Design, synthesis and molecular modelling of 1-amidinopiperidine thrombin inhibitors

Design, synthesis and biochemical evaluation of a series of novel non-covalent thrombin inhibitors with a 1-amidinopiperidine moiety are presented. Replacement of the planar benzamidine group in azaphenylalanine derivatives with 1-amidinopiperidine resulted in lower activity but higher selectivity for this type of compounds. The binding conformation of inhibitors in the active site of thrombin was revealed by molecular modelling studies.     

Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors

A library of thrombin inhibitors has been designed using statistical molecular design. An aromatic scaffold was used, with three varied positions corresponding to three pockets at the active site of thrombin (the S-, P-, and D-pockets). The selection was performed in the building block space, and previously acquired data were included in the design procedure. The design resulted in six, four, and six building blocks for the first (S), second (P), and third (D) pockets, respectively. A second round of selection applied to the combined selected building blocks resulted in a subset of 18 compounds. The selected library was synthesized in parallel and biologically evaluated. The compounds were analyzed with respect to their inhibition (pIC(50)) of thrombin; membrane permeability, estimated by migration behavior in micellar media (CE log k') and pK(a); and specificity with respect to inhibition (K(i)) of trypsin. Multivariate QSAR studies of the responses yielded valuable results and information that could only be found using statistical molecular design in combination with multivariate analysis.     

Cyanopeptide analogues: new lead structures for the design and synthesis of new thrombin inhibitors

This contribution deals with the structure-based design and syntheses of the new serine protease inhibitors RA-1001 and RA-1002, which are analogues of the blue-green algae derived cyanopeptide aeruginosin 98-B. Both compounds inhibit thrombin with Ki values of 5.6 microM and 8.7 microM, respectively.     

Dual and selective lipid inhibitors of cyclooxygenases and lipoxygenase: a molecular docking study

The side effects of non-steroidal anti-inflammatory drugs (NSAIDs) concern the public, the government, and pharmaceutical companies. NSAIDs act as inhibitors of cyclooxygenases which are the major cause of pain and inflammation in our body. However, the inhibition of cyclooxygenases could divert arachidonic acid metabolism toward the lipoxygenase pathway leading to other forms of inflammation and tissue damage. Hence a common inhibitor that could block the action of both cyclooxygenases and lipoxygenase is of interest in medicinal chemistry research. Further, the inhibition of both cyclooxygenases-1 and 2 would result in more side effects, since blocking the action of cyclooxygenase-1 would cause gastrointestinal disturbance. Therefore, there is a need to find an inhibitor that acts on cyclooxygenase-2 and lipoxygenase without disturbing the action of cyclooxygenase-1. A molecular docking study with eight lipid ligands was conducted to find the common and selective inhibitors of these three enzymes. Docking with extra precision mode and standard precision mode was performed to find the suitable docking method using the Glide software tool. Docking with extra precision mode yielded better results than with standard precision mode. The docking results are validated using a receiver operator characteristic curve. Further, molecular dynamic simulations were performed for the docked complexes of lowest binding energies. The confirmations obtained from molecular dynamic simulations are more stable and credible than the docked confirmations. Docosahexaenoic acid, eicosapentaenoic acid, 2-arachidonyl glycerol, and anandamide are identified as dual inhibitors of cyclooxygenases and lipoxygenase. α-Tocotrienols are shown to be selective inhibitors of cyclooxygenase-2 and lipoxygenase.     

Computer-aided design of selective COX-2 inhibitors: comparative molecular field analysis,comparative molecular similarity indices analysis,and docking studies of some 1,2-diarylimidazole derivatives

Comparative molecular field analysis and comparative molecular similarity indices analysis were performed on 114 analogues of 1,2-diarylimidazole to optimize their cyclooxygenase-2 (COX-2) selective antiinflammatory activities. These studies produced models with high correlation coefficients and good predictive abilities. Docking studies were also carried out wherein these analogues were docked into the active sites of both COX-1 and COX-2 to analyze the receptor ligand interactions that confer selectivity for COX-2. The most active molecule in the series (53) adopts an orientation similar to that of SC-558 (4-[5-(4-bromophenyl)-3-trifluoromethyl-1H-1-pyrozolyl]-1-benzenesulfonamide) inside the COX-2 active site while the least active molecule (101) optimizes in a different orientation. In the active site, there are some strong hydrogen-bonding interactions observed between residues His90, Arg513, and Phe518 and the ligands. Additionally, a correlation of the quantitative structure-activity relationship data and the docking results is found to validate each other and suggests the importance of the binding step in overall drug action.     

5-substituted 3,4-dihydro-3-amino-2H-1-benzopyran derivatives: synthesis and interaction with serotoninergic receptors

A new series of 3,4-dihydro-3-amino-2H-1-benzopyran derivatives (1 and 2) bearing various substituents on the 5-position was successfully prepared via palladium-mediated cross-coupling reactions. Some of the new compounds showed high affinity for 5-HT1A and 5-HT7 receptors. The best affinity for the 5-HT1A and 5-HT7 receptors was obtained for 2b (Ki = 0.3 nM for 5-HT1A and 3.1 nM for 5-HT7). The anxiolytic activity of compound 2b was evaluated.     

Design,synthesis, and molecular docking study of new monastrol analogues as kinesin spindle protein inhibitors

Lung, colorectal, and breast cancers are the top three types of cancer by incidence and are responsible for one-third of the cancer incidence and mortality. A series of 18 3,4-dihydropyrimidine analogues bearing a 1,2-methylenedioxybenzene component at position 4 with diverse side chains at positions 5 and 6 was designed and synthesized as inhibitors of the Eg5 kinesin enzyme. Target compounds were screened for their anticancer activity according to the NCI-USA protocol toward a panel of 60 cancer cell lines. Compounds 12a and 12b displayed the best antiproliferation activity against many cell lines. Interestingly, compound 12a displayed lethal effects against non-small-cell lung cancer NCI-H522 cells (−42.26%) and MDA-MB-468 breast cancer cells (−1.10%) at a single-dose assay concentration of 10⁻⁵ M. Compounds 11c, 11d, 11g, 12a – d, 13, 15 , and 18a were assayed against the kinesin enzyme, with IC₅₀ values ranging from 1.2 to 18.71 μM, which were more potent compared with monastrol (IC₅₀ = 20 μM). Cell cycle analysis of NCI-H522 cells treated with compound 12a showed cell cycle arrest at the G2/M phase. Furthermore, the expression levels of active caspase-3 and -9 were measured. A molecular docking study was performed for some demonstrative compounds as well as monastrol docked into the allosteric binding site of the kinesin spindle protein.     

Design,synthesis, and molecular docking of novel 2-arylbenzothiazole multiangiokinase inhibitors targeting breast cancer

A novel series of 2-arylbenzothiazoles 9, 10 , and 12 were designed and synthesized as VEGFR-2/FGFR-1/PDGFR-β multiangiokinase inhibitors targeting breast cancer. Structural elongation of the known 2-phenylbenzothiazole scaffold (type I protein kinase inhibitor [PKI]), was carried out to afford series of type II PKIs 9, 10 , and 12 . Compounds 9d, 9f, 9i , and 9k exhibited potent multikinase inhibitory activity with IC₅₀ values of 0.19, 0.18, 0.17, and 0.13 μM, respectively, against VEGFR-2; IC₅₀ values of 0.28, 0.37, 0.19, and 0.27 μM, respectively, against FGFR-1; and IC₅₀ values of 0.07, 0.04, 0.08, and 0.14 μM, respectively, against PDGFR-β. Moreover, the synthesized benzothiazoles demonstrated promising cytotoxic activity against the MCF-7 cell line. The most potent benzothiazoles 9d and 9i exhibited IC₅₀ values of 7.83 and 6.58 μM, respectively, on the MCF-7 cell line in comparison to sorafenib ( III ), which showed IC₅₀ = 4.33 μM. Additionally, 9d and 9i showed VEGFR-2 inhibitory activity in MCF-7 cells of 81% and 83% when compared with sorafenib ( III ), which showed 88% inhibition. Molecular docking of the designed compounds in the VEGFR-2 and FGFR-1 active sites showed the accommodation of the 2-phenylbenzothiazole moiety, as reported, in the hinge region of the receptor tyrosine kinase (RTK)-binding site, while the amide moiety is involved in hydrogen bond interactions with the key amino acids in the gate area; this in turn directs the aryl group to the hydrophobic allosteric back pocket of the RTKs in a type II-like binding mode. The synthesized benzothiazoles showed satisfactory ADME properties for further optimization in drug discovery.     

Phosphorohydrazines of 4-oxo-4H-1-benzopyran and 1-benzopyran-2,4-dione exhibit antitumor activity against L1210 leukemia

Phosphorohydrazines and phosphorohydrazones of benzopyran-2,4-dione as well as the phosphorohydrazone of 4-hydroxycoumarine were tested for antitumor activity in lymphatic leukemia L1210 bearing mice.     

2H-1-苯并吡喃衍生物的合成及其体外抗癌活性的初步评价

目的设计并合成2H-1-苯并吡喃衍生物化合库并对其体外抗癌活性进行评价。方法以2＇-羟基查耳酮为原料通过微波促进合成得到黄酮衍生物中间体，此中间体与POCl，反应得到4-氯-2H-色原烯-3-醛，通过微波辅助液相平行合成的方法，此醛与ROCONHNH2反应得到2H-1-苯并吡喃衍生物化合库。利用HL-60细胞系评价该化合物库的体外抗癌活性。结果与结论合成了含有32个化合物的2H-1-苯并吡喃衍生物库，体外活性评价表明。部分化合物对HL-60细胞的增殖有一定的抑制作用，其中。化合物9e在浓度为30μmol·L^-1的抑制率为70．8％。     

Secondary structure peptide mimetics: design, synthesis, and evaluation of beta-strand mimetic thrombin inhibitors

Constrained dipeptide mimetic templates were designed to mimic the secondary structure of peptides in a beta-strand conformation. Two templates corresponding to the D-Phe-Pro portion of the thrombin inhibitor D-Phe-Pro-ArgCH2Cl were synthesized and converted into nine alpha-ketoamide and alpha-ketoheterocycle inhibitors of thrombin. Additionally, a template corresponding to L-Phe-Pro was synthesized and converted to a thrombin inhibitor. The in vitro inhibition of thrombin by these compounds was determined, and those corresponding to the D-Phe-Pro were found to be more potent inhibitors than the L-Phe-Pro mimetic. The alpha-ketoamides were found to be more potent than the alpha-ketoheterocycles but had much slower on rates. By comparison of a series of alpha-ketoamide analogues, it is apparent that the there is a preference for binding of bulky hydrophobic substituents in the P' portion of the thrombin active site. Three of the inhibitors (MOL098, MOL144, and MOL174) were screened against a series of coagulation and anticoagulation enzymes and found to be selective for inhibition of the coagulation enzymes. Two of the inhibitors were tested in in vitro models of intestinal absorption and found to have low absorption potential. The compounds were then tested in vivo in both rats and primates, and one of them (MOL144) was approximately 25% absorbed in both species. This study has delineated the synthesis of constrained dipeptide beta-strand mimetics and validated the potential for compounds of this type as potent thrombin inhibitors and possible drug leads.     

Design,synthesis, molecular docking,and anticancer activity of benzoxazole derivatives as VEGFR‐2 inhibitors

Novel series of benzoxazole s 4 _a‐f ‐16 were designed, synthesized, and evaluated for anticancer activity against HepG2, HCT‐116, and MCF‐7 cells. HCT‐116 was the most sensitive cell line to the influence of the new derivatives. In particular, compound 5 _e was found to be the most potent against HepG2, HCT‐116, and MCF‐7 with IC₅₀ = 4.13 ± 0.2, 6.93 ± 0.3, and 8.67 ± 0.5 µM, respectively. Compounds 5 _c , 5 _f , 6 _b , 5 _d , and 6 _c showed the highest anticancer activities against HepG2 cells with IC₅₀ of 5.93 ± 0.2, 6.58 ± 0.4, 8.10 ± 0.7, 8.75 ± 0.7, and 9.95 ± 0.9 µM, respectively; HCT‐116 cells with IC₅₀ of 7.14 ± 0.4, 9.10 ± 0.8, 7.91 ± 0.6, 9.52 ± 0.5, and 12.48 ± 1.1 µM, respectively; and MCF‐7 cells with IC₅₀ of 8.93 ± 0.6, 10.11 ± 0.9, 12.31 ± 1.0, 9.95 ± 0.8, and 15.70 ± 1.4 µM, respectively, compared with sorafenib as a reference drug with IC₅₀ of 9.18 ± 0.6, 5.47 ± 0.3, and 7.26 ± 0.3 µM, respectively. The most active compounds 5 _c‐f and 6 _b,c were further evaluated for their vascular endothelial growth factor receptor‐2 (VEGFR‐2) inhibition. Compounds 5 _e and 5 _c potently inhibited VEGFR‐2 at lower IC₅₀ values of 0.07 ± 0.01 and 0.08 ± 0.01 µM, respectively, compared with sorafenib (IC₅₀ = 0.1 ± 0.02 µM). Compound 5 _f potently inhibited VEGFR‐2 at low IC₅₀ value (0.10 ± 0.02 µM) equipotent to sorafenib. Our design was based on the essential pharmacophoric features of the VEGFR‐2 inhibitor sorafenib. Molecular docking was performed for all compounds to assess their binding pattern and affinity toward the VEGFR‐2 active site.     

Structure-based design, synthesis, and biological evaluation of potent and selective macrocyclic checkpoint kinase 1 inhibitors

Based on the crystallographic analysis of a urea-checkpoint kinase 1 (Chk1) complex and molecular modeling, a class of macrocyclic Chk1 inhibitors were designed and their biological activities were evaluated. An efficient synthetic methodology for macrocyclic ureas was developed with Grubbs metathesis macrocyclization as the key step. The structure-activity relationship studies demonstrated that the macrocyclization retains full Chk1 inhibition activity and that the 4-position of the phenyl ring can tolerate a wide variety of substituents. These novel Chk1 inhibitors exhibit excellent selectivity over a panel of more than 70 kinases. Compounds 5b, 5c, 5f, 15, 16d, 17g, 17h, 17k, 18d, and 22 were identified as ideal Chk1 inhibitors, which showed little or no single-agent activity but significantly potentiate the cytotoxicities of the DNA-damaging antitumor agents doxorubicin and camptothecin. These novel Chk1 inhibitors abrogate the doxorubicin-induced G2 and camptothecin-induced S checkpoint arrests, confirming that their potent biological activities are mechanism-based through Chk1 inhibition.     

Benzoxazole/benzothiazole‐derived VEGFR‐2 inhibitors: Design,synthesis, molecular docking,and anticancer evaluations

A novel series of benzoxazole/benzothiazole derivatives 4a–c – 11a–e were designed, synthesized, and evaluated for anticancer activity against HepG2, HCT‐116, and MCF‐7 cells. HCT‐116 was the most sensitive cell line to the influence of the new derivatives. In particular, compound 4c was found to be the most potent derivative against HepG2, HCT‐116, and MCF‐7 cells, with IC₅₀ values = 9.45 ± 0.8, 5.76 ± 0.4, and 7.36 ± 0.5 µM, respectively. Compounds 4b, 9f , and 9c showed the highest anticancer activities against HepG2 cells with IC₅₀ values of 9.97 ± 0.8, 9.99 ± 0.8, and 11.02 ± 1.0 µM, respectively, HCT‐116 cells with IC₅₀ values of 6.99 ± 0.5, 7.44 ± 0.4, and 8.15 ± 0.8 µM, respectively, and MCF‐7 cells with IC₅₀ values of 7.89 ± 0.7, 8.24 ± 0.7, and 9.32 ± 0.7 µM, respectively, in comparison with sorafenib as reference drug with IC₅₀ values of 9.18 ± 0.6, 5.47 ± 0.3, and 7.26 ± 0.3 µM, respectively. The most active compounds 4a–c, 9b,c,e,f,h , and 11c,e were further evaluated for their VEGFR‐2 inhibition. Compounds 4c and 4b potently inhibited VEGFR‐2 at IC₅₀ values of 0.12 ± 0.01 and 0.13 ± 0.02 µM, respectively, which are nearly equipotent to the sorafenib IC₅₀ value (0.10 ± 0.02 µM). Furthermore, molecular docking studies were performed for all synthesized compounds to assess their binding pattern and affinity toward the VEGFR‐2 active site.     

Design,synthesis and biological evaluation of new tricyclic spiroisoxazoline derivatives as selective COX-2 inhibitors and study of their COX-2 binding modes via docking studies

A new series of 3′-(4-substitutedphenyl)-4′-(4-(methylsulfonyl)phenyl) spiroisoxazoline derivatives containing naphthalenone and chromanonespiro-bridge were synthesized for evaluation as selective cyclooxygenase-2 (COX-2) inhibitors. A synthetic reaction based on the 1,3-dipolar cycloaddition mechanism was used for the regiospecific formation of various spiroisoxazolines. One of the analogs, i.e., compound 7h, as the representative of the series was recrystallized and characterized structurally by single-crystal X-ray diffraction method. Moreover, the 3D structures of the synthesized compounds were docked into the COX-2 binding site to determine their most probable binding modes once the drug-receptor complexes are formed.