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Gür Maz T, Dahlke P, Gizem Ergül A, Olğaç A, Jordan PM, Çalışkan B, Werz O, Banoglu E. Novel 1,3,4-oxadiazole derivatives as highly potent microsomal prostaglandin E 2 synthase-1 (mPGES-1) inhibitors. Bioorg Chem 2024; 147:107383. [PMID: 38653151 DOI: 10.1016/j.bioorg.2024.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Selective inhibition of microsomal prostaglandin E2 synthase-1 (mPGES-1) is implicated as a new therapeutic modality for the development of new-generation anti-inflammatory drugs. Here, we present the discovery of new and potent inhibitors of human mPGES-1, i.e., compounds 13, 15-25, 29-30 with IC50 values in the range of 5.6-82.3 nM in a cell-free assay of prostaglandin (PG)E2 formation. We also demonstrate that 20 (TG554, IC50 = 5.6 nM) suppresses leukotriene (LT) biosynthesis at low µM concentrations, providing a benchmark compound that dually intervenes with inflammatory PGE2 and LT biosynthesis. Comprehensive lipid mediator (LM) metabololipidomics with activated human monocyte-derived macrophages showed that TG554 selectively inhibits inflammatory PGE2 formation over all cyclooxygenase (COX)-derived prostanoids, does not cause substrate shunting towards 5-lipoxygenase (5-LOX) pathway, and does not interfere with the biosynthesis of the specialized pro-resolving mediators as observed with COX inhibitors, providing a new chemotype for effective and safer anti-inflammatory drug development.
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Affiliation(s)
- Tuğçe Gür Maz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Taç Sok. No:3 Yenimahalle 06560 Ankara, Turkey
| | - Philipp Dahlke
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, D-7743 Jena, Germany
| | - Azize Gizem Ergül
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Taç Sok. No:3 Yenimahalle 06560 Ankara, Turkey
| | - Abdurrahman Olğaç
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Taç Sok. No:3 Yenimahalle 06560 Ankara, Turkey
| | - Paul M Jordan
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, D-7743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Burcu Çalışkan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Taç Sok. No:3 Yenimahalle 06560 Ankara, Turkey
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, D-7743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Erden Banoglu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Taç Sok. No:3 Yenimahalle 06560 Ankara, Turkey.
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Huang Q, Lai T, Wang Q, Luo L. mPGES-1 Inhibitor Discovery Based on Computer-Aided Screening: Pharmacophore Models, Molecular Docking, ADMET, and MD Simulations. Molecules 2023; 28:6059. [PMID: 37630311 PMCID: PMC10458489 DOI: 10.3390/molecules28166059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
mPGES-1 is an enzyme, which, when activated by inflammatory factors, can cause prostaglandin E synthesis. Traditional non-steroidal anti-inflammatory drugs are capable of inhibiting prostaglandin production, yet they can also cause gastrointestinal reactions and coagulation disorders. mPGES-1, the enzyme at the conclusion of prostaglandin production, does not cause any adverse reactions when inhibited. Numerous studies have demonstrated that mPGES-1 is more abundant in cancerous cells than in healthy cells, indicating that decreasing the expression of mPGES-1 could be a potential therapeutic strategy for cancer. Consequently, the invention of mPGES-1 inhibitors presents a fresh avenue for the treatment of inflammation and cancer. Incorporating a database of TCM compounds, we collected a batch of compounds that had an inhibitory effect on mPGES-1 and possessed IC50 value. Firstly, a pharmacophore model was constructed, and the TCM database was screened, and the compounds with score cut-off values of more than 1 were retained. Then, the compounds retained after being screened via the pharmacodynamic model were screened for docking at the mPGES-1 binding site, followed by high-throughput virtual screening [HTVS] and standard precision [SP] and super-precision [XP] docking, and the compounds in the top 20% of the XP docking score were selected to calculate the total free binding energy of MM-GBSA. The best ten compounds were chosen by comparing their score against the reference ligand 4U9 and the MM-GBSA_dG_Bind score. ADMET analysis resulted in the selection of ten compounds, three of which had desirable medicinal properties. Finally, the binding energy of the target protein mPGES-1 and the candidate ligand compound was analyzed using a 100 ns molecular dynamics simulation of the reference ligand 4U9 and three selected compounds. After a gradual screening study and analysis, we identified a structure that is superior to the reference ligand 4U9 in all aspects, namely compound 15643. Taken together, the results of this study reveal a structure that can be used to inhibit mPGES-1 compound 15643, thereby providing a new option for anti-inflammatory and anti-tumor drugs.
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Affiliation(s)
- Qiqi Huang
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (Q.H.); (T.L.)
| | - Tianli Lai
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (Q.H.); (T.L.)
| | - Qu Wang
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China;
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China;
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
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Babaoglu ZY, Kilic D. Virtual screening, molecular simulations and bioassays: Discovering novel microsomal prostaglandin E Synthase-1 (mPGES-1) inhibitors. Comput Biol Med 2023; 155:106616. [PMID: 36780799 DOI: 10.1016/j.compbiomed.2023.106616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/05/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Microsomal prostaglandin E synthase-1 (mPGES-1) is an inducible prostaglandin E synthase expressed following exposure to pro-inflammatory stimuli. The mPGES-1 enzyme represents a new target for the therapeutic treatment of acute and chronic inflammatory disorders and cancer. In the present study, compounds from the ZINC15 database with an indole scaffold were docked at the mPGES-1 binding site using Glide (high-throughput virtual screening [HTVS], standard precision [SP] and extra precision [XP]), and the stabilities of the complexes were determined by molecular simulation studies. Following HTVS, the top 10% compounds were retained and further screened by SP. Again, the top 10% of these compounds were retained. Finally, the Glide XP scores of the compounds were determined, 20% were analyzed, and the Prime MM-GBSA total free binding energies of the compounds were calculated. The molecular simulations (100 ns) of the reference ligand, LVJ, and the two best-scoring compounds were performed with the Desmond program to analyze the dynamics of the target protein-ligand complexes. In human lung cells treated with the hit compounds, cell viability by colorimetric method and PGE2 levels by immunoassay method were determined. These in vitro experiments demonstrated that the two indole-containing hit compounds are potential novel inhibitors of mPGES-1 and are, therefore, potential therapeutic agents for cancer/inflammation therapies. Moreover, the compounds are promising lead mPGES-1 inhibitors for novel molecule design.
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Affiliation(s)
| | - Deryanur Kilic
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey.
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Tian Y, Yang Z, Wang H, Yan A. Prediction of bioactivities of microsomal prostaglandin E 2 synthase-1 inhibitors by machine learning algorithms. Chem Biol Drug Des 2023; 101:1307-1321. [PMID: 36752697 DOI: 10.1111/cbdd.14214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/24/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
There is a strong interest in the development of microsomal prostaglandin E2 synthase-1 (mPGES-1) inhibitors of their potential to safely and effectively treat inflammation. Herein, 70 QSAR models were built on the dataset (735 mPGES-1 inhibitors) characterized with RDKit descriptors by multiple linear regression (MLR), support vector machine (SVM), random forest (RF), deep neural networks (DNN), and eXtreme Gradient Boosting (XGBoost). The other three regression models on the dataset are represented by SMILES using self-attention recurrent neural networks (RNN) and Graph Convolutional Networks (GCN). For the best model (Model C2), which was developed by SVM with RDKit descriptors, the coefficient of determination (R2 ) of 0.861 and root mean squared error (RMSE) of 0.235 were achieved for the test set. Additionally, R2 of 0.692 and RMSE of 0.383 were obtained on the external test set. We investigated the applicability domain (AD) of Model C2 with the rivality index (RI), the prediction of Model C2 on 78.92% of molecules in the test set, and 78.33% of molecules in the external test set were reliable. After dissecting the RDKit descriptors of Model C2, we found important physicochemical properties of highly active mPGES-1 inhibitors. Besides, by analyzing the attention weight of each atom of each inhibitor from the attention layer, we found that the benzamide group and the trifluoromethyl cyclohexane group are favorable substructures for mPGES-1 inhibitors.
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Affiliation(s)
- Yujia Tian
- Department of Pharmaceutical Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Zhenwu Yang
- Department of Pharmaceutical Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Hongzhao Wang
- Department of Pharmaceutical Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Aixia Yan
- Department of Pharmaceutical Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
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Cao SY, Zhou Y, Ma YX, Cheng SX, Tang GM, Wang YT. Syntheses, crystal structure, luminescent behaviors and Hirshfeld surface of salts with imidazole and benzimidazole-yl scaffolds. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wang JJ, Sun W, Jia WD, Bian M, Yu LJ. Research progress on the synthesis and pharmacology of 1,3,4-oxadiazole and 1,2,4-oxadiazole derivatives: a mini review. J Enzyme Inhib Med Chem 2022; 37:2304-2319. [PMID: 36000176 PMCID: PMC9423840 DOI: 10.1080/14756366.2022.2115036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Oxadiazole is a five-membered heterocyclic compound containing two nitrogen atoms and one oxygen atom. The 1,3,4-oxadiazole and 1,2,4-oxadiazole have favourable physical, chemical, and pharmacokinetic properties, which significantly increase their pharmacological activity via hydrogen bond interactions with biomacromolecules. In recent years, oxadiazole has been demonstrated to be the biologically active unit in a number of compounds. Oxadiazole derivatives exhibit antibacterial, anti-inflammatory, anti-tuberculous, anti-fungal, anti-diabetic and anticancer activities. In this paper, we report a series of compounds containing oxadiazole rings that have been published in the last three years only (2020–2022) as there was no report or their activities described in any article in 2019, which will be useful to scientists in research fields of organic synthesis, medicinal chemistry, and pharmacology.
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Affiliation(s)
- Jing-Jing Wang
- Institute of Pharmaceutical Chemistry and Pharmacology, Inner Mongolia Minzu University, Inner Mongolia Autonomous Region, Tongliao, PR China.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Inner Mongolia Autonomous Region, Tongliao, PR China
| | - Wen Sun
- Institute of Pharmaceutical Chemistry and Pharmacology, Inner Mongolia Minzu University, Inner Mongolia Autonomous Region, Tongliao, PR China.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Inner Mongolia Autonomous Region, Tongliao, PR China
| | - Wei-Dong Jia
- Institute of Pharmaceutical Chemistry and Pharmacology, Inner Mongolia Minzu University, Inner Mongolia Autonomous Region, Tongliao, PR China.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Inner Mongolia Autonomous Region, Tongliao, PR China
| | - Ming Bian
- Institute of Pharmaceutical Chemistry and Pharmacology, Inner Mongolia Minzu University, Inner Mongolia Autonomous Region, Tongliao, PR China.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Inner Mongolia Autonomous Region, Tongliao, PR China
| | - Li-Jun Yu
- Institute of Pharmaceutical Chemistry and Pharmacology, Inner Mongolia Minzu University, Inner Mongolia Autonomous Region, Tongliao, PR China.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Inner Mongolia Autonomous Region, Tongliao, PR China
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Novel quinoline-based derivatives: A new class of PDE4B inhibitors for adjuvant-induced arthritis. Eur J Med Chem 2022; 238:114497. [PMID: 35660249 DOI: 10.1016/j.ejmech.2022.114497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
A total of 31 quinoline-based derivatives were designed and synthesized to develop novel anti-inflammatory drugs. After the toxicity of synthetic compounds to RAW264.7 cells were evaluated in vitro, their anti-inflammatory activity was assessed by inhibiting lipopolysaccharide (LPS)-induced NO production levels in the RAW264.7 cells. Among the derivatives, compound f4 had the best anti-inflammatory activity, which could reduce the production of pro-inflammatory cytokines NO, IL-1β, and TNF-α with corresponding IC50 values of 20.40 ± 0.94, 18.98 ± 0.21 and 23.48 ± 0.46 μM. Western blot showed that f4 could inhibit the expression of LPS-induced inflammatory mediators iNOS and COX-2. Molecular docking showed that f4 could also enter the PDE4B receptor binding pocket, and the cellular thermal shift assay method indicated that the PDE4B protein bound to f4 had increased stability. Meanwhile, the inhibitory effect of this compound on the PDE4B enzyme (IC50 = 0.94 ± 0.36 μM) was comparable to that of the positive drug rolipram (IC50 = 1.04 ± 0.28 μM). Finally, in vivo studies showed that f4 could improve the degree of foot swelling and knee joint pathology in adjuvant-induced arthritic rats and decrease the levels of serum inflammatory factors TNF-α and IL-1β in a dose-dependent manner. Therefore, the development and design of quinoline-based derivatives for anti-inflammatory applications could be considered opportunities and challenges.
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