1
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Alfano A, Smyth M, Wharry S, Moody TS, Baumann M. Modular Synthesis of Benzoylpyridines Exploiting a Reductive Arylation Strategy. Org Lett 2024; 26:2847-2851. [PMID: 38133578 PMCID: PMC11020167 DOI: 10.1021/acs.orglett.3c03833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Herein we disclose a telescoped flow strategy to access electronically differentiated bisaryl ketones as potentially new and tunable photosensitizers containing both electron-rich benzene systems and electron-deficient pyridyl moieties. Our approach merges a light-driven (365 nm) and catalyst-free reductive arylation between aromatic aldehydes and cyanopyridines with a subsequent oxidation process. The addition of electron-donating and withdrawing substituents on the scaffold allowed effective modification of the absorbance of these compounds in the UV-vis region, while the continuous flow process affords high yields, short residence time, and high throughput.
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Affiliation(s)
| | - Megan Smyth
- Technology
Department, Almac Sciences, Craigavon BT63 5QD, United Kingdom
| | - Scott Wharry
- Technology
Department, Almac Sciences, Craigavon BT63 5QD, United Kingdom
| | - Thomas S. Moody
- Technology
Department, Almac Sciences, Craigavon BT63 5QD, United Kingdom
- Arran
Chemical Company, Monksland Industrial
Estate, Roscommon N37 DN24, Ireland
| | - Marcus Baumann
- School
of Chemistry, University College Dublin, Science Centre South, Dublin 4, Ireland
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2
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Lagunas-Rangel FA. Prediction of resveratrol target proteins: a bioinformatics analysis. J Biomol Struct Dyn 2024; 42:1088-1097. [PMID: 37011009 DOI: 10.1080/07391102.2023.2196698] [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: 01/27/2023] [Accepted: 03/22/2023] [Indexed: 04/04/2023]
Abstract
Resveratrol is a natural compound with a wide range of biological functions that generate health benefits under normal conditions and in multiple diseases. This has attracted the attention of the scientific community, which has revealed that this compound exerts these effects through its action on different proteins. Despite the great efforts made, due to the challenges involved, not all the proteins with which resveratrol interacts have yet been identified. In this work, using protein target prediction bioinformatics systems, RNA sequencing analysis and protein-protein interaction networks, 16 proteins were identified as potential targets of resveratrol. Due to its biological relevance, the interaction of resveratrol with the predicted target CDK5 was further investigated. A docking analysis found that resveratrol can interact with CDK5 and be positioned in its ATP-binding pocket. Resveratrol forms hydrogen bonds between its three hydroxyl groups (-OH) and CDK5 residues C83, D86, K89 and D144. Molecular dynamics analysis showed that these bonds allow resveratrol to remain in the pocket and suggest inhibition of CDK5 activity. All this allows us to better understand how resveratrol acts and to consider CDK5 inhibition within its biological actions, mainly in neurodegenerative diseases where this protein has been shown to be relevant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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3
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Cai Y, Mu X, Li G, Xu D. Quantum Mechanical/Molecular Mechanical Elucidation of the Catalytic Mechanism of Leukotriene A4 Hydrolase as an Epoxidase. J Phys Chem B 2023; 127:10338-10350. [PMID: 38010510 DOI: 10.1021/acs.jpcb.3c05969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Leukotriene A4 hydrolase (LTA4H) functions as a mono-zinc bifunctional enzyme with aminopeptidase and epoxidase activities. While the aminopeptidase mechanism is well understood, the epoxidase mechanism remains less clear. In continuation of our prior research, we undertook an in-depth exploration of the LTA4H catalytic role as an epoxidase, employing a combined SCC-DFTB/CHARMM method. In the current work, we found that the conversion of LTA4 to leukotriene B4 (LTB4) involves three successive steps: epoxy ring opening (RO), nucleophilic attack (NA), and proton transfer (PT) reactions at the epoxy oxygen atom. Among these steps, the RO and NA stages constitute the potential rate-limiting step within the entire epoxidase mechanism. Notably, the NA step implicates D375 as the general base catalyst, while the PT step engages protonated E271 as the general acid catalyst. Additionally, we delved into the mechanism behind the formation of the isomer product, Δ6-trans-Δ8-cis-LTB4. Our findings debunked the feasibility of a direct LTB4 to iso-LTB4 conversion. Instead, we highlight the possibility of isomerization from LTA4 to its isomeric conjugate (iso-LTA4), showing comparable energy barriers of 5.1 and 5.5 kcal/mol in aqueous and enzymatic environments, respectively. The ensuing dynamics of iso-LTA4 hydrolysis subsequently yield iso-LTB4 via a mechanism akin to LTA4 hydrolysis, albeit with a heightened barrier. Our computations firmly support the notion that substrate isomerization exclusively takes place prior to or during the initial substrate-binding phase, while LTA4 remains the dominant conformer. Notably, our simulations suggest that irrespective of the active site's constrained L-shape, isomerization from LTA4 to its isomeric conjugate remains plausible. The mechanistic insights garnered from our simulations furnish a valuable understanding of LTA4H's role as an epoxidase, thereby facilitating potential advancements in inhibitor design.
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Affiliation(s)
- Yao Cai
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Xia Mu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116000, P. R. China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116000, P. R. China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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4
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Pletzer-Zelgert J, Ehrt C, Fender I, Griewel A, Flachsenberg F, Klebe G, Rarey M. LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments. Acta Crystallogr D Struct Biol 2023; 79:837-856. [PMID: 37561404 PMCID: PMC10478636 DOI: 10.1107/s205979832300582x] [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: 04/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Due to the structural complexity of proteins, their corresponding crystal arrangements generally contain a significant amount of solvent-occupied space. These areas allow a certain degree of intracrystalline protein flexibility and mobility of solutes. Therefore, knowledge of the geometry of solvent-filled channels and cavities is essential whenever the dynamics inside a crystal are of interest. Especially in soaking experiments for structure-based drug design, ligands must be able to traverse the crystal solvent channels and reach the corresponding binding pockets. Unsuccessful screenings are sometimes attributed to the geometry of the crystal packing, but the underlying causes are often difficult to understand. This work presents LifeSoaks, a novel tool for analyzing and visualizing solvent channels in protein crystals. LifeSoaks uses a Voronoi diagram-based periodic channel representation which can be efficiently computed. The size and location of channel bottlenecks, which might hinder molecular diffusion, can be directly derived from this representation. This work presents the calculated bottleneck radii for all crystal structures in the PDB and the analysis of a new, hand-curated data set of structures obtained by soaking experiments. The results indicate that the consideration of bottleneck radii and the visual inspection of channels are beneficial for planning soaking experiments.
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Affiliation(s)
| | - Christiane Ehrt
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Inken Fender
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Axel Griewel
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Universität Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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5
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Teder T, König S, Singh R, Samuelsson B, Werz O, Garscha U, Haeggström JZ. Modulation of the 5-Lipoxygenase Pathway by Chalcogen-Containing Inhibitors of Leukotriene A 4 Hydrolase. Int J Mol Sci 2023; 24:ijms24087539. [PMID: 37108702 PMCID: PMC10145651 DOI: 10.3390/ijms24087539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The 5-lipoxygenase (5-LOX) pathway gives rise to bioactive inflammatory lipid mediators, such as leukotrienes (LTs). 5-LOX carries out the oxygenation of arachidonic acid to the 5-hydroperoxy derivative and then to the leukotriene A4 epoxide which is converted to a chemotactic leukotriene B4 (LTB4) by leukotriene A4 hydrolase (LTA4H). In addition, LTA4H possesses aminopeptidase activity to cleave the N-terminal proline of a pro-inflammatory tripeptide, prolyl-glycyl-proline (PGP). Based on the structural characteristics of LTA4H, it is possible to selectively inhibit the epoxide hydrolase activity while sparing the inactivating, peptidolytic, cleavage of PGP. In the current study, chalcogen-containing compounds, 4-(4-benzylphenyl) thiazol-2-amine (ARM1) and its selenazole (TTSe) and oxazole (TTO) derivatives were characterized regarding their inhibitory and binding properties. All three compounds selectively inhibit the epoxide hydrolase activity of LTA4H at low micromolar concentrations, while sparing the aminopeptidase activity. These inhibitors also block the 5-LOX activity in leukocytes and have distinct inhibition constants with recombinant 5-LOX. Furthermore, high-resolution structures of LTA4H with inhibitors were determined and potential binding sites to 5-LOX were proposed. In conclusion, we present chalcogen-containing inhibitors which differentially target essential steps in the biosynthetic route for LTB4 and can potentially be used as modulators of inflammatory response by the 5-LOX pathway.
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Affiliation(s)
- Tarvi Teder
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Stefanie König
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Greifswald University, 17489 Greifswald, Germany
| | - Rajkumar Singh
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Bengt Samuelsson
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, 7743 Jena, Germany
| | - Ulrike Garscha
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Greifswald University, 17489 Greifswald, Germany
| | - Jesper Z Haeggström
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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6
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Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022; 40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fares Fenanir
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| | - Abderrahmane Semmeq
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS, Sétif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France.,IUT de Moselle-Est, Université de Lorraine, Saint-Avold, France
| | | | - Smain Amira
- Laboratory of Phytotherapy Applied to Chroniques Diseases, University Ferhat Abbas, Sétif, Algeria
| | - Hocine Laouer
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
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7
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The Role of Resveratrol in Eye Diseases—A Review of the Literature. Nutrients 2022; 14:nu14142974. [PMID: 35889930 PMCID: PMC9317487 DOI: 10.3390/nu14142974] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Resveratrol (3,5,4′-trans-trihydroxystilbene) is a polyphenolic phytoalexin belonging to the stilbene family. It is commonly found in grape skins and seeds, as well as other plant-based foods. Oxidative stress and inflammation play a key role in the initiation and progression of age-related eye disorders (glaucoma, cataracts, diabetic retinopathy, and macular degeneration) that lead to a progressive loss of vision and blindness. Even though the way resveratrol affects the human body and the course of many diseases is still the subject of ongoing scientific research, it has been shown that the broad spectrum of anti-inflammatory and neuroprotective properties of resveratrol has a beneficial effect on eye tissues. In our research, we decided to analyze the current scientific literature on resveratrol, its possible mechanisms of action, and its therapeutic application in order to assess its effectiveness in eye diseases.
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8
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Lee KH, Ali NF, Lee SH, Zhang Z, Burdick M, Beaulac ZJ, Petruncio G, Li L, Xiang J, Chung EM, Foreman KW, Noble SM, Shim YM, Paige M. Substrate-dependent modulation of the leukotriene A 4 hydrolase aminopeptidase activity and effect in a murine model of acute lung inflammation. Sci Rep 2022; 12:9443. [PMID: 35676292 PMCID: PMC9177663 DOI: 10.1038/s41598-022-13238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/12/2022] [Indexed: 11/09/2022] Open
Abstract
The aminopeptidase activity (AP) of the leukotriene A4 hydrolase (LTA4H) enzyme has emerged as a therapeutic target to modulate host immunity. Initial reports focused on the benefits of augmenting the LTA4H AP activity and clearing its putative pro-inflammatory substrate Pro-Gly-Pro (PGP). However, recent reports have introduced substantial complexity disconnecting the LTA4H modulator 4-methoxydiphenylmethane (4MDM) from PGP as follows: (1) 4MDM inhibits PGP hydrolysis and subsequently inhibition of LTA4H AP activity, and (2) 4MDM activates the same enzyme target in the presence of alternative substrates. Differential modulation of LTA4H by 4MDM was probed in a murine model of acute lung inflammation, which showed that 4MDM modulates the host neutrophilic response independent of clearing PGP. X-ray crystallography showed that 4MDM and PGP bind at the zinc binding pocket and no allosteric binding was observed. We then determined that 4MDM modulation is not dependent on the allosteric binding of the ligand, but on the N-terminal side chain of the peptide. In conclusion, our study revealed that a peptidase therapeutic target can interact with its substrate and ligand in complex biochemical mechanisms. This raises an important consideration when ligands are designed to explain some of the unpredictable outcomes observed in therapeutic discovery targeting LTA4H.
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Affiliation(s)
- Kyung Hyeon Lee
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Nadia Fazal Ali
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
| | - Soo Hyeon Lee
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Zhimin Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, PO Box 800546, Charlottesville, VA, 22908, USA
| | - Marie Burdick
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, PO Box 800546, Charlottesville, VA, 22908, USA
| | - Zachary J Beaulac
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
| | - Greg Petruncio
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
| | - Linxia Li
- Department of Obstetrics and Gynecology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, 358 Datong Road, Shanghai, 200137, China
| | - Jiangdong Xiang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Ezra M Chung
- STCube Pharmaceutical, Inc., 401 Professional Dr, Gaithersburg, MD, 20879, USA
| | - Kenneth W Foreman
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
| | - Schroeder M Noble
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.
| | - Yun M Shim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, PO Box 800546, Charlottesville, VA, 22908, USA.
| | - Mikell Paige
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA.
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9
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Ibrahim KA, Abdelgaid HA, Eleyan M, Mohamed RA, Gamil NM. Resveratrol alleviates cardiac apoptosis following exposure to fenitrothion by modulating the sirtuin1/c-Jun N-terminal kinases/p53 pathway through pro-oxidant and inflammatory response improvements: In vivo and in silico studies. Life Sci 2022; 290:120265. [PMID: 34968465 DOI: 10.1016/j.lfs.2021.120265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 02/07/2023]
Abstract
Fenitrothion (FNT), a commonly used organophosphate, can cause oxidative damage and apoptosis on various organs. However, the underlying mechanisms for FNT-induced cardiotoxicity did not formally report. Here, we have evaluated the possible ameliorative roles of resveratrol (RSV) against FNT-induced cardiac apoptosis in male rats through the sirtuin1 (SIRT1)/c-Jun N-terminal kinase (c-JNK)/p53 pathway concerning pro-oxidant and inflammatory cytokines. Forty-eight male rats were equally grouped into control, RSV (20 mg/kg), 5-FNT (5 mg/kg), 10-FNT (10 mg/kg), 20-FNT (20 mg/kg), 5-FNT-RSV, 10-FNT-RSV, and 20-FNT-RSV where all doses administrated by gavage for four weeks. The present findings demonstrated that RSV markedly diminished the level of hyperlipidemia and elevation in lactate dehydrogenase (LDH), total creatine kinase (CK-T), and troponin T (TnT) levels following FNT intoxication. Furthermore, RSV significantly reduced FNT-induced cardiac oxidative injury by reducing malondialdehyde (MDA) level and improving the levels of glutathione (GSH), glutathione reductase (GR), superoxide dismutase (SOD), catalase (CAT), and acetylcholinesterase (AchE). Also, the levels of interleukin-1β (IL1β,), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) were significantly attenuated in the co-treated groups. Moreover, RSV alleviated the histopathological changes promoted by FNT and repaired the transcript levels of SIRT1, c-JNK, and caspase-9/3 along with p53 immunoreactivity. In silico study revealed that the free binding energies of RSV complexes with protein and DNA sequences of SIRT1 were lower than docked complexes of FNT. Therefore, RSV reserved myocardial injury-induced apoptosis following exposure to FNT by modulating the SIRT1/c-JNK/p53 pathway through cellular redox status and inflammatory response improvements.
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Affiliation(s)
- Khairy A Ibrahim
- Mammalian Toxicology Department, Central Agricultural Pesticides Laboratory, Agricultural Research Center, Dokki, Giza 12618, Egypt.
| | - Hala A Abdelgaid
- Biochemistry Department, National Hepatology and Tropical Medicine Research Institute, Cairo 11796, Egypt
| | - Mohammed Eleyan
- Department of Laboratory Medical Sciences, Alaqsa University, Gaza, 4051, Palestine
| | - Rania A Mohamed
- Mammalian Toxicology Department, Central Agricultural Pesticides Laboratory, Agricultural Research Center, Dokki, Giza 12618, Egypt
| | - Noha M Gamil
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6(th) of October City, Egypt
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10
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Chalotra N, Kumar J, Naqvi T, Shah BA. Photocatalytic functionalizations of alkynes. Chem Commun (Camb) 2021; 57:11285-11300. [PMID: 34617556 DOI: 10.1039/d1cc04014f] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Visible light mediated functionalizations have significantly expanded the scope of alkynes by unraveling new mechanistic pathways and enabling their transformation to diverse structural entities. The photoredox reactions on alkynes rely on their innate capability to generate myriad carbon-centred radicals via single electron transfer (SET), thereby, allowing the introduction of new radical precursors. Moreover, an array of methods have been developed facilitating transformations such as vicinal or gem-difunctionalization, annulation, cycloaddition and oxidative reactions to construct numerous key building blocks of natural and pharmaceutically important molecules. In addition, the introduction of photoredox chemistry has successfully been used to deal with the challenges associated with alkyne functionalization such as stereoselective and regioselective control. This article accounts for several visible light mediated functionalization reactions of alkynes, wherein they have been transformed into α-oxo compounds, β-keto sulfoxides, substituted olefins, N-heterocycles, internal alkynes and sulfur containing compounds. The article has been primarily categorized into various sections based on the reaction type with particular attention being paid to mechanistic details, advancement and future applications.
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Affiliation(s)
- Neha Chalotra
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad 201002, India.,Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
| | - Jaswant Kumar
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad 201002, India.,Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
| | - Tahira Naqvi
- Govt. College for Women, MA Road, Srinagar 190001, India
| | - Bhahwal Ali Shah
- Academy of Scientific and Industrial Research (AcSIR), Ghaziabad 201002, India.,Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
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11
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Schierle S, Brunst S, Helmstädter M, Ebert R, Kramer JS, Steinhilber D, Proschak E, Merk D. Development and in vitro Profiling of Dual FXR/LTA4H Modulators. ChemMedChem 2021; 16:2366-2374. [PMID: 33856122 PMCID: PMC8453936 DOI: 10.1002/cmdc.202100118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 11/10/2022]
Abstract
Designed polypharmacology presents as an attractive strategy to increase therapeutic efficacy in multi-factorial diseases by a directed modulation of multiple involved targets with a single molecule. Such an approach appears particularly suitable in non-alcoholic steatohepatitis (NASH) which involves hepatic steatosis, inflammation and fibrosis as pathological hallmarks. Among various potential pharmacodynamic mechanisms, activation of the farnesoid X receptor (FXRa) and inhibition of leukotriene A4 hydrolase (LTA4Hi) hold promise to counteract NASH according to preclinical and clinical observations. We have developed dual FXR/LTA4H modulators as pharmacological tools, enabling evaluation of this polypharmacology concept to treat NASH and related pathologies. The optimized FXRa/LTA4Hi exhibits well-balanced dual activity on the intended targets with sub-micromolar potency and is highly selective over related nuclear receptors and enzymes rendering it suitable as tool to probe synergies of dual FXR/LTA4H targeting.
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Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Steffen Brunst
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Moritz Helmstädter
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Roland Ebert
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Jan S. Kramer
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Dieter Steinhilber
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Ewgenij Proschak
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Daniel Merk
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
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12
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Röhn TA, Numao S, Otto H, Loesche C, Thoma G. Drug discovery strategies for novel leukotriene A4 hydrolase inhibitors. Expert Opin Drug Discov 2021; 16:1483-1495. [PMID: 34191664 DOI: 10.1080/17460441.2021.1948998] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
IntroductionLeukotriene A4 hydrolase (LTA4H) is the final and rate limiting enzyme regulating the biosynthesis of leukotriene B4 (LTB4), a pro-inflammatory lipid mediator implicated in a large number of inflammatory pathologies. Inhibition of LTA4H not only prevents LTB4 biosynthesis but also induces a lipid mediator class-switch within the 5-lipoxygenase pathway, elevating biosynthesis of the anti-inflammatory lipid mediator Lipoxin A4. Ample preclinical evidence advocates LTA4H as attractive drug target for the treatment of chronic inflammatory diseases.Areas coveredThis review covers details about the biochemistry of LTA4H and describes its role in regulating pro- and anti-inflammatory mediator generation. It summarizes recent efforts in medicinal chemistry toward novel LTA4H inhibitors, recent clinical trials testing LTA4H inhibitors in pulmonary inflammatory diseases, and potential reasons for the discontinuation of former development programs.Expert opinionGiven the prominent role of LTB4 in initiating and perpetuating inflammation, LTA4H remains an appealing drug target. The reason former attempts targeting this enzyme have not met with success in the clinic can be attributed to compound-specific liabilities of first-generation inhibitors and/or choice of target indications to test this mode of action. A new generation of highly potent and selective LTA4H inhibitors is currently undergoing clinical testing in indications with a strong link to LTB4 biology.
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Affiliation(s)
- Till A Röhn
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Shin Numao
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Heike Otto
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Christian Loesche
- Translational Medicine, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Gebhard Thoma
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
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Qin R, Wang H, Yan A. Classification and QSAR models of leukotriene A4 hydrolase (LTA4H) inhibitors by machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:411-431. [PMID: 33896285 DOI: 10.1080/1062936x.2021.1910862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Leukotriene A4 hydrolase (LTA4H) is an important anti-inflammatory target which can convert leukotriene A4 (LTA4) into pro-inflammatory substance leukotriene B4 (LTB4). In this paper, we built 18 classification models for 463 LTA4H inhibitors by using support vector machine (SVM), random forest (RF) and K-Nearest Neighbour (KNN). The best classification model (Model 2A) was built from RF and MACCS fingerprints. The prediction accuracy of 88.96% and the Matthews correlation coefficient (MCC) of 0.74 had been achieved on the test set. We also divided the 463 LTA4H inhibitors into six subsets using K-Means. We found that the highly active LTA4H inhibitors mostly contained diphenylmethane or diphenyl ether as the scaffold and pyridine or piperidine as the side chain. In addition, six quantitative structure-activity relationship (QSAR) models for 172 LTA4H inhibitors were built by multiple linear regression (MLR) and SVM. The best QSAR model (Model 6A) was built by using SVM and CORINA Symphony descriptors. The coefficients of determination of the training set and the test set were equal to 0.81 and 0.79, respectively. Classification and QSAR models could be used for subsequent virtual screening, and the obtained fragments that were important for highly active inhibitors would be helpful for designing new LTA4H inhibitors.
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Affiliation(s)
- R Qin
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - H Wang
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
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14
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Lin T, Qian P, Wang YE, Ou M, Jiang L, Zhu C, Xu Y, Xiong D, Mao J. Palladium-Catalyzed Direct Arylation of 2-Pyridylmethyl Silanes with Aryl Bromides. Org Lett 2021; 23:3000-3003. [PMID: 33779175 DOI: 10.1021/acs.orglett.1c00677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The first palladium-catalyzed direct arylation of 2-pyridylmethyl silanes with aryl bromides to generate a diverse array of aryl(2-pyridyl)-methyl silane derivatives has been developed. This protocol facilitates access to various kinds of heterocycle-containing silanes in good to excellent yields (40 examples, 66-97% yield) with good functional group tolerance. The scalability of this transformation is demonstrated.
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Affiliation(s)
- Tingzhi Lin
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Pengcheng Qian
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Yan-En Wang
- College of Science, Hebei Agricultural University, Baoding 071000, P. R. China
| | - Mingjie Ou
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Long Jiang
- Institute of Advanced Synthesis (IAS), Northwestern Polytechnical University (NPU), Xi'an 710072, China.,Yangtze River Delta Research Institute of NPU, Taicang, Jiangsu 215400, P. R. China
| | - Chen Zhu
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Yuchuan Xu
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Dan Xiong
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
| | - Jianyou Mao
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211800, P. R. China
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Markert C, Thoma G, Srinivas H, Bollbuck B, Lüönd RM, Miltz W, Wälchli R, Wolf R, Hinrichs J, Bergsdorf C, Azzaoui K, Penno CA, Klein K, Wack N, Jäger P, Hasler F, Beerli C, Loetscher P, Dawson J, Wieczorek G, Numao S, Littlewood-Evans A, Röhn TA. Discovery of LYS006, a Potent and Highly Selective Inhibitor of Leukotriene A 4 Hydrolase. J Med Chem 2021; 64:1889-1903. [PMID: 33592148 DOI: 10.1021/acs.jmedchem.0c01955] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cytosolic metalloenzyme leukotriene A4 hydrolase (LTA4H) is the final and rate-limiting enzyme in the biosynthesis of pro-inflammatory leukotriene B4 (LTB4). Preclinical studies have validated this enzyme as an attractive drug target in chronic inflammatory diseases. Despite several attempts, no LTA4H inhibitor has reached the market, yet. Herein, we disclose the discovery and preclinical profile of LYS006, a highly potent and selective LTA4H inhibitor. A focused fragment screen identified hits that could be cocrystallized with LTA4H and inspired a fragment merging. Further optimization led to chiral amino acids and ultimately to LYS006, a picomolar LTA4H inhibitor with exquisite whole blood potency and long-lasting pharmacodynamic effects. Due to its high selectivity and its ability to fully suppress LTB4 generation at low exposures in vivo, LYS006 has the potential for a best-in-class LTA4H inhibitor and is currently investigated in phase II clinical trials in inflammatory acne, hidradenitis suppurativa, ulcerative colitis, and NASH.
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16
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Mishra R, Das A, Rana S. Resveratrol binding to human complement fragment 5a (hC5a) may modulate the C5aR signaling axes. J Biomol Struct Dyn 2020; 39:1766-1780. [DOI: 10.1080/07391102.2020.1738958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Richa Mishra
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
| | - Aurosikha Das
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha, India
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17
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Cole DJ, Mones L, Csányi G. A machine learning based intramolecular potential for a flexible organic molecule. Faraday Discuss 2020; 224:247-264. [DOI: 10.1039/d0fd00028k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we employ the kernel regression machine learning technique to construct an analytical potential that reproduces the quantum mechanical potential energy surface of a small, flexible, drug-like molecule, 3-(benzyloxy)pyridin-2-amine.
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Affiliation(s)
- Daniel J. Cole
- School of Natural and Environmental Sciences
- Newcastle University
- Newcastle upon Tyne NE1 7RU
- UK
| | - Letif Mones
- Engineering Laboratory
- University of Cambridge
- Cambridge CB2 1PZ
- UK
| | - Gábor Csányi
- Engineering Laboratory
- University of Cambridge
- Cambridge CB2 1PZ
- UK
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18
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Lee KH, Petruncio G, Shim A, Burdick M, Zhang Z, Shim YM, Noble SM, Paige M. Effect of Modifier Structure on the Activation of Leukotriene A 4 Hydrolase Aminopeptidase Activity. J Med Chem 2019; 62:10605-10616. [PMID: 31751136 DOI: 10.1021/acs.jmedchem.9b00663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activation of the leukotriene A4 hydrolase (LTA4H) aminopeptidase (AP) activity with 4-methoxydiphenylmethane (4MDM) promoted resolution of neutrophil infiltration in a murine cigarette smoke-induced model for emphysematous chronic obstructive pulmonary disease. Recently, 4-(4-benzylphenyl)thiazol-2-amine (ARM1) was published as a ligand for LTA4H with potential anti-inflammatory properties. To investigate the effect of modifier structure on enzyme kinetics of LTA4H, a series of analogues bearing structural features of ARM1 and 4MDM were synthesized using trifluoroborate Suzuki coupling reactions. Following, the 2.8 Å X-ray crystal structure of LTA4H complexed with 4-OMe-ARM1, a 4MDM-ARM1 hybrid molecule, was determined. Kinetic analysis showed that ARM1 and related analogues lowered affinity for the enzyme-substrate complex, resulting in a change of mechanism from hyperbolic mixed predominately catalytic activation (HMx(Sp < Ca)A) as observed for 4MDM to a predominately specific activation (HMx(Sp > Ca)A) mechanism. 4-OMe-ARM1 was then shown to dose responsively reduce LTB4 production in human neutrophils.
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Affiliation(s)
- Kyung Hyeon Lee
- Department of Chemistry & Biochemistry , George Mason University , 10920 George Mason Circle , Manassas , Virginia 20110 , United States
- Bacterial Diseases Branch, Wound Infections Department , Walter Reed Army Institute of Research , 503 Robert Grant Ave , Silver Spring , Maryland 20910 , United States
| | - Greg Petruncio
- Department of Chemistry & Biochemistry , George Mason University , 10920 George Mason Circle , Manassas , Virginia 20110 , United States
| | - Amanda Shim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine , University of Virginia , P.O. Box 800546, Charlottesville , Virginia 22908 , United States
| | - Marie Burdick
- Division of Pulmonary and Critical Care Medicine, Department of Medicine , University of Virginia , P.O. Box 800546, Charlottesville , Virginia 22908 , United States
| | - Zhimin Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine , University of Virginia , P.O. Box 800546, Charlottesville , Virginia 22908 , United States
| | - Yun M Shim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine , University of Virginia , P.O. Box 800546, Charlottesville , Virginia 22908 , United States
| | - Schroeder M Noble
- Bacterial Diseases Branch, Wound Infections Department , Walter Reed Army Institute of Research , 503 Robert Grant Ave , Silver Spring , Maryland 20910 , United States
| | - Mikell Paige
- Department of Chemistry & Biochemistry , George Mason University , 10920 George Mason Circle , Manassas , Virginia 20110 , United States
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19
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Sultan S, Bhat MUS, Rizvi MA, Shah BA. Visible Light-Mediated [2 + 2] Cycloaddition Reactions of 1,4-Quinones and Terminal Alkynes. J Org Chem 2019; 84:8948-8958. [PMID: 31251064 DOI: 10.1021/acs.joc.9b00855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single-step synthesis of 4-hydroxy-functionalized bi-aryl and aryl/alkyl ketones via oxidative coupling of terminal alkynes with benzoquinones is reported. Furthermore, with naphthoquinones, owing to the cross-resonance of carbonyl with the aromatic ring, alkene-alkyne cycloaddition is more favored to give four-membered carbocyclic adducts, thereby precluding the requirement of preactivated alkynes.
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Affiliation(s)
- Shaista Sultan
- AcSIR and Natural Product Microbes , CSIR-Indian Institute of Integrative Medicine , Jammu 180001 , India
| | - Muneer-Ul-Shafi Bhat
- AcSIR and Natural Product Microbes , CSIR-Indian Institute of Integrative Medicine , Jammu 180001 , India
| | - Masood Ahmad Rizvi
- Department of Chemistry , University of Kashmir , Srinagar 190006 , India
| | - Bhahwal Ali Shah
- AcSIR and Natural Product Microbes , CSIR-Indian Institute of Integrative Medicine , Jammu 180001 , India
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20
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Morofuji T, Kinoshita H, Kano N. Connecting a carbonyl and a π-conjugated group through a p-phenylene linker by (5+1) benzene ring formation. Chem Commun (Camb) 2019; 55:8575-8578. [PMID: 31274134 DOI: 10.1039/c9cc04012a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A benzene ring was formed to connect a carbonyl group of various methyl ketones with a π-conjugated group through a p-phenylene linker. Methyl ketones and streptocyanines were used as the C1 and C5 sources, respectively, in the (5+1) annulation, which could form donor-π-acceptor molecules.
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Affiliation(s)
- Tatsuya Morofuji
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Hanae Kinoshita
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Naokazu Kano
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
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21
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Cadel S, Darmon C, Désert A, Mahbouli M, Piesse C, Ghélis T, Lafont R, Foulon T. The effects of curcumin, mangiferin, resveratrol and other natural plant products on aminopeptidase B activity. Biochem Biophys Res Commun 2019; 512:832-837. [PMID: 30928100 DOI: 10.1016/j.bbrc.2019.02.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022]
Abstract
Aminopeptidase B (Ap-B) is a Zn2+-aminopeptidase of the M1 family which is implicated, in conjunction with the nardilysin endoprotease, in the generation of miniglucagon, a peptide involved in the maintenance of glucose homeostasis. Other in vivo physiological roles have been established for this vertebrate enzyme, such as the processing of Arg-extended forms of human insulin and cholecystokinin 9 and the degradation of viral epitopes in the cytoplasm. Among M1 family members, Ap-B is phylogenetically close to leukotriene A4 hydrolase (LTA4H), a bi-functional aminopeptidase also able to transform LTA4 in LTB4 (a lipid mediator of inflammation). As the activities of LTA4H are reported to be inhibited by resveratrol, a polyphenolic molecule from red wine, the effect of this molecule was investigated on the Ap-B activity. Several other active phenolic compounds produced in plants were also tested. Among them, curcumin and mangiferin are the most effective inhibitors. Dixon analysis indicates that curcumin is a non-competitive inhibitor with a Ki value of 46 μmol.L-1. Dixon and Lineweaver-Burk representations with mangiferin show a mixed non-competitive inhibition with Ki' and Ki values of 194 μmol.L-1 and 105 μmol.L-1, respectively. At 200 μmol.L-1, no significant effect was observed with caffeic, chlorogenic, ferulic, salicylic and sinapic acids as well as with resveratrol. Analyses on the 3D-structure of LTA4H with resveratrol (pdb: 3FTS) and the Ap-B 3D-model allow hypothesis to explain theses results.
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Affiliation(s)
- Sandrine Cadel
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France.
| | - Cécile Darmon
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
| | - Alexandre Désert
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
| | - Mouna Mahbouli
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
| | - Christophe Piesse
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Plate-forme Ingénierie des Protéines et Synthèse Peptidique, 75005, Paris, France
| | - Thanos Ghélis
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
| | - René Lafont
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
| | - Thierry Foulon
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), Equipe Biogenèse des Signaux Peptidiques (BIOSIPE), 75005, Paris, France
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Saqib U, Kelley TT, Panguluri SK, Liu D, Savai R, Baig MS, Schürer SC. Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets. Front Pharmacol 2018; 9:1201. [PMID: 30405416 PMCID: PMC6207623 DOI: 10.3389/fphar.2018.01201] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/01/2018] [Indexed: 02/03/2023] Open
Abstract
Resveratrol (3, 4', 5-trihydroxy-trans-stilbene) is a natural phytoalexin found in grapes and has long been thought to be the answer to the "French Paradox." There is no shortage of preclinical and clinical studies investigating the broad therapeutic activity of resveratrol. However, in spite of many comprehensive reviews published on the bioactivity of resveratrol, there has yet to be a report focused on the variety and complexity of its structural binding properties, and its multi-targeted role. An improved understanding of disease mechanisms at the systems level has enabled targeted polypharmacology to mature into a rational drug discovery approach. Unlike traditional hit-to-lead campaigns that typically optimize activity and selectivity for a single target, polypharmacological drugs aim to selectively target multiple proteins, while avoiding critical off target interactions. This strategy bears promise of improved efficacy and reduced clinical attrition. This review seeks to investigate whether the bioactivity of resveratrol is due to a polypharmacological effect or promiscuity of the phenolic small molecule by examining the modes of binding with its diverse collection of protein targets. We focused on annotated targets, identified via the ChEMBL database, and matched these targets to a representative structure deposited in the Protein Data Bank (PDB), as crystal structures are most informative in understanding modes of binding at the atomic level. We discuss the structural aspects of resveratrol itself that permits binding to multiple proteins in various signaling pathways. Furthermore, we suggest that resveratrol's bioactivity is a result of scaffold promiscuity rather than polypharmacology, and the variety of binding modes across targets display little similarity in the pattern of target interaction.
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Affiliation(s)
- Uzma Saqib
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, India
| | - Tanya T. Kelley
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Siva K. Panguluri
- Department of Pharmaceutical Science, University of South Florida, Tampa, FL, United States
| | - Dongfang Liu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States
| | - Rajkumar Savai
- German Center for Lung Research (DZL), Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mirza S. Baig
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, United States
- Center for Computational Science, University of Miami, Coral Gables, FL, United States
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Saqib U, Faisal SM, Saluja R, Baig MS. Structural insights of resveratrol with its binding partners in the toll‐like receptor 4 pathway. J Cell Biochem 2018; 120:452-460. [DOI: 10.1002/jcb.27401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/10/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Uzma Saqib
- Discipline of Chemistry School of Basic Sciences, Indian Institute of Technology (IIT) Indore India
| | - Syed M. Faisal
- National Institute of Animal Biotechnology (NIAB) Hyderabad India
| | - Rohit Saluja
- Department of Biochemistry All India Institute of Medical Sciences (AIIMS) Bhopal India
| | - Mirza S. Baig
- Centre for Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology (IIT) Indore India
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Vo TTL, Jang WJ, Jeong CH. Leukotriene A4 hydrolase: an emerging target of natural products for cancer chemoprevention and chemotherapy. Ann N Y Acad Sci 2018; 1431:3-13. [PMID: 30058075 DOI: 10.1111/nyas.13929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/10/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
Cancer is the second leading cause of death worldwide and has become a global burden. It has long been known that inflammation is related to cancer, as inflammatory components have been identified in the tumor microenvironment and support tumor progression. Among the key inflammatory mediators, leukotrienes were found to be involved in cancer development. In particular, leukotriene B4, which is converted from leukotriene A4 by leukotriene A4 hydrolase (LTA4H), has been implicated in several types of cancer. In addition, LTA4H has attracted attention because of purported roles in inflammation and cancer development. Herein, we review the history of LTA4H, its emerging roles in cancer development, and the development of LTA4H inhibitors in cancer prevention and therapy.
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Affiliation(s)
- Tam Thuy Lu Vo
- College of Pharmacy, Keimyung University, Daegu, the Republic of Korea
| | - Won-Jun Jang
- College of Pharmacy, Keimyung University, Daegu, the Republic of Korea
| | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Daegu, the Republic of Korea
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Mu X, Xu D. QM/MM Molecular Dynamics Investigations of the Substrate Binding of Leucotriene A4 Hydrolase: Implication for the Catalytic Mechanism. J Phys Chem B 2018; 122:7253-7263. [PMID: 29965770 DOI: 10.1021/acs.jpcb.8b04203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LTA4H is a monozinc bifunctional enzyme which exhibits both aminopeptidase and epoxide hydrolase activities. Its dual functions in anti- and pro-inflammatory roles have attracted wide attention to the inhibitor design. In this work, we tried to construct Michaelis complexes of LTA4H with both a native peptide substrate and LTA4 molecule using combined quantum mechanics and molecular mechanics molecular dynamics simulations. First of all, the zinc ion is coordinated by H295, H299, and E318. For its aminopeptidase activity, similar to conventional peptidases, the fourth ligand to the zinc ion is suggested to be an active site water, which is further hydrogen bonded with a downstream glutamic acid, E296. For the epoxide hydrolase activity, the fourth ligand to the zinc ion is found to be an epoxy oxygen atom. The potential of mean force calculation indicates about an 8.5 kcal/mol activation barrier height for the ring-opening reaction, which will generate a metastable carbenium intermediate. Subsequent frontier molecular orbital analyses suggest that the next step would be the nucleophilic attacking reaction at the C12 atom by a water molecule activated by D375. Our simulations also analyzed functions of several important residues like R563, K565, E271, Y383, and Y378 in the binding of peptide and LTA4.
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Affiliation(s)
- Xia Mu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry , Sichuan University , Chengdu , Sichuan , People's Republic of China 610064
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry , Sichuan University , Chengdu , Sichuan , People's Republic of China 610064
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Kříž K, Fanfrlík J, Lepšík M. Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Chemphyschem 2018; 19:2540-2548. [PMID: 30003638 DOI: 10.1002/cphc.201800409] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 11/10/2022]
Abstract
A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry Faculty of Science, Charles University, Hlavova 8, 128 40, Praha 2, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
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Healy EF, Cervantes L, Nabona B, Williams J. A unified mechanism for plant polyketide biosynthesis derived from in silico modeling. Biochem Biophys Res Commun 2018; 497:1123-1128. [PMID: 29496450 DOI: 10.1016/j.bbrc.2018.02.190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 01/24/2023]
Abstract
The polyketide synthases found in a variety of plants and fungi provide a varied source of biologically active compounds of pharmacological and medicinal interest. Stilbene synthase and chalcone synthase catalyze the formation of a common tetraketide intermediate, but use different cyclization mechanisms to produce distinct and separate natural products. While key structural differences have been identified to explain this functional diversity, a fuller explication of the factors responsible for this mechanistic disparity is required. Based on the energetics of our models of the bound tetraketides, and our structural analysis of the active sites we propose that a key tautomeric conversion provides a mechanistic framework common to both cyclizations. A previously unidentified active water molecule facilitates cyclization in chalcone synthase through a Claisen mechanism. Such a "Claisen switch" is comparable to the previously characterized "aldol switch" mechanism proposed for the biosynthesis of resveratrol in stilbene synthase.
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Affiliation(s)
- Eamonn F Healy
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA.
| | - Luis Cervantes
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA
| | - Barret Nabona
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA
| | - Jacob Williams
- Department of Chemistry, St. Edward's University, Austin, TX 78704, USA
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28
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Liu Z, Li M, Wang B, Deng G, Chen W, Kim BS, Zhang H, Yang X, Walsh PJ. Chemoselective synthesis of aryl(pyridinyl)methanol derivatives through Ni-NIXANTPHOS catalyzed α-arylation and tandem arylation/rearrangement of pyridylmethyl ethers. Org Chem Front 2018. [DOI: 10.1039/c8qo00207j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An efficient synthesis of aryl(pyridyl)-methanol derivatives using Ni-NIXANTPHOS catalyzed α-arylation and tandem arylation/rearrangement is described.
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Affiliation(s)
- Zhengfen Liu
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Minyan Li
- Department of Chemistry
- Roy and Diana Vagelos Laboratories
- Penn/Merck Laboratory for High-Throughput Experimentation
- University of Pennsylvania
- Philadelphia
| | - Bijun Wang
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Guogang Deng
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Wen Chen
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Byeong-Seon Kim
- Department of Chemistry
- Roy and Diana Vagelos Laboratories
- Penn/Merck Laboratory for High-Throughput Experimentation
- University of Pennsylvania
- Philadelphia
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Xiaodong Yang
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Ministry of Education and Yunnan Province
- School of Chemical Science and Technology
- Yunnan University
- Kunming
| | - Patrick J. Walsh
- Department of Chemistry
- Roy and Diana Vagelos Laboratories
- Penn/Merck Laboratory for High-Throughput Experimentation
- University of Pennsylvania
- Philadelphia
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29
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Bhatt L, Roinestad K, Van T, Springman E. Recent advances in clinical development of leukotriene B4 pathway drugs. Semin Immunol 2017; 33:65-73. [DOI: 10.1016/j.smim.2017.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 12/23/2022]
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30
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Weiskirchen S, Weiskirchen R. Resveratrol: Is It Really Good for Liver Health? HEPATITIS MONTHLY 2017; 17. [DOI: 10.5812/hepatmon.12074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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31
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Proschak E, Heitel P, Kalinowsky L, Merk D. Opportunities and Challenges for Fatty Acid Mimetics in Drug Discovery. J Med Chem 2017; 60:5235-5266. [PMID: 28252961 DOI: 10.1021/acs.jmedchem.6b01287] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fatty acids beyond their role as an endogenous energy source and storage are increasingly considered as signaling molecules regulating various physiological effects in metabolism and inflammation. Accordingly, the molecular targets involved in formation and physiological activities of fatty acids hold significant therapeutic potential. A number of these fatty acid targets are addressed by some of the oldest and most widely used drugs such as cyclooxygenase inhibiting NSAIDs, whereas others remain unexploited. Compounds orthosterically binding to proteins that endogenously bind fatty acids are considered as fatty acid mimetics. On the basis of their structural resemblance, fatty acid mimetics constitute a family of bioactive compounds showing specific binding thermodynamics and following similar pharmacokinetic mechanisms. This perspective systematically evaluates targets for fatty acid mimetics, investigates their common structural characteristics, and highlights demands in their discovery and design. In summary, fatty acid mimetics share particularly favorable characteristics justifying the conclusion that their therapeutic potential vastly outweighs the challenges in their design.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lena Kalinowsky
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
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The development of novel LTA 4H modulators to selectively target LTB 4 generation. Sci Rep 2017; 7:44449. [PMID: 28303931 PMCID: PMC5355877 DOI: 10.1038/srep44449] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/08/2017] [Indexed: 12/14/2022] Open
Abstract
The pro-inflammatory mediator leukotriene B4 (LTB4) is implicated in the pathologies of an array of diseases and thus represents an attractive therapeutic target. The enzyme leukotriene A4 hydrolase (LTA4H) catalyses the distal step in LTB4 synthesis and hence inhibitors of this enzyme have been actively pursued. Despite potent LTA4H inhibitors entering clinical trials all have failed to show efficacy. We recently identified a secondary anti-inflammatory role for LTA4H in degrading the neutrophil chemoattractant Pro-Gly-Pro (PGP) and rationalized that the failure of conventional LTA4H inhibitors may be that they inadvertently prevented PGP degradation. We demonstrate that these inhibitors do indeed fail to discriminate between the dual activities of LTA4H, and enable PGP accumulation in mice. Accordingly, we have developed novel compounds that potently inhibit LTB4 generation whilst leaving PGP degradation unperturbed. These novel compounds could represent a safer and superior class of LTA4H inhibitors for translation into the clinic.
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33
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Malhotra S, Karanicolas J. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode? J Med Chem 2016; 60:128-145. [PMID: 27982595 DOI: 10.1021/acs.jmedchem.6b00725] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Traditional hit-to-lead optimization assumes that upon elaboration of chemical structure, the ligand retains its binding mode relative to the receptor. Here, we build a large-scale collection of related ligand pairs solved in complex with the same protein partner: we find that for 41 of 297 pairs (14%), the binding mode changes upon elaboration of the smaller ligand. While certain ligand physiochemical properties predispose changes in binding mode, particularly those properties that define fragments, simple structure-based modeling proves far more effective for identifying substitutions that alter the binding mode. Some ligand pairs change binding mode because the added substituent would irreconcilably conflict with the receptor in the original pose, whereas others change because the added substituent enables new, stronger interactions that are available only in a different pose. Scaffolds that can engage their target using alternate poses may enable productive structure-based optimization along multiple divergent pathways.
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Affiliation(s)
- Shipra Malhotra
- Program in Molecular Therapeutics, Fox Chase Cancer Center , 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center , 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
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Di- and tripeptide transport in vertebrates: the contribution of teleost fish models. J Comp Physiol B 2016; 187:395-462. [PMID: 27803975 DOI: 10.1007/s00360-016-1044-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/12/2016] [Accepted: 10/20/2016] [Indexed: 02/06/2023]
Abstract
Solute Carrier 15 (SLC15) family, alias H+-coupled oligopeptide cotransporter family, is a group of membrane transporters known for their role in the cellular uptake of di- and tripeptides (di/tripeptides) and peptide-like molecules. Of its members, SLC15A1 (PEPT1) chiefly mediates intestinal absorption of luminal di/tripeptides from dietary protein digestion, while SLC15A2 (PEPT2) mainly allows renal tubular reabsorption of di/tripeptides from ultrafiltration, SLC15A3 (PHT2) and SLC15A4 (PHT1) possibly interact with di/tripeptides and histidine in certain immune cells, and SLC15A5 has unknown function. Our understanding of this family in vertebrates has steadily increased, also due to the surge of genomic-to-functional information from 'non-conventional' animal models, livestock, poultry, and aquaculture fish species. Here, we review the literature on the SLC15 transporters in teleost fish with emphasis on SLC15A1 (PEPT1), one of the solute carriers better studied amongst teleost fish because of its relevance in animal nutrition. We report on the operativity of the transporter, the molecular diversity, and multiplicity of structural-functional solutions of the teleost fish orthologs with respect to higher vertebrates, its relevance at the intersection of the alimentary and osmoregulative functions of the gut, its response under various physiological states and dietary solicitations, and its possible involvement in examples of total body plasticity, such as growth and compensatory growth. By a comparative approach, we also review the few studies in teleost fish on SLC15A2 (PEPT2), SLC15A4 (PHT1), and SLC15A3 (PHT2). By representing the contribution of teleost fish to the knowledge of the physiology of di/tripeptide transport and transporters, we aim to fill the gap between higher and lower vertebrates.
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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36
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Weiskirchen S, Weiskirchen R. Resveratrol: How Much Wine Do You Have to Drink to Stay Healthy? Adv Nutr 2016; 7:706-18. [PMID: 27422505 PMCID: PMC4942868 DOI: 10.3945/an.115.011627] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Resveratrol is a naturally occurring stilbene endowed with multiple health-promoting effects. It is produced by certain plants including several dietary sources such as grapes, apples, raspberries, blueberries, plums, peanuts, and products derived therefrom (e.g., wine). Resveratrol can be isolated and purified from these biological sources or synthesized in a few steps with an overall high yield. This compound and its glucoside, the trans-polydatin piceid, have received worldwide attention for their beneficial effects on cardiovascular, inflammatory, neurodegenerative, metabolic, and age-related diseases. These health-promoting effects are particularly attractive given the prevalence of resveratrol-based nutraceuticals and the paradoxical epidemiologic observation that wine consumption is inversely correlated to the incidence of coronary heart disease. However, the notion of resveratrol as a "magic bullet" was recently challenged by clinical trials showing that this polyphenol does not have a substantial influence on health status and mortality risk. In the present review, we discuss the proposed therapeutic attributes and the mode of molecular actions of resveratrol. We also cover recent pharmacologic efforts to improve the poor bioavailability of resveratrol and influence the transition between body systems in humans. We conclude with some thoughts about future research directions that might be meaningful for resolving controversies surrounding resveratrol.
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Affiliation(s)
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, Rheinisch-Westfaelische Technische Hochschule University Hospital Aachen, Aachen, Germany
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37
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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Huschmann FU, Linnik J, Sparta K, Ühlein M, Wang X, Metz A, Schiebel J, Heine A, Klebe G, Weiss MS, Mueller U. Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library. Acta Crystallogr F Struct Biol Commun 2016; 72:346-55. [PMID: 27139825 PMCID: PMC4854561 DOI: 10.1107/s2053230x16004623] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.
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Affiliation(s)
- Franziska U. Huschmann
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Janina Linnik
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Karine Sparta
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Monika Ühlein
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Xiaojie Wang
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Alexander Metz
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Johannes Schiebel
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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Bufexamac ameliorates LPS-induced acute lung injury in mice by targeting LTA4H. Sci Rep 2016; 6:25298. [PMID: 27126280 PMCID: PMC4850449 DOI: 10.1038/srep25298] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/14/2016] [Indexed: 11/08/2022] Open
Abstract
Neutrophils play an important role in the occurrence and development of acute lung injury (ALI). Leukotriene B4 (LTB4), a hydrolysis product of epoxide leukotriene A4 (LTA4) catalyzed by LTA4 hydrolase (LTA4H), is one of the most potent chemoattractants for neutrophil. Bufexamac is a drug widely used as an anti-inflammatory agent on the skin, however, the mechanism of action is still not fully understood. In this study, we found bufexamac was capable of specifically inhibiting LTA4H enzymatic activity and revealed the mode of interaction of bufexamac and LTA4H using X-ray crystallography. Moreover, bufexamac significantly prevented the production of LTB4 in neutrophil and inhibited the fMLP-induced neutrophil migration through inhibition of LTA4H. Finally, bufexamac significantly attenuated lung inflammation as reflected by reduced LTB4 levels and weakened neutrophil infiltration in bronchoalveolar lavage fluid from a lipopolysaccharide-induced ALI mouse model. In summary, our study indicates that bufexamac acts as an inhibitor of LTB4 biosynthesis and may have potential clinical applications for the treatment of ALI.
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Rivero AR, Kim BS, Walsh PJ. Palladium-Catalyzed Benzylic Arylation of Pyridylmethyl Silyl Ethers: One-Pot Synthesis of Aryl(pyridyl)methanols. Org Lett 2016; 18:1590-3. [PMID: 27004592 PMCID: PMC4887141 DOI: 10.1021/acs.orglett.6b00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An efficient palladium-catalyzed direct arylation of pyridylmethyl silyl ethers with aryl bromides is described. A Pd(OAc)2/NIXANTPHOS-based catalyst provides aryl(pyridyl)methyl alcohol derivatives in good to excellent yields (33 examples, 57-100% yield). This protocol is compatible with different silyl ether protecting groups, affording either the protected or the free alcohols in an effective one-pot process. The scalability of the reaction is demonstrated.
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Affiliation(s)
- Alexandra R. Rivero
- Roy and Diana Vagelos Laboratories, Penn/Merck Laboratory for High-Throughput Experimentation, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Byeong-Seon Kim
- Roy and Diana Vagelos Laboratories, Penn/Merck Laboratory for High-Throughput Experimentation, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Patrick J. Walsh
- Roy and Diana Vagelos Laboratories, Penn/Merck Laboratory for High-Throughput Experimentation, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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41
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Grove LE, Vajda S, Kozakov D. Computational Methods to Support Fragment-based Drug Discovery. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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42
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Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
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Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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43
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Zhang X, Gong Z, Li J, Lu T. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations. J Chem Inf Model 2015; 55:2138-53. [DOI: 10.1021/acs.jcim.5b00177] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuejin Zhang
- School
of Basic Science, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Zhen Gong
- State
Key Laboratory of Lead Compound Research, WuXi AppTec, 288 Fute
Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Li
- State
Key Laboratory of Lead Compound Research, WuXi AppTec, 288 Fute
Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Tao Lu
- School
of Basic Science, China Pharmaceutical University, No. 24 Tongjiaxiang, Nanjing 210009, P. R. China
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Gelin M, Delfosse V, Allemand F, Hoh F, Sallaz-Damaz Y, Pirocchi M, Bourguet W, Ferrer JL, Labesse G, Guichou JF. Combining 'dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1777-87. [PMID: 26249358 DOI: 10.1107/s1399004715010342] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/29/2015] [Indexed: 12/16/2023]
Abstract
X-ray crystallography is an established technique for ligand screening in fragment-based drug-design projects, but the required manual handling steps - soaking crystals with ligand and the subsequent harvesting - are tedious and limit the throughput of the process. Here, an alternative approach is reported: crystallization plates are pre-coated with potential binders prior to protein crystallization and X-ray diffraction is performed directly 'in situ' (or in-plate). Its performance is demonstrated on distinct and relevant therapeutic targets currently being studied for ligand screening by X-ray crystallography using either a bending-magnet beamline or a rotating-anode generator. The possibility of using DMSO stock solutions of the ligands to be coated opens up a route to screening most chemical libraries.
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Affiliation(s)
- Muriel Gelin
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | - Vanessa Delfosse
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | - Frédéric Allemand
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | - François Hoh
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | | | | | - William Bourguet
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | | | - Gilles Labesse
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | - Jean François Guichou
- CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
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45
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Ruepp MD, Brozik JA, de Esch IJP, Farndale RW, Murrell-Lagnado RD, Thompson AJ. A fluorescent approach for identifying P2X1 ligands. Neuropharmacology 2015; 98:13-21. [PMID: 26026951 PMCID: PMC4728187 DOI: 10.1016/j.neuropharm.2015.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/02/2015] [Accepted: 05/12/2015] [Indexed: 02/06/2023]
Abstract
There are no commercially available, small, receptor-specific P2X1 ligands. There are several synthetic derivatives of the natural agonist ATP and some structurally-complex antagonists including compounds such as PPADS, NTP-ATP, suramin and its derivatives (e.g. NF279, NF449). NF449 is the most potent and selective ligand, but potencies of many others are not particularly high and they can also act at other P2X, P2Y and non-purinergic receptors. While there is clearly scope for further work on P2X1 receptor pharmacology, screening can be difficult owing to rapid receptor desensitisation. To reduce desensitisation substitutions can be made within the N-terminus of the P2X1 receptor, but these could also affect ligand properties. An alternative is the use of fluorescent voltage-sensitive dyes that respond to membrane potential changes resulting from channel opening. Here we utilised this approach in conjunction with fragment-based drug-discovery. Using a single concentration (300 μM) we identified 46 novel leads from a library of 1443 fragments (hit rate = 3.2%). These hits were independently validated by measuring concentration-dependence with the same voltage-sensitive dye, and by visualising the competition of hits with an Alexa-647-ATP fluorophore using confocal microscopy; confocal yielded kon (1.142 × 106 M−1 s−1) and koff (0.136 s−1) for Alexa-647-ATP (Kd = 119 nM). The identified hit fragments had promising structural diversity. In summary, the measurement of functional responses using voltage-sensitive dyes was flexible and cost-effective because labelled competitors were not needed, effects were independent of a specific binding site, and both agonist and antagonist actions were probed in a single assay. The method is widely applicable and could be applied to all P2X family members, as well as other voltage-gated and ligand-gated ion channels. This article is part of the Special Issue entitled ‘Fluorescent Tools in Neuropharmacology’. A novel fluorescence-based screening approach for identifying P2X1 receptor ligand candidates. Fragment-based drug discovery applied to ligand-gated ion channels. The use of confocal microscopy to determine the kinetics and affinity of Alexa-647-ATP binding to P2X1 receptors. Alexa-647-ATP for imaging P2X1 receptors on live cells.
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Affiliation(s)
- Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - James A Brozik
- Washington State University, Department of Chemistry, Pullman, WA 99164-4630, USA
| | - Iwan J P de Esch
- Medicinal Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | - Andrew J Thompson
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK.
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46
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O'Hagan S, Kell DB. Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites. Front Pharmacol 2015; 6:105. [PMID: 26029108 PMCID: PMC4429554 DOI: 10.3389/fphar.2015.00105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/29/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND A recent comparison showed the extensive similarities between the structural properties of metabolites in the reconstructed human metabolic network ("endogenites") and those of successful, marketed drugs ("drugs"). RESULTS Clustering indicated the related but differential population of chemical space by endogenites and drugs. Differences between the drug-endogenite similarities resulting from various encodings and judged by Tanimoto similarity could be related simply to the fraction of the bitstrings set to 1. By extracting drug/endogenite substructures, we develop a novel family of fingerprints, the Drug Endogenite Substructure (DES) encodings, based on the ranked frequency of the various substructures. These provide a natural assessment of drug-endogenite likeness, and may be used as descriptors with which to derive quantitative structure-activity relationships (QSARs). CONCLUSIONS "Drug-endogenite likeness" seems to have utility, and leads to a simple, novel and interpretable substructure-based molecular encoding for cheminformatics.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, The University of Manchester Manchester, UK ; The Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; The Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
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47
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Moser D, Wittmann SK, Kramer J, Blöcher R, Achenbach J, Pogoryelov D, Proschak E. PENG: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation, and Virtual Screening for Novel Ligands of LTA4H. J Chem Inf Model 2015; 55:284-93. [DOI: 10.1021/ci500618u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Moser
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK), 60590 Frankfurt, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sandra K. Wittmann
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - Jan Kramer
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - René Blöcher
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - Janosch Achenbach
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
- BASF SE, 67056 Ludwigshafen, Germany
| | - Denys Pogoryelov
- Institute of Biochemistry, Goethe University, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
- German Cancer Consortium (DKTK), 60590 Frankfurt, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Hall RJ, Mortenson PN, Murray CW. Efficient exploration of chemical space by fragment-based screening. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:82-91. [PMID: 25268064 DOI: 10.1016/j.pbiomolbio.2014.09.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 09/19/2014] [Accepted: 09/20/2014] [Indexed: 01/29/2023]
Abstract
Screening methods seek to sample a vast chemical space in order to identify starting points for further chemical optimisation. Fragment based drug discovery exploits the superior sampling of chemical space that can be achieved when the molecular weight is restricted. Here we show that commercially available fragment space is still relatively poorly sampled and argue for highly sensitive screening methods to allow the detection of smaller fragments. We analyse the properties of our fragment library versus the properties of X-ray hits derived from the library. We particularly consider properties related to the degree of planarity of the fragments.
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Affiliation(s)
- Richard J Hall
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton, Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton, Road, Cambridge CB4 0QA, United Kingdom
| | - Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton, Road, Cambridge CB4 0QA, United Kingdom.
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Sahi S, Rai S, Chaudhary M, Nain V. Modeling of human M1 aminopeptidases for in silico screening of potential Plasmodium falciparum alanine aminopeptidase (PfA-M1) specific inhibitors. Bioinformation 2014; 10:518-25. [PMID: 25258488 PMCID: PMC4166772 DOI: 10.6026/97320630010518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 06/27/2014] [Indexed: 11/23/2022] Open
Abstract
Plasmodium falciparum alanine M1-aminopeptidase (PfA-M1) is a validated target for anti-malarial drug development. Presence of significant similarity between PfA-M1 and human M1-aminopeptidases, particularly within regions of enzyme active site leads to problem of non-specificity and off-target binding for known aminopeptidase inhibitors. Molecular docking based in silico screening approach for off-target binding has high potential but requires 3D-structure of all human M1-aminopeptidaes. Therefore, in the present study 3D structural models of seven human M1-aminopeptidases were developed. The robustness of docking parameters and quality of predicted human M1-aminopeptidases structural models was evaluated by stereochemical analysis and docking of their respective known inhibitors. The docking scores were in agreement with the inhibitory concentrations elucidated in enzyme assays of respective inhibitor enzyme combinations (r2≈0.70). Further docking analysis of fifteen potential PfA-M1 inhibitors (virtual screening identified) showed that three compounds had less docking affinity for human M1-aminopeptidases as compared to PfA-M1. These three identified potential lead compounds can be validated with enzyme assays and used as a scaffold for designing of new compounds with increased specificity towards PfA-M1.
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Affiliation(s)
- Shakti Sahi
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Sneha Rai
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Meenakshi Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
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50
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Paige M, Wang K, Burdick M, Park S, Cha J, Jeffery E, Sherman N, Shim YM. Role of leukotriene A4 hydrolase aminopeptidase in the pathogenesis of emphysema. THE JOURNAL OF IMMUNOLOGY 2014; 192:5059-68. [PMID: 24771855 DOI: 10.4049/jimmunol.1400452] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The leukotriene A4 hydrolase (LTA4H) is a bifunctional enzyme with epoxy hydrolase and aminopeptidase activities. We hypothesize that the LTA4H aminopeptidase activity alleviates neutrophilic inflammation, which contributes to cigarette smoke (CS)-induced emphysema by clearing proline-glycine-proline (PGP), a triamino acid chemokine known to induce chemotaxis of neutrophils. To investigate the biological contributions made by the LTA4H aminopeptidase activity in CS-induced emphysema, we exposed wild-type mice to CS over 5 mo while treating them with a vehicle or a pharmaceutical agent (4MDM) that selectively augments the LTA4H aminopeptidase without affecting the bioproduction of leukotriene B4. Emphysematous phenotypes were assessed by premortem lung physiology with a small animal ventilator and by postmortem histologic morphometry. CS exposure acidified the airspaces and induced localization of the LTA4H protein into the nuclei of the epithelial cells. This resulted in accumulation of PGP in the airspaces by suppressing the LTA4H aminopeptidase activity. When the LTA4H aminopeptidase activity was selectively augmented by 4MDM, the levels of PGP in the bronchoalveolar lavage fluid and infiltration of neutrophils into the lungs were significantly reduced without affecting the levels of leukotriene B4. This protected murine lungs from CS-induced emphysematous alveolar remodeling. In conclusion, CS exposure promotes the development of CS-induced emphysema by suppressing the enzymatic activities of the LTA4H aminopeptidase in lung tissues and accumulating PGP and neutrophils in the airspaces. However, restoring the leukotriene A4 aminopeptidase activity with a pharmaceutical agent protected murine lungs from developing CS-induced emphysema.
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Affiliation(s)
- Mikell Paige
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 22030
| | - Kan Wang
- Center for Drug Discovery, Georgetown University Medical Center, Washington, DC 20057
| | - Marie Burdick
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA 22908; and
| | - Sunhye Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA 22908; and
| | - Josiah Cha
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA 22908; and
| | - Erin Jeffery
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908
| | - Nicholas Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908
| | - Y Michael Shim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA 22908; and
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