1
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Cheng Z, Chen J, Zhang Y, Shao Y, Sun J, Tang S. Decarboxylative Cyclization of Ethynyl Benzoxazinanones with Imidazolidines to Access 2,3-Indole-Fused 1,4-Diazocines. Org Lett 2024; 26:4863-4867. [PMID: 38833707 DOI: 10.1021/acs.orglett.4c01279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
2,3-Indole-fused 1,4-diazocines represent a new family of indole alkaloid compounds and are difficult to access by the reported protocols. Herein, we report a copper-catalyzed decarboxylative cyclization of cyclic propargylic carbamates with imidazolidines via sequential C-N/C-N/C-C bond formation to deliver a series of 2,3-indole-fused 1,4-diazocines, with a broad substrate scope and mild conditions.
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Affiliation(s)
- Zhangru Cheng
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Jiadong Chen
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Yulu Zhang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Ying Shao
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Jiangtao Sun
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Shengbiao Tang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
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2
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Basilico N, Parapini S, D'Alessandro S, Misiano P, Romeo S, Dondio G, Yardley V, Vivas L, Nasser S, Rénia L, Russell BM, Suwanarusk R, Nosten F, Sparatore A, Taramelli D. Favorable Preclinical Pharmacological Profile of a Novel Antimalarial Pyrrolizidinylmethyl Derivative of 4-amino-7-chloroquinoline with Potent In Vitro and In Vivo Activities. Biomolecules 2023; 13:biom13050836. [PMID: 37238706 DOI: 10.3390/biom13050836] [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: 03/09/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The 4-aminoquinoline drugs, such as chloroquine (CQ), amodiaquine or piperaquine, are still commonly used for malaria treatment, either alone (CQ) or in combination with artemisinin derivatives. We previously described the excellent in vitro activity of a novel pyrrolizidinylmethyl derivative of 4-amino-7-chloroquinoline, named MG3, against P. falciparum drug-resistant parasites. Here, we report the optimized and safer synthesis of MG3, now suitable for a scale-up, and its additional in vitro and in vivo characterization. MG3 is active against a panel of P. vivax and P. falciparum field isolates, either alone or in combination with artemisinin derivatives. In vivo MG3 is orally active in the P. berghei, P. chabaudi, and P. yoelii models of rodent malaria with efficacy comparable, or better, than that of CQ and of other quinolines under development. The in vivo and in vitro ADME-Tox studies indicate that MG3 possesses a very good pre-clinical developability profile associated with an excellent oral bioavailability, and low toxicity in non-formal preclinical studies on rats, dogs, and non-human primates (NHP). In conclusion, the pharmacological profile of MG3 is in line with those obtained with CQ or the other quinolines in use and seems to possess all the requirements for a developmental candidate.
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Affiliation(s)
- Nicoletta Basilico
- Dipartimento di Scienze Biomediche, Chirurgiche e Odontoiatriche (DiSBIOC), Università Degli Studi di Milano, Via Pascal 36, 20133 Milan, Italy
| | - Silvia Parapini
- Dipartimento di Scienze Biomediche per la Salute, Università Degli Studi di Milano, Via Pascal 36, 20133 Milan, Italy
| | - Sarah D'Alessandro
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DISFEB), Università Degli Studi di Milano, Via Pascal 36, 20133 Milan, Italy
| | - Paola Misiano
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DISFEB), Università Degli Studi di Milano, Via Pascal 36, 20133 Milan, Italy
| | - Sergio Romeo
- Dipartimento di Scienze Farmaceutiche (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giulio Dondio
- Aphad Srl, Via della Resistenza 65, Buccinasco, 20090 Milan, Italy
| | - Vanessa Yardley
- Department of Immunology Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine (LSHTM), Keppel Street, London WC1E 7HT, UK
| | - Livia Vivas
- Department of Immunology Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine (LSHTM), Keppel Street, London WC1E 7HT, UK
| | - Shereen Nasser
- Department of Immunology Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine (LSHTM), Keppel Street, London WC1E 7HT, UK
| | - Laurent Rénia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- A*STAR Infectious Diseases Labs, Agency for Science, Technology, and Research, Singapore 138648, Singapore
| | - Bruce M Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Rossarin Suwanarusk
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sparatore
- Dipartimento di Scienze Farmaceutiche (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Donatella Taramelli
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DISFEB), Università Degli Studi di Milano, Via Pascal 36, 20133 Milan, Italy
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3
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Synthesis, antibacterial evaluation, crystal structure, molecular interaction analysis and DFT calculations of novel N-hydroxy-2-(4-methylbenzamido)benzamide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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4
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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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5
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Tong X, Liu X, Tan X, Li X, Jiang J, Xiong Z, Xu T, Jiang H, Qiao N, Zheng M. Generative Models for De Novo Drug Design. J Med Chem 2021; 64:14011-14027. [PMID: 34533311 DOI: 10.1021/acs.jmedchem.1c00927] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Artificial intelligence (AI) is booming. Among various AI approaches, generative models have received much attention in recent years. Inspired by these successes, researchers are now applying generative model techniques to de novo drug design, which has been considered as the "holy grail" of drug discovery. In this Perspective, we first focus on describing models such as recurrent neural network, autoencoder, generative adversarial network, transformer, and hybrid models with reinforcement learning. Next, we summarize the applications of generative models to drug design, including generating various compounds to expand the compound library and designing compounds with specific properties, and we also list a few publicly available molecular design tools based on generative models which can be used directly to generate molecules. In addition, we also introduce current benchmarks and metrics frequently used for generative models. Finally, we discuss the challenges and prospects of using generative models to aid drug design.
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Affiliation(s)
- Xiaochu Tong
- 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaohong Liu
- 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaoqin Tan
- 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xutong 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jiaxin Jiang
- 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
| | - Zhaoping Xiong
- Laboratory of Health Intelligence, Huawei Technologies Co., Ltd, Shenzhen 518100, China
| | | | - Hualiang Jiang
- 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Nan Qiao
- Laboratory of Health Intelligence, Huawei Technologies Co., Ltd, Shenzhen 518100, 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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6
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Meier K, Arús‐Pous J, Reymond J. A Potent and Selective Janus Kinase Inhibitor with a Chiral 3D‐Shaped Triquinazine Ring System from Chemical Space. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kris Meier
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Josep Arús‐Pous
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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7
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Meier K, Arús‐Pous J, Reymond J. A Potent and Selective Janus Kinase Inhibitor with a Chiral 3D‐Shaped Triquinazine Ring System from Chemical Space. Angew Chem Int Ed Engl 2020; 60:2074-2077. [DOI: 10.1002/anie.202012049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/25/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Kris Meier
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Josep Arús‐Pous
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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8
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Synthesis of saturated nitrogen heterocycles by Strecker reaction – nucleophilic cyclization. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Abstract
Advances in computer processing speed and storage capacity have enabled researchers to generate virtual chemical libraries containing billions of molecules. While these numbers appear large, they are only a small fraction of the number of organic molecules that could potentially be synthesized. This review provides an overview of recent advances in the generation and use of virtual chemical libraries in medicinal chemistry. We also consider the practical implications of these libraries in drug discovery programs and highlight a number of current and future challenges.
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Affiliation(s)
- W Patrick Walters
- Relay Therapeutics , 215 First Street , Cambridge , Massachusetts 02142 , United States
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10
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Yamamoto T, Togo H. One-Pot Preparation of Aromatic Amides, 4-Arylthiazoles, and 4-Arylimidazoles from Arenes. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Takahiro Yamamoto
- Graduate School of Science; Chiba University; Yayoi-cho 1-33 263-8522 Inage-ku Chiba Japan
| | - Hideo Togo
- Graduate School of Science; Chiba University; Yayoi-cho 1-33 263-8522 Inage-ku Chiba Japan
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11
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Novel ethanocycloheptono [3,4,5-kl]benzo[a]xanthene induces apoptosis in BEL-7402 cells. Mol Cell Biochem 2018; 445:145-156. [DOI: 10.1007/s11010-017-3260-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/23/2017] [Indexed: 12/31/2022]
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12
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Visini R, Arús-Pous J, Awale M, Reymond JL. Virtual Exploration of the Ring Systems Chemical Universe. J Chem Inf Model 2017; 57:2707-2718. [PMID: 29019686 DOI: 10.1021/acs.jcim.7b00457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Josep Arús-Pous
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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13
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Sparling BA, DiMauro EF. Progress in the discovery of small molecule modulators of the Cys-loop superfamily receptors. Bioorg Med Chem Lett 2017; 27:3207-3218. [DOI: 10.1016/j.bmcl.2017.04.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022]
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14
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Gao P, Bai Z. Carbon Tetrabromide/Triphenylphosphine-Activated Beckmann Rearrangement of Ketoximes for Synthesis of Amides. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201700191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Peng Gao
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering; Baoji University of Arts and Sciences; Baoji Shaanxi 721013 China
| | - Zijing Bai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering; Baoji University of Arts and Sciences; Baoji Shaanxi 721013 China
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15
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Abstract
To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity. The database is available at www.gdb.unibe.ch for download and free use, together with an interactive visualization application and a Web-based nearest neighbor search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
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16
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Pradhan S, Shahi CK, Bhattacharyya A, Chauhan N, Ghorai MK. Divergent and Stereospecific Routes to Five to Eight-Membered 1,3- and 1,4-Di-Aza-Heterocycles via Ring-Opening Cyclization of Activated Aziridines with Aryl Amines. ChemistrySelect 2017. [DOI: 10.1002/slct.201602062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sajan Pradhan
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur 208016, Uttar Pradesh India
| | - Chandan Kumar Shahi
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur 208016, Uttar Pradesh India
| | - Aditya Bhattacharyya
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur 208016, Uttar Pradesh India
| | - Navya Chauhan
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur 208016, Uttar Pradesh India
| | - Manas K. Ghorai
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur 208016, Uttar Pradesh India
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17
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Bürgi JJ, Bertrand S, Marger F, Bertrand D, Reymond J. Fluorescent Agonists of the
α
7 Nicotinic Acetylcholine Receptor Derived from 3‐Amino‐Quinuclidine. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Justus J. Bürgi
- Department of Chemistry and Biochemistry University of Berne Freiestrasse 3 CH‐3012 Berne
| | - Sonia Bertrand
- HiQScreen Sàrl 6 route de Compois CH‐1222 Vésenaz Geneva
| | - Fabrice Marger
- HiQScreen Sàrl 6 route de Compois CH‐1222 Vésenaz Geneva
| | | | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Berne Freiestrasse 3 CH‐3012 Berne
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18
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Momeni Z, Ebrahimi A. The influence of CH…π interaction on hydrogen bonding ability of –CONH2 functional group of benzamide. Struct Chem 2016. [DOI: 10.1007/s11224-016-0745-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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20
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Momeni Z, Ebrahimi A. Investigation of the effect of π–π stacking interaction on the properties of –CONH2 functional group of benzamide. Struct Chem 2015. [DOI: 10.1007/s11224-015-0615-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Abstract
One of the simplest questions that can be asked about molecular diversity is how many organic molecules are possible in total? To answer this question, my research group has computationally enumerated all possible organic molecules up to a certain size to gain an unbiased insight into the entire chemical space. Our latest database, GDB-17, contains 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens, by far the largest small molecule database reported to date. Molecules allowed by valency rules but unstable or nonsynthesizable due to strained topologies or reactive functional groups were not considered, which reduced the enumeration by at least 10 orders of magnitude and was essential to arrive at a manageable database size. Despite these restrictions, GDB-17 is highly relevant with respect to known molecules. Beyond enumeration, understanding and exploiting GDBs (generated databases) led us to develop methods for virtual screening and visualization of very large databases in the form of a "periodic system of molecules" comprising six different fingerprint spaces, with web-browsers for nearest neighbor searches, and the MQN- and SMIfp-Mapplet application for exploring color-coded principal component maps of GDB and other large databases. Proof-of-concept applications of GDB for drug discovery were realized by combining virtual screening with chemical synthesis and activity testing for neurotransmitter receptor and transporter ligands. One surprising lesson from using GDB for drug analog searches is the incredible depth of chemical space, that is, the fact that millions of very close analogs of any molecule can be readily identified by nearest-neighbor searches in the MQN-space of the various GDBs. The chemical space project has opened an unprecedented door on chemical diversity. Ongoing and yet unmet challenges concern enumerating molecules beyond 17 atoms and synthesizing GDB molecules with innovative scaffolds and pharmacophores.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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22
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Li GB, Yang LL, Yuan Y, Zou J, Cao Y, Yang SY, Xiang R, Xiang M. Virtual screening in small molecule discovery for epigenetic targets. Methods 2015; 71:158-66. [DOI: 10.1016/j.ymeth.2014.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/27/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022] Open
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23
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Cui B, Yu J, Yu FC, Li YM, Chang KJ, Shen Y. Synthesis of (1R,4R)-2,5-diazabicyclo[2.2.1]heptane derivatives by an epimerization–lactamization cascade reaction. RSC Adv 2015. [DOI: 10.1039/c4ra13611j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An epimerization–lactamization cascade of functionalized (2S,4R)-4-aminoproline methyl esters is developed and applied in synthesizing (1R,4R)-2,5-diazabicyclo[2.2.1]heptane (DBH) derivatives.
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Affiliation(s)
- Benqiang Cui
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
| | - Jie Yu
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
| | - Fu-Chao Yu
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
| | - Ya-Min Li
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
| | - Kwen-Jen Chang
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
| | - Yuehai Shen
- Faculty of Life Sciences and Technology
- Kunming University of Science and Technology
- Kunming
- China
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Thiazole: a promising heterocycle for the development of potent CNS active agents. Eur J Med Chem 2014; 92:1-34. [PMID: 25544146 DOI: 10.1016/j.ejmech.2014.12.031] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/10/2014] [Accepted: 12/18/2014] [Indexed: 01/15/2023]
Abstract
Thiazole is a valuable scaffold in the field of medicinal chemistry and has accounted to display a variety of biological activities. Thiazole and its derivatives have attracted continuing interest to design various novel CNS active agents. In the past few decades, thiazoles have been widely used to develop a variety of therapeutic agents against numerous CNS targets. Thiazole containing drug molecules are currently being used in treatment of various CNS disorders and a number of thiazole derivatives are also presently in clinical trials. A lot of research has been carried out on thiazole and their analogues, which has proved their efficacy to overcome several CNS disorders in rodent as well as primate models. The aim of present review is to highlights diverse CNS activities displayed by thiazole and their derivatives. SAR of this nucleus has also been well discussed. This review covers the recent updates present in literature and will surely provide a greater insight for the designing and development of potent thiazole based CNS active agents in future.
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Awale M, Reymond JL. Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. J Chem Inf Model 2014; 54:1892-907. [DOI: 10.1021/ci500232g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mahendra Awale
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne Switzerland
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Bürgi JJ, Awale M, Boss SD, Schaer T, Marger F, Viveros-Paredes JM, Bertrand S, Gertsch J, Bertrand D, Reymond JL. Discovery of potent positive allosteric modulators of the α3β2 nicotinic acetylcholine receptor by a chemical space walk in ChEMBL. ACS Chem Neurosci 2014; 5:346-59. [PMID: 24593915 DOI: 10.1021/cn4002297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
While a plethora of ligands are known for the well studied α7 and α4β2 nicotinic acetylcholine receptor (nAChR), only very few ligands address the related α3β2 nAChR expressed in the central nervous system and at the neuromuscular junction. Starting with the public database ChEMBL organized in the chemical space of Molecular Quantum Numbers (MQN, a series of 42 integer value descriptors of molecular structure), a visual survey of nearest neighbors of the α7 nAChR partial agonist N-(3R)-1-azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) pointed to N-(2-halobenzyl)-3-aminoquinuclidines as possible nAChR modulators. This simple "chemical space walk" was performed using a web-browser available at www.gdb.unibe.ch . Electrophysiological recordings revealed that these ligands represent a new and to date most potent class of positive allosteric modulators (PAMs) of the α3β2 nAChR, which also exert significant effects in vivo. The present discovery highlights the value of surveying chemical space neighbors of known drugs within public databases to uncover new pharmacology.
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Affiliation(s)
- Justus J. Bürgi
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Silvan D. Boss
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Tifany Schaer
- HiQScreen, 6 rte de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Fabrice Marger
- HiQScreen, 6 rte de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Juan M. Viveros-Paredes
- Departamento
de Farmacobiología CUCEI, Universidad de Guadalajara, 44430 Guadalajara, Jalisco, México
| | - Sonia Bertrand
- HiQScreen, 6 rte de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Jürg Gertsch
- Institute
of Biochemistry and Molecular Medicine, University of Berne, Bühlstrasse 28, 3012 Berne, Switzerland
| | - Daniel Bertrand
- HiQScreen, 6 rte de Compois, 1222 Vésenaz, Geneva, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Molgó J, Aráoz R, Benoit E, Iorga BI. Physical and virtual screening methods for marine toxins and drug discovery targeting nicotinic acetylcholine receptors. Expert Opin Drug Discov 2013; 8:1203-23. [DOI: 10.1517/17460441.2013.822365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ruddigkeit L, Blum LC, Reymond JL. Visualization and virtual screening of the chemical universe database GDB-17. J Chem Inf Model 2013; 53:56-65. [PMID: 23259841 DOI: 10.1021/ci300535x] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The chemical universe database GDB-17 contains 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens obeying rules for chemical stability, synthetic feasibility, and medicinal chemistry. GDB-17 was analyzed using 42 integer value descriptors of molecular structure which we term "Molecular Quantum Numbers" (MQN). Principal component analysis and representation of the (PC1, PC2)-plane provided a graphical overview of the GDB-17 chemical space. Rapid ligand-based virtual screening (LBVS) of GDB-17 using the city-block distance CBD(MQN) as a similarity search measure was enabled by a hashed MQN-fingerprint. LBVS of the entire GDB-17 and of selected subsets identified shape similar, scaffold hopping analogs (ROCS > 1.6 and T(SF) < 0.5) of 15 drugs. Over 97% of these analogs occurred within CBD(MQN) ≤ 12 from each drug, a constraint which might help focus advanced virtual screening. An MQN-searchable 50 million subset of GDB-17 is publicly available at www.gdb.unibe.ch .
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Affiliation(s)
- Lars Ruddigkeit
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Ruddigkeit L, van Deursen R, Blum LC, Reymond JL. Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. J Chem Inf Model 2012; 52:2864-75. [DOI: 10.1021/ci300415d] [Citation(s) in RCA: 629] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lars Ruddigkeit
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Ruud van Deursen
- Biomolecular Screening Facility,
NCCR Chemical Biology, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015
Lausanne, Switzerland
| | - Lorenz C. Blum
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Abstract
Cyanoguanidine is an inexpensive commodity chemical and it is found to be a useful reagent for the direct Friedel-Crafts carboxamidation of arenes. The reaction works best in an excess of Brønsted superacid, an observation suggesting the involvement of a superelectrophilic intermediate. Theoretical calculations indicate that the most stable diprotonated species involves protonation at the guanidine and cyano nitrogen atoms.
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