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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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Buehler Y, Reymond JL. Expanding Bioactive Fragment Space with the Generated Database GDB-13s. J Chem Inf Model 2023; 63:6239-6248. [PMID: 37722101 PMCID: PMC10598793 DOI: 10.1021/acs.jcim.3c01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Indexed: 09/20/2023]
Abstract
Identifying innovative fragments for drug design can help medicinal chemistry address new targets and overcome the limitations of the classical molecular series. By deconstructing molecules into ring fragments (RFs, consisting of ring atoms plus ring-adjacent atoms) and acyclic fragments (AFs, consisting of only acyclic atoms), we find that public databases of molecules (i.e., ZINC and PubChem) and natural products (i.e., COCONUT) contain mostly RFs and AFs of up to 13 atoms. We also find that many RFs and AFs are enriched in bioactive vs inactive compounds from ChEMBL. We then analyze the generated database GDB-13s, which enumerates 99 million possible molecules of up to 13 atoms, for RFs and AFs resembling ChEMBL bioactive RFs and AFs. This analysis reveals a large number of novel RFs and AFs that are structurally simple, have favorable synthetic accessibility scores, and represent opportunities for synthetic chemistry to contribute to drug innovation in the context of fragment-based drug discovery.
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Affiliation(s)
- Ye Buehler
- Department of Chemistry,
Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry,
Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Zhou H, Pan R, Xu M, Ma J, Lin A, Yao H. Construction of oxygenated 2-azabicyclo[2.2.1]heptanes via palladium-catalyzed 1,2-aminoacyloxylation of cyclopentenes. Chem Commun (Camb) 2023; 59:3574-3577. [PMID: 36880405 DOI: 10.1039/d2cc06581a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Herein, we describe a palladium-catalyzed 1,2-aminoacyloxylation of cyclopentenes to synthesize oxygenated 2-azabicyclo[2.2.1]heptanes. This reaction proceeds efficiently with a broad array of substrates. The products could be further functionalized to build up a library of bridged aza-bicyclic structures.
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Affiliation(s)
- Haipin Zhou
- College of Materials & Chemical Engineering, Chuzhou University, 1 West Huifeng Road, Chuzhou, 239000, P. R. China
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
| | - Rui Pan
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
| | - Menghua Xu
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
| | - Jiao Ma
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
| | - Aijun Lin
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
| | - Hequan Yao
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China.
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Buehler Y, Reymond JL. Molecular Framework Analysis of the Generated Database GDB-13s. J Chem Inf Model 2023; 63:484-492. [PMID: 36533982 PMCID: PMC9875802 DOI: 10.1021/acs.jcim.2c01107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 12/23/2022]
Abstract
The generated databases (GDBs) list billions of possible molecules from systematic enumeration following simple rules of chemical stability and synthetic feasibility. To assess the originality of GDB molecules, we compared their Bemis and Murcko molecular frameworks (MFs) with those in public databases. MFs result from molecules by converting all atoms to carbons, all bonds to single bonds, and removing terminal atoms iteratively until none remain. We compared GDB-13s (99,394,177 molecules up to 13 atoms containing simplified functional groups, 22,130 MFs) with ZINC (885,905,524 screening compounds, 1,016,597 MFs), PubChem50 (100,852,694 molecules up to 50 atoms, 1,530,189 MFs), and COCONUT (401,624 natural products, 42,734 MFs). While MFs in public databases mostly contained linker bonds and six-membered rings, GDB-13s MFs had diverse ring sizes and ring systems without linker bonds. Most GDB-13s MFs were exclusive to this database, and many were relatively simple, representing attractive targets for synthetic chemistry aiming at innovative molecules.
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Affiliation(s)
- Ye Buehler
- Department of Chemistry, Biochemistry
and Pharmaceutical Sciences, University
of Bern, Freiestrasse 3, 3012Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry
and Pharmaceutical Sciences, University
of Bern, Freiestrasse 3, 3012Bern, Switzerland
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Perebyinis M, Rognan D. Overlap of On-demand Ultra-large Combinatorial Spaces with On-the-shelf Drug-like Libraries. Mol Inform 2023; 42:e2200163. [PMID: 36072995 DOI: 10.1002/minf.202200163] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/07/2022] [Indexed: 01/12/2023]
Abstract
On-demand combinatorial spaces are shifting paradigms in early drug discovery, by considerably increasing the searchable chemical space to several billions of compounds while securing their synthetic accessibility. We here systematically compared the on-the-shelf available drug-like chemical space (9 million compounds) to three on-demand ultra-large (ODUL) combinatorial fragment spaces (REAL, CHEMriya, GalaXi) covering 32 billion of readily accessible molecules. Surprisingly, only one space (REAL) intersects almost entirely the currently available drug-like space, suggesting that it is the only ODUL widely suitable for in-stock hit expansion. Of course, expanding a preliminary ODUL hit in the same chemical space is the best possible strategy to rapidly generate structure-activity relationships. All three spaces remain well suited to early hit finding initiatives since they all provide numerous unique scaffolds that are not described by on-the shelf collections.
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Affiliation(s)
- Mariana Perebyinis
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, 74 route du Rhin, F-67400, Illkirch, France
| | - Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS-Université de Strasbourg, 74 route du Rhin, F-67400, Illkirch, France
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Cai M, Ma J, Wu Q, Lin A, Yao H. Enantioselective Syntheses of 2-Azabicyclo[2.2.1]heptanes via Brønsted Acid Catalyzed Ring-Opening of meso-Epoxides. Org Lett 2022; 24:8791-8795. [PMID: 36414324 DOI: 10.1021/acs.orglett.2c03529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A chiral phosphoric acid-catalyzed ring-opening of meso-epoxides was developed. A range of 2-azabicyclo[2.2.1]heptanes were obtained in high yields with excellent enantioselectivities. In addition, the hydroxyl and amide groups in the products provided handles for further derivatization.
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Affiliation(s)
- Min Cai
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jiao Ma
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Qimin Wu
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Aijun Lin
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hequan Yao
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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Pujol‐Giménez J, Poirier M, Bühlmann S, Schuppisser C, Bhardwaj R, Awale M, Visini R, Javor S, Hediger MA, Reymond J. Inhibitors of Human Divalent Metal Transporters DMT1 (SLC11A2) and ZIP8 (SLC39A8) from a GDB-17 Fragment Library. ChemMedChem 2021; 16:3306-3314. [PMID: 34309203 PMCID: PMC8596699 DOI: 10.1002/cmdc.202100467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/06/2022]
Abstract
Solute carrier proteins (SLCs) are membrane proteins controlling fluxes across biological membranes and represent an emerging class of drug targets. Here we searched for inhibitors of divalent metal transporters in a library of 1,676 commercially available 3D-shaped fragment-like molecules from the generated database GDB-17, which lists all possible organic molecules up to 17 atoms of C, N, O, S and halogen following simple criteria for chemical stability and synthetic feasibility. While screening against DMT1 (SLC11A2), an iron transporter associated with hemochromatosis and for which only very few inhibitors are known, only yielded two weak inhibitors, our approach led to the discovery of the first inhibitor of ZIP8 (SLC39A8), a zinc transporter associated with manganese homeostasis and osteoarthritis but with no previously reported pharmacology, demonstrating that this target is druggable.
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Affiliation(s)
- Jonai Pujol‐Giménez
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Marion Poirier
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Sven Bühlmann
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Céline Schuppisser
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Rajesh Bhardwaj
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Mahendra Awale
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Ricardo Visini
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Sacha Javor
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Matthias A. Hediger
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Jean‐Louis Reymond
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
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