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Beato A, Gori A, Boucherle B, Peuchmaur M, Haudecoeur R. β-Carboline as a Privileged Scaffold for Multitarget Strategies in Alzheimer's Disease Therapy. J Med Chem 2021; 64:1392-1422. [PMID: 33528252 DOI: 10.1021/acs.jmedchem.0c01887] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The natural β-carboline alkaloids display similarities with neurotransmitters that can be favorably exploited to design bioactive and bioavailable drugs for Alzheimer's disease (AD) therapy. Several AD targets are currently and intensively being investigated, divided in different hypotheses: mainly the cholinergic, the amyloid β (Aβ), and the Tau hypotheses. To date, only symptomatic treatments are available involving acetylcholinesterase and NMDA inhibitors. On the basis of plethoric single-target structure-activity relationship studies, the β-carboline scaffold was identified as a powerful tool for fostering activity and molecular interactions with a wide range of AD-related targets. This knowledge can undoubtedly be used to design multitarget-directed ligands, a highly relevant strategy preferred in the context of multifactorial pathology with intricate etiology such as AD. In this review, we first individually discuss the AD targets of the β-carbolines, and then we focus on the multitarget strategies dedicated to the deliberate design of new efficient scaffolds.
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Affiliation(s)
| | - Anthonin Gori
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France.,CHANEL Parfums Beauté, F-93500 Pantin, France
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Synthesis and pharmacological evaluation of pyrazolo[4,3-c]quinolinones as high affinity GABAA-R ligands and potential anxiolytics. Bioorg Med Chem 2018; 26:3967-3974. [DOI: 10.1016/j.bmc.2018.06.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/20/2018] [Accepted: 06/14/2018] [Indexed: 11/22/2022]
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ELİK M, Serdaroğlu G. A Computational Study of 1-substituted methyl 9-methyl-9H-pyrido[3,4-b]indole-3-carboxylate: Quantum Chemical Descriptors, FMO and NBO Analysis. ACTA ACUST UNITED AC 2017. [DOI: 10.17776/csj.356185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Good AC, Richards WG. The Extension and Application of Molecular Similarity Calculations to Drug Design. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/009286159603000206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Andrew C. Good
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California
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Phani Babu Tiruveedhula VVN, Methuku KR, Deschamps JR, Cook JM. Synthesis of aza and carbocyclic β-carbolines for the treatment of alcohol abuse. Regiospecific solution to the problem of 3,6-disubstituted β- and aza-β-carboline specificity. Org Biomol Chem 2016; 13:10705-15. [PMID: 26349488 DOI: 10.1039/c5ob01572c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel two step protocol was developed to gain regiospecific access to 3-substituted β- and aza-β-carbolines, 3-PBC (1), 3-ISOPBC (2), βCCt (3), 6-aza-3-PBC (4) and 6-aza-3-ISOPBC (5). These β-carbolines (1-3) are potential clinical agents to reduce alcohol self-administration, especially 3-ISOPBC·HCl (2·HCl) which appears to be a potent anti-alcohol agent active against binge drinking in a rat model of maternally deprived (MD) rats. The method consists of two consecutive palladium-catalyzed reactions: a Buchwald-Hartwig amination followed by an intramolecular Heck-type cyclization in high yield.
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Affiliation(s)
| | - Kashi Reddy Methuku
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA.
| | - Jeffrey R Deschamps
- Center for Bimolecular Science and Engineering, Naval Research Laboratory, Code 6930, Washington, D. C. 20375, USA
| | - James M Cook
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA.
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A Review of the Updated Pharmacophore for the Alpha 5 GABA(A) Benzodiazepine Receptor Model. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2015; 2015:430248. [PMID: 26682068 PMCID: PMC4657098 DOI: 10.1155/2015/430248] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/16/2015] [Accepted: 07/02/2015] [Indexed: 12/22/2022]
Abstract
An updated model of the GABA(A) benzodiazepine receptor pharmacophore of the α5-BzR/GABA(A) subtype has been constructed prompted by the synthesis of subtype selective ligands in light of the recent developments in both ligand synthesis, behavioral studies, and molecular modeling studies of the binding site itself. A number of BzR/GABA(A) α5 subtype selective compounds were synthesized, notably α5-subtype selective inverse agonist PWZ-029 (1) which is active in enhancing cognition in both rodents and primates. In addition, a chiral positive allosteric modulator (PAM), SH-053-2′F-R-CH3 (2), has been shown to reverse the deleterious effects in the MAM-model of schizophrenia as well as alleviate constriction in airway smooth muscle. Presented here is an updated model of the pharmacophore for α5β2γ2 Bz/GABA(A) receptors, including a rendering of PWZ-029 docked within the α5-binding pocket showing specific interactions of the molecule with the receptor. Differences in the included volume as compared to α1β2γ2, α2β2γ2, and α3β2γ2 will be illustrated for clarity. These new models enhance the ability to understand structural characteristics of ligands which act as agonists, antagonists, or inverse agonists at the Bz BS of GABA(A) receptors.
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I. Marzouk M, A. Farghaly T, A. El-Hashash M, A. Shaker S, M. Hussein S. Transformation of Benzoxazinone Derivatives to Some Interesting Heterocyclic Compounds with Expected Biological Activity. HETEROCYCLES 2015. [DOI: 10.3987/com-15-13218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kroemer RT, Hecht P, Liedl KR. Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials. J Comput Chem 2014; 17:1296-308. [PMID: 25400148 DOI: 10.1002/(sici)1096-987x(199608)17:11<1296::aid-jcc2>3.0.co;2-h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/1995] [Accepted: 10/23/1995] [Indexed: 11/11/2022]
Abstract
Comparative molecular field analysis (CoMFA) is a three-dimensional quantitative structure-activity relationship (3D-QSAR) method which correlates precalculated fields surrounding a set of molecules with some target property. Among others, the electrostatic fields are commonly used. These are usually generated by calculating the Coulomb potential between a probe and the molecules bearing atom-centered point charges. The present study was performed in order to investigate up to which extent different methods to calculate electrostatic potentials can influence the results of a CoMFA. Therefore, a variety of charge calculation methods was applied to a data set consisting of 37 ligands of the benzodiazepine receptor inverse agonist-antagonist active site. These methods included Gasteiger-Marsili, semiempirical (MNDO, AM1, and PM3), and ab initio (HF/STO-3G, HF/3-21G*, and HF/6-31G*) charges. Semiempirical as well as ab initio electron populations were derived both from the Mulliken population analysis (MPA) or from fitting the charges to the molecular electrostatic potential (ESPFIT charges). In addition, the molecular electrostatic potentials (MEPs) resulting from ab initio calculations were mapped directly onto the CoMFA grid. With regard to the cross-validated r(2) values (r(2) cv ) of the resulting QSAR models, the ESPFIT-derived potentials yielded generally higher r(2) cv values than those resulting from MPA charges. For example, at the HF/3-21G* level the r(2) cv rose from 0.61 (MPA-derived potentials) to 0.76 (ESPFIT fields). The MEPs mapped directly onto the CoMFA grid were not superior to the corresponding ESPFIT-derived potentials. Semiempirical ESPFIT charges appeared to be of similar quality compared with ab initio ESPFIT electron populations in the CoMFAs. When no scaling between the steric and electrostatic descriptor matrices was applied, the electrostatic contributions were influenced to a high degree by the magnitude of the corresponding field values. © 1996 by John Wiley & Sons, Inc.
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Affiliation(s)
- R T Kroemer
- Sandoz Forschungsinstitut GmbH, Brunnerstrasse 59, A-1235 Vienna, Austria
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Lorendeau D, Dury L, Genoux-Bastide E, Lecerf-Schmidt F, Simões-Pires C, Carrupt PA, Terreux R, Magnard S, Di Pietro A, Boumendjel A, Baubichon-Cortay H. Collateral sensitivity of resistant MRP1-overexpressing cells to flavonoids and derivatives through GSH efflux. Biochem Pharmacol 2014; 90:235-45. [DOI: 10.1016/j.bcp.2014.05.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
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Ghoshal N, Vijayan RSK. Pharmacophore models for GABA(A) modulators: implications in CNS drug discovery. Expert Opin Drug Discov 2012; 5:441-60. [PMID: 22823129 DOI: 10.1517/17460441003789363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD GABA(A) ion channel is a validated drug target, implicated in the pathophysiology of various neurological and psychiatric disorders. Structural investigations on GABA(A) are currently precluded in the absence of experimentally resolved structure. Pharmacophore modeling circumvents such issues and proves to be a powerful and successful method in drug discovery. AREAS COVERED IN THIS REVIEW The present reviews encompass pharmacophoric models available in the literature for the orthosteric GABA and the allosteric benzodiazepine binding site. Success stories from these simplistic pharmacophore models in scaffold hopping and strategic lead optimization have been highlighted. Recent advances in pharmacophore modeling that can leverage CNS drug discovery programs and deliver astounding results have been reviewed. WHAT THE READER WILL GAIN Readers are bound to gain a comprehensive insight on different computational techniques used by different groups to arrive at simple, yet sophisticated pharmacophore models. In the absence of experimentally unresolved active site geometry of GABA(A), these models will provide the reader an opportunity to translate these pharmacophoric features to the microscopic phenomenon of supramolecular ligand interaction. TAKE HOME MESSAGE Pharmacophore modeling has now evolved as a mainstay approach for lead generation and optimization in drug discovery programs. Of late, many advances in pharmacophore perception have emerged. Such advancements should be used to confront activity profiling and early stage risk assessment in a high-throughput fashion. Extending such technologies has the potential not only to reduce time and cost, but also to prevent late stage attrition in drug discovery.
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Affiliation(s)
- Nanda Ghoshal
- Indian Institute of Chemical Biology (A unit of CSIR), Structural Biology and Bioinformatics Division, 4, Raja S.C. Mullick Road, Kolkata-700032, India +91 33 2473 3491 ext. 854 ; +91 33 2473 5197 ;
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Islam MA, Pal R, Hossain T, Mukherjee A, Saha A. Molecular modeling studies on structural requirement of diarylpropionitrile for selectivity to estrogen receptor subtypes. Med Chem Res 2012. [DOI: 10.1007/s00044-011-9790-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Namjoshi OA, Gryboski A, Fonseca GO, Van Linn ML, Wang ZJ, Deschamps JR, Cook JM. Development of a two-step route to 3-PBC and βCCt, two agents active against alcohol self-administration in rodent and primate models. J Org Chem 2011; 76:4721-7. [PMID: 21495660 DOI: 10.1021/jo200425m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To gain access to 3-propoxy-β-carboline hydrochloride (3-PBC·HCl) (1·HCl) and β-carboline-3-carboxylate-tert-butyl ester (βCCt) (2), potential clinical agents active against alcohol self-administration, a two-step route was developed. This process involves a palladium-catalyzed Buchwald-Hartwig coupling and an intramolecular Heck reaction. This two-step route provides rapid access to multigram quantities of 3-PBC (1) and βCCt (2), as well as analogues for studies of alcohol self-administration. The overall yield of 3-PBC (1) was improved from 8% to 50% by this route.
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Affiliation(s)
- Ojas A Namjoshi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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Smirnova OB, Golovko TV, Granik VG. Carbolines. Part I: Comparison of some methods for the synthesis of α-, γ-, and δ-carbolines (a review). Pharm Chem J 2011. [DOI: 10.1007/s11094-011-0540-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yin W, Majumder S, Clayton T, Petrou S, VanLinn ML, Namjoshi OA, Ma C, Cromer BA, Roth BL, Platt DM, Cook JM. Design, synthesis, and subtype selectivity of 3,6-disubstituted β-carbolines at Bz/GABA(A)ergic receptors. SAR and studies directed toward agents for treatment of alcohol abuse. Bioorg Med Chem 2010; 18:7548-64. [PMID: 20888240 PMCID: PMC2972656 DOI: 10.1016/j.bmc.2010.08.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 11/29/2022]
Abstract
A series of 3,6-disubstituted β-carbolines was synthesized and evaluated for their in vitro affinities at α(x)β(3)γ(2) GABA(A)/benzodiazepine receptor subtypes by radioligand binding assays in search of α(1) subtype selective ligands to treat alcohol abuse. Analogues of β-carboline-3-carboxylate-t-butyl ester (βCCt, 1) were synthesized via a CDI-mediated process and the related 6-substituted β-carboline-3-carboxylates 6 including WYS8 (7) were synthesized via a Sonogashira or Stille coupling processes from 6-iodo-βCCt (5). The bivalent ligands of βCCt (32 and 33) were also designed and prepared via a palladium-catalyzed homocoupling process to expand the structure-activity relationships (SAR) to larger ligands. Based on the pharmacophore/receptor model, a preliminary SAR study on 34 analogues illustrated that large substituents at position-6 of the β-carbolines were well tolerated. As expected, these groups are proposed to project into the extracellular domain (L(Di) region) of GABA(A)/Bz receptors (see 32 and 33). Moreover, substituents located at position-3 of the β-carboline nucleus exhibited a conserved stereo interaction in lipophilic pocket L(1), while N(2) presumably underwent a hydrogen bonding interaction with H(1). Three novel β-carboline ligands (βCCt, 3PBC and WYS8), which preferentially bound to α1 BzR subtypes permitted a comparison of the pharmacological efficacies with a range of classical BzR antagonists (flumazenil, ZK93426) from several different structural groups and indicated these β-carbolines were 'near GABA neutral antagonists'. Based on the SAR, the most potent (in vitro) α(1) selective ligand was the 6-substituted acetylenyl βCCt (WYS8, 7). Earlier both βCCt and 3PBC had been shown to reduce alcohol self-administration in alcohol preferring (P) and high alcohol drinking (HAD) rats but had little or no effect on sucrose self-administration.(1-3) Moreover, these two β-carbolines were orally active, and in addition, were anxiolytic in P rats but were only weakly anxiolytic in rodents. These data prompted the synthesis of the β-carbolines presented here.
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Affiliation(s)
- Wenyuan Yin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201-0413
| | - Samarpan Majumder
- Department of Pharmacology and Division of Medicinal Chemistry, University of North Carolina-Chapel Hill Medical School and School of Pharmacy and NIMH Psychoactive Drug Screening Program, 120 Mason Farm Road, 4072 Genetics Medicine Bldg, Chapel Hill, NC 27599-7365
| | - Terry Clayton
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201-0413
| | - Steven Petrou
- Howard Florey Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael L. VanLinn
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201-0413
| | | | - Chunrong Ma
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201-0413
| | - Brett A. Cromer
- Howard Florey Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Bryan L. Roth
- Department of Pharmacology and Division of Medicinal Chemistry, University of North Carolina-Chapel Hill Medical School and School of Pharmacy and NIMH Psychoactive Drug Screening Program, 120 Mason Farm Road, 4072 Genetics Medicine Bldg, Chapel Hill, NC 27599-7365
| | - Donna M. Platt
- Harvard Medical School, New England Primate Research Center, One Pine Hill Drive, Box 9102, Southborough, MA 01772-9102
| | - James M. Cook
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201-0413
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Nagar S, Saha A. Modeling of diarylalkyl-imidazole and diarylalkyl-triazole derivatives as potent aromatase inhibitors for treatment of hormone-dependent cancer. J Comput Chem 2010; 31:2342-53. [PMID: 20340106 DOI: 10.1002/jcc.21528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Aromatase is an enzyme that catalyzes the final step in the conversion of androgen to estrogen. It has become an attractive target for the treatment of estrogen responsive breast cancer. The study has been focused on designing aromatase inhibitors (AIs) that can be selected as probable drug candidate for the treatment of breast cancer. In the present study, long chain diarylalkyl-imidazole and -triazole scaffolds have been considered for exploring pharmacophores as potent AIs using QSAR (Quantitative SAR) and pharmacophore mapping studies. The model generated in linear free energy QSAR study (R(2) = 0.905, Q(2)= 0.885, R(2)(pred(ts)) = 0.763) showed the importance of hydrophobicity, size and shape of the molecule, van der Waals surface and hydrogen atom contribution influence the activity. 3D QSAR of comparative molecular field analysis (CoMFA, R(2)= 0.921, Q(2) = 0.741, R(2)(pred(ts))= 0.583) showed that steric and electrostatic features along with hydrophobicity and electronic charge contribution at C(4) (Fig. 1) influence on the inhibitory activity. Comparative molecular similarity analysis (CoMSIA, R(2) = 0.874, Q(2) = 0.716, R(2)(pred(ts)) = 0.591) study adjudged the presence of steric, electrostatic and hydrophobic fields together with hydrogen bond (HB) donor and acceptor play significant role in inhibitory activity to aromatase enzyme. Further pharmacophore mapping study (Q(2) = 0.947, Delta(cost) = 113.171, R(2)(pred(ts)) = 0.857) suggested that presence of HB acceptor, hydrophobicity with aromatic ring, and the importance of steric contribution influence on the activity. The critical distances among the features are also important for the inhibitor activity.
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Affiliation(s)
- Shuchi Nagar
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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Synthesis, pharmacological studies and molecular modeling of some tetracyclic 1,3-diazepinium chlorides. Bioorg Med Chem 2009; 18:909-21. [PMID: 19962901 DOI: 10.1016/j.bmc.2009.11.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/12/2009] [Accepted: 11/14/2009] [Indexed: 11/22/2022]
Abstract
Seven new 1,3-diazepinium chlorides exhibiting some structural similarities to the 1,4-benzodiazepines were synthesized. In a Hippocratic screen using mice, three of these salts, 3-methoxy-6-oxo-7,13-dihydro-6H-benzofuro[2,3-e]pyrido[1,2-a][1,3]diazepin-12-ium chloride (8a), 3-methoxy-9-methyl-6-oxo-7,13-dihydro-6H-benzofuro[2,3-e]pyrido[1,2-a][1,3]diazepin-12-ium chloride (8c) and 3-methoxy-11-methyl-6-oxo-7,13-dihydro-6H-benzofuro[2,3-e]pyrido[1,2-a][1,3]diazepin-12-ium chloride (8e) were examined for their effect on the central nervous system, and their activities compared to that of diazepam. On their own, salts 8a, 8c and 8e solicited no sedative effects on the behaviour of the animals. However, they elicited significant effects in combination with diazepam on diazepam-induced activities such as decreased motor activity, ataxia and loss of righting reflex. Compounds 8a and 8c were fitted into the pharmacophore/receptor model developed by Cook et al. with interaction at the L(1), H(1) and A(2) sites indicating that they are potential inverse agonists of the Bz receptor. The compounds displayed some affinity for the alpha1 isoform of the GABA(A)/BzR (L(Di) interaction) but are non-selective for alpha5 (no L(2) interaction). Results of binding affinity studies showed that compound 8a is mildly selective for the alpha1 receptor although not very potent (K(i)=746.5nM). The significant potentiation of diazepam-induced ataxia and decreased motor activity by compounds 8a and 8c in the Hippocratic screen may be associated with alpha1 selectivity.
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Alekseyev RS, Kurkin AV, Yurovskaya MA. γ-Carbolines and their hydrogenated derivatives. 1. Aromatic γ-carbolines: methods of synthesis, chemical and biological properties (review). Chem Heterocycl Compd (N Y) 2009. [DOI: 10.1007/s10593-009-0373-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Neaz MM, Muddassar M, Pasha FA, Cho SJ. 2D-QSAR of non-benzodiazepines to benzodiazepines receptor (BZR). Med Chem Res 2008. [DOI: 10.1007/s00044-008-9111-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Nagar S, Islam MA, Das S, Mukherjee A, Saha A. Pharmacophore mapping of flavone derivatives for aromatase inhibition. Mol Divers 2008; 12:65-76. [PMID: 18506592 DOI: 10.1007/s11030-008-9077-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 04/20/2008] [Indexed: 11/30/2022]
Abstract
Aromatase, which catalyses the final step in the steroidogenesis pathway of estrogen, has been target for the design of inhibitor in the treatment of hormone dependent breast cancer for postmenopausal women. The extensive SAR studies performed in the last 30 years to search for potent, selective and less toxic compounds, have led to the development of second and third generation of non-steroidal aromatase inhibitors (AI). Besides the development of synthetic compounds, several naturally occurring and synthetic flavonoids, which are ubiquitous natural phenolic compounds and mediate the host of biological activities, are found to demonstrate inhibitory effects on aromatase. The present study explores the pharmacophores, i.e., the structural requirements of flavones (Fig. 1) for inhibition of aromatase activity, using quantitative structure activity relationship (QSAR) and space modeling approaches. The classical QSAR studies generate the model (R (2) = 0.924, Q (2) = 0.895, s = 0.233) that shows the importance of aromatic rings A and C, along with substitutional requirements in meta and para positions of ring C for the activity. 3D QSAR of Comparative Molecular Field Analysis (CoMFA, R (2) = 0.996, R(2)(cv) = 0.791) and Comparative Molecular Similarity Analysis (CoMSIA, R (2) = 0.992, R(2)(cv) = 0.806) studies show contour maps of steric and hydrophobic properties and contribution of acceptor and donor of the molecule, suggesting the presence of steric hindrance due to ring C and R''-substituent, bulky hydrophobic substitution in ring A, along with acceptors at positions 11, and alpha and gamma of imidazole ring, and donor in ring C favor the inhibitory activity. Further space modeling (CATALYST) study (R = 0.941, Delta( cost ) = 96.96, rmsd = 0.876) adjudge the presence of hydrogen bond acceptor (keto functional group), hydrophobic (ring A) and aromatic rings (steric hindrance) along with critical distance among features are important for the inhibitory activity.
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Affiliation(s)
- Shuchi Nagar
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
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Pasha FA, Muddassar M, Cho SJ, Ahmad K, Beg Y. 3D and quantum QSAR of non-benzodiazepine compounds. Eur J Med Chem 2008; 43:2361-72. [PMID: 18346822 DOI: 10.1016/j.ejmech.2008.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 12/19/2007] [Accepted: 01/10/2008] [Indexed: 11/19/2022]
Abstract
A combined physicochemical and 3D technique is used to establish the QSAR of four series of non-benzodiazepines towards BzR. In physicochemical QSAR study, the semi-empirical PM3 based parameters like hardness, electronegativity, electrophilicity index, molar refractivity, heat of formation, solvent assessable surface area and logP were used as descriptors. The heat of formation (HF) and logP are recognized as the most important descriptors for binding affinity of such compounds to BzR. The 3D QSAR study reveals that beta-Carbolines of series "A" and Imidazo[1, 2-alpha]pyrimidines of series "C" show steric bulk interaction, the beta-Carbolines of series "B" and di-substituted purines of series "D" have dominance of electrostatic interaction with BzR. The CoMSIA also indicate the same trend in terms of steric and electrostatic interaction. The CoMSIA reveals that only in case of series "D", the hydrophobic field effect is important. Some possible candidates for all four series were designed and their probable activities were estimated by using different QSAR models. The activities of designed molecules are in better range and developed models might be helpful to design the potent ligands of BzR.
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Affiliation(s)
- F A Pasha
- Computational Science Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, Republic of Korea.
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Guan H, Chen H, Peng W, Ma Y, Cao R, Liu X, Xu A. Design of β-carboline derivatives as DNA-targeting antitumor agents. Eur J Med Chem 2006; 41:1167-79. [PMID: 16790297 DOI: 10.1016/j.ejmech.2006.05.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/29/2006] [Accepted: 05/05/2006] [Indexed: 11/21/2022]
Abstract
This research studied the structure-activity relationship of beta-carboline derivatives as antitumor agents, in which 41 synthesized compounds and their cytotoxicity to tumor and normal cell lines were assayed. It was proved that substituent in position-9 of the beta-carboline ring could reinforce the DNA intercalating ability and consequently cytotoxicity to tumor cell lines, and the amidation of amino group at the end of the DNA targeting side chain in position-3 could cripple the DNA intercalating activity of these compounds, which resultingly initiated the cytotoxic selectivity to tumor cell lines rather than to normal ones. Furthermore, the S and G2-M arrest induced by these compounds confirmed that they could target DNA and lead to DNA destructions in Hela cells. In short, this study may provide a framework to design a novel antitumor drug that could surpass Adriamycin.
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Affiliation(s)
- Huaji Guan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135, Xin Gang Xi Road, Guangzhou 510275, China
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23
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24
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Chang WJ, Kulkarni MV, Sun CM. Traceless and Stereoselective Synthesis of Tetrahydro-β-carbolinethiohydantoins by Microwave Irradiation. ACTA ACUST UNITED AC 2006; 8:141-4. [PMID: 16529504 DOI: 10.1021/cc050098j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wong-Jin Chang
- Laboratory of Combinatorial Drug Discovery, Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300-10, Taiwan
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25
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Ferlin MG, Chiarelotto G, Dall'Acqua S, Maciocco E, Mascia MP, Pisu MG, Biggio G. Novel anellated pyrazoloquinolin-3-ones: synthesis and in vitro BZR activity. Bioorg Med Chem 2005; 13:3531-41. [PMID: 15848766 DOI: 10.1016/j.bmc.2005.02.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 02/10/2005] [Accepted: 02/18/2005] [Indexed: 10/25/2022]
Abstract
A series of pyrazolo[4,3-c]pyrrolo[3,2-f]quinolin-3-one derivatives 6, 7a-c, 8a,b, 9a,b and 10-12 were synthesized as modified pyrazoloquinolinone analogs (PQs) and evaluated for their ability to inhibit radioligand to central and peripheral benzodiazepine receptors (BZRs) and their effect on GABA(A) alpha1beta2gamma2L receptors expressed in Xenopus laevis oocytes. Multistep synthesis starting from 5-nitroindole, via the Gould-Jacobs reaction to the quinoline nucleus, yielded key intermediates 9-chloro-3H-pyrrolo[3,2-f]quinoline-8-carboxylates. The reaction of the latter with methyl-hydrazine and various phenyl-hydrazines furnished the final compounds. In order to confirm the expected tetracyclic 2-substituted-2H-pyrazolopyrroloquinolin-3-one structure, IR spectrophotometric, mono-1H and 13C and bi-dimensional spectrometric and HRMS analyses were carried out: all compounds were found to be 2-substituted 3-keto tautomers; compound 6 only differed because it turned out to be 1-methyl-2H-pyrazolo[4,3-c]pyrrolo[3,2-f]quinolin-3-olo. The results of this work are consistent with those previously reported for PQs: 7-9 show high potency in displacing specific [3H]flunitrazepam from its receptor site; no compound was active in inhibiting the binding of [3H]PK 11195. They all act as antagonists at central BZR.
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Affiliation(s)
- Maria Grazia Ferlin
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Padova, Via Marzolo 5, 35131 Padova, Italy.
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26
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Ivanov I, Nikolova S, Statkova-Abeghe S. A Simple Method for the Synthesis of 1-Substituted β-Carboline Derivatives from Tryptamine and Carboxylic Acids in Polyphosphoric Acid. HETEROCYCLES 2005. [DOI: 10.3987/com-05-10484] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Bracher F, Hildebrand D, Häberlein H. 1-Substituted β-Carboline-3-Carboxylates with high affinities to the Benzodiazepine recognition site. Nat Prod Res 2004; 18:391-6. [PMID: 15248604 DOI: 10.1080/14786410310001630483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Naturally occurring derivatives of beta-carboline-3-carboxylic acid bearing acetyl or vinyl groups at C-1 were prepared by Pd-catalyzed cross-coupling reactions of methyl 1-chloro-beta-carboline-3-carboxylate with appropriate organostannanes. Esters with chloro or acetyl groups at C-1 showed high affinity for the brain benzodiazepine recognition site. Thus, in contrast to 1-alkyl and 1-aryl analogs, these beta-carboline-3-carboxylates with electron-withdrawing substituents at C-1 show high affinities.
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Affiliation(s)
- Franz Bracher
- Department Pharmazie-Zentrum für Pharmaforschung, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
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28
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Hadjipavlou-Litina D, Garg R, Hansch C. Comparative Quantitative Structure−Activity Relationship Studies (QSAR) on Non-Benzodiazepine Compounds Binding to Benzodiazepine Receptor (BzR). Chem Rev 2004; 104:3751-94. [PMID: 15352779 DOI: 10.1021/cr0304469] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotelian University of Thessaloniki, Greece.
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29
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30
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Hou T, Xu X. A new molecular simulation software package--Peking University Drug Design System (PKUDDS) for structure-based drug design. J Mol Graph Model 2002; 19:455-65, 474-5. [PMID: 11552694 DOI: 10.1016/s1093-3263(00)00094-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We present a comprehensive molecular simulation program package, the Peking University Drug Design System (PKUDDS), which runs on personal computers. PKUDDS has been developed mainly for computer-aided drug design using the methods of two-dimensional quantitative structure-activity relationships, three-dimensional quantitative structure-activity relationships, molecular docking, and database screening. This study presents an overview of its functionality, especially of methods developed in our group. PKUDDS uses genetic algorithms in molecular docking, conformational analysis, and quantitative structure-activity relationships as the most useful optimization technique. A user-friendly graphical interface provides easy access to many functions of PKUDDS. We report some examples of our considerable research using PKUDDS.
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Affiliation(s)
- T Hou
- Department of Chemistry and Molecular Engineering, Peking University, Beijing People's Republic of China
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31
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Verli H, Albuquerque MG, Bicca de Alencastro R, Barreiro EJ. Local intersection volume: a new 3D descriptor applied to develop a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands. Eur J Med Chem 2002; 37:219-29. [PMID: 11900866 DOI: 10.1016/s0223-5234(02)01334-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this work, we have developed a new descriptor, named local intersection volume (LIV), in order to compose a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands. The LIV can be classified as a 3D local shape descriptor in contraposition to the global shape descriptors. We have selected from the literature 49 non-benzodiazepine compounds as a training data set and the model was obtained and evaluated by genetic algorithms (GA) and partial least-squares (PLS) methods using LIVs as descriptors. The LIV 3D-QSAR model has a good predictive capacity according the cross-validation test by "leave-one-out" procedure (Q(2)=0.72). The developed model was compared to a comprehensive and extensive SAR pharmacophore model, recently proposed by Cook and co-workers, for benzodiazepine receptor ligands [J. Med. Chem. 43 (2000) 71]. It showed a relevant correlation with the pharmacophore groups pointed out in that work. Our LIV 3D-QSAR model was also able to predict affinity values for a series of nine compounds (test data set) that was not included into the training data set.
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Affiliation(s)
- Hugo Verli
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Departamento de Fármacos, Faculdade de Farmácia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, CP 68006, Rio de Janeiro, RJ 21944-970, Brazil
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32
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Papamicaël C, Quéguiner G, Bourguignon J, Dupas G. A convenient synthesis of 3,4-difunctionalized δ-carbolines. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00435-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Savini L, Chiasserini L, Pellerano C, Biggio G, Maciocco E, Serra M, Cinone N, Carrieri A, Altomare C, Carotti A. High affinity central benzodiazepine receptor ligands. Part 2: quantitative structure-activity relationships and comparative molecular field analysis of pyrazolo[4,3-c]quinolin-3-ones. Bioorg Med Chem 2001; 9:431-44. [PMID: 11249135 DOI: 10.1016/s0968-0896(00)00262-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large series of 2-aryl(heteroaryl)-2,5-dihydropyrazolo[4,3-c]quinolin-3(3H)-ones (PQ, 106 compounds), carrying appropriate substituents at the quinoline and N2-phenyl rings, were designed, prepared and tested as central benzodiazepine receptor ligands. Compounds with an affinity significantly higher than the parent compound CGS-8216 were obtained, the most active ligand showing a pIC50 = 10.35. Hansch and comparative molecular field analyses gave coherent results suggesting the main structural requirements of high receptor binding affinity. The possible formation of a three-centred hydrogen bond (HB) at the HB donor site H2, as a key interaction for high receptor binding affinity, was assessed by the calculation and comparison of the molecular electrostatic potentials of a series of selected ligands.
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Affiliation(s)
- L Savini
- Dipartimento Farmaco Chimico, Università degli Studi, Bari, Italy
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34
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Indolocarhazoles. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)80012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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35
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DeSimone RW, Blum CA. Substituted 3-(2-benzoxazyl)-benzimidazol-2-(1H)-ones: a new class of GABA(A) brain receptor ligands. Bioorg Med Chem Lett 2000; 10:2723-6. [PMID: 11133077 DOI: 10.1016/s0960-894x(00)00550-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel class of potent benzodiazepine receptor (BZR) ligands has been designed and synthesized aided by molecular modeling of known benzodiazepine ligands such as CGS-8216 and the use of known pharmacophore models.
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36
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De Sarro G, Carotti A, Campagna F, Mckernan R, Rizzo M, Falconi U, Palluotto F, Giusti P, Rettore C, De Sarro A. Benzodiazepine receptor affinities, behavioral, and anticonvulsant activity of 2-aryl-2,5-dihydropyridazino[4,3-b]indol- 3(3H)-ones in mice. Pharmacol Biochem Behav 2000; 65:475-87. [PMID: 10683488 DOI: 10.1016/s0091-3057(99)00230-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The anticonvulsant properties of 1,4-benzodiazepines (BDZs), pyrazoloquinolones (CGS), 2-aryl-2,5-dihydropyridazino[4, 3-b]indol-3(3H)-ones (PIs) 1 1i 1d 1f 1e 1b 1c 1h, and 1a, the latter being inactive against audiogenic seizures. Some PIs 1 and abecarnil showed anticonvulsant properties against seizures induced by PTZ with a potency lower than that observed in audiogenic seizures. The pharmacological actions of 1d, 1f, and 1i were significantly reduced by a treatment with flumazenil (8.24 micromol/kg IP), suggesting a clear involvement of benzodiazepine mechanisms in the anticonvulsant activity of these compounds or their metabolites. The anticonvulsant activity of 1d, 1f, and 1i was also evaluated against seizures induced by two beta-carbolines namely methyl-beta-carboline-3-carboxylate (beta-CCM) and methyl-6, 7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate (DMCM), in DBA/2 mice: they gave better protection against seizures induced by beta-CCM than the ones by DMCM. The potency of various BDZs and PIs as inhibitors of specific [3H]flumazenil binding to neuronal membranes, was also evaluated. The radioligand binding study, carried out on stable cell lines expressing definite combinations of benzodiazepine receptor subunits, demonstrated that 1b, 1e, 1d, and 1h have preferential interaction with alpha(1), beta(3), gamma(2), receptor subtypes.
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Affiliation(s)
- G De Sarro
- Chair of Pharmacology, Department of Experimental and Clinical Medicine, School of Medicine, University of Catanzaro, Catanzaro, Italy
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37
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Primofiore G, Da Settimo F, Taliani S, Marini AM, La Motta C, Novellino E, Greco G, Gesi M, Trincavelli L, Martini C. 3-Aryl-[1,2,4]triazino[4,3-a]benzimidazol-4(10H)-ones: tricyclic heteroaromatic derivatives as a new class of benzodiazepine receptor ligands. J Med Chem 2000; 43:96-102. [PMID: 10633040 DOI: 10.1021/jm991131h] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of 3-substituted [1,2,4]triazino[4,3-c]benzimidazoles V were prepared and tested at the central benzodiazepine receptor (BzR). These compounds were designed as rigid analogues of the previously described N-benzylindolylglyoxylylamide derivatives IV. The title compounds V showed an affinity which depended directly on the presence of the N(10)-H group and an aromatic ring at position 3. Some of them elicited a 2- or 3-fold higher affinity with respect to that of the indolylglyoxylylamide derivatives IV (R = H). The GABA ratio and [(35)S]-tert-butylcyclophosphorothionate binding data revealed an efficacy profile of partial inverse agonists/antagonists for compounds 1c,e,f,j,k, and of a partial agonist for 2c. This last compound proved to be effective in antagonizing pentylenetetrazole-induced seizures in mice. Attempts were made to interpret the structure-affinity relationships of compounds V in the light of possible tautomeric equilibria involving the ligands.
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Affiliation(s)
- G Primofiore
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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38
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Huang Q, He X, Ma C, Liu R, Yu S, Dayer CA, Wenger GR, McKernan R, Cook JM. Pharmacophore/receptor models for GABA(A)/BzR subtypes (alpha1beta3gamma2, alpha5beta3gamma2, and alpha6beta3gamma2) via a comprehensive ligand-mapping approach. J Med Chem 2000; 43:71-95. [PMID: 10633039 DOI: 10.1021/jm990341r] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pharmacophore/receptor models for three recombinant GABA(A)/BzR subtypes (alpha1beta3gamma2, alpha5beta3gamma2, and alpha6beta3gamma2) have been established via an SAR ligand-mapping approach. This study was based on the affinities of 151 BzR ligands at five distinct (alpha1-3,5,6beta3gamma2) recombinant GABA(A)/BzR receptor subtypes from at least nine different structural families. Examination of the included volumes of the alpha1-, alpha5-, and alpha6-containing subtypes indicated that region L(2) for the alpha5-containing subtype appeared to be larger in size than the analogous region of the other receptor subtypes. Region L(Di), in contrast, appeared to be larger in the alpha1 subtype than in the other two subtypes. Moreover, region L(3) in the alpha6 subtype is either very small or nonexistent in this diazepam-insensitive subtype (see Figure 16 for details) as compared to the other subtypes. Use of the pharmacophore/receptor models for these subtypes has resulted in the design of novel BzR ligands (see 27) selective for the alpha5beta3gamma2 receptor subtype. alpha5-Selective ligand 27 when injected directly into the hippocampus did enhance memory in one paradigm (Bailey et al., unpublished observations); however, systemic administration of either 9 or 27 into animals did not provide an observable enhancement. This result is in complete agreement with the observation of Liu (1996). It has been shown (Liu, 1996; Wisden et al., 1992) that in the central nervous system of the rat (as well as monkeys and pigeons) there are several native subtypes of the GABA(A) receptor which exhibit different functions, regional distributions, and neuronal locations. Although 27 binds more potently at alpha5beta3gamma2 receptor subtypes and is clearly an inverse agonist (Liu et al., 1996; Liu, 1996), it is possible that this ligand acts as an agonist at one or more subtypes. Liu (1996) clearly showed that a number of imidazobenzodiazepines were negative modulators at one subtype and agonists at another. Therefore, selectivity for a particular subtype at this point is not sufficient to rule out some physiological effect at other GABA(A)/BzR subtypes. The inability of 27 to potentiate memory when given systemically is again in support of this hypothesis, especially since alpha1beta2gamma2 subtypes are distributed throughout the brain (Wisden et al., 1992). A drug delivered systemically is far more likely to interact with all subtypes than one delivered to a specific brain region. This observation (systemic vs intrahippocampal) provides further support for the design of more subtype-specific ligands at the BzR to accurately define their pharmacology, one key to the design of new drugs with fewer side effects.
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Affiliation(s)
- Q Huang
- Department of Chemistry, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, Wisconsin 53201, USA
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39
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Dekermendjian K, Kahnberg P, Witt MR, Sterner O, Nielsen M, Liljefors T. Structure-activity relationships and molecular modeling analysis of flavonoids binding to the benzodiazepine site of the rat brain GABA(A) receptor complex. J Med Chem 1999; 42:4343-50. [PMID: 10543878 DOI: 10.1021/jm991010h] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The affinities for the benzodiazepine binding site of the GABA(A) receptor of 21 flavonoids have been studied using [(3)H]flumazenil binding to rat cortical membranes in vitro. We show that flavonoids with high affinity for the benzodiazepine receptor in vitro spanning the whole efficacy range from agonists (1q) to inverse agonists (1l) can be synthesized. The receptor binding properties of the flavonoids studied can successfully be rationalized in terms of a comprehensive pharmacophore model recently developed by Cook and co-workers (Drug Des. Dev. 1995, 12, 193-248), supporting the validity of this model. However, in contrast to the requirement by the model that an interaction with the hydrogen bond-accepting site A2 is necessary for compounds to display inverse agonistic activity, 6-methyl-3'-nitroflavone (1l), which cannot engage in such an interaction, nevertheless displays inverse agonism. The analysis of the binding affinities of 3'- and 4'-substituted flavones in terms of the pharmacophore model has yielded new information for the further development of the pharmacophore model.
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Affiliation(s)
- K Dekermendjian
- Research Institute of Biological Psychiatry, Sct. Hans Hospital, DK-4000 Roskilde, Denmark.
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40
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Campagna F, Palluotto F, Carotti A, Casini G, Genchi G. Synthesis and structure-affinity relationships at the central benzodiazepine receptor of pyridazino[4,3-b]indoles and indeno[1,2-c]pyridazines. Bioorg Med Chem 1999; 7:1533-8. [PMID: 10482445 DOI: 10.1016/s0968-0896(99)00093-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 2-aryl-3-chloro-2H-pyridazino[4,3-b]indoles, 2-aryl-3-methoxy-2H-pyridazino[4,3-b]indoles, and 2-aryl-2,5-dihydroindeno[1,2-c]pyridazino-3(3H)-ones has been prepared and tested for their ability to inhibit the [3H]flunitrazepam binding to the central benzodiazepine receptor. SAR are presented and discussed in comparison with existing pharmacophore models.
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Affiliation(s)
- F Campagna
- Dipartimento Farmacochimico, Università di Bari, Italy.
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41
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Guerrini G, Costanzo A, Bruni F, Ciciani G, Selleri S, Gratteri P, Costa B, Martini C, Lucacchini A. Benzodiazepine receptor ligands. III. Synthesis and biological evaluation of 2- and/or 3-substituted pyrazolo[5,1-c][1,2,4]benzotriazine 5-oxides. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 1999; 54:375-89. [PMID: 10576777 DOI: 10.1016/s0014-827x(99)00044-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new series of 2- and/or 3-substituted pyrazolo [5,1-c][benzotriazine 5-oxides and their 8-chloro derivatives were synthesized, and their benzodiazepine receptor (BZR) affinities were evaluated in vitro in comparison to lead compound 3-ethoxycarbonyl-8-chloropyrazolo[5,1-c][1,2,4]benzotriazine 5-oxide (29) [1,2]. None of the new compounds showed significant affinity for BZR. On the basis of a pharmacophore/receptor model suggested for lead compound 29, some hypotheses to explain the inactivity of new derivatives are discussed.
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Affiliation(s)
- G Guerrini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Firenze, Florence, Italy
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42
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Synthesis, benzodiazepine receptor affinity and in vivo testing of 3-aryl-4,7-dihydro-6-(N1′-alkylpyrazol-3′ - or 5′-yl)pyrazolo[1,5-a]pyrimidin-7-ones. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(97)89638-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Podlogar BL, Paterlini MG, Ferguson DM, Leo GC, Demeter DA, Brown FK, Reitz AB. Conformational analysis of the endogenous mu-opioid agonist endomorphin-1 using NMR spectroscopy and molecular modeling. FEBS Lett 1998; 439:13-20. [PMID: 9849868 DOI: 10.1016/s0014-5793(98)01202-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Endomorphin-1 (Tyr-Pro-Trp-Phe-NH2) is a highly selective and potent agonist of the mu-opioid receptor. To identify structural attributes unique to this opioid peptide and potential sites of recognition, a conformational analysis has been performed using multidimensional NMR and molecular modeling techniques. The spectroscopic results, derived from experiments in both DMSO and water, indicate that endomorphin-1 exists in the cis- and trans-configuration with respect to the Pro-omega bond in approximately 25% and 75% populations, respectively. In DMSO, the cis-configuration adopts a compact sandwich conformation in which the Tyr and Trp aromatic rings pack against the proline ring, whereas the trans-configuration adopts an extended conformation. Although non-random structure was not observed in water, condensed phase molecular dynamics calculations indicate that trans-isomers dominate the population in this higher dielectric medium. Structural comparison of the cis- and trans-configurations with morphine and selective mu-peptide ligands PL-017 and D-TIPP, as well as the delta-selective peptide ligands TIPP (delta-antagonist, mu-agonist) and DPDPE were also performed and suggest the trans-isomer is likely the bioactive form. A hypothesis is proposed to explain mu- and delta-selectivity based on the presence of spatially distinct selectivity pockets among these ligands.
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Affiliation(s)
- B L Podlogar
- Department of Medicinal Chemistry, The R.W. Johnson Pharmaceutical Research Institute, Raritan, NJ 08869, USA.
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44
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Demeter DA, Weintraub HJ, Knittel JJ. The local minima method (LMM) of pharmacophore determination: a protocol for predicting the bioactive conformation of small, conformationally flexible molecules. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1998; 38:1125-36. [PMID: 9845967 DOI: 10.1021/ci980404z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Software has been developed for potential energy surface analysis and the local minima method of pharmacophore determination. LMM is rigorous and systematic and employs multiple conformations which are the local minima from the potential energy surface of each compound in the data set. It produces a series of possible pharmacophores from a postulated set of pharmacophore elements. The best pharmacophore is then determined by performing a comparative molecular field analysis (CoMFA) on each one. The pharmacophore which produces the most self-consistent model is deemed the best. Local minima on the gas-phase potential energy surface are shown to be a reasonably close approximation to protein bound conformations, and these conformations can be found through systematic conformational searches followed by minimization of the local minima. LMM was used to develop a 3D-QSAR model for dopamine beta-hydroxylase (DBH) inhibitors which was highly predictive (predictive R2 = 0.71 and standard error of predictions = 0.41). The model predicted that the phenyl and thienyl series of inhibitors were acting as bioisosteres. Examination of compounds overlayed in the model indicated a possible hydrogen bond acceptor in the DBH active site. Three tyrosine residues previously labeled by mechanism based inhibitors may be acting as the acceptor and therefore represent excellent candidates for site-directed mutagenesis studies.
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Affiliation(s)
- D A Demeter
- R.W. Johnson Pharmaceutical Research Institute, Raritan, New Jersey 08869, USA.
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45
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Cox ED, Diaz-Arauzo H, Huang Q, Reddy MS, Ma C, Harris B, McKernan R, Skolnick P, Cook JM. Synthesis and evaluation of analogues of the partial agonist 6-(propyloxy)-4-(methoxymethyl)-beta-carboline-3-carboxylic acid ethyl ester (6-PBC) and the full agonist 6-(benzyloxy)-4-(methoxymethyl)-beta-carboline-3-carboxylic acid ethyl ester (Zk 93423) at wild type and recombinant GABAA receptors. J Med Chem 1998; 41:2537-52. [PMID: 9651158 DOI: 10.1021/jm970460b] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A pharmacophore and an alignment rule have previously been reported for BzR agonist ligands. The design and synthesis of 6-(propyloxy)-4-(methoxymethyl)-beta-carboline-3-carboxylic acid ethyl ester (6-PBC, 24, IC50 = 8.1 nM) was based on this pharmacophore. When evaluated in vivo this ligand exhibited anticonvulsant/anxiolytic activity but was devoid of the muscle relaxant/ataxic effects of "classical" 1,4-benzodiazepines (i.e., diazepam). Significantly, 6-PBC 24 also reversed diazepam-induced muscle relaxation in mice. The 3-substituted analogues 40-46 and 48 of 6-PBC 24 and Zk 93423 27(IC50 = 1 nM) were synthesized and evaluated in vitro to determine what affect these modifications would have on the binding affinity at recombinant BzR subtypes. With the exception of the 3-amino ligands 40 and 41, all the beta-carbolines were found to exhibit high binding affinity at BzR sites. The 3-propyl ether derivative 45 was also evaluated in vivo and found to be devoid of any proconvulsant or anticonvulsant activity at doses up to 40 mg/kg. The 6-(1-naphthylmethyloxy) and 6-octyloxy analogues 25, 26, 28, and 29 of 6-PBC 24 were synthesized to further evaluate the proposed alignment of agonists vs inverse agonists in the pharmacophore of the BzR. In addition, ligands 26 and 29 were designed to probe the dimensions of lipophilic pocket L3 at the agonist site. The activity of 29 was evaluated in vivo; however, this analogue elicited no pharmacological effects at doses up to 80 mg/kg. These and other related beta-carbolines were also examined in five recombinant GABAA receptor subtypes. Ligands 52-61 all exhibited moderate to high affinity at GABAA receptors containing alpha1 subunits. These ligands will be useful in further defining the pharmacophore at alpha1 beta3 gamma2 receptors.
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Affiliation(s)
- E D Cox
- Department of Chemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
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46
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Savini L, Massarelli P, Nencini C, Pellerano C, Biggio G, Maciocco A, Tuligi G, Carrieri A, Cinone N, Carotti A. High affinity central benzodiazepine receptor ligands: synthesis and structure-activity relationship studies of a new series of pyrazolo[4,3-c]quinolin-3-ones. Bioorg Med Chem 1998; 6:389-99. [PMID: 9597183 DOI: 10.1016/s0968-0896(97)10039-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A large series of 2-aryl(heteroaryl)-2,5-dihydropyrazolo[4,3-c]quinolin- 3-(3H)-ones, carrying appropriate substituents at the quinoline and N2-phenyl rings, were prepared and tested as central benzodiazepine receptor ligands. Results from structure-affinity relationship studies were in full agreement with previously proposed pharmacophore models and, in addition, quantitative structure-activity analysis gave further significant insight into the main molecular determinants of high benzodiazepine receptor affinity. The intrinsic activity of some active ligands was also determined and preliminary discussed.
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Affiliation(s)
- L Savini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi, Siena, Italy
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47
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So SS, Karplus M. Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications. J Med Chem 1997; 40:4360-71. [PMID: 9435905 DOI: 10.1021/jm970488n] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Validation of a method that uses a genetic neural network with electrostatic and steric similarity matrices (SM/GNN) to obtain quantitative structure-activity relationships (QSARs) is performed with eight data sets. Biological and physicochemical properties from a broad range of chemical classes are correlated and predicted using this technique. Quantitatively the results compare favorably with the benchmarks obtained by a number of well-established QSAR methods; qualitatively the models are consistent with the published descriptions on the relative contribution of steric and electrostatic factors. The results demonstrate the general utility of this method in deriving QSARs. The implication of the importance of molecular alignment and possible methodological improvements are discussed.
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Affiliation(s)
- S S So
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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48
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Parretti MF, Kroemer RT, Rothman JH, Richards WG. Alignment of molecules by the Monte Carlo optimization of molecular similarity indices. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(199708)18:11<1344::aid-jcc2>3.0.co;2-l] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Arzel E, Rocca P, Marsais F, Godard A, Quéguiner G. A new synthesis of α-substituted δ-carbolines. J Heterocycl Chem 1997. [DOI: 10.1002/jhet.5570340418] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Da Settimo A, Primofiore G, Da Settimo F, Marini AM, Novellino E, Greco G, Martini C, Giannaccini G, Lucacchini A. Synthesis, structure-activity relationships, and molecular modeling studies of N-(indol-3-ylglyoxylyl)benzylamine derivatives acting at the benzodiazepine receptor. J Med Chem 1996; 39:5083-91. [PMID: 8978839 DOI: 10.1021/jm960240i] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of N-(indol-3-ylglyoxylyl)benzylamine derivatives were synthesized and tested for [3H]flunitrazepam displacing activity in bovine brain membranes. Some of these derivatives (9, 12, 14, 15, 17, 27, 34, 35, 38, 41, and 45) exhibited high affinity for the benzodiazepine receptor (BzR) with Ki values ranging from 67 to 11 nM. The GABA ratio and [35S]-tert-butylbicyclophosphorothionate binding data, determined for the most active compounds, showed that they elicit an efficacy profile at the BzR which depends on the kind of substituent present on the phenyl ring of the benzylamine moiety. Moreover, lengthening (propylamine derivatives 1-3) and shortening (aniline derivatives 46-54) of the distance between the phenyl ring and the amide group of the side chain gave compounds with a drastically lower binding potency. The biological results are discussed in the light of a recently proposed pharmacophore model and compared, by molecular modeling studies, with those obtained from effective BzR ligands.
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Affiliation(s)
- A Da Settimo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Italy
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