation, Indiana Biosciences Research
Institute, Indianapolis, Indiana 64202, United States
| | - Monique P. C. Mulder
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul Workman
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London, Sutton SM2 5NG, United Kingdom
- Chemical
Probes Portal, https://www.chemicalprobes.org/
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16
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Fruergaard MU, Nielsen CJF, Kjeldsen CR, Iversen L, Andersen JL, Nissen P. Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases. Life Sci Alliance 2023; 6:e202201425. [PMID: 36806093 PMCID: PMC9941302 DOI: 10.26508/lsa.202201425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
The p90 ribosomal S6 kinases (RSKs) contain two distinct catalytic kinase domains, the N-terminal and C-terminal kinase domains (NTKD and CTKD, respectively). The activation of CTKD is regulated by phosphorylation by extracellular signal-regulated kinase (ERK1/2) and an autoinhibitory αL helix. Through a mutational series in vitro of the RSK CTKDs, we found a complex mechanism lifting autoinhibition that led us to design constitutively active RSK CTKDs. These are based on a phosphomimetic mutation and a C-terminal truncation (e.g., RSK2 T577E D694*) where a high activity in absence of ERK phosphorylation is obtained. Using these constructs, we characterize IC50 values of ATP-competitive inhibitors and provide a setup for determining specificity constants (kinact/Ki) of covalent CTKD inhibitors.
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Affiliation(s)
- Marlene Uglebjerg Fruergaard
- Department of Molecular Biology and Genetics, DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, Denmark
| | - Christine Juul Fælled Nielsen
- Department of Molecular Biology and Genetics, DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, Denmark
| | - Cecilia Rosada Kjeldsen
- Department of Clinical Medicine- The Department of Dermatology and Venereology, Aarhus N, Denmark
| | - Lars Iversen
- Department of Clinical Medicine- The Department of Dermatology and Venereology, Aarhus N, Denmark
| | | | - Poul Nissen
- Department of Molecular Biology and Genetics, DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, Denmark
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17
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Bonatto V, Lameiro RF, Rocho FR, Lameira J, Leitão A, Montanari CA. Nitriles: an attractive approach to the development of covalent inhibitors. RSC Med Chem 2023; 14:201-217. [PMID: 36846367 PMCID: PMC9945868 DOI: 10.1039/d2md00204c] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Nitriles have broad applications in medicinal chemistry, with more than 60 small molecule drugs on the market containing the cyano functional group. In addition to the well-known noncovalent interactions that nitriles can perform with macromolecular targets, they are also known to improve drug candidates' pharmacokinetic profiles. Moreover, the cyano group can be used as an electrophilic warhead to covalently bind an inhibitor to a target of interest, forming a covalent adduct, a strategy that can present benefits over noncovalent inhibitors. This approach has gained much notoriety in recent years, mainly with diabetes and COVID-19-approved drugs. Nevertheless, the application of nitriles in covalent ligands is not restricted to it being the reactive center, as it can also be employed to convert irreversible inhibitors into reversible ones, a promising strategy for kinase inhibition and protein degradation. In this review, we introduce and discuss the roles of the cyano group in covalent inhibitors, how to tune its reactivity and the possibility of achieving selectivity only by replacing the warhead. Finally, we provide an overview of nitrile-based covalent compounds in approved drugs and inhibitors recently described in the literature.
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Affiliation(s)
- Vinícius Bonatto
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Rafael F Lameiro
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Fernanda R Rocho
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Jerônimo Lameira
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
- Institute of Biological Science, Federal University of Pará Rua Augusto Correa S/N Belém PA Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
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18
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Bum-Erdene K, Yeh IJ, Gonzalez-Gutierrez G, Ghozayel MK, Pollok K, Meroueh SO. Small-Molecule Cyanamide Pan-TEAD·YAP1 Covalent Antagonists. J Med Chem 2023; 66:266-284. [PMID: 36562717 DOI: 10.1021/acs.jmedchem.2c01189] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcriptional enhanced associate domains (TEADs) are transcription factors that bind to cotranscriptional activators like the yes-associated protein (YAP) or its paralog transcriptional coactivator with a PDZ-binding motif (TAZ). TEAD·YAP/TAZ target genes are involved in tissue and immune homeostasis, organ size control, tumor growth, and metastasis. Here, we report isoindoline and octahydroisoindole small molecules with a cyanamide electrophile that forms a covalent bond with a conserved cysteine in the TEAD palmitate-binding cavity. Time- and concentration-dependent studies against TEAD1-4 yielded second-order rate constants kinact/KI greater than 100 M-1 s-1. Compounds inhibited YAP1 binding to TEADs with submicromolar IC50 values. Cocrystal structures with TEAD2 enabled structure-activity relationship studies. In mammalian cells, compounds suppressed CTGF mRNA levels and inhibited TEAD1-4 transcriptional activity with submicromolar IC50 values. Inhibition of TEAD binding to YAP1 in mammalian cells was also observed. Several compounds inhibited the cell viability of sarcoma, hepatocellular carcinoma, glioblastoma, and breast cancer cells with single-digit micromolar IC50 values.
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Affiliation(s)
- Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - I-Ju Yeh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, Indiana 47405, United States
| | - Mona K Ghozayel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Karen Pollok
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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19
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Jain NK, Tailang M, Jain HK, Chandrasekaran B, Sahoo BM, Subramanian A, Thangavel N, Aldahish A, Chidambaram K, Alagusundaram M, Kumar S, Selvam P. Therapeutic implications of current Janus kinase inhibitors as anti-COVID agents: A review. Front Pharmacol 2023; 14:1135145. [PMID: 37021053 PMCID: PMC10067607 DOI: 10.3389/fphar.2023.1135145] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/09/2023] [Indexed: 04/07/2023] Open
Abstract
Severe cases of COVID-19 are characterized by hyperinflammation induced by cytokine storm, ARDS leading to multiorgan failure and death. JAK-STAT signaling has been implicated in immunopathogenesis of COVID-19 infection under different stages such as viral entry, escaping innate immunity, replication, and subsequent inflammatory processes. Prompted by this fact and prior utilization as an immunomodulatory agent for several autoimmune, allergic, and inflammatory conditions, Jakinibs have been recognized as validated small molecules targeting the rapid release of proinflammatory cytokines, primarily IL-6, and GM-CSF. Various clinical trials are under investigation to evaluate Jakinibs as potential candidates for treating COVID-19. Till date, there is only one small molecule Jakinib known as baricitinib has received FDA-approval as a standalone immunomodulatory agent in treating critical COVID-19 patients. Though various meta-analyses have confirmed and validated the safety and efficacy of Jakinibs, further studies are required to understand the elaborated pathogenesis of COVID-19, duration of Jakinib treatment, and assess the combination therapeutic strategies. In this review, we highlighted JAK-STAT signalling in the pathogenesis of COVID-19 and clinically approved Jakinibs. Moreover, this review described substantially the promising use of Jakinibs and discussed their limitations in the context of COVID-19 therapy. Hence, this review article provides a concise, yet significant insight into the therapeutic implications of Jakinibs as potential anti-COVID agents which opens up a new horizon in the treatment of COVID-19, effectively.
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Affiliation(s)
- Nem Kumar Jain
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Mukul Tailang
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Hemant Kumar Jain
- Department of General Medicine, Government Medical College, Datia, Madhya Pradesh, India
| | - Balakumar Chandrasekaran
- Faculty of Pharmacy, Philadelphia University, Amman, Jordan
- *Correspondence: Balakumar Chandrasekaran, ; Palani Selvam,
| | - Biswa Mohan Sahoo
- Roland Institute of Pharmaceutical Sciences, Berhampur, Odisha, India
| | - Anandhalakshmi Subramanian
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Neelaveni Thangavel
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Afaf Aldahish
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - M. Alagusundaram
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
| | - Santosh Kumar
- School of Sciences, ITM University, Gwalior, Madhya Pradesh, India
| | - Palani Selvam
- School of Medicine, College of Medicine and Health Sciences, Jijiga University, Jijiga, Ethiopia
- *Correspondence: Balakumar Chandrasekaran, ; Palani Selvam,
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20
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Wang X, Ji Z, Liu J, Wang B, Jin H, Zhang L. Advances in Organocatalytic Asymmetric Reactions Involving Thioesters. ACTA CHIMICA SINICA 2023. [DOI: 10.6023/a22100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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21
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Yang L, Zhang K, Xu M, Xie Y, Meng X, Wang H, Wei D. Mechanism-Guided Computational Design of ω-Transaminase by Reprograming of High-Energy-Barrier Steps. Angew Chem Int Ed Engl 2022; 61:e202212555. [PMID: 36300723 DOI: 10.1002/anie.202212555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 11/06/2022]
Abstract
ω-Transaminases (ω-TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism-guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high-energy-barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate-limiting transition state with the aid of the Rosetta design. The 14 top-ranked variants showed 16.9-143-fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660-fold increase in kcat /Km and a 1.5-26.8-fold increase in turnover number (TON) towards various indanone derivatives.
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Affiliation(s)
- Lin Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Kaiyue Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Meng Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Youyu Xie
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
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22
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Henry SP, Liosi ME, Ippolito JA, Menges F, Newton AS, Schlessinger J, Jorgensen WL. Covalent Modification of the JH2 Domain of Janus Kinase 2. ACS Med Chem Lett 2022; 13:1819-1826. [PMID: 36385940 PMCID: PMC9661697 DOI: 10.1021/acsmedchemlett.2c00414] [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: 09/09/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Probe molecules that covalently modify the JAK2 pseudokinase domain (JH2) are reported. Selective targeting of JH2 domains over the kinase (JH1) domains is a necessary feature for ligands intended to evaluate JH2 domains as therapeutic targets. The JH2 domains of three Janus kinases (JAK1, JAK2, and TYK2) possess a cysteine residue in the catalytic loop that does not occur in their JH1 domains. Starting from a non-selective kinase binding molecule, computer-aided design directed attachment of substituents terminating in acrylamide warheads to modify Cys675 of JAK2 JH2. Successful covalent attachment was demonstrated first through observation of enhanced binding with increasing incubation time in fluorescence polarization experiments. Covalent binding also increased selectivity to as much as ca. 30-fold for binding the JAK2 JH2 domain over the JH1 domain after a 20-h incubation. Covalency was confirmed through HPLC electrospray quadrupole time-of-flight HRMS experiments, which revealed the expected mass shifts.
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Affiliation(s)
- Sean P. Henry
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maria-Elena Liosi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Fabian Menges
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana S. Newton
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph Schlessinger
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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23
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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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24
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Xu WY, Li YJ, Gong TJ, Fu Y. Synthesis of gem-Difluorinated 1,3-Dienes via Synergistic Cu/Pd-Catalyzed Borodifluorovinylation of Alkynes. Org Lett 2022; 24:5884-5889. [PMID: 35926100 DOI: 10.1021/acs.orglett.2c01875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
gem-Difluoroalkenes (=CF2), which normally act as metabolically stable bioisosteres for carbonyl groups (C═O), are widely applied in agrochemicals and pharmaceuticals and are also used as building blocks in organic synthesis. Herein, an example of Cu/Pd-catalyzed borodifluorovinylation was achieved using alkynes, difluoroethylene bromide, and B2pin2 as chemical feedstocks, providing the corresponding conjugated gem-difluoroalkene scaffold with good functional group compatibility. Moreover, an array of fluorinated synthons can be obtained through further transformations.
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Affiliation(s)
- Wen-Yan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yu-Jie Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Tian-Jun Gong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.,Institute of Energy, Hefei Comprehensive National Science Center, Hefei, Anhui 230031, People's Republic of China
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25
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Li S, Si H, Song X, Lei C, He X, Wang J, Liu Y, Zhou Y, Song JG, Peng L, Tang X, Chan S, Ren X, Tu Z, Li Z, Wang Z, Zhang Z, Ding K. Discovery of Hexahydrofuro[3,2- b]furans as New Kinase-Selective and Orally Bioavailable JAK3 Inhibitors for the Treatment of Leukemia Harboring a JAK3 Activating Mutant. J Med Chem 2022; 65:10674-10690. [PMID: 35860875 DOI: 10.1021/acs.jmedchem.2c00922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Janus kinase 3 (JAK3) is a potential target for the treatment of hematological malignancies. Herein, we report the discovery of a series of new orally bioavailable irreversible JAK3 kinase inhibitors. The representative compound 12n potently inhibited JAK3 kinase activity with an IC50 value of 1.2 nM and was more than 900-fold selective over JAK1, JAK2, and Tyk2. Cell-based assays revealed that 12n significantly suppressed phosphorylation of JAK3 and the downstream effectors STAT3/5 and also robustly restrained proliferation of BaF3 cells transfected with JAK3M511I activating mutation and human leukemia U937 cells harboring JAK3M511I with IC50 values of 22.9 and 20.2 nM, respectively. More importantly, 12n showed reasonable pharmacokinetic (PK) properties, and oral administration of 12n at a dose of 50 mg/kg twice daily led to tumor regression in a U937 cell inoculated xenograft mouse model. Thus, 12n represents a promising lead compound for further optimization to discover new therapeutic agents for hematological malignancies.
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Affiliation(s)
- Shan Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Hongfei Si
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Chong Lei
- State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
| | - Xiaoqiang He
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jie Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yiling Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jian-Guo Song
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Lijie Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xia Tang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Shingpan Chan
- Guangzhou Lixin Pharmaceuticals, Guangzhou 510530, China
| | - Xiaomei Ren
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhengchao Tu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhen Wang
- State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.,State Key Laboratory of Bioorganic Chemistry and Natural Products, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Lingling Road, Shanghai 200032, China.,The First Affiliated Hospital (Huaqiao Hospital), Jinan University, #601 Huangpu Avenue West, Guangzhou 510632, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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26
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Su W, Chen Z, Liu M, He R, Liu C, Li R, Gao M, Zheng M, Tu Z, Zhang Z, Xu T. Design, synthesis and structure-activity relationship studies of pyrido[2,3-d]pyrimidin-7-ones as potent Janus Kinase 3 (JAK3) covalent inhibitors. Bioorg Med Chem Lett 2022; 64:128680. [PMID: 35306167 DOI: 10.1016/j.bmcl.2022.128680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/21/2022] [Accepted: 03/14/2022] [Indexed: 11/19/2022]
Abstract
Aberrantly activated Janus kinase 3 (JAK3) has been constantly detected in various immune disorders and hematopoietic cancers, suggesting its potential of being an attractive therapeutic target for these indications. Clinical benefits of drugs selectively targeting JAK3 versus pan-JAK inhibitors remain unclear. In this study, we report the design and synthesis of a new series of JAK3 covalent inhibitors with a pyrido[2,3-d]pyrimidin-7-one scaffold. After the extensive SAR study, compound 10f emerged to be the most potent JAK3 inhibitor with an IC50 value of 2.0 nM. It showed excellent selectively proliferation inhibitory activity against U937 cells harboring JAK3 M511I mutation, while remained weakly active to the other tested cancer cells. Compound 10f also dose-dependently inhibited the phosphorylation of JAK3 and its downstream signal STAT5 in U937 cells. Taken together, 10f may serve as a promising tool molecule for treating cancers with aberrantly activated JAK3.
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Affiliation(s)
- Wenhong Su
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Zhiwen Chen
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Meiying Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Rui He
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chaoyi Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Rui Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingshan Gao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhengchao Tu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Tianfeng Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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27
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Design of Rational JAK3 Inhibitors Based on the Parent Core Structure of 1,7-Dihydro-Dipyrrolo [2,3-b:3',2'-e] Pyridine. Int J Mol Sci 2022; 23:ijms23105437. [PMID: 35628248 PMCID: PMC9141313 DOI: 10.3390/ijms23105437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
JAK3 differs from other JAK family members in terms of tissue distribution and functional properties, making it a promising target for autoimmune disease treatment. However, due to the high homology of these family members, targeting JAK3 selectively is difficult. As a result, exploiting small changes or selectively boosting affinity within the ATP binding region to produce new tailored inhibitors of JAK3 is extremely beneficial. PubChem CID 137321159 was used as the lead inhibitor in this study to preserve the characteristic structure and to collocate it with the redesigned new parent core structure, from which a series of 1,7-dihydro-dipyrrolo [2,3-b:3′,2′-e] pyridine derivatives were obtained using the backbone growth method. From the proposed compounds, 14 inhibitors of JAK3 were found based on the docking scoring evaluation. The RMSD and MM/PBSA methods of molecular dynamics simulations were also used to confirm the stable nature of this series of complex systems, and the weak protein−ligand interactions during the dynamics were graphically evaluated and further investigated. The results demonstrated that the new parent core structure fully occupied the hydrophobic cavity, enhanced the interactions of residues LEU828, VAL836, LYS855, GLU903, LEU905 and LEU956, and maintained the structural stability. Apart from this, the results of the analysis show that the binding efficiency of the designed inhibitors of JAK3 is mainly achieved by electrostatic and VDW interactions and the order of the binding free energy with JAK3 is: 8 (−70.286 kJ/mol) > 11 (−64.523 kJ/mol) > 6 (−51.225 kJ/mol) > 17 (−42.822 kJ/mol) > 10 (−40.975 kJ/mol) > 19 (−39.754 kJ/mol). This study may provide a valuable reference for the discovery of novel JAK3 inhibitors for those patients with immune diseases.
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28
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A Comprehensive Overview of Globally Approved JAK Inhibitors. Pharmaceutics 2022; 14:pharmaceutics14051001. [PMID: 35631587 PMCID: PMC9146299 DOI: 10.3390/pharmaceutics14051001] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Janus kinase (JAK) is a family of cytoplasmic non-receptor tyrosine kinases that includes four members, namely JAK1, JAK2, JAK3, and TYK2. The JAKs transduce cytokine signaling through the JAK-STAT pathway, which regulates the transcription of several genes involved in inflammatory, immune, and cancer conditions. Targeting the JAK family kinases with small-molecule inhibitors has proved to be effective in the treatment of different types of diseases. In the current review, eleven of the JAK inhibitors that received approval for clinical use have been discussed. These drugs are abrocitinib, baricitinib, delgocitinib, fedratinib, filgotinib, oclacitinib, pacritinib, peficitinib, ruxolitinib, tofacitinib, and upadacitinib. The aim of the current review was to provide an integrated overview of the chemical and pharmacological data of the globally approved JAK inhibitors. The synthetic routes of the eleven drugs were described. In addition, their inhibitory activities against different kinases and their pharmacological uses have also been explained. Moreover, their crystal structures with different kinases were summarized, with a primary focus on their binding modes and interactions. The proposed metabolic pathways and metabolites of these drugs were also illustrated. To sum up, the data in the current review could help in the design of new JAK inhibitors with potential therapeutic benefits in inflammatory and autoimmune diseases.
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29
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Moghadam ES, Mireskandari K, Abdel-Jalil R, Amini M. An approach to pharmacological targets of pyrrole family from a medicinal chemistry viewpoint. Mini Rev Med Chem 2022; 22:2486-2561. [PMID: 35339175 DOI: 10.2174/1389557522666220325150531] [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: 11/27/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Pyrrole is one of the most widely used heterocycles in the pharmaceutical industry. Due to the importance of pyrrole structure in drug design and development, herein, we tried to conduct an extensive review of the bioactive pyrrole based compounds reported recently. The bioactivity of pyrrole derivatives varies, so in the review, we categorized them based on their direct pharmacologic targets. Therefore, readers are able to find the variety of biologic targets for pyrrole containing compounds easily. This review explains around seventy different biologic targets for pyrrole based derivatives, so, it is helpful for medicinal chemists in design and development novel bioactive compounds for different diseases. This review presents an extensive meaningful structure activity relationship for each reported structure as much as possible. The review focuses on papers published between 2018 and 2020.
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Affiliation(s)
- Ebrahim Saeedian Moghadam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Katayoon Mireskandari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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30
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Hany R, Leyris JP, Bret G, Mallié S, Sar C, Thouaye M, Hamze A, Provot O, Sokoloff P, Valmier J, Villa P, Rognan D. High-Throughput Screening for Extracellular Inhibitors of the FLT3 Receptor Tyrosine Kinase Reveals Chemically Diverse and Druggable Negative Allosteric Modulators. ACS Chem Biol 2022; 17:709-722. [PMID: 35227060 DOI: 10.1021/acschembio.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inhibiting receptor tyrosine kinases is commonly achieved by two main strategies targeting either the intracellular kinase domain by low molecular weight compounds or the extracellular ligand-binding domain by monoclonal antibodies. Identifying small molecules able to inhibit RTKs at the extracellular level would be highly desirable to gain exquisite selectivity but is believed to be challenging owing to the size of RTK endogenous ligands (cytokines, growth factors) and the topology of RTK extracellular domains. We here report the high-throughput screening of the French Chemical Library (48K compounds) for extracellular inhibitors of the Fms-like tyrosine kinase 3 (FLT3) receptor tyrosine kinase, by a homogeneous time-resolved fluorescence competition assay. A total of 679 small molecular weight ligands (1.4%) were confirmed to strongly inhibit (>75%) the binding of the fluorescent labeled FLT3 ligand (FL cytokine) to FLT3 overexpressed in HEK-293 cells, at two different concentrations (5 and 20 μM). Concentration-response curves, obtained for 111 lead-like molecules, confirmed the unexpected tolerance of the FLT3 extracellular domain for low molecular weight druggable inhibitors exhibiting submicromolar potencies, chemical diversity, and promising pharmacokinetic properties. Further investigation of one hit confirmed inhibitory properties in dorsal root ganglia neurons and in a mouse model of neuropathic pain.
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Affiliation(s)
- Romain Hany
- Plate-forme de Chimie Biologique Intégrative de Strasbourg (PCBIS), UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch Cedex, France
| | - Jean-Philippe Leyris
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
- BIODOL Therapeutics, CAP Alpha, 34830 Clapiers, France
| | - Guillaume Bret
- Laboratoire d’Innovation Thérapeutique (LIT), UMR7200 CNRS-Université de Strasbourg, 67400 Illkirch, France
| | - Sylvie Mallié
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Chamroeun Sar
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Maxime Thouaye
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Abdallah Hamze
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Olivier Provot
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | | | - Jean Valmier
- Institut des Neurosciences de Montpellier (INM), INSERM, Institut National de la Santé et de la Recherche Médicale, UMR1051, Hôpital Saint-Eloi, 34000 Montpellier, France
- Université de Montpellier, 34000 Montpellier, France
| | - Pascal Villa
- Plate-forme de Chimie Biologique Intégrative de Strasbourg (PCBIS), UAR3286 CNRS-Université de Strasbourg, Institut du Médicament de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67412 Illkirch Cedex, France
| | - Didier Rognan
- Laboratoire d’Innovation Thérapeutique (LIT), UMR7200 CNRS-Université de Strasbourg, 67400 Illkirch, France
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31
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Oyamada Y, Inaba K, Sasamori T, Nakamura S. Enantioselective reaction of N-cyano imines: decarboxylative Mannich-type reaction with malonic acid half thioesters. Chem Commun (Camb) 2022; 58:2172-2175. [PMID: 35060982 DOI: 10.1039/d1cc07191b] [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
The enantioselective reaction of imines bearing a cyano group as an activating group with malonic acid half thioesters gave chiral cyanamide derivatives with high enantioselectivity. The density functional theory (DFT) calculation clarified the stereochemical outcome and importance of the N-cyano group for imines.
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Affiliation(s)
- Yusuke Oyamada
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan.
| | - Kazuto Inaba
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan.
| | - Takahiro Sasamori
- Faculty of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science (TREMS) University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Shuichi Nakamura
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan. .,Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan
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32
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Zhang Z, Wang Y, Chen X, Song X, Tu Z, Chen Y, Zhang Z, Ding K. Characterization of an aromatic trifluoromethyl ketone as a new warhead for covalently reversible kinase inhibitor design. Bioorg Med Chem 2021; 50:116457. [PMID: 34670167 DOI: 10.1016/j.bmc.2021.116457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
An aromatic trifluoromethyl ketone moiety was characterized as a new warhead for covalently reversible kinase inhibitor design to target the non-catalytic cysteine residue. Potent and selective covalently reversible inhibitors of FGFR4 kinase were successfully designed and synthesized by utilizing this new warhead. The binding mode of a representative inhibitor was fully characterized by using multiple technologies including MALDI-TOF mass spectrometry, dialysis assay and X-ray crystallographic studies etc. This functional group was also successfully applied to discovery of a new JAK3 inhibitor, suggesting its potential application in designing other kinase inhibitors.
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Affiliation(s)
- Zhen Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Song
- Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhimin Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; The First Affiliated Hospital, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
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33
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Qiu H, Ali Z, Bowlan J, Caldwell R, Gardberg A, Glaser N, Goutopoulos A, Head J, Johnson T, Maurer C, Georgi K, Grenningloh R, Fang Z, Morandi F, Rohdich F, Schmidt R, Follis AV, Sherer B. Discovery of Covalent Bruton's Tyrosine Kinase Inhibitors with Decreased CYP2C8 Inhibitory Activity. ChemMedChem 2021; 16:3653-3662. [PMID: 34582626 DOI: 10.1002/cmdc.202100453] [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: 06/22/2021] [Revised: 09/27/2021] [Indexed: 11/07/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a member of the Tec kinase family that is expressed in cells of hematopoietic lineage. Evidence has shown that inhibition of BTK has clinical benefit for the treatment of a wide array of autoimmune and inflammatory diseases. Previously we reported the discovery of a novel nicotinamide selectivity pocket (SP) series of potent and selective covalent irreversible BTK inhibitors. The top molecule 1 of that series strongly inhibited CYP2C8 (IC50 =100 nM), which was attributed to the bridged linker group. However, our effort on the linker replacement turned out to be fruitless. With the study of the X-ray crystal structure of compound 1, we envisioned the opportunity of removal of this liability via transposition of the linker moiety in 1 from C6 to C5 position of the pyridine core. With this strategy, our optimization led to the discovery of a novel series, in which the top molecule 18 A displayed reduced CYP inhibitory activity and good potency. To further explore this new series, different warheads besides acrylamide, for example cyanamide, were also tested. However, this effort didn't lead to the discovery of molecules with better potency than 18 A. The loss of potency in those molecules could be related to the reduced reactivity of the warhead or reversible binding mode. Further profiling of 18 A disclosed that it had a strong hERG (human Ether-a-go-go Related Gene) inhibition, which could be related to the phenoxyphenyl group.
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Affiliation(s)
- Hui Qiu
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Zahid Ali
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Julian Bowlan
- Repare Therapeutics, 1 Broadway, 15th Floor, Cambridge, MA, 02142, USA
| | - Richard Caldwell
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Anna Gardberg
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA, 02142, USA
| | - Nina Glaser
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Andreas Goutopoulos
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Jared Head
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Theresa Johnson
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | | | - Katrin Georgi
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Roland Grenningloh
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Zhizhou Fang
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Federica Morandi
- Cellular Enzymology, F. Hoffmann-La Roche AG, Konzern-Hauptsitz, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Felix Rohdich
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Ralf Schmidt
- Merck KGaA, Frankfurter Str. 250, Darmstadt, 64293, Germany
| | - Ariele Viacava Follis
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Brian Sherer
- EMD Serono Research & Development Institute, 45 A Middlesex Turnpike, Billerica, MA, 01821, USA
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Guan I, Williams K, Pan J, Liu X. New Cysteine Covalent Modification Strategies Enable Advancement of Proteome‐wide Selectivity of Kinase Modulators. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ivy Guan
- School of Chemistry The Heart Research Institute The University of Sydney Sydney New South Wales 2006 Australia
| | - Kayla Williams
- School of Chemistry The University of Sydney Sydney New South Wales 2006 Australia
| | - Jolyn Pan
- Faculty of Science & Engineering The University of Waikato 124 Hillcrest Road, Hillcrest Hamilton 3216 New Zealand
| | - Xuyu Liu
- School of Chemistry The Heart Research Institute The University of Sydney Sydney New South Wales 2006 Australia
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Abstract
In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
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The advantages of describing covalent inhibitor in vitro potencies by IC 50 at a fixed time point. IC 50 determination of covalent inhibitors provides meaningful data to medicinal chemistry for SAR optimization. Bioorg Med Chem 2020; 29:115865. [PMID: 33285410 DOI: 10.1016/j.bmc.2020.115865] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 01/07/2023]
Abstract
Recent years have seen a resurgence in drug discovery efforts aimed at the identification of covalent inhibitors which has led to an explosion of literature reports in this area and most importantly new approved therapies. These reports and breakthroughs highlight the significant investments made across the industry in SAR campaigns to optimize inhibitors. The potency of covalent inhibitors is generally considered to be more accurately described by the time-independent kinetic parameter kinact/Ki rather than a by a simple IC50 since the latter is a time-dependent parameter. Enzyme substrate concentrations are an additional important factor to consider when attempting to translate parameters derived from enzymology experiments to phenotypic behavior in a physiologically relevant cell-based system. Theoretical and experimental investigations into the relationship between IC50, time, substrate concentration and Kinact/Ki provided us with an effective approach to provide meaningful data for SAR optimization. The data we generated for our JAK3 irreversible covalent inhibitor program using IC50 values provided by enzyme assays with long incubations (>1h) coupled with physiological substrate concentration provided the medicinal chemist with optimal information in a rapid and efficient manner. We further document the wide applicability of this method by applying it to other enzymes systems where we have run covalent inhibitor programs.
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37
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Bao Q, Zhang L, Wang N, Gabet B, Yang W, Gao X, You Q, Jiang Z. Hydrogen Peroxide Inducible JAK3 Covalent Inhibitor: Prodrug for the Treatment of RA with Enhanced Safety Profile. ACS Med Chem Lett 2020; 11:2182-2189. [PMID: 33214827 DOI: 10.1021/acsmedchemlett.0c00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Selective inhibition of Janus kinases (JAKs) is an arising strategy in drug discovery. Covalent inhibitors targeting a unique cysteine in JAK3 exhibit ultraselectivity among JAK family members. However, safety and tissue specific concerns still remain. A prodrug of a known JAK3 covalent inhibitor sensitive to H2O2 was designed and synthesized and its therapeutic effect was evaluated in the CIA (collagen-induced arthritis) mice model of RA (rheumatoid arthritis). The prodrug strategy relied on the introduction of a hydrogen peroxide-sensitive borate trigger group to avoid random covalent binding to thiol functionalities in biomacromolecules. The results show that the prodrug can be activated and released under pathophysiological concentration of H2O2. In addition, the prodrug demonstrated stability to the physiological environment. In comparison to the parent compound, the prodrug showed a similar therapeutic effect in the CIA model but notably exhibited lower toxicity and a larger therapeutic window.
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Affiliation(s)
- Qichao Bao
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Liangying Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Nan Wang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Brian Gabet
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Weikang Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xingyang Gao
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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38
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Mondal S, Malakar S. Synthesis of sulfonamide and their synthetic and therapeutic applications: Recent advances. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131662] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Duchamp E, Hanessian S. Cyanide-Free Synthesis of Air Stable N-Substituted Li and K Cyanamide Salts from Tetrazoles. Applications toward the Synthesis of Primary and Secondary Cyanamides as Precursors to Amidines. Org Lett 2020; 22:8487-8491. [PMID: 33090802 DOI: 10.1021/acs.orglett.0c03085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A practical two-step synthesis of N,N'-disubstituted cyanamides consists in the low-temperature metalation of N-substituted 5H-tetrazoles that undergo spontaneous cycloreversion at 0 °C releasing dinitrogen, and forming N-metalated cyanamides that can be reacted in situ with a variety of electrophiles. Remarkably, the N-substituted Li and K cyanamides are air stable white solids at room temperature. Addition of lithium organometallics to the N,N'-disubstituted cyanamides provides a new method for accessing N,N'-disubstituted amidines.
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Affiliation(s)
- Edouard Duchamp
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ., Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ., Centre-ville, Montréal, Québec, Canada H3C 3J7
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40
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Cong X, Zhan G, Mo Z, Nishiura M, Hou Z. Diastereodivergent [3 + 2] Annulation of Aromatic Aldimines with Alkenes via C-H Activation by Half-Sandwich Rare-Earth Catalysts. J Am Chem Soc 2020; 142:5531-5537. [PMID: 32148027 DOI: 10.1021/jacs.0c01171] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stereodivergent catalysis is of great importance, as it can allow efficient access to all possible stereoisomers of a given product with multiple stereocenters from the same set of starting materials. We report herein the first diastereodivergent [3 + 2] annulation of aromatic aldimines with alkenes via C-H activation by half-sandwich rare-earth catalysts. This protocol provides an efficient and general route for the selective synthesis of both trans and cis diastereoisomers of multisubstituted 1-aminoindanes from the same set of aldimines and alkenes, featuring 100% atom efficiency, excellent diastereoselectivity, broad substrate scope, and good functional group compatibility. The diastereodivergence is achieved by fine-tuning the sterics or ligand/metal combination of the half-sandwich rare-earth metal complexes.
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Affiliation(s)
- Xuefeng Cong
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Gu Zhan
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zhenbo Mo
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masayoshi Nishiura
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zhaomin Hou
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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41
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Xu P, Shen P, Yu B, Xu X, Ge R, Cheng X, Chen Q, Bian J, Li Z, Wang J. Janus kinases (JAKs): The efficient therapeutic targets for autoimmune diseases and myeloproliferative disorders. Eur J Med Chem 2020; 192:112155. [PMID: 32120325 DOI: 10.1016/j.ejmech.2020.112155] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023]
Abstract
The Janus kinases or JAKs are a family of intracellular tyrosine kinases that play an essential role in the signaling of numerous cytokines that have been implicated in the pathogenesis of autoimmune diseases and myeloproliferative disorders. JAKs are activated upon ligand induced receptor homo- or heterodimerization, which results in the immediate phosphorylation of tyrosine residues and the phosphotyrosines then serve as docking sites for cytoplasmic signal transducer and activator of transcription (STAT) proteins which become phosphorylated by the JAKs upon recruitment to the receptor complex. The phosphorylated STAT proteins dimerize and travel to the cellular nucleus, where they act as transcription factors. Interfering in the JAK-STAT pathway has yielded the only approved small molecule kinase inhibitors for immunological indications. Numerous medicinal chemistry studies are currently aimed at the design of novel and potent inhibitors for JAKs. Additionally, whether the second-generation inhibitors which possessed selectivity for JAKs are more efficient are under research. This Perspective summarizes the progress in the discovery and development of JAKs inhibitors, including the potential binding site and approaches for identifying small-molecule inhibitors, as well as future therapeutic perspectives in autoimmune diseases and myeloproliferative disorders are also put forward in order to provide reference and rational for the drug discovery of novel and potent JAKs inhibitors.
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Affiliation(s)
- Pengfei Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Pei Shen
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Bin Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Xi Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Raoling Ge
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650000, China
| | - Xinying Cheng
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Qiuyu Chen
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Jinlei Bian
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 21009, China
| | - Zhiyu Li
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 21009, China.
| | - JuBo Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 21009, China.
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42
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Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
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43
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Dai J, Yang L, Addison G. Current Status in the Discovery of Covalent Janus Kinase 3 (JAK3) Inhibitors. Mini Rev Med Chem 2019; 19:1531-1543. [PMID: 31288716 DOI: 10.2174/1389557519666190617152011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/09/2023]
Abstract
The search for inhibitors of the Janus kinase family (JAK1, JAK2, JAK3 and TYK2) has been ongoing for several decades and has resulted in a number of JAK inhibitors being approved for use in patients, such as tofacitinib for the treatment of autoimmune diseases such as Rheumatoid Arthritis (RA). Although initially thought to be a JAK3 selective inhibitor, tofacitinib was subsequently found to possess significant activity to inhibit JAK1 and JAK2 which has contributed to some adverse side effects. A selective JAK3 inhibitor should only have an effect within the immune system since JAK3 is solely expressed in lymphoid tissue; this makes JAK3 a target of interest in the search for treatments of autoimmune diseases. A method to obtain selectivity for JAK3 over the other JAK family members, which has attracted more scientific attention recently, is the targeting of the active site cysteine residue, unique in JAK3 within the JAK family, with compounds containing electrophilic warheads which can form a covalent bond with the nucleophilic thiol of the cysteine residue. This review encompasses the historical search for a covalent JAK3 inhibitor and the most recently published research which hasn't been reviewed to date. The most important compounds from the publications reviewed the activity and selectivity of these compounds together with some of the more important biological results are condensed in to an easily digested form that should prove useful for those interested in the field.
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Affiliation(s)
- Jun Dai
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
| | - LiXi Yang
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
| | - Glynn Addison
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
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44
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Yang M, Tao B, Chen C, Jia W, Sun S, Zhang T, Wang X. Machine Learning Models Based on Molecular Fingerprints and an Extreme Gradient Boosting Method Lead to the Discovery of JAK2 Inhibitors. J Chem Inf Model 2019; 59:5002-5012. [DOI: 10.1021/acs.jcim.9b00798] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Minjian Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
- Joint Laboratory of Artificial Intelligence of the Institute of Materia Medica and Yuan Qi Zhi Yao, Beijing 100050, P.R. China
| | - Bingzhong Tao
- Joint Laboratory of Artificial Intelligence of the Institute of Materia Medica and Yuan Qi Zhi Yao, Beijing 100050, P.R. China
| | - Chengjuan Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Wenqiang Jia
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Shaolei Sun
- Joint Laboratory of Artificial Intelligence of the Institute of Materia Medica and Yuan Qi Zhi Yao, Beijing 100050, P.R. China
| | - Tiantai Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Xiaojian Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
- Joint Laboratory of Artificial Intelligence of the Institute of Materia Medica and Yuan Qi Zhi Yao, Beijing 100050, P.R. China
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45
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Leonard WJ, Lin JX, O'Shea JJ. The γ c Family of Cytokines: Basic Biology to Therapeutic Ramifications. Immunity 2019; 50:832-850. [PMID: 30995502 DOI: 10.1016/j.immuni.2019.03.028] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/15/2022]
Abstract
The common cytokine receptor γ chain, γc, is a component of the receptors for interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21. Mutation of the gene encoding γc results in X-linked severe combined immunodeficiency in humans, and γc family cytokines collectively regulate development, proliferation, survival, and differentiation of immune cells. Here, we review the basic biology of these cytokines, highlighting mechanisms of signaling and gene regulation that have provided insights for immunodeficiency, autoimmunity, allergic diseases, and cancer. Moreover, we discuss how studies of this family stimulated the development of JAK3 inhibitors and present an overview of current strategies targeting these pathways in the clinic, including novel antibodies, antagonists, and partial agonists. The diverse roles of these cytokines on a range of immune cells have important therapeutic implications.
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Affiliation(s)
- Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA.
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA.
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Metabolic, and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-1674, USA.
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46
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van den Bedem H, Wilson MA. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:958-966. [PMID: 31274417 PMCID: PMC6613112 DOI: 10.1107/s160057751900568x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Cysteine is a rare but functionally important amino acid that is often subject to covalent modification. Cysteine oxidation plays an important role in many human disease processes, and basal levels of cysteine oxidation are required for proper cellular function. Because reactive cysteine residues are typically ionized to the thiolate anion (Cys-S-), their formation of a covalent bond alters the electrostatic and steric environment of the active site. X-ray-induced photo-oxidation to sulfenic acids (Cys-SOH) can recapitulate some aspects of the changes that occur under physiological conditions. Here we propose how site-specific cysteine photo-oxidation can be used to interrogate ensuing changes in protein structure and dynamics at atomic resolution. Although this powerful approach can connect cysteine covalent modification to global protein conformational changes and function, careful biochemical validation must accompany all such studies to exclude misleading artifacts. New types of X-ray crystallography experiments and powerful computational methods are creating new opportunities to connect conformational dynamics to catalysis for the large class of systems that use covalently modified cysteine residues for catalysis or regulation.
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Affiliation(s)
- Henry van den Bedem
- Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
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47
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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48
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Spergel SH, Mertzman ME, Kempson J, Guo J, Stachura S, Haque L, Lippy JS, Zhang RF, Galella M, Pitt S, Shen G, Fura A, Gillooly K, McIntyre KW, Tang V, Tokarski J, Sack JS, Khan J, Carter PH, Barrish JC, Nadler SG, Salter-Cid LM, Schieven GL, Wrobleski ST, Pitts WJ. Discovery of a JAK1/3 Inhibitor and Use of a Prodrug To Demonstrate Efficacy in a Model of Rheumatoid Arthritis. ACS Med Chem Lett 2019; 10:306-311. [PMID: 30891131 DOI: 10.1021/acsmedchemlett.8b00508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022] Open
Abstract
The four members of the Janus family of nonreceptor tyrosine kinases play a significant role in immune function. The JAK family kinase inhibitor, tofacitinib 1, has been approved in the United States for use in rheumatoid arthritis (RA) patients. A number of JAK inhibitors with a variety of JAK family selectivity profiles are currently in clinical trials. Our goal was to identify inhibitors that were functionally selective for JAK1 and JAK3. Compound 22 was prepared with the desired functional selectivity profile, but it suffered from poor absorption related to physical properties. Use of the phosphate prodrug 32 enabled progression to a murine collagen induced arthritis (CIA) model. The demonstration of a robust efficacy in the CIA model suggests that use of phosphate prodrugs may resolve issues with progressing this chemotype for the treatment of autoimmune diseases such as RA.
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Affiliation(s)
- Steven H. Spergel
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Michael E. Mertzman
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - James Kempson
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Junqing Guo
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Sylwia Stachura
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Lauren Haque
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Jonathan S. Lippy
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Rosemary F. Zhang
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Michael Galella
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Sidney Pitt
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Guoxiang Shen
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Aberra Fura
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Kathleen Gillooly
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Kim W. McIntyre
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Vicky Tang
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - John Tokarski
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - John S. Sack
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Javed Khan
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Percy H. Carter
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Joel C. Barrish
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Steven G. Nadler
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Luisa M. Salter-Cid
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Gary L. Schieven
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - Stephen T. Wrobleski
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
| | - William J. Pitts
- Research and Development, Bristol-Myers Squibb Company, Route 206 and Provinceline Road, Princeton, New Jersey 08543-4000, United States
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49
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 378] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
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