Molecular docking and competitive binding study discovered different binding modes of microsomal prostaglandin E synthase-1 inhibitors

MOZART, a QSAR Multi-Target Web-Based Tool to Predict Multiple Drug-Enzyme Interactions

Developing models able to predict interactions between drugs and enzymes is a primary goal in computational biology since these models may be used for predicting both new active drugs and the interactions between known drugs on untested targets. With the compilation of a large dataset of drug-enzyme pairs (62,524), we recognized a unique opportunity to attempt to build a novel multi-target machine learning (MTML) quantitative structure-activity relationship (QSAR) model for probing interactions among different drugs and enzyme targets. To this end, this paper presents an MTML-QSAR model based on using the features of topological drugs together with the artificial neural network (ANN) multi-layer perceptron (MLP). Validation of the final best model found was carried out by internal cross-validation statistics and other relevant diagnostic statistical parameters. The overall accuracy of the derived model was found to be higher than 96%. Finally, to maximize the diffusion of this model, a public and accessible tool has been developed to allow users to perform their own predictions. The developed web-based tool is public accessible and can be downloaded as free open-source software.

Computer-Aided Drug Design of Anti-inflammatory Agents Targeting Microsomal Prostaglandin E2 Synthase-1 (mPGES-1)

Inflammation is a natural process in response to external stimuli associated with organism protection. However, this reaction could be exaggerated, leading to severe damages related to physiopathological processes, such as rheumatoid arthritis, cancer, diabetes, allergies, infections, among others. Inflammation is mainly characterized by pain, increased temperature, flushing, and edema, which can be controlled using anti-inflammatory drugs. In this context, prostaglandin E2 (PGE2) inhibition has been targeted for designing new compounds with anti-inflammatory properties. It is a bioactive lipid overproduced during an inflammatory process, in which its increased production is carried out mainly by COX-1, COX-2, and microsomal prostaglandin E2 synthase-1 (mPGES-1). Recently, studies have demonstrated that mPGES-1 inhibition is a safe strategy to develop anti-inflammatory agents, which could protect against pain, acute inflammation, arthritis, autoimmune diseases, and different types of cancers. To decrease production costs and increase the probability of discovering active substances, computer-aided drug design (CADD) approaches have been increasingly used for designing new inhibitors. Thus, this review will cover all aspects involving high-throughput virtual screening, molecular docking, dynamics, fragment-based drug design, quantitative structure-activity relationship in seeking new promising mPGES-1 inhibitors.

Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study

BACKGROUND

Aryl hydrocarbon receptor (AhR) ligands may act as potential carcinogens or anti-tumor agents. Understanding how some of the residues in AhR ligand binding domain (AhRLBD) modulate their interactions with ligands would be useful in assessing their divergent roles including toxic and beneficial effects. To this end, we have analysed the nature of AhRLBD interactions with 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), 6-formylindolo[3,2-b]carbazole (FICZ), indole-3-carbinol (I3C) and its degradation product, 3,3'-diindolylmethane (DIM), Resveratrol (RES) and its analogue, Piceatannol (PTL) using molecular modeling approach followed by molecular dynamic simulations.

RESULTS

Results showed that each of the AhR ligands, TCDD, FICZ, I3C, DIM, RES and PTL affect the local and global conformations of AhRLBD.

CONCLUSION

The data presented in this study provide a structural understanding of AhR with its ligands and set the basis for its functions in several pathways and their related diseases.

Docking Methodologies and Recent Advances

Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.

Hit-to-lead optimization of phenylsulfonyl hydrazides for a potent suppressor of PGE2 production: Synthesis, biological activity, and molecular docking study

Preliminary hit-to-lead optimization of a novel series of phenylsulfonyl hydrazide derivatives, which were derived from the high throughput screening hit compound 1 (IC50=5700nM against PGE2 production), for a potent suppressor of PGE2 production is described. Subsequent optimization led to the identification of the potent lead compound 8n with IC50 values of 4.5 and 6.9nM, respectively, against LPS-induced PGE2 production and NO production in RAW 264.7 macrophage cells. In addition, 8n was about 30- and >150-fold more potent against mPGES-1 enzyme in a cell-free assay (IC50=70nM) than MK-886 and hit compound 1, respectively. Molecular docking suggests that compound 8n could inhibit PGE2 production by blocking the PGH2 binding site of human mPGES-1 enzyme.

Targeting microsomal prostaglandin E2synthase-1 (mPGES-1): the development of inhibitors as an alternative to non-steroidal anti-inflammatory drugs (NSAIDs)

AA cascade and several key residues in the 3D structure of mPGES-1.

Targeting inflammation: multiple innovative ways to reduce prostaglandin E₂

The PGE2 pathway is important in inflammation-driven diseases and specific targeting of the inducible mPGES-1 is warranted due to the cardiovascular problems associated with the long-term use of COX-2 inhibitors. This review focuses on patents issued on methods of measuring mPGES-1 activity, on drugs targeting mPGES-1 and on other modulators of free extracellular PGE2 concentration. Perspectives and conclusions regarding the status of these drugs are also presented. Importantly, no selective inhibitors targeting mPGES-1 have been identified and, despite the high number of published patents, none of these drugs have yet made it to clinical trials.

Exploration of the dihydropyrimidine scaffold for the development of new potential anti-inflammatory agents blocking prostaglandin E₂ synthase-1 enzyme (mPGES-1)

Agents targeting microsomal prostaglandin E2 synthase-1 (mPGES-1) would inhibit only PGE2 production induced by inflammatory stimuli and thus could represent a valuable alternative to non-steroidal anti-inflammatory drugs (NSAIDs) as they should be free from the severe side effects of the classic anti-inflammatory drugs. Although several mPGES-1 inhibitors have been so far identified, none of them is currently in clinical trials, therefore the discovery of new molecular platforms, able to interfere with this interesting target, is urgently required. Here, we report the results of a focused collection of dyhidropyrimidin-2(1H)-one based molecules projected by Virtual Screening computational techniques. The key interactions with the receptor counterpart were introduced as a qualitative filter for the selection of the most promising compounds. The biological data obtained are consistent with the computer-aided suggestions and disclosed two interesting molecules showing in vitro mPGES-1 inhibitory activity in the low μM range.

Hypoxia-inducible factor-2α is essential in activating the COX2/mPGES-1/PGE2 signaling axis in colon cancer

Cyclooxygenase 2 (COX2) is overexpressed in 80% of colon adenocarcinomas. However, the mechanism leading to aberrant COX2 expression in tumors is unclear. Intestinal epithelium-specific disruption of the von Hippel-Lindau tumor suppressor protein (VHL) in adenomatous polyposis coli (Apc)(min/+) mice (Vhl(ΔIE)/Apc(min/+)) resulted in constitutive activation of hypoxia-inducible factor (HIF), robustly enhanced colon carcinogenesis and potentiated COX2 expression in normal colon epithelium and tumors. In this study, we hypothesize that HIF regulates COX2 expression in colon tumors, and this regulation is critical for HIF-mediated colon carcinogenesis. COX2 was demonstrated to be a direct target gene of HIF-2α, and genetic disruption of HIF-2α abolished the induction of COX2 in tumors. Furthermore, inhibition of COX2 by nimesulide reduced HIF-2α-induced colon tumor formation. Interestingly, the levels of prostaglandin E(2) (PGE(2)), the downstream effector of COX2, remained elevated in normal and tumor tissues of the nimesulide-treated Vhl(ΔIE)/Apc(min/+) mice. Further examination revealed that the terminal PGE(2) synthesis enzyme microsomal prostaglandin E synthase 1 (mPGES-1) was overexpressed in the colon of Vhl(ΔIE)/Apc(min/+) mice. mPGES-1 was demonstrated to be a direct target gene of HIF-2α, and genetic disruption of HIF-2α abolished the induction of mPGES-1 in colon tumors. Together, our findings demonstrate that HIF-2α is a major regulator of COX2/mPGES-1/PGE(2) pathway in colon tumors.

Microsomal Prostaglandin E2 Synthase-1

The prostanoids and leukotrienes (LTs) formed from arachidonic acid (AA) via the cyclooxygenase (COX)-1/2 and 5-lipoxygenase (5-LO) pathway, respectively, mediate inflammatory responses, chronic tissue remodelling, cancer, asthma and autoimmune disorders, but also possess homeostatic functions in the gastrointestinal tract, uterus, brain, kidney, vasculature and host defence. Based on the manifold functions of these eicosanoids, the clinical use of non-steroidal anti-inflammatory drugs (NSAIDs), a class of drugs that block formation of all prostanoids, is hampered by severe side-effects including gastrointestinal injury, renal irritations and cardiovascular risks. Therefore, anti-inflammatory agents interfering with eicosanoid biosynthesis require a well-balanced pharmacological profile to minimize these on-target side-effects. Current anti-inflammatory research aims at identifying compounds that can suppress the massive formation of pro-inflammatory prostaglandin (PG)E2 without affecting homeostatic PGE2 and PGI2 synthesis. The inducible microsomal prostaglandin E2 synthase-1 (mPGES-1) is one promising target enzyme. We will give an overview about the structure, regulation and function of mPGES-1 and then present novel inhibitors of mPGES-1 that may possess a promising pharmacological profile.