2001
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Griffen E, Leach AG, Robb GR, Warner DJ. Matched Molecular Pairs as a Medicinal Chemistry Tool. J Med Chem 2011; 54:7739-50. [DOI: 10.1021/jm200452d] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ed Griffen
- Oncology Innovative Medicines Unit, AstraZeneca Pharmaceuticals, Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Andrew G. Leach
- Cardiovascular and Gastrointestinal Innovative Medicines Unit, AstraZeneca Pharmaceuticals, 30S373 Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Graeme R. Robb
- Cardiovascular and Gastrointestinal Innovative Medicines Unit, AstraZeneca Pharmaceuticals, 30S373 Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Daniel J. Warner
- Department of Medicinal Chemistry, AstraZeneca R&D Montreal, Montreal, Quebec, H4S 1Z9, Canada
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2002
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Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, Yu B, Zhang J, Bryant SH. PubChem3D: a new resource for scientists. J Cheminform 2011; 3:32. [PMID: 21933373 PMCID: PMC3269824 DOI: 10.1186/1758-2946-3-32] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/20/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. DESCRIPTION PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. CONCLUSIONS The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.
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Affiliation(s)
- Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jie Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lianyi Han
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Siqian He
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Wenyao Shi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Vahan Simonyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yan Sun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Paul A Thiessen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Bo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jian Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
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2003
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Ballatore C, Soper JH, Piscitelli F, James M, Huang L, Atasoylu O, Huryn DM, Trojanowski JQ, Lee VMY, Brunden KR, Smith AB. Cyclopentane-1,3-dione: a novel isostere for the carboxylic acid functional group. Application to the design of potent thromboxane (A2) receptor antagonists. J Med Chem 2011; 54:6969-83. [PMID: 21863799 DOI: 10.1021/jm200980u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclopentane-1,3-diones are known to exhibit pK(a) values typically in the range of carboxylic acids. To explore the potential of the cyclopentane-1,3-dione unit as a carboxylic acid isostere, the physical-chemical properties of representative congeners were examined and compared with similar derivatives bearing carboxylic acid or tetrazole residues. These studies suggest that cyclopentane-1,3-diones may effectively substitute for the carboxylic acid functional group. To demonstrate the use of the cyclopentane-1,3-dione isostere in drug design, derivatives of a known thromboxane A(2) prostanoid (TP) receptor antagonist, 3-(3-(2-(4-chlorophenylsulfonamido)ethyl)phenyl)propanoic acid (12), were synthesized and evaluated in both functional and radioligand-binding assays. A series of mono- and disubstituted cyclopentane-1,3-dione derivatives (41-45) were identified that exhibit nanomolar IC(50) and K(d) values similar to 12. Collectively, these studies demonstrate that the cyclopentane-1,3-dione moiety comprises a novel isostere of the carboxylic acid functional group. Given the combination of the relatively strong acidity, tunable lipophilicity, and versatility of the structure, the cyclopentane-1,3-dione moiety may constitute a valuable addition to the palette of carboxylic acid isosteres.
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Affiliation(s)
- Carlo Ballatore
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States.
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2004
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Cheng YD, Hwang TL, Wang HH, Pan TL, Wu CC, Chang WY, Liu YT, Chu TC, Hsieh PW. Anthranilic acid-based inhibitors of phosphodiesterase: design, synthesis, and bioactive evaluation. Org Biomol Chem 2011; 9:7113-25. [PMID: 21847495 DOI: 10.1039/c1ob05714f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Our previous studies identified two 2-benzoylaminobenzoate derivatives 1, which potently inhibited superoxide (O(2)˙(-)) generation induced by formyl-L-methionyl-L-leucyl-L-phenylalanine (FMLP) in human neutrophils. In an attempt to improve their activities, a series of anthranilic acid derivatives were synthesized and their anti-inflammatory effects and underlying mechanisms were investigated in human neutrophils. Of these, compounds 17, 18, 46, 49, and 50 showed the most potent inhibitory effect on FMLP-induced release of O(2)˙(-) in human neutrophils with IC(50) values of 0.20, 0.16, 0.15, 0.06, and 0.29 μM, respectively. SAR analysis showed that the activities of most compounds were dependent on the ester chain length in the A ring. Conversely, a change in the linker between the A and B ring from amide to sulfonamide or N-methyl amide, as well as exchanges in the benzene rings (A or B rings) by isosteric replacements were unfavorable. Further studies indicated that inhibition of O(2)˙(-) production in human neutrophils by these anthranilic acids was associated with an elevation in cellular cAMP levels through the selective inhibition of phosphodiesterase 4. Compound 49 could be approved as a lead for the development of new drugs in the treatment of neutrophilic inflammatory diseases.
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Affiliation(s)
- Yih-Dih Cheng
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan, 33302, Taiwan
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2005
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Abstract
Direct methods for the trifluoromethylation of heteroaromatic systems are in extremely high demand in nearly every sector of chemical industry. Here we report the discovery of a general procedure using a benchtop stable trifluoromethyl radical source that functions broadly on a variety of electron deficient and rich heteroaromatic systems and demonstrates high functional group tolerance. This C-H trifluoromethylation protocol is operationally simple (avoids gaseous CF(3)I), scalable, proceeds at ambient temperature, can be used directly on unprotected molecules, and is demonstrated to proceed at the innately reactive positions of the substrate. The unique and orthogonal reactivity of the trifluoromethyl radical relative to aryl radicals has also been investigated on both a complex natural product and a pharmaceutical agent. Finally, preliminary data suggest that the regioselectivity of C-H trifluoromethylation can be fine-tuned simply by judicious solvent choice.
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2006
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Frant J, Veerendhar A, Chernilovsky T, Nedvetzki S, Vaksman O, Hoffman A, Breuer E, Reich R. Orally active, antimetastatic, nontoxic diphenyl ether-derived carbamoylphosphonate matrix metalloproteinase inhibitors. ChemMedChem 2011; 6:1471-7. [PMID: 21656908 DOI: 10.1002/cmdc.201100153] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/10/2011] [Indexed: 11/07/2022]
Abstract
Seven 4-phenoxybenzenesulfonamidopolymethylene carbamoylphosphonates (CPOs) bearing two to eight methylene units in the polymethylene chain were synthesized and evaluated as matrix metalloproteinase (MMP) inhibitors. The five lowest homologues [(CH₂)₂-₆] are selective MMP-2 inhibitors, whereas the two with the longest linkers [(CH₂)₇,₈] lack inhibitory activity. The most potent homologues are those with (CH₂)₅,₆; these two were evaluated for antimetastatic activity in a murine melanoma model and showed good potency both by oral and intraperitoneal administration without any toxic--including musculoskeletal--side effects. In contrast to the previously reported cis-ACCP, which was shown to inhibit MMP-2 for ∼30 min, the new compounds inhibit MMP activity for the duration of measurement, lasting several hours. Pharmacokinetic evaluation revealed, on the one hand, low oral bioavailability; on the other hand, a relatively large calculated volume of distribution, consistent with the observed reversible absorption of CPO 5 to hydroxyapatite, as a model for bone.
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Affiliation(s)
- Julia Frant
- Institute for Drug Research, The Hebrew University of Jerusalem, School of Pharmacy, P.O. Box 12065, Jerusalem 91120, Israel
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2007
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Moriaud F, Adcock SA, Vorotyntsev A, Doppelt-Azeroual O, Richard SB, Delfaud F. A Computational Fragment Approach by Mining the Protein Data Bank: Library Design and Bioisosterism. LIBRARY DESIGN, SEARCH METHODS, AND APPLICATIONS OF FRAGMENT-BASED DRUG DESIGN 2011. [DOI: 10.1021/bk-2011-1076.ch005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- F. Moriaud
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
| | - S. A. Adcock
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
| | - A. Vorotyntsev
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
| | - O. Doppelt-Azeroual
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
| | - S. B. Richard
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
| | - F. Delfaud
- Felix Concordia SARL, 400 av Roumanille Bât. 7, BP 309 06906 Sophia-Antipolis, France
- MEDIT SA, 2 rue du Belvedere, 91120 Palaiseau, France
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