Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques

c-Yes kinase is considered as one of the attractive targets for anti-cancer drug design. The DFG (Asp-Phe-Gly) motif present in most of the kinases will adopt active and inactive conformations, known as DFG-in and DFG-out and their inhibitors are classified into type I and type II, respectively. In the present study, two screening protocols were followed for identification of c-Yes kinase inhibitors. (i) Structure-based virtual screening (SBVS) and (ii) Structure-based (SB) and Pharmacophore-based (PB) tandem screening. In SBVS, the c-Yes kinase structure was obtained from homology modeling and seven ensembles with different active site scaffolds through molecular dynamics (MD) simulations. For SB-PB tandem screening, we modeled ligand bound active and inactive conformations. Physicochemical properties of inhibitors of Src kinase family and c-Yes kinase were used to prepare target focused libraries for screenings. Our screening procedure along with docking showed 520 probable hits in SBVS and tandem screening (120 and 400, respectively). Out of 5000 compounds identified from different computational methods, 2410 were examined using kinase inhibition assays. It includes 266 compounds (5.32%) identified from our method. We observed that 14 compounds (12%) are identified by the present method out of 168 that showed > 30% inhibition. Among them, three compounds are novel, unique, and showed good inhibition. Further, we have studied the binding of these compounds at the DFG-in and DFG-out conformations and reported the probable class (type I or type II). Hence, we suggest that these compounds could be novel drug leads for regulation of colorectal cancer.     

Structure-based design of eugenol analogs as potential estrogen receptor antagonists

Eugenol is an essential oil mainly found in the buds and leaves of clove (Syzygium aromaticum (L.) Merrill and Perry), which has been reported to have activity on inhibition of cell proliferation and apoptosis induction in human MCF-7 breast cancer cells. This biological activity is correlated to its activity as an estrogen receptor antagonist. In this article, we present the construction and validation of structure-based virtual screening (SBVS) protocols to identify the potent estrogen receptor α (ER) antagonists. The selected protocol, which gave acceptable enrichment factors as a virtual screening protocol, subsequently used to virtually screen eugenol, its analogs and their dimers. Based on the virtual screening results, dimer eugenol of 4-[4-hydroxy-3-(prop-2-en-1- yl)phenyl]-2-(prop-2-en-1-yl)phenol is recommended to be developed further in order to discover novel and potent ER antagonists.     

Recent progress on the prospective application of machine learning to structure-based virtual screening

As more bioactivity and protein structure data become available, scoring functions (SFs) using machine learning (ML) to leverage these data sets continue to gain further accuracy and broader applicability. Advances in our understanding of the optimal ways to train and evaluate these ML-based SFs have introduced further improvements. One of these advances is how to select the most suitable decoys (molecules assumed inactive) to train or test an ML-based SF on a given target. We also review the latest applications of ML-based SFs for prospective structure-based virtual screening (SBVS), with a focus on the observed improvement over those using classical SFs. Finally, we provide recommendations for future prospective SBVS studies based on the findings of recent methodological studies.     

Additive neuroprotective effects of creatine and cyclooxygenase 2 inhibitors in a transgenic mouse model of amyotrophic lateral sclerosis

There is substantial evidence implicating both inflammation and mitochondrial dysfunction in amyotrophic lateral sclerosis (ALS) pathogenesis. We investigated the therapeutic effects of cyclooxygenase 2 (COX-2) inhibitors both alone and in combination with creatine in the G93A transgenic mouse model of ALS. Oral administration of either celecoxib or rofecoxib significantly improved motor performance, attenuated weight loss and extended survival. The administration of COX-2 inhibitors significantly reduced prostaglandin E2 levels at 110 days of age. The combination of creatine with COX-2 inhibitors produced additive neuroprotective effects and extended survival by approximately 30%. The COX-2 inhibitors significantly protected against depletion of anterior horn motor neurons and creatine with COX-2 inhibitors showed greater protection than COX-2 inhibitors alone. These results suggest that combinations of therapies targeting different disease mechanisms may be a useful strategy in the treatment of ALS.     

An alphabetic code based atomic level molecular similarity search in databases

Atomic level molecular similarity and diversity studies have gained considerable importance through their wide application in Bioinformatics and Chemo-informatics for drug design. The availability of large volumes of data on chemical compounds requires new methodologies for efficient and effective searching of its archives in less time with optimal computational power. We describe an alphabetic algorithm for similarity searching based on atom-atom bonding preference for ligands. We represented 170 cyclindependent kinase 2 inhibitors using strings of pre-defined alphabets for searching using known protein sequence alignment tools. Thus, a common pattern was extracted using this set of compounds for database searching to retrieve similar active compounds. Area under the receiver operating characteristic (ROC) curve was used for the discrimination of similar and dissimilar compounds in the databases. An average retrieval rate of about 60% is obtained in cross-validation using the home-grown dataset and the directory of useful decoys (DUD, formally known as the ZINC database) data. This will help in the effective retrieval of similar compounds using database search.     

Design,Synthesis and Biological Evaluation of New N-Acyl Hydrazones with a Methyl Sulfonyl Moiety as Selective COX-2 Inhibitors

The mechanism of action of nonsteroidal anti-inflammatory drugs (NSAIDs) is inhibition of specific prostaglandin (PG) synthesis by inhibition of cyclooxygenase (COX) enzymes. The two COX isoenzymes show 60 % similarity. It is known that the nonspecific side effects of conventional NSAIDs are physiologically caused by inhibition of the COX-1 enzyme. Therefore, the use of COX-2 selective inhibitors is seen to be a more beneficial approach in reducing these negative effects. However, some of the existing COX-2 selective inhibitors show cardiovascular side effects. Therefore, studies on the development of new selective COX-2 inhibitors remain necessary. It is important to develop new COX-2 inhibitors in the field of medicinal chemistry. Accordingly, novel N-acyl hydrazone derivatives were synthesized as new COX-2 inhibitors in this study. The hydrazone structure, also known for its COX activity, is important in terms of many biological activities and was preferred as the main structure in the design of these compounds. A methyl sulfonyl pharmacophore was added to the structure in order to increase the affinity for the polar side pocket present in the COX-2 enzyme. It is known that methyl sulfonyl groups are suitable for polar side pockets. The synthesis of the compounds ( 3a – 3j ) was characterized by spectroscopic methods. Evaluation of in vitro COX-1/COX-2 enzyme inhibition was performed by fluorometric method. According to the enzyme inhibition results, the obtained compounds displayed the predicted selectivity for COX-2 enzyme inhibition. Compound 3j showed important COX-2 inhibition with a value of IC₅₀=0.143 uM. Interaction modes between the COX-2 enzyme and compound 3j were investigated by docking studies.     

Assessing aural and visual cueing as tools for seabird management

Social attraction, that is, mimicking of active and productive colonies via audio playback of calls of breeding conspecifics and the use of decoys, is commonly used to attract birds to newly established or restored breeding sites. However, little is known about the relative importance of aural versus visual cues for identify nesting areas. Such information is important for design and evaluation of management protocols. We studied the effectiveness of decoys (visual cues) and playbacks (audio cues) as methods for restoring a colony of common terns (Sterna hirundo) at Muskeget Island, Massachusetts, USA. We used a 2-year, crossover experiment with 3 treatment areas: audio and visual, audio only, and visual only. We reversed treatment areas in the second year to control for previous nesting area or substrate preference. In both years, nests were built 9–101 m downwind of loudspeakers. There was no overlap in areas used for nesting between years and no nests were built within decoy plots in either year. Behavioral observations showed that birds responded to decoys only when within range of sound treatments. Conspecific vocalizations appear to be important proximate cues for seabird colony site selection and should be given priority in management protocols using social attraction. © 2011 The Wildlife Society.     

环氧化酶-2对肿瘤细胞的作用机理研究

主要检测环氧化酶-2对肿瘤细胞的影响,分析讨论了环氧化酶-2引起细胞凋亡的潜在机制。不同浓度的环氧化酶-2处理肿瘤细胞的结果表明:环氧化酶-2对肿瘤细胞的抑制作用为时间和浓度依赖型。转染Bax-YFP与DsRed-Mit质粒并经环氧化酶-2处理3 h后的结果显示:肿瘤细胞中Bax明显聚集,细胞形态发生变化。实验证明环氧化酶-2促使肿瘤细胞凋亡是经过线粒体途径而发生的。     

基于机器学习的环氧合酶-2抑制剂分类模型的构建

摘要 目的：构建环氧合酶-2（Cyclooxygenase-2,COX-2）抑制剂分类模型,用以筛选和优化COX-2抑制剂。方法：基于八种机器学习算法构建模型,比较不同模型的预测性能,筛选出最优模型后利用Y随机验证法对其进行测试,最后运用SHAP（Shapley Additive eXplanation）算法对最优模型进行可解释性分析。结果：八种不同模型的性能比较结果显示,基于随机森林算法建立的模型最优,其预测准确率、平衡准确率、马修斯相关系数、特征曲线下面积和F1分数（分别为0.893、0.825、0.673、0.909和0.933）最高;Y随机验证结果表明最优模型的预测结果并非偶然;此外,通过SHAP算法挖掘出20个最有可能影响COX-2抑制剂活性的结构片段。结论：本研究为新型COX-2抑制剂的开发提供理论依据,可供本领域其他研究人员对先导化合物进行优化或设计更好的COX-2抑制剂。     

Prostaglandin E2 EP3 receptor regulates cyclooxygenase-2 expression in the kidney

Cyclooxygenase-2 (COX-2) is constitutively expressed and highly regulated in the thick ascending limb (TAL). As COX-2 inhibitors (Coxibs) increase COX-2 expression, we tested the hypothesis that a negative feedback mechanism involving PGE(2) EP3 receptors regulates COX-2 expression in the TAL. Sprague-Dawley rats were treated with a Coxib [celecoxib (20 mg·kg(-1)·day(-1)) or rofecoxib (10 mg·kg(-1)·day(-1))], with or without sulprostone (20 μg·kg(-1)·day(-1)). Sulprostone was given using two protocols, namely, previous to Coxib treatment (prevention effect; Sulp7-Coxib5 group) and 5 days after initiation of Coxib treatment (regression effect; Coxib10-Sulp5 group). Immunohistochemical and morphometric analysis revealed that the stained area for COX-2-positive TAL cells (μm(2)/field) increased in Coxib-treated rats (Sham: 412 ± 56.3, Coxib: 794 ± 153.3). The Coxib effect was inhibited when sulprostone was used in either the prevention (285 ± 56.9) or regression (345 ± 51.1) protocols. Western blot analysis revealed a 2.1 ± 0.3-fold increase in COX-2 protein expression in the Coxib-treated group, an effect abolished by sulprostone using either the prevention (1.2 ± 0.3-fold) or regression (0.6 ± 0.4-fold vs. control, P < 0.05) protocols. Similarly, the 6.4 ± 0.6-fold increase in COX-2 mRNA abundance induced by Coxibs (P < 0.05) was inhibited by sulprostone; prevention: 0.9 ± 0.3-fold (P < 0.05) and regression: 0.6 ± 0.1 (P < 0.05). Administration of a selective EP3 receptor antagonist, L-798106, also increased the area for COX-2-stained cells, COX-2 mRNA accumulation, and protein expression in the TAL. Collectively, the data suggest that COX-2 levels are regulated by a novel negative feedback loop mediated by PGE(2) acting on its EP3 receptor in the TAL.     

Cyclooxygenase (COX) and 5-lipoxygenase (5-LOX) selectivity of COX inhibitors

In vitro evaluations of the selectivity of COX inhibitors are based on a great variety of experimental protocols. As a result, data available on cyclooxygenase (COX)-1/COX-2/5- lipoxygenase (LOX) selectivity of COX inhibitors lack consistency. We, therefore, performed a systematic analysis of the COX-1/COX-2/5-LOX selectivity of 14 compounds with selective COX inhibitory activity (Coxibs). The compounds belonged to different structural classes and were analyzed employing the well-recognized whole-blood assay. 5-LOX activity was also tested on isolated human polymorphonuclear leukocytes. Among COX inhibitors, celecoxib and ML-3000 (licofelone) inhibited 5-LOX in human neutrophils at micromolar ranges. Surprisingly, ML-3000 had no effect on 5-LOX product synthesis in whole-blood assay. In addition, we could show that inhibition of COX pathways did not increase the transformation of arachidonic acid by the 5-LOX pathway.     

COX-2 and iNOS in opioid-induced delayed cardioprotection in the intact rat

Cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) have been previously implicated in the late phase of cardioprotection associated with opioid-induced and ischemic preconditioning (IPC) in conscious rabbits and COX-2 in isolated rat hearts pretreated with an exogenous delta opioid agonist. However, it is not know if both iNOS and COX-2 mediate the late phase of cardioprotection induced by opioids in the intact blood-perfused rat. Therefore, we investigated the role of COX-2 and iNOS in the delayed phase of protection mediated by delta opioid receptor activation. Rats were pretreated 24 hours prior to an occlusion/reperfusion protocol with the selective non-peptide delta opioid agonists, BW373U86 (BW) and SNC-121 (SNC). NS-398, a selective COX-2 inhibitor was administered after the 24-hour recovery period just prior to index ischemia. The selective iNOS inhibitors, S-methylthiourea (SMT) and aminoguanidine (AG), were administered in conjunction with opioid pretreatment or were also given 24 hours after opioid administration just prior to index ischemia. COX-2 inhibition by NS-398 given 24 hours after opioid administration attenuated the protective effects of both BW and SNC (46 +/- 6 vs. 13 +/- 3 and 51 +/- 5 vs. 29 +/- 2, p < 0.001, respectively). Similarly, inhibition of iNOS following 24 hours of treatment with opioids also attenuated the protective effects of BW and SNC. However, the delayed protective effects of the opioids were not attenuated by pretreatment with the iNOS inhibitors 24 hours prior to the infarct protocol. These results suggest that both COX-2 and iNOS are mediators of delayed protection induced by non-peptide delta opioid agonists. It appears that the trigger effect is not dependent on the activity of iNOS or COX-2 but the late phase of cardioprotection is dependent on the upregulation of these enzymes.     

An ELISA method to measure inhibition of the COX enzymes

The cyclooxygenase (COX) reaction can be monitored by measurement of oxygen consumption, peroxidase co-substrate oxidation or prostaglandin (PG) detection. This protocol describes a procedure measuring cyclooxygenase activity by quantifying PGE2 produced by enzymatic conversion of arachidonic acid, in the presence or absence of potential inhibitors. This high-throughput method has the advantage that it directly measures cyclooxygenase activity and requires little enzyme. The first part of the assay consists of incubating arachidonic acid, cyclooxygenase and the test samples to generate prostaglandins. The second part uses an ELISA method to quantify the amount of PGE2 produced by the enzymatic reaction. The isolation of COX-1 and COX-2 enzymes is also described. This protocol can be completed in approximately 23 h, including 16-h and 4-h incubation phases. This does not include enzyme preparation (3 h for COX-1 and 24 h for COX-2) or preparation of ELISA plates (23 h, including incubation).     

Cyclooxygenase-2 inhibitors constrict the fetal lamb ductus arteriosus both in vitro and in vivo

Nonselective cyclooxygenase (COX) inhibitors are potent tocolytic agents; however, they also have adverse fetal effects such as constriction of the fetal ductus arteriosus. Recently, selective COX-2 inhibitors have been used in the management of preterm labor in the hope of avoiding fetal complications. However, both COX-1 and -2 are expressed by cells of the ductus arteriosus. We used fetal lambs (0.88 gestation) to assess the ability of selective COX-2 inhibitors celecoxib and NS398 to affect the ductus arteriosus. Both selective COX-2 inhibitors decreased PGE(2) and 6ketoPGF(1alpha) production in vitro; both inhibitors constricted the isolated ductus in vitro. The nonselective COX-1/COX-2 inhibitor indomethacin produced a further reduction in PG release and an additional increase in ductus tension in vitro. We used a prodrug of celecoxib to achieve 1.4 +/- 0.6 microg/ml, mean +/- standard deviation, of the active drug in vivo. This concentration of celecoxib produced both an increase in pressure gradient and resistance across the ductus; celecoxib also decreased fetal plasma concentrations of PGE(2) and 6ketoPGF(1alpha). Indomethacin (0.7 +/- 0.2 microg/ml) produced a significantly greater fall in ductus blood flow than celecoxib and tended to have a greater effect on ductus resistence in vivo. We conclude that caution should be used when recommending COX-2 inhibitors for use in pregnant women, because COX-2 appears to play a significant role in maintaining patency of the fetal ductus arteriosus.     

Structure-based discovery of inhibitors of the YycG histidine kinase: New chemical leads to combat Staphylococcus epidermidis infections

Background

Coagulase-negative Staphylococcus epidermidis has become a major frequent cause of infections in relation to the use of implanted medical devices. The pathogenicity of S. epidermidis has been attributed to its capacity to form biofilms on surfaces of medical devices, which greatly increases its resistance to many conventional antibiotics and often results in chronic infection. It has an urgent need to design novel antibiotics against staphylococci infections, especially those can kill cells embedded in biofilm.

Results

In this report, a series of novel inhibitors of the histidine kinase (HK) YycG protein of S. epidermidis were discovered first using structure-based virtual screening (SBVS) from a small molecular lead-compound library, followed by experimental validation. Of the 76 candidates derived by SBVS targeting of the homolog model of the YycG HATPase_c domain of S. epidermidis, seven compounds displayed significant activity in inhibiting S. epidermidis growth. Furthermore, five of them displayed bactericidal effects on both planktonic and biofilm cells of S. epidermidis. Except for one, the compounds were found to bind to the YycG protein and to inhibit its auto-phosphorylation in vitro, indicating that they are potential inhibitors of the YycG/YycF two-component system (TCS), which is essential in S. epidermidis. Importantly, all these compounds did not affect the stability of mammalian cells nor hemolytic activities at the concentrations used in our study.

Conclusion

These novel inhibitors of YycG histidine kinase thus are of potential value as leads for developing new antibiotics against infecting staphylococci. The structure-based virtual screening (SBVS) technology can be widely used in screening potential inhibitors of other bacterial TCSs, since it is more rapid and efficacious than traditional screening technology.     

Thalidomide and its analogues as cyclooxygenase inhibitors

Thalidomide showed cyclooxygenase (COX)-1/2 inhibitory activity with a potency comparable to that of aspirin. Structural development studies of thalidomide resulted in potent COX-1/2 inhibitors, and COX-1-selective and COX-2-selective inhibitors.     

FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data

We demonstrate a new approach to the development of scoring functions through the formulation and parameterization of a new function, which can be used both for rapidly ranking the binding of ligands to proteins and for estimating relative aqueous molecular solubilities. The intent of this work is to introduce a new paradigm for creation of scoring functions, wherein we impose the following criteria upon the function: (1) simple; (2) intuitive; (3) requires no postparameterization tweaking; (4) can be applied (without reparameterization) to multiple target systems; and (5) can be rapidly evaluated for any potential ligand. Following these criteria, a new function, FURSMASA (function for rapid scoring using an MD-averaged grid and the accessible surface area) has been developed. Three novel features of the function include: (1) use of an MD-averaged potential energy grid for ligand-protein interactions, rather than a simple static grid; (2) inclusion of a term that depends on the change in the solvent-accessible surface area changes on an atomic (not molecular) basis; and (3) use of the recently derived predictive index (PI) target when optimizing the function, which focuses the function on its intended purpose of relative ranking. A genetic algorithm is used to optimize the function against test data sets that include ligands for the following proteins: IMPDH, p38, gyrase B, HIV-1, and TACE, as well as the Syracuse Research solubility database. We find that the function is predictive, and can simultaneously fit all the test data sets with cross-validated predictive indices ranging from 0.68 to 0.82. As a test of the ability of this function to predict binding for systems not in the training set, the resulting fitted FURSAMA function is then applied to 23 ligands of the COX-2 enzyme. Comparing the results for COX-2 against those obtained using a variety of well-known rapid scoring functions demonstrates that FURSMASA outperforms all of them in terms of the PI and correlation coefficient. We also find that the FURSAMA function is able to reliably predict the water solubility for 1032 compounds from the Syracuse Research solubility database with a cross-correlated PI of 0.84 and a correlation coefficient R(2) of 0.69. This prediction, which is based solely on a term derived from the atom-based solvent-accessible surface areas, compares favorably with the best prediction methods in the literature, most of which are more complex and/or require experimental data. Finally, as a rigorous test of the applicability to database screening, we apply FURSMASA to large active/decoy ligand databases for IMPDH (400 actives vs. 10,000 decoys), p38 (502 actives vs. 10,000 decoys), and HIV (787 actives vs. 10,000 decoys) used in earlier work to critically evaluate many popular scoring functions, and find that FURSMASA performs surprisingly well for IMPDH and HIV.     

Design and synthesis of novel celecoxib analogues as selective cyclooxygenase-2 (COX-2) inhibitors: replacement of the sulfonamide pharmacophore by a sulfonylazide bioisostere

A group of celecoxib analogues in which the para-SO(2)NH(2) substituent on the N(1)-phenyl ring was replaced by a para-sulfonylazido (SO(2)N(3)) 4, or a meta-SO(2)N(3) 8, substituent were designed for evaluation as selective cyclooxygenase-2 (COX-2) inhibitors. In vitro COX-1 and COX-2 inhibition studies showed that 4-[5-(4-methylphenyl)-3-trifluoromethyl-1H-pyrazol-1-yl]benzenesulfonyl azide (4) with a para-SO(2)N(3) substituent was a selective COX-1 inhibitor. In contrast, 3-[5-(4-methylphenyl)-3-trifluoromethylpyrazol-1-yl]benzenesulfonyl azide (8a) having a meta-SO(2)N(3) substituent (COX-1 IC(50) >100microM; COX-2 IC(50)=5.16microM; COX-2 selectivity index >19.3) is a selective COX-2 inhibitor. A molecular modeling (docking) study showed that the SO(2)N(3) group of 8a inserts deep inside the secondary pocket of the COX-2 binding site. The SO(2)N(3) moiety of 8a can undergo a dual H-bonding interaction via one of its SO(2) oxygen-atoms, and an electrostatic (ion-ion) interaction via the terminal azido (N(3)) nitrogen-atom, to the guanidino NH(2) of Arg(513) in the secondary pocket of COX-2. These observations indicate that an appropriately positioned SO(2)N(3) moiety is a novel alternative bioisostere to the traditional SO(2)NH(2) and SO(2)Me pharmacophores present in selective COX-2 inhibitors, that are only capable of H-bonding interactions with the COX-2 isozyme, for use in drug design.     

Extracellular calcium induces COX-2 in osteoblasts via a PKA pathway

We have shown that extracellular calcium [Ca(+2)](e) induces cyclooxygenase-2 (COX-2) expression and prostaglandin E(2) (PGE(2)) production via an ERK signaling pathway in osteoblasts. In this study, we examined the roles of protein kinase C (PKC) and A (PKA) signaling pathways in the [Ca(+2)](e) induction of COX-2 in primary calvarial osteoblasts from mice transgenic for -371 bp of the COX-2 promoter fused to a luciferase reporter. Neither PKC specific inhibitors nor downregulation of the PKC pathway by phorbol myristate acetate (PMA) affected the [Ca(+2)](e) stimulation of COX-2 mRNA or promoter activity. In contrast, PKA inhibitors, used at doses that inhibited forskolin-stimulated luciferase activity by 90%, reduced [Ca(+2)](e)-stimulated COX-2 mRNA expression and promoter activity by 80-90%. [Ca(+2)](e) also stimulated a 2- to 3-fold increase in cAMP production. Hence, the [Ca(+2)](e) induction of COX-2 mRNA expression and promoter activity was independent of the PKC pathway and dependent on the PKA signaling pathway.