Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors

The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by -substituted indomethacin ethanolamide inhibitors.     

COX抑制剂——氟比洛芬衍生物的作用方式及选择性研究

用DOCK4.0程序搜索氟比洛芬衍生物与环氧合酶结合的构象。用Cscore综合评 分体系确定最佳构象，复合物经分子力学优化后，发现衍生物在COX-1中的取向和 位置与X射线衍射测犁晶体复合物中氟比洛芬作用方式相同；衍生物在COX-2中也有 与氟比洛芬类似的结合方式。衍生物对COX-2/COX-1 的选择掏性与衍生物作用于两 种酶的结合自由能之差有较好的相关性。相关系数     

Development of energetic pharmacophore for the designing of 1,2,3,4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2 inhibitors

We present here the Energetic pharmacophore model representing complementary features of the 1,2,3,4-tetrahydropyrimidine for selective cyclooxygenase-2 (COX-2) inhibition. For the development of pharmacophore hypothesis, a total of 43 previously reported compounds were docked on active site of COX-2 enzyme. The generated pharmacophore features were ranked using energetic terms of Glide XP docking for 1,2,3,4-tetrahydropyrimidine scaffold to optimize its structure requirement for COX-2 inhibition. The thirty new 4,5,6-triphenyl-1,2,3,4-tetrahydropyrimidine derivatives were synthesized and assessed for selective COX-2 inhibitory activity. Two compounds 4B1 and 4B11 were found to be potent and selective COX-2 inhibitors. The molecular docking studies revealed that the newly synthesized compounds can be docked into COX-2 binding site and also provide the molecular basis for their activity.     

Drug Design,Synthesis and Biological Evaluation of Heterocyclic Molecules as Anti-Inflammatory Agents

Non-steroidal anti-inflammatory drugs (NSAIDs) are generally utilized for numerous inflammatory ailments. The long-term utilization of NSAIDs prompts adverse reactions such as gastrointestinal ulceration, renal dysfunction and hepatotoxicity; however, selective COX-2 inhibitors prevent these adverse events. Various scientific approaches have been employed to identify safer COX-2 inhibitors, as in any case, a large portion of particular COX-2 inhibitors have been retracted from the market because of severe cardiovascular events. This study aimed to develop and synthesize a novel series of indomethacin analogues with potential anti-inflammatory properties and fewer side effects, wherein carboxylic acid moiety was substituted using DCC/DMAP coupling. This study incorporates the docking of various indomethacin analogues to detect the binding interactions with COX-2 protein (PDB ID: 3NT1). MD simulation was performed to measure the stability and flexibility of ligand–protein interactions at the atomic level, for which the top-scoring ligand–protein complex was selected. These compounds were evaluated in vitro for COX enzymes inhibition. Likewise, selected compounds were screened in vivo for anti-inflammatory potential using the carrageenan-induced rat paw oedema method and their ulcerogenic potential. The acute toxicity of compounds was also predicted using in silico tools. Most of the compounds exhibited the potent inhibition of both COX enzymes; however, 3e and 3c showed the most potent COX-2 inhibition having IC50 0.34 µM and 1.39 µM, respectively. These compounds also demonstrated potent anti-inflammatory potential without ulcerogenic liability. The biological evaluation revealed that the compound substituted with 4-nitrophenyl was most active.     

Bioassay-guided isolation of human carboxylesterase 2 inhibitory and antioxidant constituents from Laportea bulbifera: Inhibition interactions and molecular mechanism

Laportea bulbifera (Sieb. et. Zucc.) Wedd has long been utilized in Traditional Chinese Medicines (TCM) for the treatment of rheumatoid arthritis. However, the study of systematic anti-inflammatory chemical constituents in L. bulbifera has never been reported. Thus, bioassay-guided isolation for its roots part led to 46 compounds, including 38 phenolic derivatives. Their structures were determined on the basis of ¹H and ¹³C NMR and MS spectra. All compounds were isolated from L. bulbifera for the first time except for 13 compounds. Most of the compounds showed good COX-2 inhibitory activity (IC₅₀: 0.13–3.94 μM) and DPPH radical-scavenging activity (IC₅₀: 1.57–9.55 μM). Four compounds (4, 17, 35, and 43) with different skeletons showed preferential COX-2 over COX-1 inhibition with selective indices ranging from 12 to 171. High content active compounds are important for elucidating the basis of the active substance of TCM. Compound 4 (COX-2, IC₅₀ 0.24 μM), a high content compound, represented one of the best selective COX-2 inhibitors. Another high content active compound (35) with a different skeleton might have different mechanism. Further study for the inhibition kinetics against COX-2 indicated compounds 4 and 35 were noncompetitive and competitive COX-2 inhibitors, respectively. Moreover, molecular docking and molecular dynamics simulation data further indicated that compound 4 could bind in the cavity of COX-2 and interacted with key residues VAL-538, PHE-142, and GLY-225 of COX-2 through hydrogen bonds. The results indicated that L. bulbifera roots could be applied as antioxidant and anti-inflammatory agents due to their potent selective COX-2 inhibitory and antioxidant activity of phenolic compounds.     

Determination of Celecoxib, Rofecoxib, Sodium Diclofenac and Niflumic Acid in Human Serum Samples by HPLC with DAD Detection

A reverse-phase high-performance liquid chromatographic method has been developed for the separation and simultaneous determination of two COX-2 inhibitors, celecoxib and rofecoxib, in addition to two well-known non-steroidal anti-inflammatory drugs (NSAIDs), sodium diclofenac and niflumic acid in human serum samples. Good chromatographic separation was achieved using a C18 bonded silica column applying a gradient with acetronitrile and water, from 15 to 60% acetonitrile. The mobile phase contained 0.1% trifluoroacetic acid as an organic modifier. Detection was made using a diode array detector (DAD) and the analytical parameters were established at the wavelength maximum in the UV spectrum of each drug. Linearity was studied up to 100.0 mg L⁻¹. Calibration functions, quantification and detection limits, intra- and inter-day reproducibility and accuracy were estimated for each drug. Solid phase extraction was needed to separate and concentrate the drugs from human serum samples. The method was successfully applied to determine the drugs in human serum samples at levels of 1.0 mg L⁻¹.     

Characterization and Molecular Docking Study of New 4-Acetamidoalkyl Pyrazoles As B-Raf /Cox-2 Inhibitors

Several new 4-acetamidoalkyl pyrazoles are synthesized by an efficient, one-pot three-component reaction of 3,5-dimethyl-1-phenyl-1H-pyrazole or 3-methyl-1-phenyl-1H-pyrazol-5-ol, aromatic aldehydes, and acetonitrile in the presence of chlorosulfonic acid at room temperature. The products are characterized based on IR, ¹H and ¹³C NMR data and evaluated as potential COX-2 and B-Raf inhibitors by molecular docking studies. All the products showed the potency of B-Raf and COX-2 inhibitory effects with a greater binding affinity to B-Raf than COX-2 protein.     

Stimulatory action of cyclooxygenase inhibitors on hematopoiesis: a review

The presented review summarizes experimental data obtained with a mouse model when investigating the relationship between inhibition of prostaglandin production and hematopoiesis. While prostaglandin E₂ acts in a negative feedback control of myelopoiesis, inhibition of cyclooxygenases, responsible for its production, shifts the feedback to positive control. Based on these relationships, agents inhibiting cyclo-oxygenases, known as non-steroidal anti-inflammatory drugs (NSAIDs), can activate hematopoiesis and be protective or curative under myelosuppressive states. The effectiveness of therapeutic use of NSAIDs in these situations is expressive especially under the selective inhibition of cyclooxygenase-2 (COX-2), when undesirable side effects of cyclooxygenase-1 inhibition, like gastrointestinal damage, are absent. The effects of the clinically approved selective COX-2 inhibitor, meloxicam, were investigated and demonstrated significant hematopoiesis-stimulating and survival-enhancing actions of this drug in sublethally or lethally γ-irradiated mice. These effects were connected with the ability of meloxicam to increase serum levels of the granulocyte colony-stimulating factor. It can be inferred from these findings that selective COX-2 inhibitors might find their use in the treatment of myelosuppressions of various etiologies.     

Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs

The prostaglandin-endoperoxide H synthase-1 (PGHS-1) and prostaglandin-endoperoxide H synthase-2 (PGHS-2) are the targets of nonsteroidal anti-inflammatory drugs (NSAIDs).It appears that the high degree of selectivity for inhibition of PGHS-2 shown by certain compounds is the result of two mechanisms (time-dependent, time-independent inhibition), by which they interact with each isoform. Molecular models of the complexes formed by indomethacin, sulindac, fenamates, 2-phenylpropionic acids and selective cyclooxygenase-2 (COX-2) inhibitors with the cyclooxygenase active site of human PGHS-2 have been built, paying particular attention to water molecules that participate in the hydrogen-bonding network at the polar active site entrance. The stability of the complexes has been assessed by molecular dynamics simulations and interaction energy decomposition analysis, and their biological significance has been discussed in light of available X-ray crystallographic and kinetic results. The selective PGHS-2 inhibitors exploit the extra space of a side-pocket in the active site of PGHS-2 that is not found in PGHS-1. The results suggest that active site hydration together with residues Tyr³⁵⁵, Glu⁵²⁴, Arg¹²⁰ and Arg⁵¹³ are crucial to understand the time-dependent inhibition mechanism. A marked relationship between the isoform selectivity and tightly interactions with residues into the side pocket bordered by Val⁵²³ is also found.     

Facile air oxidation of the conjugate base of rofecoxib (Vioxx), a possible contributor to chronic human toxicity

The COX-2 inhibitor rofecoxib (Vioxx^™, 1) ionizes under physiological conditions to an anion that reacts readily with dioxygen to form inter alia the reactive maleic anhydride derivative 6, a potentially toxic compound.     

二芳基取代-1,2,4-三唑类化合物的合成及其抗炎活性研究

以选择性环氧化酶-2(COX-2)抑制剂Celecoxib为先导,根据其构效关系和分子模拟研究结果,应用生物电子等排原理等药物设计方法,设计合成了19个结构全新的二芳基取代-1,2,4-三唑类衍生物,其结构经IR,¹HNMR,MS和元素分析确证.初步的药理试验结果表明,部分目标化合物具有一定的抗炎活性.     

Heterocyclic inflammation inhibitors

Non steroidal anti-inflammatory drugs are the most widely used medicines for relief of pain. These drugs have some side effects, particularly toxicity in the gastrointestinal tract and kidneys. Various approaches have been used for obtaining safer anti-inflammatory drugs. In this review we have summarized the recent developments in the following areas; (i) mode of action of NSAIDs (ii) Role of COX-1 & COX-2 in inflammation, (iii) Different approaches used to improve gastric tolerance i.e. chemical manipulation, formulation & co-administration, development of non specific (COX-1 & COX-2 inhibitors) and specific (COX-2 inhibitors) inflammation inhibitors, and development of inflammation inhibitors having a mode of action other than COX-1 & COX-2 inhibition. We have also focused on the safety of COX-2 inhibitors and the synthesis of heterocyclic compounds and their role as inflammation inhibitors.     

Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition

Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD₅₀ in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.     

A rapid and sensitive high-performance liquid chromatography assay for rofecoxib in human serum

Rofecoxib is a selective cyclooxygenase (COX)-2 inhibitor that is approved for the treatment of acute pain and osteoarthritis in adults. A sensitive and rapid high-performance liquid chromatographic (HPLC) method of determining rofecoxib in human serum is described. Alkalinized plasma samples are extracted into an organic solvent containing an internal standard and evaporated under nitrogen. The dried sample residues are reconstituted with mobile phase and analyzed by HPLC. The method uses 100 microL of the sample and is linear from 20 to 2000 ng/mL of rofecoxib. Precision and accuracy studies are performed. Stability of the drug in serum over four weeks is documented. This new method is simple, sensitive, precise, and accurate. Its use will translate into faster laboratory turnaround time, and the small sample volume required (100 microL) makes this assay suitable for pediatric patients. This assay will expedite pharmacokinetic studies and the therapeutic drug monitoring of rofecoxib and possibly other COX-2 inhibitors.     

机器学习方法用于选择性环氧化酶-2抑制剂活性预测模型的建立

与传统的非甾体类消炎药相比,选择性环氧化酶-2抑制剂具有无胃肠道粘膜损伤,溃疡和肾功能障碍等严重的副作用,设计选择性环氧化酶-2抑制剂具有重要意义。本文用支持矢量学习机和神经网络两种机器学习方法建立选择性环氧化酶-2抑制剂的活性预测模型,以期为选择性环氧化酶-2抑制剂药物的合成提供先导化合物。我们将467个环氧化酶-2抑制剂用Kennard-Stone方法分为训练集,验证集和独立测试集,对每一抑制剂分子我们计算了463个包含组成描述符和拓扑描述符的分子描述符来表征其分子结构,并通过F-Score方法选取最重要的分子描述符用于分类模型的建立。结果表明,SVM方法通过变量筛选后具有很好的预测能力,其预测正确率达到93.30%。     

Antiinflammation Derived Suzuki-Coupled Fenbufens as COX-2 Inhibitors: Minilibrary Construction and Bioassay

A small fenbufen library comprising 18 compounds was prepared via Suzuki Miyara coupling. The five-step preparations deliver 9–17% biphenyl compounds in total yield. These fenbufen analogs exert insignificant activity against the IL-1 release as well as inhibiting cyclooxygenase 2 considerably. Both the para-amino and para-hydroxy mono substituents display the most substantial COX-2 inhibition, particularly the latter one showing a comparable activity as celecoxib. The most COX-2 selective and bioactive disubstituted compound encompasses one electron-withdrawing methyl and one electron-donating fluoro groups in one arene. COX-2 is selective but not COX-2 to bioactive compounds that contain both two electron-withdrawing groups; disubstituted analogs with both resonance-formable electron-donating dihydroxy groups display high COX-2 activity but inferior COX-2 selectivity. In silico simulation and modeling for three COX-2 active—p-fluoro, p-hydroxy and p-amino—fenbufens show a preferable docking to COX-2 than COX-1. The most stabilization by the p-hydroxy fenbufen with COX-2 predicted by theoretical simulation is consistent with its prominent COX-2 inhibition resulting from experiments.     

Synthesis,anti-inflammatory activities and docking studies of amide derivatives of meclofenamic acid

NSAIDs constitute a heterogeneous class of pharmacological agents widely prescribed for the treatment of inflammation, pain and edema, as well as osteoarthritis, rheumatoid arthritis and musculoskeletal disorders. This class of drugs has proved efficacious on account of their analgesic, anti-pyretic and anti-inflammatory activities, but gastrointestinal toxicity exists as the biggest problem associated with their chronic use. Many attempts have been made to structurally modify conventional NSAIDs as selective COX-2 inhibitors based on the old and still prevalent common belief that selective inhibition of COX-2 would provide safer NSAIDs. The present work thus focused on the synthesis of amide derivatives of one of the conventional non-selective NSAID, meclofenamic acid utilizing the one pot procedure involving a selective agent, bis (2-oxo-3-oxazolidinyl) phosphonic chloride. The synthesized compounds were tested for their in vivo inflammatory activity using carrageenan rat paw edema assay, and were subsequently docked on COX-2 PDB code 4COX to have better insights into their mechanism of action. The amide derivative with N-4-methoxybenzyl moiety (TSN4) proved to have anti-inflammatory potential (72.8%) better than meclofenamic acid (56.75%). This compound also docked with the highest dock score among the synthesized compounds and was found to have both hydrogen bonding with Arg120 and Tyr355 and hydrophobic interactions with Val349, Leu352, Ser353, Tyr385, Trp387, Met522, Val523, Ala527 and Ser530. N-4-methoxybenzyl amide derivative (TSN4) followed by benzyl amide derivative (TSN1) of meclofenamic acid were identified as potential anti-inflammatory compounds in both in vivo and in silico studies.