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Robello M, Barresi E, Baglini E, Salerno S, Taliani S, Settimo FD. The Alpha Keto Amide Moiety as a Privileged Motif in Medicinal Chemistry: Current Insights and Emerging Opportunities. J Med Chem 2021; 64:3508-3545. [PMID: 33764065 PMCID: PMC8154582 DOI: 10.1021/acs.jmedchem.0c01808] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the years, researchers in drug discovery have taken advantage of the use of privileged structures to design innovative hit/lead molecules. The α-ketoamide motif is found in many natural products, and it has been widely exploited by medicinal chemists to develop compounds tailored to a vast range of biological targets, thus presenting clinical potential for a plethora of pathological conditions. The purpose of this perspective is to provide insights into the versatility of this chemical moiety as a privileged structure in drug discovery. After a brief analysis of its physical-chemical features and synthetic procedures to obtain it, α-ketoamide-based classes of compounds are reported according to the application of this motif as either a nonreactive or reactive moiety. The goal is to highlight those aspects that may be useful to understanding the perspectives of employing the α-ketoamide moiety in the rational design of compounds able to interact with a specific target.
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Affiliation(s)
- Marco Robello
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Taliani S, Da Settimo F, Martini C, Laneri S, Novellino E, Greco G. Exploiting the Indole Scaffold to Design Compounds Binding to Different Pharmacological Targets. Molecules 2020; 25:molecules25102331. [PMID: 32429433 PMCID: PMC7287756 DOI: 10.3390/molecules25102331] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Several indole derivatives have been disclosed by our research groups that have been collaborating for nearly 25 years. The results of our investigations led to a variety of molecules binding selectively to different pharmacological targets, specifically the type A γ-aminobutyric acid (GABAA) chloride channel, the translocator protein (TSPO), the murine double minute 2 (MDM2) protein, the A2B adenosine receptor (A2B AR) and the Kelch-like ECH-associated protein 1 (Keap1). Herein, we describe how these works were conceived and carried out thanks to the versatility of indole nucleus to be exploited in the design and synthesis of drug-like molecules.
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Affiliation(s)
- Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
- Correspondence: (S.T.); (G.G.); Tel.: +39-050-2219547 (S.T.); +39-081-678645 (G.G.)
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy; (F.D.S.); (C.M.)
| | - Sonia Laneri
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
| | - Giovanni Greco
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy; (S.L.); (E.N.)
- Correspondence: (S.T.); (G.G.); Tel.: +39-050-2219547 (S.T.); +39-081-678645 (G.G.)
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3
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Simeon S, Montanari D, Gleeson MP. Investigation of Factors Affecting the Performance of
in silico
Volume Distribution QSAR Models for Human, Rat, Mouse, Dog & Monkey. Mol Inform 2019; 38:e1900059. [DOI: 10.1002/minf.201900059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/03/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Saw Simeon
- Interdisciplinary Graduate Program in Bioscience, Faculty of ScienceKasetsart University Bangkok 10900 Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced StudiesKasetsart University Bangkok 10900 Thailand
| | - Dino Montanari
- DMPK and Bioanalysis, Aptuit Via Alessandro Fleming, 4 37135 Verona VR Italy
| | - Matthew Paul Gleeson
- Department of Chemistry, Faculty of ScienceKasetsart University Bangkok 10900 Thailand
- Department of Biomedical Engineering, Faculty of EngineeringKing Mongkut's Institute of Technology Ladkrabang Bangkok 10520 Thailand
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Marchand P, Antoine M, Le Baut G, Czech M, Baasner S, Günther E. Synthesis and structure-activity relationships of N-aryl(indol-3-yl)glyoxamides as antitumor agents. Bioorg Med Chem 2009; 17:6715-27. [PMID: 19682911 DOI: 10.1016/j.bmc.2009.07.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/15/2009] [Accepted: 07/22/2009] [Indexed: 11/15/2022]
Abstract
The synthesis and study of the structure-activity relationships of cytotoxic compounds based on N-pyridinyl or N-aryl-2-(1-benzylindol-3-yl)glyoxamide skeleton, represented by the lead structures D-24241 and D-24851, are described. The presence of N-(pyridin-4-yl) moiety was crucial for activity and 2-[1-(4-chloro-3-nitrobenzyl)-1H-indol-3-yl]-2-oxo-N-(pyridin-4-yl)acetamide (55), the most potent derivative, showed IC(50)=39 nM, 51 nM and 11 nM against HeLa/KB (human cervix carcinoma), L1210 (murine leukemia) and SKOV3 (human ovarian carcinoma) cell lines proliferation assay, respectively, as active as the lead compounds.
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Affiliation(s)
- Pascal Marchand
- Nantes Université, Nantes Atlantique Universités, Département de Pharmacochimie, IICiMed UPRES EA 1155, Faculté de Pharmacie, 1 rue Gaston Veil 44035 Nantes, France.
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Primofiore G, Settimo FD, Taliani S, Marini AM, Novellino E, Greco G, Lavecchia A, Besnard F, Trincavelli L, Costa B, Martini C. Novel N-(arylalkyl)indol-3-ylglyoxylylamides targeted as ligands of the benzodiazepine receptor: synthesis, biological evaluation, and molecular modeling analysis of the structure-activity relationships. J Med Chem 2001; 44:2286-97. [PMID: 11428922 DOI: 10.1021/jm010827j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of N-(arylalkyl)indol-3-ylglyoxylylamides (4-8) was synthesized as ligands of the benzodiazepine receptor (BzR) and tested for their ability to displace [(3)H]flumazenil from bovine brain membranes. The new compounds, bearing a branched (4) or a geometrically constrained benzyl/phenylethyl amide side chain (5-8), represent the continuation of our research on N-benzylindol-3-ylglyoxylylamides 1 (Da Settimo et al., 1996), N'-phenylindol-3-ylglyoxylohydrazides 2 (Da Settimo et al., 1998), and N-(indol-3-ylglyoxylyl)alanine derivatives 3 (Primofiore et al., 1989). A few indoles belonging to the previously investigated benzylamides 1 and phenylhydrazides 2 were synthesized and tested to enrich the SARs in these two series. The affinities and the GABA ratios of selected compounds for clonal mammalian alpha(1)beta(2)gamma(2), alpha(3)beta(2)gamma(2), and alpha(5)beta(3)gamma(2) BzR subtypes were also determined. It was hypothesized that the reduced flexibility of indoles 4-8 would both facilitate the mapping of the BzR binding cleft and increase the chances of conferring selectivity for the considered receptor subtypes. In the series of indoles 4, the introduction of a methyl group on the benzylic carbon with the R configuration improved affinity of the 5-substituted (5-Cl and 5-NO(2)) derivatives, whereas it was detrimental for their 5-unsubtituted (5-H) counterparts. All S enantiomers were less potent than the R ones. Replacement of the methyl with hydrophilic substituents on the benzylic carbon lowered affinity. The isoindolinylamide side chain was tolerated if the 5-position was unsubstituted (K(i) of 5a = 123 nM), otherwise affinity was abolished (5b, c). All the 2-indanylamides 6 and (S)-1-indanylamides 8 were devoid of any appreciable affinity. The 5-Cl and 5-NO(2) (R)-1-indanylamides 7b (K(i) 80 nM) and 7c (K(i) 28 nM) were the most potent among the indoles 5-8 geometrically constrained about the side chain. The 5-H (R)-1-indanylamide 7a displayed a lower affinity (K(i) 675 nM). The SARs developed from the new compounds, together with those collected from our previous studies, confirmed the hypothesis of different binding modes for 5-substituted and 5-unsubstituted indoles, suggesting that the shape of the lipophilic pocket L(1) (notation in accordance with Cook's BzR topological model) is asymmetric and highlighted the stereoelectronic and conformational properties of the amide side chain required for high potency. Several of the new indoles showed selectivity for the alpha(1)beta(2)gamma(2) subtype compared with the alpha(3)beta(2)gamma(2) and alpha(5)beta(3)gamma(2) subtypes (e.g.: 4t and 7c bind to these three BzR isoforms with K(i) values of 14 nM, 283 nM, 239 nM, and 9 nM, 1960 nM, 95 nM, respectively). The GABA ratios close to unity exhibited by all the tested compounds on each BzR subtype were predictive of an efficacy profile typical of antagonists.
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Affiliation(s)
- G Primofiore
- Dipartimento di Scienze Farmaceutiche and Dipartimento di Psichiatria, Neurobiologia, Farmacologia e Biotecnologie, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
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6
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Collins I, Davey WB, Rowley M, Quirk K, Bromidge FA, McKernan RM, Thompson SA, Wafford KA. N-(indol-3-ylglyoxylyl)piperidines: high affinity agonists of human GABA-A receptors containing the alpha1 subunit. Bioorg Med Chem Lett 2000; 10:1381-4. [PMID: 10890169 DOI: 10.1016/s0960-894x(00)00245-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new class of N-(indol-3-ylglyoxylyl)piperidines are high affinity agonists at the benzodiazepine binding site of human GABA-A receptor ion-channels, with modest selectivity for receptors containing the alpha1 subunit over alpha2 and alpha3. All three receptor subtypes discriminate substantially between the two enantiomers of the chiral ligand 10.
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Affiliation(s)
- I Collins
- Department of Medicinal Chemistry, Merck Sharp & Dohme Research Laboratories, Neuroscience Research Centre, Harlow, Essex, UK.
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Da Settimo A, Primofiore G, Da Settimo F, Marini AM, Novellino E, Greco G, Gesi M, Martini C, Giannaccini G, Lucacchini A. N'-Phenylindol-3-ylglyoxylohydrazide derivatives: synthesis, structure-activity relationships, molecular modeling studies, and pharmacological action on brain benzodiazepine receptors. J Med Chem 1998; 41:3821-30. [PMID: 9748357 DOI: 10.1021/jm9800301] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A series of N'-phenylindol-3-ylglyoxylohydrazides, isosters of the N-benzylindol-3-ylglyoxylamide derivatives previously described by us, were synthesized and tested for their ability to displace [3H]Ro 15-1788 from bovine brain membranes. These compounds were designed with the aim of obtaining products which could exert an in vivo activity, thanks to a higher hydrosolubility and consequently a better bioavailability. Affinity was restricted to the derivatives unsubstituted in the 5 position of the indole nucleus (1, 6, 9, 12, 15, 18, 23, and 26), with Ki values ranging from 510 to 11 nM. The most active compounds (6, 9, 23, and 29) proved to be effective in antagonizing pentylenetetrazole-induced seizures. Molecular modeling studies were performed to rationalize the lack of affinity of hydrazides with a chloro or a nitro group in the 5 position of the indole nucleus. It was hypothesized that the conformational preference of the hydrazide side chain, characterized by a gauche disposition of lone pairs and substituents about the N-N bond, prevents all hydrazides from binding to the receptor similarly to other classes of indole analogues previously investigated. The potency of 5-H hydrazides was attributed to a binding mode which is not feasible for 5-Cl and 5-NO2 counterparts. This theoretical model of ligand-receptor interaction permitted a more stringent interpretation of structure-affinity relationships of hydrazides and of recently described benzylamide derivatives (Da Settimo et al. J. Med. Chem. 1996, 39, 5083-5091).
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Affiliation(s)
- A Da Settimo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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8
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Gupta SP. Recent advances in benzodiazepine receptor (BZR) binding studies. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 1995; 45:67-106. [PMID: 8545542 DOI: 10.1007/978-3-0348-7164-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- S P Gupta
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, India
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9
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Campagna F, Carotti A, Casini G, Palluotto F, Genchi G, De Sarro GB. 2-Aryl-2,5-dihydropyridazino[4,3-b]indol-3(3H)-ones: novel rigid planar benzodiazepine receptor ligands. Bioorg Med Chem 1993; 1:437-46. [PMID: 8087565 DOI: 10.1016/s0968-0896(00)82154-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A series of 2-aryl-2,5-dihydropyridazino[4,3-b]indol-3(3H)-ones 5 were prepared and evaluated for their ability to inhibit radioligand binding to BZR, and to prevent sound and pentylenetetrazole (PTZ) induced seizures in mice. The biological and pharmacological results are discussed in the light of some recently proposed pharmacophore models and compared through molecular orbital and molecular modeling studies to those obtained from the close pyrazoloquinoline analogs 6.
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Affiliation(s)
- F Campagna
- Dipartimento Farmacochimico, University of Bari, Italy
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10
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Trapani G, Carotti A, Franco M, Latrofa A, Genchi G, Liso G. Structure-affinity relationships of some alkoxycarbonyl-2H-or-4H-pyrimido [2,1-b]benzothiazol-2- or 4-one benzodiazepine receptor ligands. Eur J Med Chem 1993. [DOI: 10.1016/0223-5234(93)90074-o] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Bertucci C, Salvadori P, Belfiore S, Martini C, Lucacchini A. Characterization of the enantiomeric 3-substituted-1,4-benzodiazepin-2-ones binding to the GABA-BDZ-chloride ionophore receptor complex. J Pharm Biomed Anal 1992; 10:359-63. [PMID: 1324740 DOI: 10.1016/0731-7085(92)80053-p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- C Bertucci
- Centro Studio del CNR per le Macromolecole Stereordinate Otticamente Attive, Dipartimento di Chimica e Chimica Industriale, Pisa, Italy
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12
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13
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Cecchi L, Colotta V, Melani F, Palazzino G, Filacchioni G, Martini C, Giannaccini G, Lucacchini A. Synthesis of 1,5-diaryl-3-methyl-1H-pyrazolo[4,5-c]isoquinolines and studies of binding to specific peripheral benzodiazepine binding sites. J Pharm Sci 1989; 78:437-42. [PMID: 2547927 DOI: 10.1002/jps.2600780602] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Some 1,5-diaryl-3-methyl-1H-pyrazolo[4,5-c]isoquinolines were synthesized and tested for their ability to displace [3H]clonazepam or [3H]Ro 5-4864 from their specific binding on the central and peripheral benzodiazepine receptors. None of the tested compounds showed any activity as central binding inhibitors, while most of them were specific as peripheral binding inhibitors, although they were not very potent.
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Affiliation(s)
- L Cecchi
- Dipartimento di Scienze Farmaceutiche, Università di Firenze, Italy
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Salvadori P, Bertucci C, Domenici E, Giannaccini G. Chiral 1,4-benzodiazepin-2-ones: relationship between stereochemistry and pharmacological activity. J Pharm Biomed Anal 1989; 7:1735-42. [PMID: 2562315 DOI: 10.1016/0731-7085(89)80188-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pure enantiomers of 3-substituted-1,4-benzodiazepin-2-ones, obtained by HPLC resolution on chiral stationary phases, show significant differences in their pharmacological activity. The occurrence of biotransformation during the pharmacological test is monitored using a new chromatographic method. The reliability of the pharmacological activity data is discussed.
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Affiliation(s)
- P Salvadori
- Centro di Studio del CNR per le Macromolecole Stereordinate Otticamente Attive, Dipartimento di Chimica e Chimica Industriale, Pisa, Italy
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15
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Martini C, Marrucci W, Lucacchini A, Biagi G, Livi O. Specific inhibition of benzodiazepine receptor binding by some 1,2,3-triazole derivatives. J Pharm Sci 1988; 77:977-80. [PMID: 2852246 DOI: 10.1002/jps.2600771117] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Certain 1,2,3-triazole derivatives were prepared and tested for their ability to displace [3H]diazepam from bovine brain membranes. From these compounds, the quinolytriazole derivatives (14, 15, 16, 17) were clearly the most potent, while the naphthyl- and the naphthyridyl-triazoles were considerably less active. The p-nitrophenyl derivative (15) was the compound that bound with the highest affinity within the quinolyltriazole compounds class. The replacement of the p-nitrophenyl group with other substituents greatly decreased the binding activity. From a Lineweaver-Burk analysis of 11, it appears that the inhibition is competitive.
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Affiliation(s)
- C Martini
- Istituto Policattedra di Discipline Biologiche, Università di Pisa, Italy
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16
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Da Settimo A, Primofiore G, Marini AM, Ferrarini PL, Franzone J, Cirillo R, Reboani MC. N-(Indol-3-ylglyoxylyl)methionine derivatives: preparation and gastric anti-secretory activity. Eur J Med Chem 1988. [DOI: 10.1016/0223-5234(88)90162-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Melani F, Cecchi L, Palazzino G, Filacchioni G, Martini C, Pennacchi E, Lucacchini A. Pyrazolo[4,5-c]quinolines. 3. Synthesis, receptor binding, and 13C NMR study. J Pharm Sci 1986; 75:1175-9. [PMID: 3031269 DOI: 10.1002/jps.2600751212] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Some 1-aryl-3-methylpyrazolo[4,5-c]quinolin-4-ones, were prepared and tested for their ability to displace specific [3H]flunitrazepam binding from bovine brain membranes. The 1-meta-aryl derivatives were the compounds that bound with the highest affinity within this class. Our 13C NMR study suggested a correlation between the binding affinity and the chemical shift value of a carbon atom of the tricyclic system.
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