1
|
Mokrov GV. Multitargeting in cardioprotection: An example of biaromatic compounds. Arch Pharm (Weinheim) 2023; 356:e2300196. [PMID: 37345968 DOI: 10.1002/ardp.202300196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
A multitarget drug design approach is actively developing in modern medicinal chemistry and pharmacology, especially with regard to multifactorial diseases such as cardiovascular diseases, cancer, and neurodegenerative diseases. A detailed study of many well-known drugs developed within the single-target approach also often reveals additional mechanisms of their real pharmacological action. One of the multitarget drug design approaches can be the identification of the basic pharmacophore models corresponding to a wide range of the required target ligands. Among such models in the group of cardioprotectors is the linked biaromatic system. This review develops the concept of a "basic pharmacophore" using the biaromatic pharmacophore of cardioprotectors as an example. It presents an analysis of possible biological targets for compounds corresponding to the biaromatic pharmacophore and an analysis of the spectrum of biological targets for the five most known and most studied cardioprotective drugs corresponding to this model, and their involvement in the biological effects of these drugs.
Collapse
|
2
|
Polishchuk P. Interpretation of Quantitative Structure–Activity Relationship Models: Past, Present, and Future. J Chem Inf Model 2017; 57:2618-2639. [DOI: 10.1021/acs.jcim.7b00274] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Pavel Polishchuk
- Institute of Molecular and
Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská
1333/5, 779 00 Olomouc, Czech Republic
| |
Collapse
|
3
|
Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ. From Homology Models to a Set of Predictive Binding Pockets-a 5-HT 1A Receptor Case Study. J Chem Inf Model 2017; 57:311-321. [PMID: 28055203 PMCID: PMC5361891 DOI: 10.1021/acs.jcim.6b00263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite its remarkable importance in the arena of drug design, serotonin 1A receptor (5-HT1A) has been elusive to the X-ray crystallography community. This lack of direct structural information not only hampers our knowledge regarding the binding modes of many popular ligands (including the endogenous neurotransmitter-serotonin), but also limits the search for more potent compounds. In this paper we shed new light on the 3D pharmacological properties of the 5-HT1A receptor by using a ligand-guided approach (ALiBERO) grounded in the Internal Coordinate Mechanics (ICM) docking platform. Starting from a homology template and set of known actives, the method introduces receptor flexibility via Normal Mode Analysis and Monte Carlo sampling, to generate a subset of pockets that display enriched discrimination of actives from inactives in retrospective docking. Here, we thoroughly investigated the repercussions of using different protein templates and the effect of compound selection on screening performance. Finally, the best resulting protein models were applied prospectively in a large virtual screening campaign, in which two new active compounds were identified that were chemically distinct from those described in the literature.
Collapse
Affiliation(s)
- Dawid Warszycki
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Manuel Rueda
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Drive, MC 0747 La Jolla, CA 92093-0747, U.S
| | - Stefan Mordalski
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Kurt Kristiansen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway
| | - Grzegorz Satała
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Krzysztof Rataj
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| | - Zdzisław Chilmonczyk
- Department of Cell Biology, National Medicines Institute, 30/34 Chełmska Street, 00-725 Warszawa, Poland
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway
| | - Ruben Abagyan
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, 9500 Gilman Drive, MC 0747 La Jolla, CA 92093-0747, U.S
| | - Andrzej J. Bojarski
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Street, 31-343 Kraków, Poland
| |
Collapse
|
4
|
Jia Q, Cui X, Li L, Wang Q, Liu Y, Xia S, Ma P. Quantitative Structure-Activity Relationship for High Affinity 5-HT1A Receptor Ligands Based on Norm Indexes. J Phys Chem B 2015; 119:15561-7. [PMID: 26605982 DOI: 10.1021/acs.jpcb.5b08980] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylpiperazine derivatives are promising 5-hydroxytryptamine (5-HT) receptor ligands which can inhibit serotonin reuptake effectively. In this work, some norm index descriptors were proposed and further utilized to develop a model for predicting 5-HT1A receptor affinity (pKi) of 88 arylpiperazine derivatives. Results showed that this new model could provide satisfactory predictions with the square of the correction coefficient (R(2)) of 0.8891 and the squared correlation coefficient of cross-validation (Q(2)) of 0.8082, respectively. In addition, the applicability domain of this model was validated by using the leverage approach and results which suggested potential large scale for further utilization of this model. The results of statistical values and validation tests demonstrated that our proposed norm index based model could be successfully applied for predicting the affinity 5-HT1A receptor ligands of arylpiperazine derivatives.
Collapse
Affiliation(s)
| | | | | | | | | | - Shuqian Xia
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| | - Peisheng Ma
- School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
| |
Collapse
|
5
|
5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists. J Comput Aided Mol Des 2013; 27:305-19. [PMID: 23625023 DOI: 10.1007/s10822-013-9647-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/13/2013] [Indexed: 01/08/2023]
Abstract
The α1-adrenoceptors (α1-ARs), in particular the α1A-AR subtype, are current therapeutic targets of choice for the treatment of urogenital conditions, such as benign prostatic hyperplasia (BPH). Due to the similarity between the transmembrane domains of the α1-AR subtypes, and the serotonin receptor subtype 1A (5-HT1A-R), currently used α1-AR subtype-selective drugs to treat BPH display considerable off-target affinity for the 5-HT1A-R, leading to side effects. We describe the construction and validation of pharmacophores for 5-HT1A-R agonists and antagonists. Through the structural diversity of the training sets used in their development, these pharmacophores define the properties of a compound needed to bind to 5-HT1A receptors. Using these and previously published pharmacophores in virtual screening and profiling, we have identified unique chemical compounds (hits) that fit the requirements to bind to our target, the α1A-AR, selectively over the off-target, the 5-HT1A-R. Selected hits have been obtained and their affinities for α1A-AR, α1B-AR and 5-HT1A-R determined in radioligand binding assays, using membrane preparations which contain human receptors expressed individually. Three of the tested hits demonstrate statistically significant selectivity for α1A-AR over 5-HT1A-R. All seven tested hits bind to α1A-AR, with two compounds displaying K i values below 1 μM, and a further two K i values of around 10 μM. The insights and knowledge gained through the development of the new 5-HT1A-R pharmacophores will greatly aid in the design and synthesis of derivatives of our lead compound, and allow the generation of more efficacious and selective ligands.
Collapse
|
6
|
Kuz'min VE, Polishchuk PG, Artemenko AG, Andronati SA. Interpretation of QSAR Models Based on Random Forest Methods. Mol Inform 2011; 30:593-603. [DOI: 10.1002/minf.201000173] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 05/13/2011] [Indexed: 11/07/2022]
|
7
|
Pharmacophore models based studies on the affinity and selectivity toward 5-HT1A with reference to α1-adrenergic receptors among arylpiperazine derivatives of phenytoin. Bioorg Med Chem 2011; 19:1349-60. [DOI: 10.1016/j.bmc.2010.11.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Revised: 11/17/2010] [Accepted: 11/20/2010] [Indexed: 11/19/2022]
|
8
|
Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT1A receptor ligands. Eur J Med Chem 2010; 45:1508-14. [PMID: 20133028 DOI: 10.1016/j.ejmech.2009.12.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/18/2009] [Indexed: 11/21/2022]
Abstract
5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds.
Collapse
|
9
|
Machado A, Tejera E, Cruz-Monteagudo M, Rebelo I. Application of desirability-based multi(bi)-objective optimization in the design of selective arylpiperazine derivates for the 5-HT1A serotonin receptor. Eur J Med Chem 2009; 44:5045-54. [DOI: 10.1016/j.ejmech.2009.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 07/06/2009] [Accepted: 09/06/2009] [Indexed: 10/20/2022]
|
10
|
Leifert WR. An overview on GPCRs and drug discovery: structure-based drug design and structural biology on GPCRs. Methods Mol Biol 2009; 552:51-66. [PMID: 19513641 PMCID: PMC7122359 DOI: 10.1007/978-1-60327-317-6_4] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) represent 50-60% of the current drug targets. There is no doubt that this family of membrane proteins plays a crucial role in drug discovery today. Classically, a number of drugs based on GPCRs have been developed for such different indications as cardiovascular, metabolic, neurodegenerative, psychiatric, and oncologic diseases. Owing to the restricted structural information on GPCRs, only limited exploration of structure-based drug design has been possible. Much effort has been dedicated to structural biology on GPCRs and very recently an X-ray structure of the beta2-adrenergic receptor was obtained. This breakthrough will certainly increase the efforts in structural biology on GPCRs and furthermore speed up and facilitate the drug discovery process.
Collapse
|
11
|
Weber KC, da Silva ABF. A chemometric study of the 5-HT1A receptor affinities presented by arylpiperazine compounds. Eur J Med Chem 2008; 43:364-72. [PMID: 17562349 DOI: 10.1016/j.ejmech.2007.03.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 11/24/2022]
Abstract
Arylpiperazine compounds are promising 5-HT(1A) receptor ligands that can contribute for accelerating the onset of therapeutic effect of selective serotonin reuptake inhibitors. In the present work, the chemometric methods HCA, PCA, KNN, SIMCA and PLS were employed in order to obtain SAR and QSAR models relating the structures of arylpiperazine compounds to their 5-HT(1A) receptor affinities. A training set of 52 compounds was used to construct the models and the best ones were obtained with nine topological descriptors. The classification and regression models were externally validated by means of predictions for a test set of 14 compounds and have presented good quality, as verified by the correctness of classifications, in the case of pattern recognition studies, and by the high correlation coefficients (q(2)=0.76, r(2)=0.83) and small prediction errors for the PLS regression. Since the results are in good agreement with previous SAR studies, we can suggest that these findings can help in the search for 5-HT(1A) receptor ligands that are able to improve antidepressant treatment.
Collapse
Affiliation(s)
- Karen C Weber
- Instituto de Química de São Carlos, Universidade de São Paulo, P.O. Box 780, 13566-590 São Carlos, SP, Brazil
| | | |
Collapse
|
12
|
Carrupt PA, Testa B, Gaillard P. Computational Approaches to Lipophilicity: Methods and Applications. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125885.ch5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
13
|
Mälkiä A, Murtomäki L, Urtti A, Kontturi K. Drug permeation in biomembranes. Eur J Pharm Sci 2004; 23:13-47. [PMID: 15324921 DOI: 10.1016/j.ejps.2004.05.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Revised: 05/13/2004] [Accepted: 05/24/2004] [Indexed: 11/21/2022]
Abstract
In the past decades, it has become increasingly apparent that in addition to therapeutic effect, drugs need to exhibit favourable absorption, distribution, metabolism and excretion (ADME) characteristics to produce a desirable response in vivo. As the recent progress in drug discovery technology enables rapid synthesis of vast numbers of potential drug candidates, robust methods are required for the effective screening of compounds synthesized within such programs, so that compounds with poor pharmacokinetic properties can be rejected at an early stage of drug development. Furthermore, a viable in silico method would save resources by enabling virtual screening of drug candidates already prior to synthesis. This review gives a general overview of the approaches aimed at predicting biological permeation, one of the cornerstones behind the ADME behaviour of drugs. The most important experimental and computational models are reviewed. Physicochemical factors underlying the permeation process are discussed.
Collapse
Affiliation(s)
- Annika Mälkiä
- Laboratory of Physical Chemistry and Electrochemistry, Helsinki University of Technology, P.O. Box 6100, FIN-02015 HUT, Finland
| | | | | | | |
Collapse
|
14
|
Jung D, Floyd J, Gund TM. A comparative molecular field analysis (CoMFA) study using semiempirical, density functional,ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands. J Comput Chem 2004; 25:1385-99. [PMID: 15185333 DOI: 10.1002/jcc.10410] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Comparative Molecular Field Analysis (CoMFA) was developed to investigate a three-dimensional quantitative structure activity relationship (3D-QSAR) model of ligands for the sigma 1 receptor. The starting geometry of sigma-1 receptor ligands was obtained from the Tripos force field minimizations and conformations were decided from DISCOtech using the SYBYL 6.8. program. The structures of 48 molecules were fully optimized at the ab initio HF/3-21G* and semiempirical AM1 calculations using GAUSSIAN 98. The electrostatic charges were calculated using several methods such as semiempirical AM1, density functional B3LYP/3-21G*, and ab initio HF/3-21G*, MP2/3-21G* calculations within GAUSSIAN 98. Using the optimized geometries, the CoMFA results derived from the HF/3-21G method were better than those from AM1. The best CoMFA was obtained from HF/3-21G* optimized geometry and charges (R2 = 0.977). Using the optimized geometries, the CoMFA results derived from the HF/3-21G methods were better than those from AM1 calculations. The training set of 43 molecules gave higher R2 (0.989-0.977) from HF/3-21G* optimized geometries than R2 (0.966-0.911) values from AM1 optimized geometries. The test set of five molecules also suggested that HF/3-21G* optimized geometries produced good CoMFA models to predict bioactivity of sigma 1 receptor ligands but AM1 optimized geometries failed to predict reasonable bioactivity of sigma 1 receptor ligands using different calculations for atomic charges.
Collapse
Affiliation(s)
- Dawoon Jung
- Department of Chemistry, and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 17102-1982
| | | | | |
Collapse
|
15
|
Asproni B, Pau A, Bitti M, Melosu M, Cerri R, Dazzi L, Seu E, Maciocco E, Sanna E, Busonero F, Talani G, Pusceddu L, Altomare C, Trapani G, Biggio G. Synthesis and pharmacological evaluation of 1-[(1,2-diphenyl-1H-4-imidazolyl)methyl]-4-phenylpiperazines with clozapine-like mixed activities at dopamine D(2), serotonin, and GABA(A) receptors. J Med Chem 2002; 45:4655-68. [PMID: 12361392 DOI: 10.1021/jm020848t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 18 1-[(1,2-diphenyl-1H-4-imidazolyl)methyl]-4-piperazines (1a-r) were designed and synthesized as possible ligands with mixed dopamine (DA) D(2)/serotonin 5-HT(1A) affinity, with the aim of identifying novel compounds with neurochemical and pharmacological properties similar to those of clozapine. The binding profile at D(2) like, 5-HT(1A), and 5-HT(2A) receptors of title compounds was determined. Modifications made in the phenyl rings of the parent compound (1a) produced congeners endowed with a broad range of binding affinities for DA D(2) like, serotonin 5-HT(1A), and 5-HT(2A) receptors, with IC(50) values ranging from 25 to >10,000 nM. As for the modification of the piperazine N(4)-phenyl ring, the affinities for both D(2) like and 5-HT(1A) receptors were progressively increased by introduction of ortho-methoxy and ethoxy groups (1b,o, respectively). Data revealed the presence of a para-chloro substituent in 1g to be associated with a relatively high affinity and substantial selectivity for D(2) like receptors, whereas the meta-chloro analogue 1f exhibited preferential affinity for 5-HT(1A) receptors. A quantitative structure-affinity relationship analysis of the measured binding data resulted in regression equations that highlighted substituent physicochemical properties modulating the binding to subtypes 1A and 2A of serotonin 5-HT receptors but not to D(2) like receptors. Thus, besides an electron-withdrawing field effect and ortho substitution, which both influence binding to serotonin 5-HT receptor subtypes, though to a different extent as revealed by regression coefficients in the multiparametric regression equations, the affinity of congeners 1a-r to 5-HT(1A) receptors proved to be linearly correlated with volume/polarizability descriptors, whereas their affinity to 5-HT(2A) receptors correlated with lipophilicity constants through a parabolic relationship. 1-[(1,2-Diphenyl-1H-4-imidazolyl)methyl]-4-(2-methoxyphenyl)piperazine (1b), with a D(2)/5-HT(1A) IC(50) ratio of approximately 1, was selected for a further pharmacological study. In rats, the intraperitoneal administration of compound 1b, like that of clozapine, induced an increase in the extracellular concentration of DA measured in the medial prefrontal cortex. Furthermore, 1b and clozapine each inhibited GABA-evoked Cl(-) currents at recombinant GABA(A) receptors expressed in Xenopus oocytes. These findings suggest that compound 1b may represent an interesting prototype of a novel class of drugs endowed with a neurochemical profile similar to that of atypical antipsychotics.
Collapse
Affiliation(s)
- Battistina Asproni
- Dipartimento Farmaco Chimico Tossicologico, Facoltà di Farmacia, Università degli Studi di Sassari, 07100 Sassari, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Kowalski P, Kowalska T, Mokrosz MJ, Bojarski AJ, Charakchieva-Minol S. Biologically Active 1-Arylpiperazines. Synthesis of New N-(4-Aryl-1-piperazinyl)alkyl Derivatives of Quinazolidin-4(3H)-one, 2,3-Dihydrophthalazine-1,4-dione and 1,2-Dihydropyridazine-3,6-dione as Potential Serotonin Receptor Ligands. Molecules 2001. [PMCID: PMC6236407 DOI: 10.3390/60900784] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The synthesis of a series of new n-propyl and n-butyl chain containing 1-aryl-piperazine derivatives of quinazolidin-4(3H)-one (7) 2-phenyl-2,3-dihydrophthalazine-1,4-dione (8) and 1-phenyl-1,2-dihydropyridazine-3,6-dione (9) as potential serotonin receptor ligands is described.
Collapse
Affiliation(s)
- Piotr Kowalski
- Institute of Organic Chemistry and Technology, Cracow University of Technology, 24 Warszawska str., 31-155 Cracow, Poland
- Author to whom correspondence should be addressed; e-mail:
| | - Teresa Kowalska
- Institute of Organic Chemistry and Technology, Cracow University of Technology, 24 Warszawska str., 31-155 Cracow, Poland
| | - Maria J. Mokrosz
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna str., 31-343 Cracow, Poland
| | - Andrzej J. Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna str., 31-343 Cracow, Poland
| | - Sijka Charakchieva-Minol
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna str., 31-343 Cracow, Poland
| |
Collapse
|
17
|
Barbaro R, Betti L, Botta M, Corelli F, Giannaccini G, Maccari L, Manetti F, Strappaghetti G, Corsano S. Synthesis, biological evaluation, and pharmacophore generation of new pyridazinone derivatives with affinity toward alpha(1)- and alpha(2)-adrenoceptors. J Med Chem 2001; 44:2118-32. [PMID: 11405649 DOI: 10.1021/jm010821u] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of new pyridazin-3(2H)-one derivatives (3 and 4) were evaluated for their in vitro affinity toward both alpha(1)- and alpha(2)-adrenoceptors by radioligand receptor binding assays. All target compounds showed good affinities for the alpha(1)-adrenoceptor, with K(i) values in the low nanomolar range. The polymethylene chain constituting the spacer between the furoylpiperazinyl pyridazinone and the arylpiperazine moiety was shown to influence the affinity and selectivity of these compounds. Particularly, a gradual increase in affinity was observed by lengthening the polymethylene chain up to a maximum of seven carbon atoms. In addition, compound 3k, characterized by a very interesting alpha(1)-AR affinity (1.9 nM), was also shown to be a highly selective alpha(1)-AR antagonist, the affinity ratio for alpha(2)- and alpha(1)-adrenoceptors being 274. To gain insight into the structural features required for alpha(1) antagonist activity, the pyridazinone derivatives were submitted to a pharmacophore generation procedure using the program Catalyst. The resulting pharmacophore model showed high correlation and predictive power. It also rationalized the relationships between structural properties and biological data of, and external to, the pyridazinone class.
Collapse
Affiliation(s)
- R Barbaro
- Istituto di Chimica e Tecnologia del Farmaco, Università di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- L Savini
- Dipartimento Farmaco Chimico, Università degli Studi, Bari, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Jäger R, Schmidt F, Schilling B, Brickmann J. Localization and quantification of hydrophobicity: the molecular free energy density (MolFESD) concept and its application to sweetness recognition. J Comput Aided Mol Des 2000; 14:631-46. [PMID: 11008885 DOI: 10.1023/a:1008181611372] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A method for the localization, the quantification, and the analysis of hydrophobicity of a molecule or a molecular fragment is presented. It is shown that the free energy of solvation for a molecule or the transfer free energy from one solvent to another can be represented by a surface integral of a scalar quantity, the molecular free energy surface density (MolFESD), over the solvent accessible surface of that molecule. This MolFESD concept is based on a model approach where the solvent molecules are considered to be small in comparison to the solute molecule, and the solvent can be represented by a continuous medium with a given dielectric constant. The transfer energy surface density for a 1-octanol/water system is empirically determined employing a set of atomic increment contributions and distance dependent membership functions measuring the contribution of the increments to the surface value of the MolFESD. The MolFESD concept can be well used for the quantification of the purely hydrophobic contribution to the binding constants of molecule-receptor complexes. This is demonstrated with the sweeteners sucrose and sucralose and various halogen derivatives. Therein the relative sweetness, which is assumed to be proportional to the binding constant, nicely correlates to the surface integral over the positive, hydrophobic part of the MolFESD, indicating that the sweetness receptor can be characterized by a highly flexible hydrophobic pocket instead of a localized binding site.
Collapse
Affiliation(s)
- R Jäger
- Institute for Physical Chemistry, Darmstadt University of Technology, Germany
| | | | | | | |
Collapse
|
20
|
Guccione S, Doweyko AM, Chen H, Barretta GU, Balzano F. 3D-QSAR using 'multiconformer' alignment: the use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands. J Comput Aided Mol Des 2000; 14:647-57. [PMID: 11008886 DOI: 10.1023/a:1008136325544] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The observed 5-HT1A and alpha1-adrenergic receptor (alpha1-AR) receptor binding properties of a series of 23 thienopyrimidinones were used to develop HASL 3D-QSAR models. A single, low energy conformer of the most active analogue in the series, which was consistent with NMR structural studies, was chosen as a template molecule. Alignments of all the molecules to the template were provided by an Amber/MM2 superposition force field. In this manner, each molecule was represented by five separate low energy conformers which were subsequently used in the generation of HASL 3D-QSAR models. Models derived from multiple conformers were found to exhibit enhanced predictivity compared to models based on single, low energy conformers. In addition, the use of contour imaging of HASL multi-conformer model interactions was found to lead to a more consistent interpretation of those molecular features most significant for 5-HT1A receptor binding.
Collapse
Affiliation(s)
- S Guccione
- Dipartimento di Scienze Farmaceutiche, Università di Catania, Italy.
| | | | | | | | | |
Collapse
|
21
|
Cruciani G, Crivori P, Carrupt PA, Testa B. Molecular fields in quantitative structure–permeation relationships: the VolSurf approach. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(99)00360-7] [Citation(s) in RCA: 309] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
22
|
Zhang SX, Feng J, Kuo SC, Brossi A, Hamel E, Tropsha A, Lee KH. Antitumor agents. 199. Three-dimensional quantitative structure-activity relationship study of the colchicine binding site ligands using comparative molecular field analysis. J Med Chem 2000; 43:167-76. [PMID: 10649972 DOI: 10.1021/jm990333a] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibitors of tubulin polymerization interacting at the colchicine binding site are potential anticancer agents. We have been involved in the synthesis of a number of colchicine site agents, such as thiocolchicinoids and allocolchicinoids, which are colchicine analogues, and 2-phenyl-quinolones and 2-aryl-naphthyridinones, which are the amino analogues of cytotoxic antimitotic flavonoids. The most cytotoxic of the latter compounds strongly inhibit binding of radiolabeled colchicine to tubulin, and these agents therefore probably bind in the colchicine site of tubulin. We have applied conventional CoMFA and q(2)-GRS CoMFA to identify the essential structural requirements for increasing the ability of these compounds to form tubulin complexes. The CoMFA model for the training set of 51 compounds yielded cross-validated R(2) (q(2)) values of 0.637 for conventional CoMFA and 0.692 for q(2)-GRS CoMFA. The predictive power of this model was confirmed by successful activity prediction for a test set of 53 compounds with known potencies as inhibitors of tubulin polymerization. The activities of 88% of the compounds were predicted with absolute value of residuals of less than 0.5. The predictive q(2) values were 0.546 for conventional CoMFA and 0.426 for q(2)-GRS CoMFA. The conventional CoMFA model with the highest predictive q(2) (0.546) was analyzed in detail in terms of underlying structure-activity relationships.
Collapse
Affiliation(s)
- S X Zhang
- Natural Products Laboratory, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Cinone N, Carrieri A, Strappaghetti G, Corsano S, Barbaro R, Carotti A. Comparative molecular field analysis of some pyridazinone-containing alpha1-antagonists. Bioorg Med Chem 1999; 7:2615-20. [PMID: 10632072 DOI: 10.1016/s0968-0896(99)00211-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Diverse series of piperazines linked at N1 to 4, 5, or 6 positions of 3-(2H)-pyridazinone ring and at N4, by a suitable alkyl spacer, to some classical alpha1-adrenoceptor pharmacophore moieties, were tested in vitro for their alpha1-adrenoceptor antagonist activity. The modeling of their biological activity (pKb) by comparative molecular field analysis led to the development of a statistically significant partial least squares (PLS) model able to detect at 3-D level the main physicochemical interactions responsible for alpha1-adrenoceptor antagonist activity.
Collapse
Affiliation(s)
- N Cinone
- Dipartimento Farmaco-Chimico, Università di Bari, Italy
| | | | | | | | | | | |
Collapse
|
24
|
Pigini M, Bousquet P, Brasili L, Carrieri A, Cavagna R, Dontenwill M, Gentili F, Giannella M, Leonetti F, Piergentili A, Quaglia W, Carotti A. Ligand binding to I2 imidazoline receptor: the role of lipophilicity in quantitative structure-activity relationship models. Bioorg Med Chem 1998; 6:2245-60. [PMID: 9925287 DOI: 10.1016/s0968-0896(98)80005-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of 2-trans-styryl-imidazoline (tracizoline) congeners were designed and tested to develop 2-D and 3-D QSAR models for their binding to imidazoline (I2) receptor. The important role of lipophilicity was assessed by classical 2-D QSAR study (Hansch approach) and by comparative molecular field analysis (CoMFA) with the inclusion of the molecular lipophilicity potential (MLP), as an additional descriptor, besides standard steric and electrostatic fields. Results from these studies were compared to those obtained in a previous modeling study of I2 receptor ligands and integrated into a new, comprehensive model, based on about sixty I2 receptor ligands. This model revealed, at the three-dimensional level, the most significant steric, electrostatic, and lipophilic interactions accounting for high I2 receptor affinity.
Collapse
Affiliation(s)
- M Pigini
- Dipartimento di Scienze Chimiche, Università di Camerino, MC, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Marot C, Chavatte P, Morin-Allory L, Viaud MC, Guillaumet G, Renard P, Lesieur D, Michel A. Pharmacophoric search and 3D-QSAR comparative molecular field analysis studies on agonists of melatonin sheep receptors. J Med Chem 1998; 41:4453-65. [PMID: 9804685 DOI: 10.1021/jm980026p] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational analysis was used to characterize the agonist pharmacophore for melatonin sheep brain receptor recognition and activation. The molecular geometry shared by all conformations of the selected active ligands was determined. Assuming that all the compounds interact at the same binding site at the receptor level, 2-iodomelatonin pharmacophoric conformation served as a template for the superimposition of 64 structurally heterogeneous agonists constituting the training set used to perform a three-dimensional quantitative structure-activity relationship study via the comparative molecular field analysis method. A statistically significant model was obtained for the totality of the compounds (n = 64, q2 = 0.62, N = 6, r2 = 0.96, s = 0.28, F = 249) with steric, electrostatic, and lipophilic relative contributions of 28%, 35%, and 37%, respectively. The predictive power of the proposed model was discerned by successfully testing the 78 agonist ligands constituting the test set. The model so obtained and validated brings important structural insights to aid the design of novel melatoninergic agonist ligands prior to their synthesis.
Collapse
Affiliation(s)
- C Marot
- Institut de Chimie Organique et Analytique, associé au CNRS, Université d'Orléans, BP 6759, 45067 Orléans Cedex 2, France
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Spedding M, Newman-Tancredi A, Millan MJ, Dacquet C, Michel AN, Jacoby E, Vickery B, Tallentire D. Interaction of the anxiogenic agent, RS-30199, with 5-HT1A receptors: modulation of sexual activity in the male rat. Neuropharmacology 1998; 37:769-80. [PMID: 9707291 DOI: 10.1016/s0028-3908(98)00065-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
RS-30199 has been shown previously to have atypical interactions at 5-HT1A receptors. RS-30199 and RS-64459, an analogue of buspirone with a buspirone side chain, were compared with the classic, partial agonist at 5-HT1A receptors, 8-hydroxy-2 (di-n-propylamino) tetralin (8-OH-DPAT) and buspirone. At human (h) 5-HT1A receptors in CHO cells, RS-30199-193 (racemate) and its enantiomers (-197, -198) inhibited [3H]-8-OH-DPAT binding (RS-30199-198, ki, 29.7 +/- 11.7 nM; RS-30199-197, ki, 74.1 +/- 11.7 nM) as did RS-64459 (ki, 24.9 +/- 6.0 nM), but RS-30199-197 and -198 were almost full agonists in a [35S]-GTPgammaS binding assay, whereas RS-64459 was a partial agonist, resembling buspirone and 8-OH-DPAT. RS-64459 and the enantiomers of RS-30199 had weaker affinity for 5-HT2C and 5-HT7 receptors. These compounds did not induce the 5-HT behavioural syndrome in male rats. However, in a model where naive male rats were introduced to estrogen-progesterone primed, sexually receptive female rats, RS-30199-197 (0.1, 1, 10 mg/kg, s.c.) had a profound inhibitory effect on sexual behaviour score. Neither buspirone nor 8-OH-DPAT reduced the sexual behaviour score. Unlike 8-OH-DPAT, which shortens intromission latency, RS-30199 prolonged intromission latency. RS-30199 (10 mg/kg s.c.) fully inhibited the facilitation of sexual behaviour caused by the alpha2-adrenoceptor antagonist, delequamine (0.1 mg/kg, p.o.). In contrast, RS-64459 (100, 250, 1000 and 4000 microg/kg, s.c.) failed to modify the sexual behaviour score and did not modify intromission latency. The differences between the effects of RS-30199 and RS-64459 in binding and functional experiments are supported by molecular models of the receptor-ligand interaction, where the compounds interact in different ways with the receptor; a model is proposed for the allosteric interaction of different agents with the receptor, resulting in different functional profiles. RS-30199 can be considered an atypical agonist at 5-HT1A receptors.
Collapse
Affiliation(s)
- M Spedding
- Institut de Internationales, Servier, Croissy Research Centre, Paris, France.
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Imberty A, Mollicone R, Mikros E, Carrupt PA, Pérez S, Oriol R. How do antibodies and lectins recognize histo-blood group antigens? A 3D-QSAR study by comparative molecular field analysis (CoMFA). Bioorg Med Chem 1996; 4:1979-88. [PMID: 9007281 DOI: 10.1016/s0968-0896(96)00179-4] [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: 02/03/2023]
Abstract
The cross-reaction patterns of nine antibodies and three lectins against 12 H type 2 related oligosaccharides have been analysed by means of 3D-QSAR study. Three-dimensional descriptors of the molecular properties have been used in comparative molecular field analysis (CoMFA). Three different alignments were considered for the oligosaccharides. One, based on the superimposition of the oligosaccharide core, could be correlated to most of the antibody activities. A second alignment, based on a superimposition of the fucose residue, had to be taken into account for explaining the binding properties of Ulex europaeus isolectin I. Analysis of the QSAR data gives indications on the carbohydrate epitopes essential for antibody recognition and yields some insights about the nature of the molecular recognition. This study complements previous biochemical estimates of the H type 2 related oligosaccharide binding areas (Mollicone, R.; Cailleau, A.; Imberty, A.; Gane, P.; Pérez, S.; Oriol, R. Glycoconj. J. 1996, 13, 263-271).
Collapse
Affiliation(s)
- A Imberty
- Laboratoire de Synthèse Organique, Centre National de la Recherche Scientifique, Nantes, France
| | | | | | | | | | | |
Collapse
|
28
|
Paluchowska MH, Dereń-Wesołek A, Mokrosz JL, Charakchieva-Minol S, Chojnacka-Wójcik E. Structure-activity relationship studies of CNS agents, Part 31: Analogs of MP 3022 with a different number of nitrogen atoms in the heteroaromatic fragment--new 5-HT1A receptor ligands. Arch Pharm (Weinheim) 1996; 329:451-6. [PMID: 8933747 DOI: 10.1002/ardp.19963291006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two series of new MP 3022 analogs, i.e. 1-(o-methoxyphenyl)-4-n-propylpiperazines (3, 4a, 4b, 6-9, and 12-13) and 2-(n-propyl)-1,2,3,4-tetrahydroisoquinolines (5a, 5b, 11a, and 11b) containing a terminal heteroaromatic system with a different number of nitrogen atoms, were synthesized and their 5-HT1A/5-HT2A and alpha 1 receptor affinity was assayed. The majority of investigated piperazines may be classified as non-selective 5-HT1A/5-HT2A/alpha 1 receptor ligands. Compounds 3, 4a, 4b, 7-9a with the highest affinity for 5-HT1A receptors (Ki = 4-54 nM) were tested in vivo. Their functional activity was differentiated; while 3, 8, and 9a behaved like weak antagonists of postsynaptic 5-HT1A receptors, 4b and 7 may be classified as potential partial 5-HT1A receptors, agonists. Isomer 4a has characteristic features of a potential weak postsynaptic 5-HT1A receptor agonist.
Collapse
Affiliation(s)
- M H Paluchowska
- Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | | | | | | | | |
Collapse
|