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Song Q, Wang S, Lei X, Liu Y, Wen X, Wang Z. One-Pot Route from Halogenated Amides to Piperidines and Pyrrolidines. Molecules 2022; 27:molecules27154698. [PMID: 35897866 PMCID: PMC9331508 DOI: 10.3390/molecules27154698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Piperidine and pyrrolidine derivatives are important nitrogen heterocyclic structures with a wide range of biological activities. However, reported methods for their construction often face problems of requiring the use of expensive metal catalysts, highly toxic reaction reagents or hazardous reaction conditions. Herein, an efficient route from halogenated amides to piperidines and pyrrolidines was disclosed. In this method, amide activation, reduction of nitrile ions, and intramolecular nucleophilic substitution were integrated in a one-pot reaction. The reaction conditions were mild and no metal catalysts were used. The synthesis of a variety of N-substituted and some C-substituted piperidines and pyrrolidines became convenient, and good yields were obtained.
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Affiliation(s)
- Qiao Song
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Yibin 644000, China
- Correspondence: (Q.S.); (Z.W.)
| | - Sheng Wang
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
| | - Xiangui Lei
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Yibin 644000, China
| | - Yan Liu
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
| | - Xin Wen
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
| | - Zhouyu Wang
- Department of Chemistry, Xihua University, Chengdu 610039, China; (S.W.); (X.L.); (Y.L.); (X.W.)
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Yibin 644000, China
- Correspondence: (Q.S.); (Z.W.)
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2
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Axen SD, Huang XP, Cáceres EL, Gendelev L, Roth BL, Keiser MJ. A Simple Representation of Three-Dimensional Molecular Structure. J Med Chem 2017; 60:7393-7409. [PMID: 28731335 DOI: 10.1021/acs.jmedchem.7b00696] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Statistical and machine learning approaches predict drug-to-target relationships from 2D small-molecule topology patterns. One might expect 3D information to improve these calculations. Here we apply the logic of the extended connectivity fingerprint (ECFP) to develop a rapid, alignment-invariant 3D representation of molecular conformers, the extended three-dimensional fingerprint (E3FP). By integrating E3FP with the similarity ensemble approach (SEA), we achieve higher precision-recall performance relative to SEA with ECFP on ChEMBL20 and equivalent receiver operating characteristic performance. We identify classes of molecules for which E3FP is a better predictor of similarity in bioactivity than is ECFP. Finally, we report novel drug-to-target binding predictions inaccessible by 2D fingerprints and confirm three of them experimentally with ligand efficiencies from 0.442-0.637 kcal/mol/heavy atom.
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Affiliation(s)
- Seth D Axen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine , Chapel Hill, North Carolina 27599, United States.,National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Elena L Cáceres
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Leo Gendelev
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine , Chapel Hill, North Carolina 27599, United States.,National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina , Chapel Hill, North Carolina 27599, United States.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Michael J Keiser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, and Institute for Computational Health Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States
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3
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Levoin N, Labeeuw O, Billot X, Calmels T, Danvy D, Krief S, Berrebi-Bertrand I, Lecomte JM, Schwartz JC, Capet M. Discovery of nanomolar ligands with novel scaffolds for the histamine H4 receptor by virtual screening. Eur J Med Chem 2016; 125:565-572. [PMID: 27718472 DOI: 10.1016/j.ejmech.2016.09.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/29/2022]
Abstract
The involvement of histamine H4 receptor (H4R) in immune cells chemotaxis and mediator release makes it an attractive target for the treatment of inflammation disorders. A decade of medicinal chemistry efforts has led to several promising ligands, although the chemical structures described so far possesses a singular limited diversity. We report here the discovery of novel structures, belonging to completely different scaffolds. The virtual screening was planed as a two-steps process. First, using a "scout screening" methodology, we have experimentally probed the H4R ligand binding site using a small size chemical library with very diverse structures, and identified a hit that further assist us in refining a raw 3D homology model. Second, the refined 3D model was used to conduct a widened virtual screening. This two-steps strategy proved to be very successful, both in terms of structural diversity and hit rate (23%). Moreover, the hits have high affinity for the H4R, with most potent ligands in the nanomolar range.
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Affiliation(s)
- Nicolas Levoin
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France.
| | - Olivier Labeeuw
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Xavier Billot
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Thierry Calmels
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Denis Danvy
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | - Stéphane Krief
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | | | - Jeanne-Marie Lecomte
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
| | | | - Marc Capet
- Bioprojet-Biotech, 4rue du Chesnay Beauregard, 35762 Saint-Gregoire Cedex, France
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4
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Baumann M, Baxendale IR. An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles. Beilstein J Org Chem 2013. [DOI: 10.3762/bjoc.9.265 pmid: 24204439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This review which is the second in this series summarises the most common synthetic routes as applied to the preparation of many modern pharmaceutical compounds categorised as containing a six-membered heterocyclic ring. The reported examples are based on the top retailing drug molecules combining synthetic information from both scientific journals and the wider patent literature. It is hoped that this compilation, in combination with the previously published review on five-membered rings, will form a comprehensive foundation and reference source for individuals interested in medicinal, synthetic and preparative chemistry.
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Baumann M, Baxendale IR. An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles. Beilstein J Org Chem 2013; 9:2265-319. [PMID: 24204439 PMCID: PMC3817479 DOI: 10.3762/bjoc.9.265] [Citation(s) in RCA: 530] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/09/2013] [Indexed: 12/13/2022] Open
Abstract
This review which is the second in this series summarises the most common synthetic routes as applied to the preparation of many modern pharmaceutical compounds categorised as containing a six-membered heterocyclic ring. The reported examples are based on the top retailing drug molecules combining synthetic information from both scientific journals and the wider patent literature. It is hoped that this compilation, in combination with the previously published review on five-membered rings, will form a comprehensive foundation and reference source for individuals interested in medicinal, synthetic and preparative chemistry.
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Affiliation(s)
- Marcus Baumann
- Department of Chemistry, University of Durham, South Road, Durham, DH1 3LE, UK
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6
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Synthesis, characterization, and biological assessment of the four stereoisomers of the H3 receptor antagonist 5-fluoro-2-methyl-N-[2-methyl-4-(2-methyl[1,3′]bipyrrolidinyl-1′-yl)phenyl]benzamide. Bioorg Med Chem Lett 2013; 23:4044-7. [DOI: 10.1016/j.bmcl.2013.05.068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 11/17/2022]
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7
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Bordi F, Rivara S, Dallaturca E, Carmi C, Pala D, Lodola A, Vacondio F, Flammini L, Bertoni S, Ballabeni V, Barocelli E, Mor M. Dibasic biphenyl H3 receptor antagonists: Steric tolerance for a lipophilic side chain. Eur J Med Chem 2012; 48:214-30. [DOI: 10.1016/j.ejmech.2011.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/07/2011] [Accepted: 12/10/2011] [Indexed: 10/14/2022]
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8
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Kruger FA, Overington JP. Global analysis of small molecule binding to related protein targets. PLoS Comput Biol 2012; 8:e1002333. [PMID: 22253582 PMCID: PMC3257267 DOI: 10.1371/journal.pcbi.1002333] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/16/2011] [Indexed: 11/29/2022] Open
Abstract
We report on the integration of pharmacological data and homology information for a large scale analysis of small molecule binding to related targets. Differences in small molecule binding have been assessed for curated pairs of human to rat orthologs and also for recently diverged human paralogs. Our analysis shows that in general, small molecule binding is conserved for pairs of human to rat orthologs. Using statistical tests, we identified a small number of cases where small molecule binding is different between human and rat, some of which had previously been reported in the literature. Knowledge of species specific pharmacology can be advantageous for drug discovery, where rats are frequently used as a model system. For human paralogs, we demonstrate a global correlation between sequence identity and the binding of small molecules with equivalent affinity. Our findings provide an initial general model relating small molecule binding and sequence divergence, containing the foundations for a general model to anticipate and predict within-target-family selectivity. Many drugs are small molecules that specifically bind to proteins involved in disease related processes. In this way, drugs modulate the function of a targeted protein and ultimately the process causing the disease. The development of drugs crucially relies on assays that measure the potency of the effect a small molecule exerts on its protein target. We compared the potencies of small molecules measured for human proteins and the corresponding (orthologous) protein in rat. Our results suggest that, after subtraction of statistical noise, most human proteins are equally susceptible to small molecule binding as their orthologs in rats. However, we identified a small number of exceptions to this rule, for example the histamine H3 receptor, a protein of the central nervous system. We also compared the potency of small molecules measured against a human protein and another member of the same protein family. In drug development it is often desired to target a protein selectively over other related proteins. The observed differences were generally greater than the statistical noise, indicating that most of the small molecules in our study have some degree of selectivity within protein families.
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9
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Identification of biaryl sulfone derivatives as antagonists of the histamine H3 receptor: Discovery of (R)-1-(2-(4′-(3-methoxypropylsulfonyl)biphenyl-4-yl)ethyl)-2-methylpyrrolidine (APD916). Bioorg Med Chem Lett 2012; 22:71-5. [DOI: 10.1016/j.bmcl.2011.11.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/14/2011] [Accepted: 11/18/2011] [Indexed: 11/20/2022]
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10
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Wijtmans M, Denonne F, Célanire S, Gillard M, Hulscher S, Delaunoy C, Van houtvin N, Bakker RA, Defays S, Gérard J, Grooters L, Hubert D, Timmerman H, Leurs R, Talaga P, de Esch IJP, Provins L. Histamine H3 receptor ligands with a 3-cyclobutoxy motif: a novel and versatile constraint of the classical 3-propoxy linker. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00056f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Covel JA, Santora VJ, Smith JM, Hayashi R, Gallardo C, Weinhouse MI, Ibarra JB, Schultz JA, Park DM, Estrada SA, Hofilena BJ, Pulley MD, Smith BM, Ren A, Suarez M, Frazer J, Edwards J, Hauser EK, Lorea J, Semple G, Grottick AJ. Design and Evaluation of Novel Biphenyl Sulfonamide Derivatives with Potent Histamine H3 Receptor Inverse Agonist Activity. J Med Chem 2009; 52:5603-11. [DOI: 10.1021/jm900857n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan A. Covel
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Vincent J. Santora
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Jeffrey M. Smith
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Rena Hayashi
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | | | | | - Jason B. Ibarra
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Jeffrey A. Schultz
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Douglas M. Park
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Scott A. Estrada
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Brian J. Hofilena
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Michelle D. Pulley
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Brian M. Smith
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Albert Ren
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Marissa Suarez
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - John Frazer
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Jeffrey Edwards
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Erin K. Hauser
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Jodie Lorea
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Graeme Semple
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
| | - Andrew J. Grottick
- Arena Pharmaceuticals, 6166 Nancy Ridge Drive, San Diego, California 92121
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12
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Novel H3 receptor antagonists with improved pharmacokinetic profiles. Bioorg Med Chem Lett 2008; 18:4133-6. [DOI: 10.1016/j.bmcl.2008.05.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 05/20/2008] [Accepted: 05/21/2008] [Indexed: 11/24/2022]
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13
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Sander K, Kottke T, Stark H. Histamine H3 Receptor Antagonists Go to Clinics. Biol Pharm Bull 2008; 31:2163-81. [DOI: 10.1248/bpb.31.2163] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kerstin Sander
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Pharmazeutische Chemie
| | - Tim Kottke
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Pharmazeutische Chemie
| | - Holger Stark
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Pharmazeutische Chemie
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