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Chan BWGL, Lynch NB, Tran W, Joyce JM, Savage GP, Meutermans W, Montgomery AP, Kassiou M. Fragment-based drug discovery for disorders of the central nervous system: designing better drugs piece by piece. Front Chem 2024; 12:1379518. [PMID: 38698940 PMCID: PMC11063241 DOI: 10.3389/fchem.2024.1379518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Fragment-based drug discovery (FBDD) has emerged as a powerful strategy to confront the challenges faced by conventional drug development approaches, particularly in the context of central nervous system (CNS) disorders. FBDD involves the screening of libraries that comprise thousands of small molecular fragments, each no greater than 300 Da in size. Unlike the generally larger molecules from high-throughput screening that limit customisation, fragments offer a more strategic starting point. These fragments are inherently compact, providing a strong foundation with good binding affinity for the development of drug candidates. The minimal elaboration required to transition the hit into a drug-like molecule is not only accelerated, but also it allows for precise modifications to enhance both their activity and pharmacokinetic properties. This shift towards a fragment-centric approach has seen commercial success and holds considerable promise in the continued streamlining of the drug discovery and development process. In this review, we highlight how FBDD can be integrated into the CNS drug discovery process to enhance the exploration of a target. Furthermore, we provide recent examples where FBDD has been an integral component in CNS drug discovery programs, enabling the improvement of pharmacokinetic properties that have previously proven challenging. The FBDD optimisation process provides a systematic approach to explore this vast chemical space, facilitating the discovery and design of compounds piece by piece that are capable of modulating crucial CNS targets.
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Affiliation(s)
| | - Nicholas B. Lynch
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Jack M. Joyce
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
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2
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Wang ZZ, Yi C, Huang JJ, Xu TF, Chen KZ, Wang ZS, Xue YP, Lu JL, Nie B, Zhang YJ, Jin CF, Hao GF. Deciphering Nonbioavailable Substructures Improves the Bioavailability of Antidepressants by Serotonin Transporter. J Med Chem 2023; 66:371-383. [PMID: 36598095 DOI: 10.1021/acs.jmedchem.2c01339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Inadequate bioavailability is one of the most critical reasons for the failure of oral drug development. However, the way that substructures affect bioavailability remains largely unknown. Serotonin transporter (SERT) inhibitors are first-line drugs for major depression disorder, and improving their bioavailability may be able to decrease side-effects by reducing daily dose. Thus, it is an excellent model to probe the relationship between substructures and bioavailability. Here, we proposed the concept of "nonbioavailable substructures", referring to substructures that are unfavorable to bioavailability. A machine learning model was developed to identify nonbioavailable substructures based on their molecular properties and shows the accuracy of 83.5%. A more potent SERT inhibitor DH4 was discovered with a bioavailability of 83.28% in rats by replacing the nonbioavailable substructure of approved drug vilazodone. DH4 exhibits promising anti-depression efficacy in animal experiments. The concept of nonbioavailable substructures may open up a new venue for the improvement of drug bioavailability.
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Affiliation(s)
- Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430000, China
| | - Chao Yi
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Teng-Fei Xu
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Kang-Zhi Chen
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Zu-Sheng Wang
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Ya-Ping Xue
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Jie-Lian Lu
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Biao Nie
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Ying-Jun Zhang
- HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Chuan-Fei Jin
- Sunshine Lake Pharma Co. Ltd., Shenzhen 518000, China.,HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China.,Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430000, China
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3
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Biological Properties and Clinical Significance of Lipoprotein-Associated Phospholipase A2 in Ischemic Stroke. Cardiovasc Ther 2022; 2022:3328574. [PMID: 36313479 PMCID: PMC9586817 DOI: 10.1155/2022/3328574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/27/2022] Open
Abstract
Ischemic stroke, which occurs following blockage of the blood supply to the brain, is a leading cause of death worldwide. Its main cause is atherosclerosis, a disease of the arteries characterized by the deposition of plaques of fatty material on the inner artery walls. Multiple proteins involved in the inflammation response have been identified as diagnosing biomarkers of ischemic stroke. One of these is lipoprotein-associated phospholipase A2 (Lp-PLA2), an enzyme that can hydrolyze circulating oxidized phospholipids, generating proinflammatory lysophosphatidylcholine and promoting the development of atherosclerosis. In the last two decades, a number of studies have revealed that both the concentration and the activity of Lp-PLA2 are independent biomarkers of ischemic stroke. The US Food and Drug Administration (FDA) has approved two tests to determine Lp-PLA2 mass and activity for predicting stroke. In this review, we summarize the biological properties of Lp-PLA2, the detection sensitivity and limitations of Lp-PLA2 measurement, the clinical significance and association of Lp-PLA2 in ischemic stroke, and the prospects of therapeutic inhibition of Lp-PLA2 as an intervention and treatment.
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4
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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5
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Pan YL, Gong XM, Hao RR, Zeng SX, Shen ZR, Huang WH. The synthesis of anticancer sulfonated indolo[2,1- a]isoquinoline and benzimidazo[2,1- a]isoquinolin-6(5 H)-ones derivatives via a free radical cascade pathway. RSC Adv 2022; 12:9763-9772. [PMID: 35424925 PMCID: PMC8961271 DOI: 10.1039/d1ra06981k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/19/2022] [Indexed: 01/22/2023] Open
Abstract
A facile CuBr2 induced radical relay addition/cyclization of activated alkenes with substituted-thiosulfonates has been achieved, leading to a broad range of sulfonated indolo[2,1-a]isoquinolines and benzimidazo[2,1-a]isoquinolin-6(5H)-ones in moderate to good yields. In particular, some compounds exhibit bioactivity against cancer cell lines. This protocol shows advantages of low-cost, base-free, simple operation, and broad functional group tolerance.
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Affiliation(s)
- You-Lu Pan
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College Hangzhou Zhejiang China
| | - Xiao-Meng Gong
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College Hangzhou Zhejiang China
| | - Rong-Rong Hao
- Hangzhou Chinese Academy of Sciences, Hangzhou Medical College, Advanced Medical Technology Institute Hangzhou Zhejiang China
| | - Shen-Xin Zeng
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College Hangzhou Zhejiang China
| | - Zheng-Rong Shen
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College Hangzhou Zhejiang China
| | - Wen-Hai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College Hangzhou Zhejiang China
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6
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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7
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Wang C, Sun G, Huang HL, Liu J, Tang H, Li Y, Hu H, He S, Gao F. Visible-Light-Driven Sulfonylation/Cyclization to Access Sulfonylated Benzo[4,5]imidazo[2,1-a]isoquinolin-6(5H)-ones. Chem Asian J 2021; 16:2618-2621. [PMID: 34342941 DOI: 10.1002/asia.202100681] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/18/2021] [Indexed: 12/17/2022]
Abstract
Visible-light-driven sulfonylation/cyclization of N-methacryloyl-2-phenylbenzoimidazoles has been successfully developed. Using commercially available sulfonyl chloride as sulfonylation reagent, a wide range of sulfonylated benzo[4,5]imidazo[2,1-a]isoquinolin-6(5H)-ones with potential antitumor activity were provided in acceptable to excellent yields. This method has the advantages of mild reaction conditions and outstanding functional group tolerance, and provides a new strategy for the development of potential antitumor lead compounds.
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Affiliation(s)
- Chen Wang
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Guoquan Sun
- Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, P. R. China
| | - Hong-Li Huang
- College of Chemistry and Chemical Engineering, Liaocheng University, Shandong, 252059, P. R. China
| | - Jing Liu
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Hua Tang
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Yinghua Li
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Honggang Hu
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Shipeng He
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Fei Gao
- Institute of Translation Medicine, Shanghai University, Shanghai, 200444, P. R. China
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8
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Batsika CS, Gerogiannopoulou ADD, Mantzourani C, Vasilakaki S, Kokotos G. The design and discovery of phospholipase A 2 inhibitors for the treatment of inflammatory diseases. Expert Opin Drug Discov 2021; 16:1287-1305. [PMID: 34143707 DOI: 10.1080/17460441.2021.1942835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AREAS COVERED This review article summarizes the most important synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated Lp-PLA2), discussing their in vitro and in vivo activities as well as their recent applications and therapeutic properties. Recent findings on the role of PLA2 in the pathobiology of COVID-19 are also discussed. EXPERT OPINION Although a number of PLA2 inhibitors have entered clinical trials, none has reached the market yet. Lipoprotein-associated PLA2 is now considered a biomarker of vascular inflammation rather than a therapeutic target for inhibitors like darapladib. Inhibitors of cytosolic PLA2 may find topical applications for diseases like atopic dermatitis and psoriasis. Inhibitors of secreted PLA2, varespladib and varespladib methyl, are under investigation for repositioning in snakebite envenoming. A deeper understanding of PLA2 enzymes is needed for the development of novel selective inhibitors. Lipidomic technologies combined with medicinal chemistry approaches may be useful tools toward this goal.
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Affiliation(s)
| | | | - Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
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9
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Li X, Liao W, Huang B, Zhang Y, Wang J. A metal-free approach for the synthesis of thiosulfonates from sulfonyl hydrazides. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211014444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Without any metal catalyst, an efficient transformation of a variety of sulfonyl hydrazides into the corresponding thiosulfonates mediated by NBS/DABCO under air is developed. The method utilizes mild reaction conditions, affords moderate to good yields of product, and tolerates a broad substrate scope. A plausible mechanism is proposed for the decomposition of the sulfonyl hydrazides and the construction of S(O2)–S bonds to form thiosulfonates.
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Affiliation(s)
- Xue Li
- Drug Research Center, Traditional Chinese Medicine Institute of Jiangxi, Nanchang, P.R. China
| | - WeiBo Liao
- Drug Research Center, Traditional Chinese Medicine Institute of Jiangxi, Nanchang, P.R. China
| | - Bin Huang
- Drug Research Center, Traditional Chinese Medicine Institute of Jiangxi, Nanchang, P.R. China
| | - YuanYuan Zhang
- Drug Research Center, Traditional Chinese Medicine Institute of Jiangxi, Nanchang, P.R. China
| | - JiangWei Wang
- Drug Research Center, Traditional Chinese Medicine Institute of Jiangxi, Nanchang, P.R. China
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10
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Synthesis of sulfonylated benzimidazo[2,1-a]isoquinolin-6(5H)-ones via I2O5-induced radical relay addition/cyclization of activated alkenes with sulfonylhydrazides. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Kobauri P, Szymanski W, Cao F, Thallmair S, Marrink SJ, Witte MD, Dekker FJ, Feringa BL. Biaryl sulfonamides as cisoid azosteres for photopharmacology. Chem Commun (Camb) 2021; 57:4126-4129. [DOI: 10.1039/d1cc00950h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Biaryl sulfonamides are excellent candidates for the azologization approach that yields photoswitchable drugs more active in their metastable cis state, compared to the stable trans state.
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Affiliation(s)
- Piermichele Kobauri
- Stratingh Institute for Chemistry
- University of Groningen
- Nijenborgh 4
- Groningen
- The Netherlands
| | - Wiktor Szymanski
- Medical Imaging Center
- University of Groningen
- University Medical Center Groningen
- Hanzeplein 1
- Groningen 9713 GZ
| | - Fangyuan Cao
- Chemical and Pharmaceutical Biology
- Groningen Research Institute of Pharmacy
- University of Groningen
- A. Deusinglaan 1
- Groningen, 9713 AV
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 7
- Groningen 9747 AG
- The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials
- University of Groningen
- Nijenborgh 7
- Groningen 9747 AG
- The Netherlands
| | - Martin D. Witte
- Chemical Biology II
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen 9747 AG
- The Netherlands
| | - Frank J. Dekker
- Chemical and Pharmaceutical Biology
- Groningen Research Institute of Pharmacy
- University of Groningen
- A. Deusinglaan 1
- Groningen, 9713 AV
| | - Ben L. Feringa
- Stratingh Institute for Chemistry
- University of Groningen
- Nijenborgh 4
- Groningen
- The Netherlands
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12
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Chen T, Xiong H, Yang JF, Zhu XL, Qu RY, Yang GF. Diaryl Ether: A Privileged Scaffold for Drug and Agrochemical Discovery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9839-9877. [PMID: 32786826 DOI: 10.1021/acs.jafc.0c03369] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diaryl ether (DE) is a functional scaffold existing widely both in natural products (NPs) and synthetic organic compounds. Statistically, DE is the second most popular and enduring scaffold within the numerous medicinal chemistry and agrochemical reports. Given its unique physicochemical properties and potential biological activities, DE nucleus is recognized as a fundamental element of medicinal and agrochemical agents aimed at different biological targets. Its drug-like derivatives have been extensively synthesized with interesting biological features including anticancer, anti-inflammatory, antiviral, antibacterial, antimalarial, herbicidal, fungicidal, insecticidal, and so on. In this review, we highlight the medicinal and agrochemical versatility of the DE motif according to the published information in the past decade and comprehensively give a summary of the target recognition, structure-activity relationship (SAR), and mechanism of action of its analogues. It is expected that this profile may provide valuable guidance for the discovery of new active ingredients both in drug and pesticide research.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hao Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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13
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Huang F, Hu H, Wang K, Peng C, Xu W, Zhang Y, Gao J, Liu Y, Zhou H, Huang R, Li M, Shen J, Xu Y. Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach. J Med Chem 2020; 63:7052-7065. [DOI: 10.1021/acs.jmedchem.0c00372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Fubao Huang
- State Key Laboratory of Drug Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hangchen Hu
- CAS Key Laboratory of Receptor Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Wang
- State Key Laboratory of Drug Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chengyuan Peng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenwei Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yu Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- CAS Key Laboratory of Receptor Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yishen Liu
- Nanchang University, Nanchang 330031, China
| | - Hu Zhou
- CAS Key Laboratory of Receptor Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Wu F, Zhuo L, Wang F, Huang W, Hao G, Yang G. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead. iScience 2020; 23:101179. [PMID: 32498019 PMCID: PMC7267738 DOI: 10.1016/j.isci.2020.101179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Motivated by the growing demand for reducing the chemical optimization burden of H2L, we developed auto in silico ligand directing evolution (AILDE, http://chemyang.ccnu.edu.cn/ccb/server/AILDE), an efficient and general approach for the rapid identification of drug leads in accessible chemical space. This computational strategy relies on minor chemical modifications on the scaffold of a hit compound, and it is primarily intended for identifying new lead compounds with minimal losses or, in some cases, even increases in ligand efficiency. We also described how AILDE greatly reduces the chemical optimization burden in the design of mesenchymal-epithelial transition factor (c-Met) kinase inhibitors. We only synthesized eight compounds and found highly efficient compound 5g, which showed an ∼1,000-fold improvement in in vitro activity compared with the hit compound. 5g also displayed excellent in vivo antitumor efficacy as a drug lead. We believe that AILDE may be applied to a large number of studies for rapid design and identification of drug leads. AILDE was developed for the rapid identification of drug leads A potent drug lead targeted to c-Met was found by synthesizing only eight compounds
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Linsheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Gefei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, P. R. China.
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15
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Su H, Zou Y, Chen G, Dou H, Xie H, Yuan X, Zhang X, Zhang N, Li M, Xu Y. Exploration of Fragment Binding Poses Leading to Efficient Discovery of Highly Potent and Orally Effective Inhibitors of FABP4 for Anti-inflammation. J Med Chem 2020; 63:4090-4106. [DOI: 10.1021/acs.jmedchem.9b02107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Haixia Su
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zou
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guofeng Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huixia Dou
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hang Xie
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaojing Yuan
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglei Zhang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Mahanty K, Maiti D, De Sarkar S. Regioselective C–H Sulfonylation of 2H-Indazoles by Electrosynthesis. J Org Chem 2020; 85:3699-3708. [PMID: 32003566 DOI: 10.1021/acs.joc.9b03330] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kingshuk Mahanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Debabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Suman De Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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17
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Nikolaou A, Kokotou MG, Vasilakaki S, Kokotos G. Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A 2. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:941-956. [PMID: 30905350 PMCID: PMC7106526 DOI: 10.1016/j.bbalip.2018.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/10/2018] [Accepted: 08/16/2018] [Indexed: 11/20/2022]
Abstract
Phospholipase A2 (PLA2) enzymes are involved in various inflammatory pathological conditions including arthritis, cardiovascular and autoimmune diseases. The regulation of their catalytic activity is of high importance and a great effort has been devoted in developing synthetic inhibitors. We summarize the most important small-molecule synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated LpPLA2). We discuss recent applications of inhibitors to understand the role of each PLA2 type and their therapeutic potential. Potent and selective PLA2 inhibitors have been developed. Although some of them have been evaluated in clinical trials, none reached the market yet. Apart from their importance as potential medicinal agents, PLA2 inhibitors are excellent tools to unveil the role that each PLA2 type plays in cells and in vivo. Modern medicinal chemistry approaches are expected to generate improved PLA2 inhibitors as new agents to treat inflammatory diseases.
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Affiliation(s)
- Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Maroula G Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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18
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Huang F, Wang K, Shen J. Lipoprotein-associated phospholipase A2: The story continues. Med Res Rev 2019; 40:79-134. [PMID: 31140638 PMCID: PMC6973114 DOI: 10.1002/med.21597] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/20/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022]
Abstract
Inflammation is thought to play an important role in the pathogenesis of vascular diseases. Lipoprotein-associated phospholipase A2 (Lp-PLA2) mediates vascular inflammation through the regulation of lipid metabolism in blood, thus, it has been extensively investigated to identify its role in vascular inflammation-related diseases, mainly atherosclerosis. Although darapladib, the most advanced Lp-PLA2 inhibitor, failed to meet the primary endpoints of two large phase III trials in atherosclerosis patients cotreated with standard medical care, the research on Lp-PLA2 has not been terminated. Novel pathogenic, epidemiologic, genetic, and crystallographic studies regarding Lp-PLA2 have been reported recently, while novel inhibitors were identified through a fragment-based lead discovery strategy. More strikingly, recent clinical and preclinical studies revealed that Lp-PLA2 inhibition showed promising therapeutic effects in diabetic macular edema and Alzheimer's disease. In this review, we not only summarized the knowledge of Lp-PLA2 established in the past decades but also emphasized new findings in recent years. We hope this review could be valuable for helping researchers acquire a much deeper insight into the nature of Lp-PLA2, identify more potent and selective Lp-PLA2 inhibitors, and discover the potential indications of Lp-PLA2 inhibitors.
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Affiliation(s)
- Fubao Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China
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19
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Jacquemard C, Drwal MN, Desaphy J, Kellenberger E. Binding mode information improves fragment docking. J Cheminform 2019; 11:24. [PMID: 30903304 PMCID: PMC6431075 DOI: 10.1186/s13321-019-0346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Docking is commonly used in drug discovery to predict how ligand binds to protein target. Best programs are generally able to generate a correct solution, yet often fail to identify it. In the case of drug-like molecules, the correct and incorrect poses can be sorted by similarity to the crystallographic structure of the protein in complex with reference ligands. Fragments are particularly sensitive to scoring problems because they are weak ligands which form few interactions with protein. In the present study, we assessed the utility of binding mode information in fragment pose prediction. We compared three approaches: interaction fingerprints, 3D-matching of interaction patterns and 3D-matching of shapes. We prepared a test set composed of high-quality structures of the Protein Data Bank. We generated and evaluated the docking poses of 586 fragment/protein complexes. We observed that the best approach is twice as accurate as the native scoring function, and that post-processing is less effective for smaller fragments. Interestingly, fragments and drug-like molecules both proved to be useful references. In the discussion, we suggest the best conditions for a successful pose prediction with the three approaches.![]()
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Affiliation(s)
- Célien Jacquemard
- Laboratoire d'innovation thérapeutique, UMR7200, CNRS, Université de Strasbourg, 67400, Illkirch, France
| | - Malgorzata N Drwal
- Laboratoire d'innovation thérapeutique, UMR7200, CNRS, Université de Strasbourg, 67400, Illkirch, France
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Esther Kellenberger
- Laboratoire d'innovation thérapeutique, UMR7200, CNRS, Université de Strasbourg, 67400, Illkirch, France.
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20
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Mortenson PN, Erlanson DA, de Esch IJP, Jahnke W, Johnson CN. Fragment-to-Lead Medicinal Chemistry Publications in 2017. J Med Chem 2018; 62:3857-3872. [PMID: 30462504 DOI: 10.1021/acs.jmedchem.8b01472] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This Miniperspective is the third in a series reviewing fragment-to-lead publications from a given year. Following our reviews for 2015 and 2016, this Miniperspective provides tabulated summaries of relevant articles published in 2017 along with some general observations. In addition, we discuss insights obtained from analysis of the combined data set of 85 examples from all three years of publications.
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Affiliation(s)
- Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ , Amsterdam , The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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