- Molecular modeling studies, synthesis and biological evaluation of dabigatran analogues as thrombin inhibitors
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In this work, 48 thrombin inhibitors based on the structural scaffold of dabigatran were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models based on three alignments for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for thrombin protein inhibition. In addition to the 3D-QSAR study, Topomer CoMFA model also was established with a higher leave-one-out cross-validation q2 and a non-cross-validation r2, which suggest that the three models have good predictive ability. The results indicated that the steric, hydrophobic and electrostatic fields play key roles in QSAR model. Furthermore, we employed molecular docking and re-docking simulation explored the binding relationship of the ligand and the receptor protein in detail. Molecular docking simulations identified several key interactions that were also indicated through 3D-QSAR analysis. On the basis of the obtained results, two compounds were designed and predicted by three models, the biological evaluation in vitro (IC50) demonstrated that these molecular models were effective for the development of novel potent thrombin inhibitors.
- Dong, Ming-Hui,Chen, Hai-Feng,Ren, Yu-Jie,Shao, Fang-Ming
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Read Online
- Synthesis of a secretoglobin 3A2 type C (98–139) fragment by Dawson's native chemical ligation
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A secretoglobin 3A2 type C (98–139) peptide was synthesized by native chemical ligation between 115Ile and 116Cys residues using Dawson's linker. The peptide-N-acyl-benzimidazolinone-glycine amide, a C-terminal thioesters precursor, was provided from 3-amino-4-(methylamino)benzoic acid. In addition, an N-terminal cysteine fragment, the (116–139) peptide, was prepared by ordinary Fmoc-solid phase peptide synthesis. Native chemical ligation of the (98–115) fragment with the Dawson's linker and the (116–139) peptide smoothly proceeded to give SCGB3A2 type C (98–139) peptide.
- Kikuchi, Mariko,Kurotani, Reiko,Konno, Hiroyuki
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- A chemical approach for the synthesis of the DNA-binding domain of the oncoprotein MYC
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We describe the first chemical synthesis of a functional mutant of the DNA binding domain of the oncoprotein MYC, using two alternative strategies which involve either one or two Native Chemical Ligations (NCLs). Both routes allowed the efficient synthesis of a miniprotein which is capable of heterodimerizing with MAX, and replicate the DNA binding of the native protein. The versatility of the reported synthetic approach enabled the straightforward preparation of MYC and Omomyc analogues, as well as fluorescently labeled derivatives.
- Calo-Lapido, Renata,Penas, Cristina,Jiménez-Balsa, Adrián,Vázquez, M. Eugenio,Mascare?as, José L.
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- Chemical Protein Synthesis Using a Second-Generation N-Acylurea Linker for the Preparation of Peptide-Thioester Precursors
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The broad utility of native chemical ligation (NCL) in protein synthesis has fostered a search for methods that enable the efficient synthesis of C-terminal peptide-thioesters, key intermediates in NCL. We have developed an N-acylurea (Nbz) approach for the synthesis of thioester peptide precursors that efficiently undergo thiol exchange yielding thioester peptides and subsequently NCL reaction. However, the synthesis of some glycine-rich sequences revealed limitations, such as diacylated products that can not be converted into N-acylurea peptides. Here, we introduce a new N-acylurea linker bearing an o-amino(methyl)aniline (MeDbz) moiety that enables in a more robust peptide chain assembly. The generality of the approach is illustrated by the synthesis of a pentaglycine sequence under different coupling conditions including microwave heating at coupling temperatures up to 90 C, affording the unique and desired N-acyl-N′-methylacylurea (MeNbz) product. Further extension of the method allowed the synthesis of all 20 natural amino acids and their NCL reactions. The kinetic analysis of the ligations using model peptides shows the MeNbz peptide rapidly converts to arylthioesters that are efficient at NCL. Finally, we show that the new MeDbz linker can be applied to the synthesis of cysteine-rich proteins such the cyclotides Kalata B1 and MCoTI-II through a one cyclization/folding step in the ligation/folding buffer. (Chemical Equation Presented).
- Blanco-Canosa, Juan B.,Nardone, Brunello,Albericio, Fernando,Dawson, Philip E.
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Read Online
- Design, synthesis and biological activity evaluation of novel methyl substituted benzimidazole derivatives
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Ten new dabigatran derivatives (7a–j) with high docking scoring were designed, synthesised and biologically evaluated. The inhibitory in vitro activity of these compounds on thrombin was evaluated on the basis of preliminary activity screening results. The IC50 values of compounds 7a, 7d and 7j were 1.92, 2.17 and 1.54 nM, respectively, and are equivalent to the dabigatran (IC50 = 1.20 nM). Therefore, the most active compound, 7j, was selected to further investigate the anticoagulant activity in rats. Compound 7j presented excellent in vivo inhibitory effects on arteriovenous thrombosis, and the inhibition rate was (84.19 ± 1.14) %. The anticoagulant activity of compound 7k synthesised in the previous work was evaluated in vivo, and its inhibition rate was (85.58 ± 2.89) %. This rate was nearly equivalent to that of dabigatran (85.07 ± 0.61) %. Results indicated that compounds 7a, 7d, 7j and 7k can be further studied as novel antithrombin drug candidates.
- Liu, Qianqian,Ren, Yujie,Zhang, Tianrong
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- “On Water” promoted N-arylation reactions using Cu (0)/myo-inositol catalytic system
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Myo-inositol is originally applied as a cardiovascular medicine in clinic, which can be multi-ton manufactured via extraction from the byproducts in agricultural product processing such as defatted rice bran and corn-soaking water. Herein, the application of myo-inositol (MI) as a novel versatile tridentate O-donor ligand has been first described for promoting Cu-catalyzed amination reaction in aqueous medium.
- Zhou, Qifan,Du, Fangyu,Chen, Yuanguang,Fu, Yang,Chen, Guoliang
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supporting information
p. 1938 - 1941
(2019/06/24)
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- Computer-aid drug design, synthesis, and anticoagulant activity evaluation of novel dabigatran derivatives as thrombin inhibitors
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In this study, computer-aided drug design techniques were adopted to explore the structural and chemical features for dabigatran and design novel derivatives. The built 3D-QSAR models demonstrated significant statistical quality and excellent predictive ability by internal and external validation. Based on QSAR information, 11 novel dabigatran derivatives (12a–12k) were designed and predicted, then ADME prediction and molecular docking were performed. Furthermore, all designed compounds were synthesized and characterized by 1H NMR, 13C NMR and HR-MS. Finally, they were evaluated for anticoagulant activity in vitro. The activity results showed that the 10 obtained compounds exhibited comparable activity to the reference dabigatran (IC50 = 9.99 ± 1.48 nM), except for compound 12i. Further analysis on molecular docking was performed on three compounds (12a, 12c and 12g) with better activity (IC50 = 11.19 ± 1.70 nM, IC50 = 10.94 ± 1.85 nM and IC50 = 11.19 ± 1.70 nM). MD simulations (10 ns) were carried out, and their binding free energies were calculated, which showed strong hydrogen bond and pi–pi stacking interactions with key residues Gly219, Asp189 and Trp60D. The 10 novel dabigatran derivatives obtained can be further studied as anticoagulant candidate compounds.
- Huang, Shanshan,Ren,Peng, Xiuxiu,Qian, Pingping,Meng, Lingwei
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- One-Pot Peptide Ligation-Oxidative Cyclization Protocol for the Preparation of Short-/Medium-Size Disulfide Cyclopeptides
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Native chemical ligation (NCL) employing the N-methylbenzimidazolinone (MeNbz) linker readily provided the linear precursor of a 16-mer peptide that is difficult to obtain by stepwise solid-phase peptide synthesis. NCL and the workup conditions were improved toward a protocol that allows for quantitative removal of the 4-hydroxymercaptophenol additive and subsequent formation of the disulfide bridge in the NCL cocktail by oxidation in air, tolerated by the presence of tris(hydroxypropyl)phosphine.
- Spengler, Jan,Blanco-Canosa, Juan B.,Forni, Luciano,Albericio, Fernando
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supporting information
p. 4306 - 4309
(2018/07/29)
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- Structure-activity relationship study based on autoinducing peptide (AIP) from dog pathogen S. schleiferi
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Herein, an effective protocol for solid-phase synthesis of peptide thiolactones by concomitant ring closure and cleavage from the solid support is reported. The strategy was applied for mapping the importance of the structural features in S. schleiferi AIP (5) by performing an alanine scan and truncation of this natural compound. This furnished some of the most potent inhibitors of accessory gene regulator (agr)-I in the human pathogen S. aureus reported to date.
- Gless, Bengt H.,Peng, Pai,Pedersen, Katja D.,Gotfredsen, Charlotte H.,Ingmer, Hanne,Olsen, Christian A.
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supporting information
p. 5276 - 5279
(2017/11/06)
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- BENZOIMIDAZOLE DERIVATIVES AS PAD4 INHIBITORS
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Compounds of formula (I): wherein X, Y, R1 and R3-R11 are as herein defined, and salts thereof are PAD4 inhibitors and may be useful in the treatment of various disorders, for example rheumatoid arthritis, vasculitis, systemic lupus erythematosus, ulcerative colitis, cancer, cystic fibrosis, asthma, cutaneous lupus erythematosis, and psoriasis.
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- Design, synthesis, biological evaluation and molecular docking studies of dabigatran analogs as potential thrombin inhibitors
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A series of fluorinated dabigatran analogs were designed and synthesized. All the target compounds were characterized by 1H NMR, 13C NMR, and FT-ICR-MS. The thrombin inhibitory activities of the new synthesized compounds were also evaluated in vitro. The results show that compound 12a has the highest IC50 of thrombin inhibition (IC50 = 5.41 nM). Moreover, molecular docking simulation was carried out to elucidate the conformations of the compounds and key amino acid residues at the active site of thrombin protein. The results show there is an appropriate relationship between IC50 and the docking scores for compounds 12a-e. We suggest that the hydrogen bond interaction between Asp189, Gly219 of thrombin and the compounds appear to play major role in thrombin inhibition.
- Chen, Hai-Feng,Dong, Ming-Hui,Ren, Yu-Jie,Wang, Fei
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p. 347 - 357
(2016/01/09)
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- Multi-substituted 4-methyl ester derivative of amino benzonitrile trunk and its preparation and use
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The invention provides new ester derivatives with a general formula (I) shown in the specification of multi-substituted 4-methylamino-benzamidine or pharmaceutically acceptable salts, wherein A1, A2, A3 and A4 in the formula are as defined in the specification. The compounds have an anticoagulant effect and can be used for preparing medicaments for preventing and treating thromboembolic diseases.
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Paragraph 0096; 0105-0107
(2018/01/19)
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- Synthesis and biological evaluation of novel dabigatran derivatives as thrombin inhibitors
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A novel series of 3-[{2-[(4-carbamimidoylphenylamino)methyl]-1-substituted-1H-benzoimidazole-5-carbonyl}(3-chloro-4-fluorophenyl)amino]propionic derivatives of dabigatran was synthesized. The structures of the compounds were characterized by 1H NMR, 13C NMR, HRMS, and elemental analysis. The compounds were screened for in vitro thrombin inhibitory activity. The results indicated that the compounds had low to moderate inhibitory activity. The compounds with N-methyl and N-ethyl side chains had much greater inhibitory activity against thrombin than those with other side chains.
- Li, Chun Lei,Ren, Yu Jie
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p. 735 - 752
(2016/04/26)
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- 2-(AZAINDOL-2-YL)BENZIMIDAZOLES AS PAD4 INHIBITORS
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Compounds of formula (I): wherein; R1 is hydrogen or C1-6alkyl;R2 is hydrogen, C1-6alkyl, perhalomethylC0-5alkyl-O—, or C1-6alkoxy;R3 is hydrogen, C1-6alkyl, or C1-6alkoxyC1-6alkyl;R4 is hydrogen, C1-6alkyl, perhalomethylC1-6alkyl; or unsubstituted C3-6cycloalkylC1-6 alkyl;A is C—R5 or N;B is C—R6 or N;D is C—R7 or N;with the proviso that at least one of A, B, and D, is N;R5 is hydrogen or C1-6alkyl;R6 is hydrogen or C1-6alkyl;R7 is hydrogen, C1-6alkyl, C1-6alkoxy, or hydroxy;R8 is hydrogen or C1-6alkyl, with the proviso that one of R4 and R8 is hydrogen;R9 is hydrogen or hydroxy;R10 is hydrogen or C1-6alkyl; and salts thereof are PAD4 inhibitors and may be useful in the treatment of various disorders, for example rheumatoid arthritis, vasculitis, systemic lupus erythematosus, ulcerative colitis, cancer, cystic fibrosis, asthma, cutaneous lupus erythematosis, and psoriasis.
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- BENZAMIDE DERIVATIVE USEFUL AS FASN INHIBITORS FOR THE TREATMENT OF CANCER
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The present invention is directed to benzamide derivatives, pharmaceutical compositions containing them, and their use as FASN inhibitors, in for example, the treatment of cancer, obesity related disorders, liver related disorders and viral infections. Such compounds are represented by formula (I) as follows: wherein R1, R2, R3, R4, R5, m, n, (II) and (III) are defined herein.
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(2015/06/18)
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- A PROCESS FOR PREPARATION OF DABIGATRAN ETEXILATE MESYLATE AND INTERMEDIATES THEREOF
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The present invention relates to an improved process for the preparation of Dabigatran etexilate and its acid addition salts thereof, wherein the said process substantially eliminates the potential impurities. The present invention also relates to an intermediate of Dabigatran etexilate and process for preparation thereof.
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Page/Page column 40; 41
(2015/09/28)
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- PROCESS FOR THE PREPARATION OF DABIGATRAN ETEXILATE MESYLATE AND POLYMORPHS OF INTERMEDIATES THEREOF
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The present invention provides crystalline form of intermediates of Formula 2A, The present invention also provides process for the preparation of dabigatran etexilate mesylate; polymorph of intermediates thereof; particularly processes for the preparation of crystalline form of intermediates. The present invention also relates to the use of crystalline intermediates for the preparation of dabigatran etexilate mesylate.
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Paragraph 0117-0118
(2015/02/18)
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- Process For The Preparation Of Benzimidazole Derivatives And Salts Thereof
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Provided are novel salts of benzimidazole derivatives, preferably salts of benzimidazole derivatives which are useful intermediates in the synthesis of pure 1-methyl-2-[N-[4-(N-n-hexyloxycarbonylamidino)phenyl]aminomethyl]benzimidazol-5-yl-carboxylicacid-N-(2-pyridyl)-N-(2-ethoxycarbonylethyl)amide and its salts.
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Paragraph 0218
(2015/03/31)
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- 2 - (AZAINDOL- 2 -YL) BENZ IMIDAZOLES AS PAD4 INHIBITORS
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Compounds of formula (I) wherein; R1 is hydrogen or C1-6alkyl; R2 is hydrogen, C1-6alkyl, perhalomethylC0-5alkyl-O-, or C1-6alkoxy; R3 is hydrogen, C1-6alkyl, or C1-6alkoxyC1-6alkyl; R4 is hydrogen, C1-6alkyl, perhalomethylC1-6alkyl; or unsubstituted C3-6cycloalkylC1-6alkyl; A is C-R5 or N; B is C-R6 or N; D is C-R7 or N; with the proviso that at least one of A, B, and D, is N; R5 is hydrogen or C1-6alkyl; R6 is hydrogen or C1-6alkyl; R7 is hydrogen, C1-6alkyl, C1-6alkoxy, or hydroxy; R8 is hydrogen or C1-6alkyl, with the proviso that one of R4 and R8 is hydrogen; R9 is hydrogen or hydroxy; R10 is hydrogen or C1-6alkyl; and salts thereof are PAD4 inhibitors and may be useful in the treatment of various disorders, for example rheumatoid arthritis, vasculitis, systemic lupus erythematosus, ulcerative colitis, cancer, cystic fibrosis, asthma, cutaneous lupus erythematosis, and psoriasis.
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- NOVEL ARYLALKENE DERIVATIVES AND USE THEREOF AS SELECTIVE ESTROGEN RECEPTOR MODULATORS
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The invention provides novel ethylene derivatives represented by Formula I, which may be used as selective estrogen receptor modulators (SERMs) and useful in the prophylaxis and/or treatment of estrogen-dependent conditions or conditions.
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Paragraph 0291
(2013/07/19)
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- PROCESS FOR THE PREPARATION OF DABIGATRAN ETEXILATE MESYLATE AND POLYMORPHS OF INTERMEDIATES THEREOF
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The present invention provides crystalline form of intermediates of Formula 2A, Formula 2B and Formula E. The present invention also provides process for the preparation of dabigatran etexilate mesylate; polymorph of intermediates thereof; particularly processes for the preparation of crystalline form of intermediates. The present invention also relates to the use of crystalline intermediates for the preparation of dabigatran etexilate mesylate.
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Page/Page column 17
(2013/08/15)
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- HETEROCYCLIC COMPOUNDS FOR THE INHIBITION OF PASK
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Disclosed herein are new heterocyclic compounds and compositions and their application as pharmaceuticals for the treatment of disease. Methods of inhibiting PAS Kinase (PASK) activity in a human or animal subject are also provided for the treatment of diseases such as diabetes mellitus.
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(2012/11/08)
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- Dabigatran etexilate and related substances, processes and compositions, and use of the substances as reference standards and markers
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The present invention relates to dabigatran etexilate and related substances and use of the substances as reference standards and markers. There are also provided processes of detecting the substances in samples of dabigatran etexilate, or pharmaceutically acceptable salts or solvates thereof, and also for analyzing the purity of samples of dabigatran etexilate, or pharmaceutically acceptable salts or solvates thereof. There are still further provided processes of preparing dabigatran etexilate and related substances, and pharmaceutical compositions containing the same.
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(2012/12/13)
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- DABIGATRAN ETEXILATE AND RELATED SUBSTANCES, PROCESSES AND COMPOSITIONS, AND USE OF THE SUBSTANCES AS REFERENCE STANDARDS AND MARKERS
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The present invention relates to dabigatran etexilate and related substances and use of the substances as reference standards and markers. There are also provided processes of detecting the substances in samples of dabigatran etexilate, or pharmaceutically acceptable salts or solvates thereof, and also for analyzing the purity of samples of dabigatran etexilate, or pharmaceutically acceptable salts or solvates thereof.There are still further provided processes of preparing dabigatran etexilate and related substances, and pharmaceutical compositions containing the same.
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Page/Page column 39-40
(2012/12/13)
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- Substituted Fused Imidazole Derivatives, Pharmaceutical Compositions, and Methods of Use Thereof
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Substituted fused imidazole derivatives, methods of their preparation, pharmaceutical compositions comprising a substituted fused imidazole derivative, and methods of use in treating inflammation are provided. The substituted fused imidazole derivatives may control the activity or the amount or both the activity and the amount of heme-oxygenase.
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Page/Page column 115; 117
(2011/09/14)
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- 3H-IMIDAZO [4, 5 -C] PYRIDINE- 6 -CARBOXAMIDES AS ANTI- INFLAMMATORY AGENTS
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The present invention relates to compounds of general formula (I) in which A, L, M, Q2, Q3, Q4, R1, R5, Ra, Rb, Rc, W, X, Y, Z1, Z2, Z3 are defined in the description, the salts thereof, particularly the physiologically acceptable salts thereof. The compounds are of potential utility in the treatment and/or prevention of inflammatory diseases and associated conditions, in particular, in the treatment and/or prevention of pain. The invention also relates to the use of such compounds as medicaments, to pharmaceutical compositions containing them, and to their preparation.
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Page/Page column 81-82
(2010/09/18)
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- Total synthesis of hypermodified epothilone analogs with potent in vitro antitumor activity
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The convergent total synthesis of hypermodified epothilone analogs 1 and 2 has been achieved with the stereoselective cyclopropanation of allylic alcohol 17 and ring-closing olefin metathesis with diene 22 as the key steps. In spite of significant structural differences between these analogs and the natural epothilone scaffold, 1 and 2 are potent inducers of tubulin polymerization and inhibit the growth of human cancer cells in vitro with sub-nM IC50 values.
- Kuzniewski, Christian N.,Gertsch, Jurg,Wartmann, Markus,Altmann, Karl-Heinz
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supporting information; experimental part
p. 1183 - 1186
(2009/04/06)
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- Methods for Chk2 inhibitor patient selection
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The present invention contemplates a method to identify subjects that either have a tumor, or are at risk for tumor development, that are responsive to various inhibitors of an activated-Chk2 protein. Such Chk2 inhibitors may comprise a benzimidazole core structure, and derivatives thereof. Other Chk2 inhibitors may comprise nucleic acids, such as silencing interference RNA's specific for a Chk2 expression. Other Chk2 inhibitors may comprises proteins, such as antibodies. For example, the present invention contemplates that when a Chk2 inhibitor is administered during, or after, ionizing radiation tumor cell apoptosis is increased.
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Page/Page column 15-16
(2008/12/05)
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- 3-Nitro-4-amino benzoic acids and 6-amino nicotinic acids are highly selective agonists of GPR109b
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A series of 3-nitro-4-substituted-aminobenzoic acids were prepared and found to act as potent and highly selective agonists of the orphan human GPCR GPR109b, a low affinity receptor for niacin. No activity was observed at the closely homologous high affinity niacin receptor, GPR109a. A second series, comprising 6-amino-substituted nicotinic acids was, also prepared and several analogues showed comparable activity to the nitroaryl series.
- Skinner, Philip J.,Cherrier, Martin C.,Webb, Peter J.,Sage, Carleton R.,Dang, Huong T.,Pride, Cameron C.,Chen, Ruoping,Tamura, Susan Y.,Richman, Jeremy G.,Connolly, Daniel T.,Semple, Graeme
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p. 6619 - 6622
(2008/04/02)
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- Novel non-benzimidazole chk2 kinase inhibitors
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In a recent paper, [Arienti, K. L.; Brunmark, A.; Axe, F. U.; McClure, K. M.; Lee, A.; Blevitt, J.; Neff, D. K.; Huang, L.; Crawford, S.; Chennagiri, R. P.; Karlsson, L.; Brietenbucher, J. G. J. Med. Chem. 2005, 48, 1873], we described the discovery of a class of benzimidazole chk2 kinase inhibitors, exemplified by compound 1, which had radio-protective effects in human T-cells subjected to ionizing radiation. Here, a series of non-benzimidazole analogs intended to define the scope of the SAR about this new series of inhibitor, and allow for refinement of the binding model of these compounds to the chk2 kinase is described.
- McClure, Kelly J.,Huang, Liming,Arienti, Kristen L.,Axe, Frank U.,Brunmark, Anders,Blevitt, Jon,Guy Breitenbucher
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p. 1924 - 1928
(2007/10/03)
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- INHIBITORS OF HISTONE DEACETYLASE
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The invention relates to the inhibition of histone deacetylase. The invention provides compounds and methods for inhibiting histone deacetylase enzymatic activity. The invention also provides compositions and methods for treating cell proliferative diseases and conditions.
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Page/Page column 244
(2010/02/11)
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- Novel compounds and compositions for treating diseases asociated with protease activity
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Novel compounds, compositions and methods effective for the prevention and treatment of mast-cell mediated inflammatory disorders are described. The compounds, compositions and methods are effective for the prevention and treatment of inflammatory diseases associated with the respiratory tract, such as asthma and allergic rhinitis, as well as other types of immunomediated inflammatory disorders, such as rheumatoid arthritis, conjunctivitis and inflammatory bowel disease, various dermatological conditions, as well as certain viral conditions. The compounds comprise potent and selective inhibitors of the mast cell protease tryptase. The compositions for treating these conditions include oral, inhalant, topical and parenteral preparations as well as devices comprising such preparations.
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- Design and synthesis of a novel water soluble benzotetrazepinone
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In order to confer water solubility to the benzotetrazepinone ring system, the synthesis of 12 was undertaken. The design and synthesis of 12 were based upon previously established structural requirements for the stability of the 1,2,3,5-tetrazepin-4-one ring system. Tetrazepinone 12 was extremely water soluble and was 10-fold more potent than its imidazo-1,2,3,5-tetrazin-4-one counterpart 1a, against the human MCF-7 breast cancer cell line. (C) 2000 Elsevier Science Ltd.
- Dumont-Hornebeck, Beatrice,Strube, Yi Ning,Vasilescu, Daniela,Jean-Claude, Bertrand Jacques
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p. 2325 - 2327
(2007/10/03)
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