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Ji Y, Li R, Tian Y, Chen G, Yan A. Classification models and SAR analysis on thromboxane A 2 synthase inhibitors by machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:429-462. [PMID: 35678125 DOI: 10.1080/1062936x.2022.2078880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Thromboxane A2 synthase (TXS) is a promising drug target for cardiovascular diseases and cancer. In this work, we conducted a structure-activity relationship (SAR) study on 526 TXS inhibitors for bioactivity prediction. Three types of descriptors (MACCS fingerprints, ECFP4 fingerprints, and MOE descriptors) were utilized to characterize inhibitors, 24 classification models were developed by support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), and deep neural networks (DNN). Then we reduced the number of fingerprints according to the contribution of descriptors to the models, and constructed 16 extra models on simplified fingerprints. In general, Model_4D built by DNN algorithm and 67 bits MACCS fingerprints performs best. The prediction accuracy of the model on the test set is 0.969, and Matthews correlation coefficient (MCC) is 0.936. The distance between compound and model (dSTD-PRO) was used to characterize the application domain of the model. In the test set of Model_4D, dSTD-PRO of 91.5% compounds is lower than the corresponding training set threshold (threshold0.90 = 0.1055), and the accuracy of these compounds is 0.983. In addition, the important descriptors were summarized and further analyzed. It showed that aromatic nitrogenous heterocyclic groups were beneficial to improve the bioactivity of TXS inhibitors.
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Affiliation(s)
- Y Ji
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - R Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Y Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - G Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
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2
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Synthesis and in Vitro and in Vivo Anticoagulant and Antiplatelet Activities of Amidino- and Non-Amidinobenzamides. Molecules 2016; 21:molecules21050676. [PMID: 27213328 PMCID: PMC6273990 DOI: 10.3390/molecules21050676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 12/26/2022] Open
Abstract
Three amidino- and ten non-amidinobenzamides were synthesized as 3-aminobenzoic acid scaffold-based anticoagulant and antiplatelet compounds. The anticoagulant activities of thirteen synthesized compounds 1-13, and 2b and 3b as prodrugs were preliminary evaluated by screening the prolongation of activated partial thromboplastin time (aPTT) and prothrombin time (PT) in vitro. From the aPTT results obtained, two amidinobenzamides, N-(3'-amidinophenyl)-3-(thiophen-2''-ylcarbonylamino) benzamide (1, 33.2 ± 0.7 s) and N-(4'-amidinophenyl)-3-(thiophen-2''-ylcarbonylamino) benzamide (2, 43.5 ± 0.6 s) were selected to investigate the further anticoagulant and antiplatelet activities. The aPTT results of 1 (33.2 ± 0.7 s) and 2 (43.5 ± 0.6 s) were compared with heparin (62.5 ± 0.8 s) in vitro at 30 μM. We investigated the effect of 1 and 2 on blood anticoagulant activity (ex vivo) and on tail bleeding time (in vivo) on mice. A tail cutting/bleeding time assay revealed that both 1 and 2 prolonged bleeding time in mice at a dose of 24.1 g/mouse and above. Compounds 1 and 2 dose-dependently inhibited thrombin-catalyzed fibrin polymerization and platelet aggregation. In addition, 1 and 2 were evaluated on the inhibitory activities of thrombin and FXa as well as the generation of thrombin and FXa in human umbilical vein endothelial cells (HUVECs). Collectively, 1 and 2 possess some antiplatelet and anticoagulant activities and offer a basis for development of a novel antithrombotic product.
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Prajapti SK, Shrivastava S, Bihade U, Gupta AK, Naidu VGM, Banerjee UC, Babu BN. Synthesis and biological evaluation of novel Δ2-isoxazoline fused cyclopentane derivatives as potential antimicrobial and anticancer agents. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00525b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel Δ2-isoxazoline fused cyclopentane derivatives have been synthesized and evaluated for their antimicrobial and anticancer activities.
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Affiliation(s)
- Santosh Kumar Prajapti
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Shweta Shrivastava
- Department of Pharmacology and Toxicology
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Umesh Bihade
- Department of Pharmaceutical Technology
- National Institute of Pharmaceutical Education and Research (NIPER)
- S. A. S. Nagar
- India
| | - Ajay Kumar Gupta
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - V. G. M. Naidu
- Department of Pharmacology and Toxicology
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Uttam Chand Banerjee
- Department of Pharmaceutical Technology
- National Institute of Pharmaceutical Education and Research (NIPER)
- S. A. S. Nagar
- India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
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4
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Wang X, Liu L, Huang L, Herbst-Robinson K, Cornec AS, James MJ, Sugiyama S, Bassetto M, Brancale A, Trojanowski JQ, Lee VMY, Smith AB, Brunden KR, Ballatore C. Potent, long-acting cyclopentane-1,3-Dione thromboxane (A2)-receptor antagonists. ACS Med Chem Lett 2014; 5:1015-20. [PMID: 25221659 DOI: 10.1021/ml5002085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/17/2014] [Indexed: 11/29/2022] Open
Abstract
A series of derivatives of the known thromboxane A2 prostanoid (TP) receptor antagonists, 3-(6-((4-chlorophenyl)sulfonamido)-5,6,7,8-tetrahydronaphthalen-1-yl)propanoic acid and 3-(3-(2-((4-chlorophenyl)sulfonamido)ethyl)phenyl) propanoic acid, were synthesized in which the carboxylic acid functional group was replaced with substituted cyclopentane-1,3-dione (CPD) bioisosteres. Characterization of these molecules led to the discovery of remarkably potent new analogues, some of which were considerably more active than the corresponding parent carboxylic acid compounds. Depending on the choice of the C2 substituent of the CPD unit, these new derivatives can produce either a reversible or an apparent irreversible inhibition of the human TP receptor. Given the potency and the long-lasting inhibition of TP receptor signaling, these novel antagonists may comprise promising leads for the development of antithromboxane therapies.
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Affiliation(s)
| | | | | | | | | | | | | | - Marcella Bassetto
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Andrea Brancale
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
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5
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Evaluation of the cyclopentane-1,2-dione as a potential bio-isostere of the carboxylic acid functional group. Bioorg Med Chem Lett 2014; 24:4171-5. [PMID: 25127105 DOI: 10.1016/j.bmcl.2014.07.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 11/20/2022]
Abstract
Cycloalkylpolyones hold promise in drug design as carboxylic acid bio-isosteres. To investigate cyclopentane-1,2-diones as potential surrogates of the carboxylic acid functional group, the acidity, tautomerism, and geometry of hydrogen bonding of representative compounds were evaluated. Prototypic derivatives of the known thromboxane A2 prostanoid (TP) receptor antagonist, 3-(3-(2-((4-chlorophenyl)sulfonamido)-ethyl)phenyl)propanoic acid, in which the carboxylic acid moiety is replaced by the cyclopentane-1,2-dione unit, were synthesized and evaluated as TP receptor antagonists. Cyclopentane-1,2-dione derivative 9 was found to be a potent TP receptor antagonist with an IC50 value comparable to that of the parent carboxylic acid. These results indicate that the cyclopentane-1,2-dione may be a potentially useful carboxylic acid bio-isostere.
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Abstract
The carboxylic acid functional group can be an important constituent of a pharmacophore, however, the presence of this moiety can also be responsible for significant drawbacks, including metabolic instability, toxicity, as well as limited passive diffusion across biological membranes. To avoid some of these shortcomings while retaining the desired attributes of the carboxylic acid moiety, medicinal chemists often investigate the use of carboxylic acid (bio)isosteres. The same type of strategy can also be effective for a variety other purposes, for example, to increase the selectivity of a biologically active compound or to create new intellectual property. Several carboxylic acid isosteres have been reported, however, the outcome of any isosteric replacement cannot be readily predicted as this strategy is generally found to be dependent upon the particular context (i.e., the characteristic properties of the drug and the drug-target). As a result, screening of a panel of isosteres is typically required. In this context, the discovery and development of novel carboxylic acid surrogates that could complement the existing palette of isosteres remains an important area of research. The goal of this Minireview is to provide an overview of the most commonly employed carboxylic acid (bio)isosteres and to present representative examples demonstrating the use and utility of each isostere in drug design.
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Affiliation(s)
- Carlo Ballatore
- Department of Chemistry, University of Pennsylvania, 231 South 34th St., Philadelphia, PA 19104, USA.
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Hamada Y, Kiso Y. The application of bioisosteres in drug design for novel drug discovery: focusing on acid protease inhibitors. Expert Opin Drug Discov 2012; 7:903-22. [PMID: 22873630 DOI: 10.1517/17460441.2012.712513] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION A bioisostere is a powerful concept for medicinal chemistry. It allows the improvement of the stability; oral absorption; membrane permeability; and absorption, distribution, metabolism and excretion (ADME) of drug candidate, while retaining their biological properties. The term 'bioisostere' is derived from 'isostere', whose physical and chemical properties, such as steric size, hydrophobicity, and electronegativity, are similar to those of a functional or atomic group, and is considered to possess biological properties. Here, the authors highlight the recent applications of bioisosteres in drug design, mainly based on our drug discovery studies. AREAS COVERED This review discusses the application of bioisosteres for novel drug discovery with focus on the authors' drug discovery studies such as renin, HIV-protease, and β-secretase inhibitors. The authors highlight that some bioisosteres can form the scaffolding for drug candidates, namely substrate transition state, amide/ester, and carboxylic acid bioisosteres. Moreover, the authors propose the new terms 'electron-donor bioisostere' and 'conformational bioisostere' for drug discovery. EXPERT OPINION The authors discuss the importance of bioisostere's design concept based on specific interaction with the corresponding biomolecule. In addition, some strategies for drug discovery based on the bioisostere concept are introduced. Many bioisosteres, which are recognized by corresponding target biomolecules as exhibiting similar biological properties, have been reported to date; most of the recently developed bioisosteres were designed by cheminformatics approaches. Some molecular design softwares and databases are introduced.
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Affiliation(s)
- Yoshio Hamada
- Faculty of Pharmaceutical Sciences , Kobe Gakuin University, Minatojima, Chuo-ku, Kobe, Japan
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8
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Ballatore C, Soper JH, Piscitelli F, James M, Huang L, Atasoylu O, Huryn DM, Trojanowski JQ, Lee VMY, Brunden KR, Smith AB. Cyclopentane-1,3-dione: a novel isostere for the carboxylic acid functional group. Application to the design of potent thromboxane (A2) receptor antagonists. J Med Chem 2011; 54:6969-83. [PMID: 21863799 DOI: 10.1021/jm200980u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclopentane-1,3-diones are known to exhibit pK(a) values typically in the range of carboxylic acids. To explore the potential of the cyclopentane-1,3-dione unit as a carboxylic acid isostere, the physical-chemical properties of representative congeners were examined and compared with similar derivatives bearing carboxylic acid or tetrazole residues. These studies suggest that cyclopentane-1,3-diones may effectively substitute for the carboxylic acid functional group. To demonstrate the use of the cyclopentane-1,3-dione isostere in drug design, derivatives of a known thromboxane A(2) prostanoid (TP) receptor antagonist, 3-(3-(2-(4-chlorophenylsulfonamido)ethyl)phenyl)propanoic acid (12), were synthesized and evaluated in both functional and radioligand-binding assays. A series of mono- and disubstituted cyclopentane-1,3-dione derivatives (41-45) were identified that exhibit nanomolar IC(50) and K(d) values similar to 12. Collectively, these studies demonstrate that the cyclopentane-1,3-dione moiety comprises a novel isostere of the carboxylic acid functional group. Given the combination of the relatively strong acidity, tunable lipophilicity, and versatility of the structure, the cyclopentane-1,3-dione moiety may constitute a valuable addition to the palette of carboxylic acid isosteres.
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Affiliation(s)
- Carlo Ballatore
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States.
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9
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Shetty RS, Lee Y, Liu B, Husain A, Joseph RW, Lu Y, Nelson D, Mihelcic J, Chao W, Moffett KK, Schumacher A, Flubacher D, Stojanovic A, Bukhtiyarova M, Williams K, Lee KJ, Ochman AR, Saporito MS, Moore WR, Flynn GA, Dorsey BD, Springman EB, Fujimoto T, Kelly MJ. Synthesis and pharmacological evaluation of N-(3-(1H-indol-4-yl)-5-(2-methoxyisonicotinoyl)phenyl)methanesulfonamide (LP-261), a potent antimitotic agent. J Med Chem 2010; 54:179-200. [PMID: 21126027 DOI: 10.1021/jm100659v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis and optimization of a series of orally bioavailable 1-(1H-indol-4-yl)-3,5-disubstituted benzene analogues as antimitotic agents are described. A functionalized dibromobenzene intermediate was used as a key scaffold, which when modified by sequential Suzuki coupling and Buchwald-Hartwig amination provided a flexible entry to 1,3,5-trisubstituted phenyl compounds. A 1H-indol-4-yl moiety at the 1-position was determined to be a critical feature for optimal potency. The compounds have been shown to induce cell cycle arrest at the G2/M phase and demonstrate efficacy in both cell viability and cell proliferation assays. The primary site of action for these agents is revealed by their colchicine competitive inhibition of tubulin polymerization, and a computational model has been developed for the association of these compounds to tubulin. An optimized lead LP-261 significantly inhibits growth of a human non-small-cell lung tumor (NCI-H522) in a mouse xenograft model.
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Affiliation(s)
- Rupa S Shetty
- Ansaris, Four Valley Square, Blue Bell, Pennsylvania 19401, United States.
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10
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Roy S, Zych AJ, Herr RJ, Cheng C, Shipps GW. Direct synthesis of Cbz-protected (2-amino)-6-(2-aminoethyl)pyridines. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Bruno O, Brullo C, Schenone S, Bondavalli F, Ranise A, Tognolini M, Ballabeni V, Barocelli E. Synthesis and pharmacological evaluation of 5H-[1]benzopyrano[4,3-d]pyrimidines effective as antiplatelet/analgesic agents. Bioorg Med Chem 2004; 12:553-61. [PMID: 14738964 DOI: 10.1016/j.bmc.2003.11.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis and pharmacological screening of new 2-methylthio/2-methanesulfonyl/2-methoxy-5H-[1]benzopyrano[4,3-d]pyrimidines were planned in order to study the effects of the 5-substitution with alkoxy/phenoxy/alkylthio and phenylthio groups both on in vitro antiplatelet and in vivo antinociceptive activities. Antiplatelet activity was assessed in vitro against ADP, Arachidonic acid and U46619 induced aggregation, in rabbit plasma. Anti-inflammatory, analgesic and antipyretic activities were tested in rat paw edema, mouse writhing test and LPS induced rat fever, respectively. Amongst test compounds, 2-methylthio derivatives displayed an ASA-like antiplatelet activity whereas 2-methoxy and, particularly, 2-methanesulfonyl derivatives showed a broad spectrum of antiplatelet action, inhibiting both the ADP- and the AA- and U46619-induced aggregation. With regard to the in vivo pharmacological activities, mainly the 2-methoxy derivatives showed a significant analgesic effect comparable to that of indomethacin. SAR considerations, also in comparison with a number of previously described compounds, were performed.
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Affiliation(s)
- Olga Bruno
- Dipartimento di Scienze Farmaceutiche-Università degli Studi, V.le Benedetto XV, 3-16132 Genova, Italy.
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12
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Dack KN, Dickinson RP, Long CJ, Steele J. Thromboxane modulating agents. 4. Design and synthesis of 3-(2-[[(4-chlorophenyl)sulfonyl]-amino]ethyl)benzenepropanoic acid derivatives as potent thromboxane receptor antagonists. Bioorg Med Chem Lett 1998; 8:2061-6. [PMID: 9873486 DOI: 10.1016/s0960-894x(98)00242-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The design of a series of thromboxane receptor antagonists based on 3-(2-[[(4-chlorophenyl)sulfonyl]amino]ethyl)benzenepropanoic acid (1) is described. Addition of an arylmethyl group at the 5-position of 1 gave exceptionally potent agents in vitro and in vivo, with 13a (UK-147,535) giving complete blockade of the TxA2 receptor for greater than 12 hours in dogs, following an oral dose of 0.1 mg/kg.
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Affiliation(s)
- K N Dack
- Department of Discovery Chemistry, Pfizer Central Research, Sandwich, Kent, U.K.
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