1
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Isigkeit L, Hörmann T, Schallmayer E, Scholz K, Lillich FF, Ehrler JHM, Hufnagel B, Büchner J, Marschner JA, Pabel J, Proschak E, Merk D. Automated design of multi-target ligands by generative deep learning. Nat Commun 2024; 15:7946. [PMID: 39261471 PMCID: PMC11390726 DOI: 10.1038/s41467-024-52060-8] [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: 01/10/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
Generative deep learning models enable data-driven de novo design of molecules with tailored features. Chemical language models (CLM) trained on string representations of molecules such as SMILES have been successfully employed to design new chemical entities with experimentally confirmed activity on intended targets. Here, we probe the application of CLM to generate multi-target ligands for designed polypharmacology. We capitalize on the ability of CLM to learn from small fine-tuning sets of molecules and successfully bias the model towards designing drug-like molecules with similarity to known ligands of target pairs of interest. Designs obtained from CLM after pooled fine-tuning are predicted active on both proteins of interest and comprise pharmacophore elements of ligands for both targets in one molecule. Synthesis and testing of twelve computationally favored CLM designs for six target pairs reveals modulation of at least one intended protein by all selected designs with up to double-digit nanomolar potency and confirms seven compounds as designed dual ligands. These results corroborate CLM for multi-target de novo design as source of innovation in drug discovery.
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Affiliation(s)
- Laura Isigkeit
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Tim Hörmann
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Espen Schallmayer
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Katharina Scholz
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Felix F Lillich
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
| | - Johanna H M Ehrler
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Benedikt Hufnagel
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Jasmin Büchner
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Julian A Marschner
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Jörg Pabel
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Ewgenij Proschak
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany.
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany.
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Phong NV, Thao NP, Vinh LB, Luyen BTT, Minh CV, Yang SY. Inhibition of Soluble Epoxide Hydrolase by Cembranoid Diterpenes from Soft Coral Sinularia maxima: Enzyme Kinetics, Molecular Docking, and Molecular Dynamics. Mar Drugs 2024; 22:373. [PMID: 39195489 DOI: 10.3390/md22080373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/16/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024] Open
Abstract
Soluble epoxide hydrolase (sEH) is essential for converting epoxy fatty acids, such as epoxyeicosatrienoic acids (EETs), into their dihydroxy forms. EETs play a crucial role in regulating blood pressure, mediating anti-inflammatory responses, and modulating pain, making sEH a key target for therapeutic interventions. Current research is increasingly focused on identifying sEH inhibitors from natural sources, particularly marine environments, which are rich in bioactive compounds due to their unique metabolic adaptations. In this study, the sEH inhibitory activities of ten cembranoid diterpenes (1-10) isolated from the soft coral Sinularia maxima were evaluated. Among them, compounds 3 and 9 exhibited considerable sEH inhibition, with IC50 values of 70.68 μM and 78.83 μM, respectively. Enzyme kinetics analysis revealed that these two active compounds inhibit sEH through a non-competitive mode. Additionally, in silico approaches, including molecular docking and molecular dynamics simulations, confirmed their stability and interactions with sEH, highlighting their potential as natural therapeutic agents for managing cardiovascular and inflammatory diseases.
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Affiliation(s)
- Nguyen Viet Phong
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Nguyen Phuong Thao
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Le Ba Vinh
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Bui Thi Thuy Luyen
- Faculty of Pharmaceutical Chemistry and Technology, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi 11021, Vietnam
| | - Chau Van Minh
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Seo Young Yang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea
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3
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Gazzillo E, Colarusso E, Giordano A, Chini MG, Potenza M, Hofstetter RK, Iorizzi M, Werz O, Lauro G, Bifulco G. Repositioning of Small Molecules through the Inverse Virtual Screening in silico Tool: Case of Benzothiazole-Based Inhibitors of Soluble Epoxide Hydrolase (sEH). Chempluschem 2024:e202400234. [PMID: 38753468 DOI: 10.1002/cplu.202400234] [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: 03/28/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Computational techniques accelerate drug discovery by identifying bioactive compounds for specific targets, optimizing molecules with moderate activity, or facilitating the repositioning of inactive items onto new targets. Among them, the Inverse Virtual Screening (IVS) approach is aimed at the evaluation of one or a small set of molecules against a panel of targets for addressing target identification. In this work, a focused library of benzothiazole-based compounds was re-investigated by IVS. Four items, originally synthesized and tested on bromodomain-containing protein 9 (BRD9) but yielding poor binding, were critically re-analyzed, disclosing only a partial fit with 3D structure-based pharmacophore models, which, in the meanwhile, were developed for this target. Afterwards, these compounds were re-evaluated through IVS on a panel of proteins involved in inflammation and cancer, identifying soluble epoxide hydrolase (sEH) as a putative interacting target. Three items were subsequently confirmed as able to interfere with sEH activity, leading to inhibition percentages spanning from 70 % up to 30 % when tested at 10 μM. Finally, one benzothiazole-based compound emerged as the most promising inhibitor featuring an IC50 in the low micromolar range (IC50=6.62±0.13 μM). Our data confirm IVS as a predictive tool for accelerating the target identification and repositioning processes.
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Affiliation(s)
- Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, Pozzuoli, I-80078, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Marianna Potenza
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Robert Klaus Hofstetter
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Maria Iorizzi
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
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4
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Feng ZQ, Ding J, Zhu MZ, Xie WS, Liu RC, Liu SS, Liu SM, Yu MJ, Zhu XH, Liang JH. Discovery of a novel lead characterized by a stilbene-extended scaffold against sepsis as soluble epoxide hydrolase inhibitors. Eur J Med Chem 2024; 266:116113. [PMID: 38215588 DOI: 10.1016/j.ejmech.2023.116113] [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: 11/01/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/14/2024]
Abstract
Recently, some inhibitors of soluble epoxide hydrolase (sEH) showed limited potential in treating sepsis by increasing survival time, but they have unfortunately failed to improve survival rates. In this study, we initially identified a new hit 11D, belonging to a natural skeleton known as stilbene and having an IC50 of 644 nM on inhibiting murine sEH. Natural scaffold-based sEH inhibitors are paid less attention. A combination of structure-activity relationships (SARs)-guided structural optimization and computer-aided skeleton growth led to a highly effective lead compound 70P (IC50: 4.0 nM). The dose-response study indicated that 70P (at doses of 0.5-5 mg/kg, ip.) significantly increased survival rates and survival time by reducing the levels of the inflammatory factors TNF-α and IL-6 in the liver. Interestingly, 70P exhibited much higher accumulation in the liver than in plasma (AUC ratio: 175). In addition, 70P exhibits equal IC50 value (1.5 nM) on inhibiting human sEH as EC5026 (1.7 nM). In conclusion, the natural scaffold-extended sEH inhibitor 70P has the potential to become a new promising lead for addressing the unmet medical need in sepsis treatment, which highlighted the importance of natural skeleton in developing sEH inhibitors.
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Affiliation(s)
- Zi-Qiang Feng
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Jing Ding
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Min-Zhen Zhu
- Research Center for Brain Health, PazhouLab, Guangzhou, 510330, China
| | - Wei-Song Xie
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Rui-Chen Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Si-Si Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Si-Meng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Ming-Jia Yu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China.
| | - Xin-Hong Zhu
- Research Center for Brain Health, PazhouLab, Guangzhou, 510330, China.
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China.
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5
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Oanh VT, Phong NV, Min BS, Yang SY, Kim JA. Insights into the inhibitory activities of neolignans and diarylnonanoid derivatives from nutmeg ( Myristica fragrans Houtt.) seeds on soluble epoxide hydrolase using in vitro and in silico approaches. J Enzyme Inhib Med Chem 2023; 38:2251099. [PMID: 37638797 PMCID: PMC10464555 DOI: 10.1080/14756366.2023.2251099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/05/2023] [Accepted: 08/18/2023] [Indexed: 08/29/2023] Open
Abstract
Two new neolignans, myrifralignans F-G (14 and 18), four new diarylnonanoid derivatives, myrifragranones A-D (21-24), and 18 known compounds were isolated and structurally elucidated from nutmeg (Myristica fragrans Houtt.) seeds. The absolute configurations of these secondary metabolites were determined using the electronic circular dichroism technique. The inhibitory potential of these isolated compounds on soluble epoxide hydrolase (sEH) was investigated for the first time. Among them, malabaricones B and C (19 and 20) and four new compounds 21-24 displayed inhibitory activities against sEH, with IC50 values ranging from 14.24 to 46.35 µM. Additionally, the binding mechanism, key binding interactions, stability, and dynamic behaviour of the active compounds with the sEH enzyme were analysed using in silico molecular docking and dynamics simulations. Our findings suggest that nutmeg could become a promising natural source for discovering and developing new sEH inhibitors.
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Affiliation(s)
- Vu Thi Oanh
- Vessel-Organ Interaction Research Center, VOICE (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
- Biotechnology Department, Vietnam – Korea Institute of Science and Technology, Thach Hoa, Thach That, Hanoi, Vietnam
| | - Nguyen Viet Phong
- Vessel-Organ Interaction Research Center, VOICE (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Sun Min
- College of Pharmacy, Drug Research and Development Center, Daegu Catholic University, Gyeongbuk, Republic of Korea
| | - Seo Young Yang
- Department of Pharmaceutical Engineering, Sangji University, Wonju, Republic of Korea
| | - Jeong Ah Kim
- Vessel-Organ Interaction Research Center, VOICE (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
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6
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Characterization reveals a putative Epoxide hydrolase from Yarrowia lipolytica with the ability to convert rac-1,2-epoxyhexane to (R)-diol. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Repositioning of Quinazolinedione-Based Compounds on Soluble Epoxide Hydrolase (sEH) through 3D Structure-Based Pharmacophore Model-Driven Investigation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123866. [PMID: 35744994 PMCID: PMC9228872 DOI: 10.3390/molecules27123866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
The development of new bioactive compounds represents one of the main purposes of the drug discovery process. Various tools can be employed to identify new drug candidates against pharmacologically relevant biological targets, and the search for new approaches and methodologies often represents a critical issue. In this context, in silico drug repositioning procedures are required even more in order to re-evaluate compounds that already showed poor biological results against a specific biological target. 3D structure-based pharmacophoric models, usually built for specific targets to accelerate the identification of new promising compounds, can be employed for drug repositioning campaigns as well. In this work, an in-house library of 190 synthesized compounds was re-evaluated using a 3D structure-based pharmacophoric model developed on soluble epoxide hydrolase (sEH). Among the analyzed compounds, a small set of quinazolinedione-based molecules, originally selected from a virtual combinatorial library and showing poor results when preliminarily investigated against heat shock protein 90 (Hsp90), was successfully repositioned against sEH, accounting the related built 3D structure-based pharmacophoric model. The promising results here obtained highlight the reliability of this computational workflow for accelerating the drug discovery/repositioning processes.
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8
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Lum PT, Sekar M, Gan SH, Jeyabalan S, Bonam SR, Rani NNIM, Ku-Mahdzir KM, Seow LJ, Wu YS, Subramaniyan V, Fuloria NK, Fuloria S. Therapeutic potential of mangiferin against kidney disorders and its mechanism of action: A review. Saudi J Biol Sci 2022; 29:1530-1542. [PMID: 35280538 PMCID: PMC8913403 DOI: 10.1016/j.sjbs.2021.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/13/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
There is a swing in research developments concerning the utilization of natural products as effective pharmacotherapeutic agents due to their comparatively lower toxicities than synthetic compounds. Among natural products, mangiferin is a natural C-glucosyl xanthonoid polyphenol with remarkable pharmacological activities. Emerging evidence indicates the therapeutic benefits of mangiferin against various kidney disorders, including renal injury, diabetic nephropathy, renal fibrosis, hyperuricemic nephropathy, and lupus nephritis, in experimental animal models. The mangiferin induced antioxidant response resulting in vital functions, such as protection against renal inflammation, inhibits renal cell apoptosis, activates autophagy, causes immunomodulation, regulates renal urate transporters and modulates cell signalling pathways. The purpose of this review provide a brief overview of the in vitro/in vivo reno-protective effect of mangiferin and the underlying mechanism(s) in protecting against kidney disorders. Understanding the pharmacological actions of mangiferin is prominence due to its excellent therapeutic potential in managing kidney disorders. Thus, in addition to this review, in-silico molecular docking is performed against nuclear factor kappa B (NF-κB) and soluble epoxide hydrolase (sEH) to study the mechanism of action of mangiferin. It is believed that mangiferin is a safe reno-protective molecule. The observed positive effects are attributed to the inhibition of inflammation caused by NF-κB and sEH upregulation and oxidative stress activation. Studies on the efficacy and safety of mangiferin in clinical trials are further warranted to confirm its medicinal potential as therapeutic agent for kidney disorders in humans.
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Charles RL, Abis G, Fernandez BF, Guttzeit S, Buccafusca R, Conte MR, Eaton P. A thiol redox sensor in soluble epoxide hydrolase enables oxidative activation by intra-protein disulfide bond formation. Redox Biol 2021; 46:102107. [PMID: 34509915 PMCID: PMC8436062 DOI: 10.1016/j.redox.2021.102107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022] Open
Abstract
Soluble epoxide hydrolase (sEH), an enzyme that broadly regulates the cardiovascular system, hydrolyses epoxyeicosatrienoic acids (EETs) to their corresponding dihydroxyeicosatrienoic acids (DHETs). We previously showed that endogenous lipid electrophiles adduct within the catalytic domain, inhibiting sEH to lower blood pressure in angiotensin II-induced hypertensive mice. As angiotensin II increases vascular H2O2, we explored sEH redox regulation by this oxidant and how this integrates with inhibition by lipid electrophiles to regulate vasotone. Kinetics analyses revealed that H2O2 not only increased the specific activity of sEH but increased its affinity for substrate and increased its catalytic efficiency. This oxidative activation was mediated by formation of an intra-disulfide bond between C262 and C264, as determined by mass spectrometry and substantiated by biotin-phenylarsinate and thioredoxin-trapping mutant assays. C262S/264S sEH mutants were resistant to peroxide-induced activation, corroborating the disulfide-activation mechanism. The physiological impact of sEH redox state was determined in isolated arteries and the effect of the pro-oxidant vasopressor angiotensin II on arterial sEH redox state and vasodilatory EETs indexed in mice. Angiotensin II induced the activating intra-disulfide in sEH, causing a decrease in plasma EET/DHET ratios that is consistent with the pressor response to this hormone. Although sEH C262-C264 disulfide formation enhances hydrolysis of vasodilatory EETs, this modification also sensitized sEH to inhibition by lipid electrophiles. This explains why angiotensin II decreases EETs and increases blood pressure, but when lipid electrophiles are also present, that EETs are increased and blood pressure lowered.
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Affiliation(s)
- Rebecca L Charles
- Queen Mary University of London, William Harvey Research Institute, Charterhouse Square, London, EC1M 6BQ, UK
| | - Giancarlo Abis
- King's College London, Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, London, SE1 1UL, UK
| | - Beatriz F Fernandez
- King's College London, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Sebastian Guttzeit
- King's College London, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital, London, SE1 7EH, UK
| | - Roberto Buccafusca
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Maria R Conte
- King's College London, Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, London, SE1 1UL, UK.
| | - Philip Eaton
- Queen Mary University of London, William Harvey Research Institute, Charterhouse Square, London, EC1M 6BQ, UK.
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10
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Bzówka M, Mitusińska K, Hopko K, Góra A. Computational insights into the known inhibitors of human soluble epoxide hydrolase. Drug Discov Today 2021; 26:1914-1921. [PMID: 34082135 DOI: 10.1016/j.drudis.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023]
Abstract
Human soluble epoxide hydrolase (hsEH) is involved in the hydrolysis of epoxyeicosatrienoic acids (EETs), which have potent anti-inflammatory properties. Given that EET conversion generates nonbioactive molecules, inhibition of this enzyme would be beneficial. Past decades of work on hsEH inhibitors resulted in numerous potential compounds, of which a hundred hsEH-ligand complexes were crystallized and deposited in the Protein Data Bank (PDB). We analyzed all deposited hsEH-ligand complexes to gain insight into the binding of inhibitors and to provide feedback on the future drug design processes. We also reviewed computationally driven strategies that were used to propose novel hsEH inhibitors.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland; Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, ul. Krzywoustego 4, Faculty of Chemistry, Silesian University of Technology, Gliwice 44-100, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Katarzyna Hopko
- Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland.
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11
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Fakhar Z, Hejazi L, Tabatabai SA, Munro OQ. Discovery of novel heterocyclic amide-based inhibitors: an integrative in-silico approach to targeting soluble epoxide hydrolase. J Biomol Struct Dyn 2021; 40:7114-7128. [PMID: 33650467 DOI: 10.1080/07391102.2021.1894987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inhibition of soluble epoxide hydrolase (sEH) is considered as an emerging druggable target to reduce blood pressure, improve insulin sensitivity, and decrease inflammation. Despite the availability of different classes of sEH small molecule inhibitors for the potential treatment of hypertension, only a few candidates have reached clinical trials, making the optimal control of blood pressure presently unattainable. This necessity motivated us to explore a series of novel quinazoline-4(3H)-one and 4,6-disubstituted pyridin-2(1H)-one derivatives targeting sEH enzyme. Herein, comprehensive computational investigations were performed to probe the inhibition efficacy of these potent compounds in terms of inhibitor-enzyme interactions against sEH. In this study, the 39 in-house with a focused library comprising 39 in-house synthesized compounds were selected. The structure-based pharmacophore modeling was developed based on the crystal structure of sEH with its co-crystallized biologically active inhibitor. The generated hypotheses were applied for virtual screening-based PHASE fitness scores. Docking-based virtual screening workflows were used to generate lead compounds using HTVS, SP and XP based GLIDE G-score values. The candidate leads were filtered using ADMET pharmacological and physicochemical properties screening. A 100-ns of molecular dynamics simulations with Molecular dynamics simulations (100 ns) were performed to explore the binding affinities of the considered compounds. Our study identified four best candidates from quinazoline-4(3H)-one derivatives, which indicated that a quinazolinone ring serves as a suitable scaffold to develop novel small molecule sEH inhibitors.
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Affiliation(s)
- Zeynab Fakhar
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - Leila Hejazi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Abbas Tabatabai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Orde Q Munro
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
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12
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Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 PMCID: PMC7888625 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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13
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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Das Mahapatra A, Choubey R, Datta B. Small Molecule Soluble Epoxide Hydrolase Inhibitors in Multitarget and Combination Therapies for Inflammation and Cancer. Molecules 2020; 25:molecules25235488. [PMID: 33255197 PMCID: PMC7727688 DOI: 10.3390/molecules25235488] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
The enzyme soluble epoxide hydrolase (sEH) plays a central role in metabolism of bioactive lipid signaling molecules. The substrate-specific hydrolase activity of sEH converts epoxyeicosatrienoic acids (EETs) to less bioactive dihydroxyeicosatrienoic acids. EETs exhibit anti-inflammatory, analgesic, antihypertensive, cardio-protective and organ-protective properties. Accordingly, sEH inhibition is a promising therapeutic strategy for addressing a variety of diseases. In this review, we describe small molecule architectures that have been commonly deployed as sEH inhibitors with respect to angiogenesis, inflammation and cancer. We juxtapose commonly used synthetic scaffolds and natural products within the paradigm of a multitarget approach for addressing inflammation and inflammation induced carcinogenesis. Structural insights from the inhibitor complexes and novel strategies for development of sEH-based multitarget inhibitors are also presented. While sEH inhibition is likely to suppress inflammation-induced carcinogenesis, it can also lead to enhanced angiogenesis via increased EET concentrations. In this regard, sEH inhibitors in combination chemotherapy are described. Urea and amide-based architectures feature prominently across multitarget inhibition and combination chemotherapy applications of sEH inhibitors.
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Affiliation(s)
- Amarjyoti Das Mahapatra
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
| | - Rinku Choubey
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
| | - Bhaskar Datta
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India; (A.D.M.); (R.C.)
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar 382355, India
- Correspondence: ; Tel.: +079-2395-2073; Fax: +079-2397-2622
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15
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Shamsara J. A Random Forest Model to Predict the Activity of a Large Set of Soluble Epoxide Hydrolase Inhibitors Solely Based on a Set of Simple Fragmental Descriptors. Comb Chem High Throughput Screen 2020; 22:555-569. [PMID: 31622216 DOI: 10.2174/1386207322666191016110232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/02/2019] [Accepted: 09/19/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND The Soluble Epoxide Hydrolase (sEH) is a ubiquitously expressed enzyme in various tissues. The inhibition of the sEH has shown promising results to treat hypertension, alleviate pain and inflammation. OBJECTIVE In this study, the power of machine learning has been employed to develop a predictive QSAR model for a large set of sEH inhibitors. METHODS In this study, the random forest method was employed to make a valid model for the prediction of sEH inhibition. Besides, two new methods (Treeinterpreter python package and LIME, Local Interpretable Model-agnostic Explanations) have been exploited to explain and interpret the model. RESULTS The performance metrics of the model were as follows: R2=0.831, Q2=0.565, RMSE=0.552 and R2 pred=0.595. The model also demonstrated good predictability on the two extra external test sets at least in terms of ranking. The Spearman's rank correlation coefficients for external test set 1 and 2 were 0.872 and 0.673, respectively. The external test set 2 was a diverse one compared to the training set. Therefore, the model could be used for virtual screening to enrich potential sEH inhibitors among a diverse compound library. CONCLUSION As the model was solely developed based on a set of simple fragmental descriptors, the model was explained by two local interpretation algorithms, and this could guide medicinal chemists to design new sEH inhibitors. Moreover, the most important general descriptors (fragments) suggested by the model were consistent with the available crystallographic data. The model is available as an executable binary at http://www.pharm-sbg.com and https://github.com/shamsaraj.
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Affiliation(s)
- Jamal Shamsara
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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16
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Lee KSS, Ng JC, Yang J, Hwang SH, Morisseau C, Wagner K, Hammock BD. Preparation and evaluation of soluble epoxide hydrolase inhibitors with improved physical properties and potencies for treating diabetic neuropathic pain. Bioorg Med Chem 2020; 28:115735. [PMID: 33007552 DOI: 10.1016/j.bmc.2020.115735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/18/2022]
Abstract
Soluble epoxide hydrolase (sEH), a novel therapeutic target for neuropathic pain, is a largely cytosolic enzyme that degrades epoxy-fatty acids (EpFAs), an important class of lipid signaling molecules. Many inhibitors of sEH have been reported, and to date, the 1,3-disubstituted urea has the highest affinity reported for the sEH among the central pharmacophores evaluated. An earlier somewhat water soluble sEH inhibitor taken to the clinic for blood pressure control had mediocre potency (both affinity and kinetics) and a short in vivo half-life. We undertook a study to overcome these difficulties, but the sEH inhibitors carrying a 1,3-disubstituted urea often suffer poor physical properties that hinder their formulation. In this report, we described new strategies to improve the physical properties of sEH inhibitors with a 1,3-disubstituted urea while maintaining their potency and drug-target residence time (a complementary in vitro parameter) against sEH. To our surprise, we identified two structural modifications that substantially improve the potency and physical properties of sEH inhibitors carrying a 1,3-disubstituted urea pharmacophore. Such improvements will greatly facilitate the movement of sEH inhibitors to the clinic.
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Affiliation(s)
| | - Jen C Ng
- Department of Entomology and Nematology, One Shields Ave, University of California-Davis, Davis, CA 95616, United States
| | - Jun Yang
- EicOsis Human Health, 140 B Street, Suite 5, Number 346, Davis, CA 95616, United States
| | - Sung-Hee Hwang
- EicOsis Human Health, 140 B Street, Suite 5, Number 346, Davis, CA 95616, United States
| | - Christophe Morisseau
- Department of Entomology and Nematology, One Shields Ave, University of California-Davis, Davis, CA 95616, United States
| | - Karen Wagner
- EicOsis Human Health, 140 B Street, Suite 5, Number 346, Davis, CA 95616, United States
| | - Bruce D Hammock
- Synthia LLC, Davis, CA 95616, United States; Department of Entomology and Nematology, One Shields Ave, University of California-Davis, Davis, CA 95616, United States; EicOsis Human Health, 140 B Street, Suite 5, Number 346, Davis, CA 95616, United States
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17
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Li HX, Heo M, Go Y, Kim YS, Kim YH, Yang SY, Li W. Coumarin and Moracin Derivatives from Mulberry Leaves ( Morus alba L.) with Soluble Epoxide Hydrolase Inhibitory Activity. Molecules 2020; 25:molecules25173967. [PMID: 32878149 PMCID: PMC7504814 DOI: 10.3390/molecules25173967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/23/2022] Open
Abstract
This study identified three coumarins (1-3), and six moracin derivatives (4-9). The structures of these natural compounds were determined by the spectroscopic methods, including 1D and 2D NMR methods, and comparison with previous reported data. All of the isolated compounds were assessed for the effects on the soluble epoxide hydrolase (sEH) inhibitory activity. Among them, compounds 1-7 exhibited significant inhibitory effect with 100% inhibitory, with IC50 values of 6.9, 0.2, 15.9, 1.1, 1.2, 9.9, and 7.7 µM, respectively. A kinetic study revealed that compounds 1-4, and 6 were competitive types of inhibitors, compounds 5 and 7 were mixed types of inhibitors. These results suggest that moracin and coumarin derivatives from mulberry leaves are significant sEH inhibitors.
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Affiliation(s)
- Hong Xu Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Myungsook Heo
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (M.H.); (Y.H.K.)
| | - Younghoon Go
- Korean Medicine (KM) Application Center, Korea Institute of Oriental Medicine, Daegu 41062, Korea; (Y.G.); (Y.S.K.)
| | - Young Soo Kim
- Korean Medicine (KM) Application Center, Korea Institute of Oriental Medicine, Daegu 41062, Korea; (Y.G.); (Y.S.K.)
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (M.H.); (Y.H.K.)
| | - Seo Young Yang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (M.H.); (Y.H.K.)
- Correspondence: (S.Y.Y.); (W.L.); Tel.: +82-42-821-5933 (S.Y.Y.); +82-53-940-3874 (W.L.)
| | - Wei Li
- Korean Medicine (KM) Application Center, Korea Institute of Oriental Medicine, Daegu 41062, Korea; (Y.G.); (Y.S.K.)
- Correspondence: (S.Y.Y.); (W.L.); Tel.: +82-42-821-5933 (S.Y.Y.); +82-53-940-3874 (W.L.)
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18
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Mahlooji I, Shokri M, Manoochehri R, Mahboubi-Rabbani M, Rezaee E, Tabatabai SA. Discovery of phthalimide derivatives as novel inhibitors of a soluble epoxide hydrolase. Arch Pharm (Weinheim) 2020; 353:e2000052. [PMID: 32484272 DOI: 10.1002/ardp.202000052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 11/08/2022]
Abstract
Soluble epoxide hydrolase (sEH) inhibitors are effective in reducing blood pressure, inflammation, and pain in a number of mammalian disease models. As most classical urea-based sEH inhibitors suffer from poor solubility and pharmacokinetic properties, the development of novel sEH inhibitors with an improved pharmacokinetic specification has received a great deal of attention. In this study, a series of amide-based sEH inhibitors bearing a phthalimide ring as the novel secondary pharmacophore (P2 ) was designed, synthesized, and evaluated. Docking results illustrated that the amide group as the primary pharmacophore (P1 ) was placed at a suitable distance from the three key amino acids (Tyr383, Tyr466, and Asp335) for an effective hydrogen bonding. In agreement with these findings, most of the newly synthesized compounds demonstrated moderate to high sEH inhibitory activities, relative to 12-(3-adamantan-1-yl-ureido)dodecanoic acid as the reference standard. Compound 12e with a 4-methoxybenzoyl substituent exhibited the highest sEH inhibitory activity, with an IC50 value of 1.06 nM. Moreover, the ADME properties of the compounds were evaluated in silico, and the results revealed appropriate predictions.
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Affiliation(s)
- Iman Mahlooji
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Shokri
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rana Manoochehri
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahboubi-Rabbani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Rezaee
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Abbas Tabatabai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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19
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Khattri RB, Morris DL, Bilinovich SM, Manandhar E, Napper KR, Sweet JW, Modarelli DA, Leeper TC. Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead. Molecules 2019; 25:E147. [PMID: 31905878 PMCID: PMC6983068 DOI: 10.3390/molecules25010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.
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Affiliation(s)
- Ram B. Khattri
- Department of Physiology and Functional genomics, University of Florida, Gainesville, FL 32610, USA;
| | - Daniel L. Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Stephanie M. Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Kahlilah R. Napper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Jacob W. Sweet
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - David A. Modarelli
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Thomas C. Leeper
- Department of Chemistry and Biochemistry, Kennesaw State University, GA 30144, USA
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20
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Bhagwati S, Siddiqi MI. Identification of potential soluble epoxide hydrolase (sEH) inhibitors by ligand-based pharmacophore model and biological evaluation. J Biomol Struct Dyn 2019; 38:4956-4966. [DOI: 10.1080/07391102.2019.1691659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sudha Bhagwati
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
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21
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Abis G, Charles RL, Kopec J, Yue WW, Atkinson RA, Bui TTT, Lynham S, Popova S, Sun YB, Fraternali F, Eaton P, Conte MR. 15-deoxy-Δ 12,14-Prostaglandin J 2 inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanism. Commun Biol 2019; 2:188. [PMID: 31123712 PMCID: PMC6525171 DOI: 10.1038/s42003-019-0426-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 01/01/2023] Open
Abstract
Human soluble epoxide hydrolase (hsEH) is an enzyme responsible for the inactivation of bioactive epoxy fatty acids, and its inhibition is emerging as a promising therapeutical strategy to target hypertension, cardiovascular disease, pain and insulin sensitivity. Here, we uncover the molecular bases of hsEH inhibition mediated by the endogenous 15-deoxy-Δ12,14-Prostaglandin J2 (15d-PGJ2). Our data reveal a dual inhibitory mechanism, whereby hsEH can be inhibited by reversible docking of 15d-PGJ2 in the catalytic pocket, as well as by covalent locking of the same compound onto cysteine residues C423 and C522, remote to the active site. Biophysical characterisations allied with in silico investigations indicate that the covalent modification of the reactive cysteines may be part of a hitherto undiscovered allosteric regulatory mechanism of the enzyme. This study provides insights into the molecular modes of inhibition of hsEH epoxy-hydrolytic activity and paves the way for the development of new allosteric inhibitors.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Rebecca L. Charles
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Jolanta Kopec
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - R. Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Tam T. T. Bui
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, The James Black Centre, King’s College London, London, SE5 9NU UK
| | - Simona Popova
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Philip Eaton
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
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22
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Abis G, Charles RL, Eaton P, Conte MR. Expression, purification, and characterisation of human soluble Epoxide Hydrolase (hsEH) and of its functional C-terminal domain. Protein Expr Purif 2018; 153:105-113. [PMID: 30218745 PMCID: PMC6189638 DOI: 10.1016/j.pep.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/30/2018] [Accepted: 09/05/2018] [Indexed: 12/30/2022]
Abstract
The human soluble Epoxide Hydrolase (hsEH) is an enzyme involved in the hydrolysis of endogenous anti-inflammatory and cardio-protective signalling mediators known as epoxyeicosatrienoic acids (EETs). EETs’ conversion into the corresponding diols by hsEH generates non-bioactive molecules, thereby the enzyme inhibition would be expected to enhance the EETs bioavailability, and their beneficial properties. Numerous inhibitors have been developed to target the enzyme, some of which are showing promising antihypertensive and anti-inflammatory properties in vivo. Thus far, the preparation of the recombinant enzyme for enzymatic and structural in vitro studies has been performed mainly using a baculovirus expression system. More recently, it was reported that the enzyme could be exogenously expressed and isolated from E. coli, although limited amounts of active protein were obtained. We herein describe two novel methods to yield pure recombinant enzyme. The first describes the expression and purification of the full-length enzyme from eukaryotic cells HEK293-F, whilst the second concerns the C-terminal domain of hsEH obtained from the cost-effective and rapid E. coli prokaryotic system. The two methods successfully generated satisfactory amounts of functional enzyme, with virtually identical enzymatic activity. Overall, the protocols described in this paper can be employed for the recombinant expression and purification of active hsEH, to be used in future biomedical investigations and for high-throughput screening of inhibitors for potential use in the treatment of cardiovascular disease. hsEH is a key regulator of cardiovascular homeostasis. A HEK293-F mammalian expression system for hsEH full-length (FL) was developed. An E. coli expression system for the hsEH C-terminal Domain (CTD) was established. Both proteins exhibited the same enzymatic specific activity in vitro. The CTD preparation provides benefits of easy operation, and high yield and purity.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Excellence, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, United Kingdom.
| | - Rebecca L Charles
- Cardiovascular Division and British Heart Foundation Centre of Excellence, The Rayne Institute, King´s College London, St Thomas' Hospital, London, SE1 7EH, United Kingdom
| | - Philip Eaton
- Cardiovascular Division and British Heart Foundation Centre of Excellence, The Rayne Institute, King´s College London, St Thomas' Hospital, London, SE1 7EH, United Kingdom
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Excellence, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, United Kingdom.
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23
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Blacklock KM, Yang L, Mulligan VK, Khare SD. A computational method for the design of nested proteins by loop-directed domain insertion. Proteins 2018; 86:354-369. [PMID: 29250820 DOI: 10.1002/prot.25445] [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: 07/24/2017] [Revised: 12/04/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022]
Abstract
The computational design of novel nested proteins-in which the primary structure of one protein domain (insert) is flanked by the primary structure segments of another (parent)-would enable the generation of multifunctional proteins. Here we present a new algorithm, called Loop-Directed Domain Insertion (LooDo), implemented within the Rosetta software suite, for the purpose of designing nested protein domain combinations connected by flexible linker regions. Conformational space for the insert domain is sampled using large libraries of linker fragments for linker-to-parent domain superimposition followed by insert-to-linker superimposition. The relative positioning of the two domains (treated as rigid bodies) is sampled efficiently by a grid-based, mutual placement compatibility search. The conformations of the loop residues, and the identities of loop as well as interface residues, are simultaneously optimized using a generalized kinematic loop closure algorithm and Rosetta EnzymeDesign, respectively, to minimize interface energy. The algorithm was found to consistently sample near-native conformations and interface sequences for a benchmark set of structurally similar but functionally divergent domain-inserted enzymes from the α/β hydrolase superfamily, and discriminates well between native and nonnative conformations and sequences, although loop conformations tended to deviate from the native conformations. Furthermore, in cross-domain placement tests, native insert-parent domain combinations were ranked as the best-scoring structures compared to nonnative domain combinations. This algorithm should be broadly applicable to the design of multi-domain protein complexes with any combination of inserted or tandem domain connections.
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Affiliation(s)
- Kristin M Blacklock
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Lu Yang
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Vikram K Mulligan
- Institute for Protein Design and Department of Biochemistry, University of Washington, Seattle, Washington
| | - Sagar D Khare
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
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An JU, Song YS, Kim KR, Ko YJ, Yoon DY, Oh DK. Biotransformation of polyunsaturated fatty acids to bioactive hepoxilins and trioxilins by microbial enzymes. Nat Commun 2018; 9:128. [PMID: 29317615 PMCID: PMC5760719 DOI: 10.1038/s41467-017-02543-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/08/2017] [Indexed: 12/18/2022] Open
Abstract
Hepoxilins (HXs) and trioxilins (TrXs) are involved in physiological processes such as inflammation, insulin secretion and pain perception in human. They are metabolites of polyunsaturated fatty acids (PUFAs), including arachidonic acid, eicosapentaenoic acid and docosahexaenoic acid, formed by 12-lipoxygenase (LOX) and epoxide hydrolase (EH) expressed by mammalian cells. Here, we identify ten types of HXs and TrXs, produced by the prokaryote Myxococcus xanthus, of which six types are new, namely, HXB5, HXD3, HXE3, TrXB5, TrXD3 and TrXE3. We succeed in the biotransformation of PUFAs into eight types of HXs (>35% conversion) and TrXs (>10% conversion) by expressing M. xanthus 12-LOX or 11-LOX with or without EH in Escherichia coli. We determine 11-hydroxy-eicosatetraenoic acid, HXB3, HXB4, HXD3, TrXB3 and TrXD3 as potential peroxisome proliferator-activated receptor-γ partial agonists. These findings may facilitate physiological studies and drug development based on lipid mediators. Hepoxilins (HXs) and trioxilins (TrXs) are lipid metabolites with roles in inflammation and insulin secretion. Here, the authors discover a prokaryotic source of HXs and TrXs, identify the biosynthetic enzymes and heterologously express HXs and TrXs in E. coli.
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Affiliation(s)
- Jung-Ung An
- Department of Integrative Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yong-Seok Song
- Department of Integrative Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Kyoung-Rok Kim
- Department of Integrative Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yoon-Joo Ko
- National Center for Inter-University Research Facilities (NCIRF), Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Do-Young Yoon
- Department of Integrative Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Integrative Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
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25
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Wilson C, De Oliveira GS, Adriani PP, Chambergo FS, Dias MV. Structure of a soluble epoxide hydrolase identified in Trichoderma reesei. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1039-1045. [DOI: 10.1016/j.bbapap.2017.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/14/2017] [Accepted: 05/08/2017] [Indexed: 01/01/2023]
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26
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Aliagas I, Berger R, Goldberg K, Nishimura RT, Reilly J, Richardson P, Richter D, Sherer EC, Sparling BA, Bryan MC. Sustainable Practices in Medicinal Chemistry Part 2: Green by Design. J Med Chem 2017; 60:5955-5968. [DOI: 10.1021/acs.jmedchem.6b01837] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ignacio Aliagas
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Raphaëlle Berger
- MRL, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kristin Goldberg
- Innovative Medicines Unit, AstraZeneca, Building 310, Milton Science Park, Cambridge, CB4 0FZ, U.K
| | - Rachel T. Nishimura
- Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California 92121, United States
| | - John Reilly
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paul Richardson
- Pfizer Global Research and Development, 10777 Science Center Drive (CB2), San Diego, California 92121, United States
| | - Daniel Richter
- Pfizer Global Research and Development, 10777 Science Center Drive (CB2), San Diego, California 92121, United States
| | - Edward C. Sherer
- MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Brian A. Sparling
- Amgen, Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marian C. Bryan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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27
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Discovery of the first dual inhibitor of the 5-lipoxygenase-activating protein and soluble epoxide hydrolase using pharmacophore-based virtual screening. Sci Rep 2017; 7:42751. [PMID: 28218273 PMCID: PMC5317001 DOI: 10.1038/srep42751] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/13/2017] [Indexed: 11/09/2022] Open
Abstract
Leukotrienes (LTs) are pro-inflammatory lipid mediators derived from arachidonic acid (AA) with roles in inflammatory and allergic diseases. The biosynthesis of LTs is initiated by transfer of AA via the 5-lipoxygenase-activating protein (FLAP) to 5-lipoxygenase (5-LO). FLAP inhibition abolishes LT formation exerting anti-inflammatory effects. The soluble epoxide hydrolase (sEH) converts AA-derived anti-inflammatory epoxyeicosatrienoic acids (EETs) to dihydroxyeicosatetraenoic acids (di-HETEs). Its inhibition consequently also counteracts inflammation. Targeting both LT biosynthesis and the conversion of EETs with a dual inhibitor of FLAP and sEH may represent a novel, powerful anti-inflammatory strategy. We present a pharmacophore-based virtual screening campaign that led to 20 hit compounds of which 4 targeted FLAP and 4 were sEH inhibitors. Among them, the first dual inhibitor for sEH and FLAP was identified, N-[4-(benzothiazol-2-ylmethoxy)-2-methylphenyl]-N'-(3,4-dichlorophenyl)urea with IC50 values of 200 nM in a cell-based FLAP test system and 20 nM for sEH activity in a cell-free assay.
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28
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Karami L, Saboury AA, Rezaee E, Tabatabai SA. Investigation of the binding mode of 1, 3, 4-oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:445-459. [PMID: 27928588 DOI: 10.1007/s00249-016-1188-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/03/2016] [Accepted: 11/17/2016] [Indexed: 01/24/2023]
Abstract
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH. The results obtained from the binding free energy (ΔG binding) calculation and normal mode analysis indicate that the major favorable contributors are the van der Waals and electrostatic terms, whereas the polar solvation term opposes binding. In addition, a good agreement between the calculated ΔG binding and the experimental IC50 was obtained [correlation coefficient, r 2 = 0.89 (with) and 0.87 (without) entropy]. Besides, comparison of the enthalpy changes (ΔG MM-GBSA) with entropy changes (-TΔS) indicates that binding process of all inhibitors to sEH is enthalpy-driven. Based on the ΔG binding on per residue decomposition, Asp335 and Tyr383 residues from the active site and Trp336, Leu499 and His524 residues from hydrophobic pockets contribute the most to ΔG binding. Moreover, hydrogen bond analysis reveals that Tyr383, Tyr466 and Asp335 residues have an important role in the binding to inhibitors by forming hydrogen bonds with high occupancies. Our obtained results are useful for the understanding of the sEH-inhibitor interactions and may have great importance in the design of future sEH inhibitors.
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Affiliation(s)
- Leila Karami
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Elham Rezaee
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Abbas Tabatabai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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29
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Amour A, Barton N, Cooper AWJ, Inglis G, Jamieson C, Luscombe CN, Morrell J, Peace S, Perez D, Rowland P, Tame C, Uddin S, Vitulli G, Wellaway N. Evolution of a Novel, Orally Bioavailable Series of PI3Kδ Inhibitors from an Inhaled Lead for the Treatment of Respiratory Disease. J Med Chem 2016; 59:7239-51. [DOI: 10.1021/acs.jmedchem.6b00799] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Augustin Amour
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Nick Barton
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | | | - Graham Inglis
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Craig Jamieson
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow G1 1XL, U.K
| | | | - Josie Morrell
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Simon Peace
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - David Perez
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Paul Rowland
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Chris Tame
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Sorif Uddin
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
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30
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Gee CT, Arntson KE, Urick AK, Mishra NK, Hawk LML, Wisniewski AJ, Pomerantz WCK. Protein-observed (19)F-NMR for fragment screening, affinity quantification and druggability assessment. Nat Protoc 2016; 11:1414-27. [PMID: 27414758 DOI: 10.1038/nprot.2016.079] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are able to provide dynamic structural information toward understanding protein folding and function. Changes in these spectra upon the addition of fragment molecules can be observed and quantified. This protocol describes the sequence-selective labeling of three proteins (the first bromodomains of Brd4 and BrdT, and the KIX domain of the CREB-binding protein) using commercially available fluorinated aromatic amino acids and fluorinated precursors as example applications of the method developed by our research group. Fragment-screening approaches are discussed, as well as Kd determination, ligand-efficiency calculations and druggability assessment, i.e., the ability to target these proteins using small-molecule ligands. Experiment times on the order of a few minutes and the simplicity of the NMR spectra obtained make this approach well-suited to the investigation of small- to medium-sized proteins, as well as the screening of multiple proteins in the same experiment.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keith E Arntson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Neeraj K Mishra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura M L Hawk
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea J Wisniewski
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
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31
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Waltenberger B, Garscha U, Temml V, Liers J, Werz O, Schuster D, Stuppner H. Discovery of Potent Soluble Epoxide Hydrolase (sEH) Inhibitors by Pharmacophore-Based Virtual Screening. J Chem Inf Model 2016; 56:747-62. [DOI: 10.1021/acs.jcim.5b00592] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Birgit Waltenberger
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ulrike Garscha
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Veronika Temml
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Josephine Liers
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Oliver Werz
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | | | - Hermann Stuppner
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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32
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Xue Y, Olsson T, Johansson CA, Öster L, Beisel HG, Rohman M, Karis D, Bäckström S. Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration. ChemMedChem 2016; 11:497-508. [PMID: 26845235 DOI: 10.1002/cmdc.201500575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/20/2022]
Abstract
Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high-throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose-response analysis to confirm the hits, the identified actives were then effectively triaged by a structure-based hit-classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right-hand side of the active-site pocket with hydrogen bonds to the protein. The 2-phenylbenzimidazole-4-sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2-phenylbenzimidazole-4-sulfonamide series.
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Affiliation(s)
- Yafeng Xue
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Thomas Olsson
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Carina A Johansson
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Linda Öster
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Hans-Georg Beisel
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Mattias Rohman
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - David Karis
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Stefan Bäckström
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.
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33
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Li J, Bai F, Liu H, Gramatica P. Ligand Efficiency Outperforms pIC50on Both 2D MLR and 3D CoMFA Models: A Case Study on AR Antagonists. Chem Biol Drug Des 2015. [PMID: 26198098 DOI: 10.1111/cbdd.12619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jiazhong Li
- School of Pharmacy; Lanzhou University; 199 West Donggang Road 730000 Lanzhou China
- The Separating Scientific Institute of Lanzhou; 3 Weiyi Road 730000 Lanzhou China
| | - Fang Bai
- School of Pharmacy; Lanzhou University; 199 West Donggang Road 730000 Lanzhou China
| | - Huanxiang Liu
- School of Pharmacy; Lanzhou University; 199 West Donggang Road 730000 Lanzhou China
| | - Paola Gramatica
- Department of Theoretical and Applied Sciences; University of Insubria; via Dunant 3 21100 Varese Italy
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34
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Lee GY, Kim JH, Choi SK, Kim YH. Constituents of the seeds of Cassia tora with inhibitory activity on soluble expoxide hydrolease. Bioorg Med Chem Lett 2015; 25:5097-101. [PMID: 26483136 DOI: 10.1016/j.bmcl.2015.10.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/17/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
Abstract
Efforts to extract soluble epoxide hydrolase (sEH) inhibitors from food sources through bioactivity-guided fractionation of Cassia tora seed extracts led to the isolation of one new compound, 1, and 15 known compounds, 2-16. Structural elucidations were performed using 1D/2D NMR spectroscopy and mass spectrometry. Compounds 1, 3, 4, 6, 10, 11, and 13-16 exhibited inhibitory activities on sEH with IC50 values of 2.2±2.1-40.6±3.4 μM. Compound 13 was particularly active and exhibited a reversible-uncompetitive behavior in enzyme kinetic studies. A binding site on the enzyme for compound 13 was also predicted by Autodock 4.2 simulations.
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Affiliation(s)
- Ga Young Lee
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Jang Hoon Kim
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea; Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-852, Republic of Korea
| | - Seung-Kook Choi
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-852, Republic of Korea
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea.
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35
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Cortés-Cabrera Á, Gago F, Morreale A. A computational fragment-based de novo design protocol guided by ligand efficiency indices (LEI). Methods Mol Biol 2015; 1289:89-100. [PMID: 25709035 DOI: 10.1007/978-1-4939-2486-8_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new protocol aimed at the structure-based design of drug-like molecules using a fragment approach. It starts from a suitably placed and well-defined "base fragment" and then uses an incremental construction algorithm and a scoring function to grow the molecule into prioritized candidates. The selection of the most promising solutions for synthesis and validation is guided by the optimization of the calculated ligand efficiency indices known as binding efficiency index (BEI) and surface efficiency index (SEI), which allow the user to navigate proficiently in chemico-biological space. A test case for the protocol is exemplified here using published data for inhibitors of protein kinase B, aka AKT, a key enzyme in several signal transduction pathways. Our procedure was able to identify the main features responsible for the binding of inhibitors and guided the selection process towards molecules that included or resembled those shown as the most active in the original studies.
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Affiliation(s)
- Álvaro Cortés-Cabrera
- Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM, Madrid, Spain
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36
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Sugaya N. Ligand efficiency-based support vector regression models for predicting bioactivities of ligands to drug target proteins. J Chem Inf Model 2014; 54:2751-63. [PMID: 25220713 DOI: 10.1021/ci5003262] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The concept of ligand efficiency (LE) indices is widely accepted throughout the drug design community and is frequently used in a retrospective manner in the process of drug development. For example, LE indices are used to investigate LE optimization processes of already-approved drugs and to re-evaluate hit compounds obtained from structure-based virtual screening methods and/or high-throughput experimental assays. However, LE indices could also be applied in a prospective manner to explore drug candidates. Here, we describe the construction of machine learning-based regression models in which LE indices are adopted as an end point and show that LE-based regression models can outperform regression models based on pIC50 values. In addition to pIC50 values traditionally used in machine learning studies based on chemogenomics data, three representative LE indices (ligand lipophilicity efficiency (LLE), binding efficiency index (BEI), and surface efficiency index (SEI)) were adopted, then used to create four types of training data. We constructed regression models by applying a support vector regression (SVR) method to the training data. In cross-validation tests of the SVR models, the LE-based SVR models showed higher correlations between the observed and predicted values than the pIC50-based models. Application tests to new data displayed that, generally, the predictive performance of SVR models follows the order SEI > BEI > LLE > pIC50. Close examination of the distributions of the activity values (pIC50, LLE, BEI, and SEI) in the training and validation data implied that the performance order of the SVR models may be ascribed to the much higher diversity of the LE-based training and validation data. In the application tests, the LE-based SVR models can offer better predictive performance of compound-protein pairs with a wider range of ligand potencies than the pIC50-based models. This finding strongly suggests that LE-based SVR models are better than pIC50-based models at predicting bioactivities of compounds that could exhibit a much higher (or lower) potency.
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Affiliation(s)
- Nobuyoshi Sugaya
- Drug Discovery Department, Research & Development Division, PharmaDesign, Inc. , Hatchobori 2-19-8, Chuo-ku, Tokyo 104-0032, Japan
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37
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Amano Y, Yamaguchi T, Tanabe E. Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Bioorg Med Chem 2014; 22:2427-34. [DOI: 10.1016/j.bmc.2014.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 12/22/2022]
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38
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Structure-based optimization of cyclopropyl urea derivatives as potent soluble epoxide hydrolase inhibitors for potential decrease of renal injury without hypotensive action. Bioorg Med Chem 2014; 22:1548-57. [DOI: 10.1016/j.bmc.2014.01.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 01/11/2023]
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39
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Joseph-McCarthy D, Campbell AJ, Kern G, Moustakas D. Fragment-Based Lead Discovery and Design. J Chem Inf Model 2014; 54:693-704. [DOI: 10.1021/ci400731w] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Diane Joseph-McCarthy
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Arthur J. Campbell
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gunther Kern
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Demetri Moustakas
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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40
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Abstract
More research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. The enzyme DHPS has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. The use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. Despite the large amount of structural information available for DHPS, few recent publications address the possibility of using this knowledge for novel drug design. This article reviews the relevant papers and patents that report promising new small-molecule inhibitors of DHPS, and discuss these data in light of new insights into the DHPS catalytic mechanism and recently determined crystal structures of DHPS bound to potent small-molecule inhibitors. This new functional understanding confirms that DHPS deserves further consideration as an antimicrobial drug target.
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41
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de la Vega de León A, Bajorath J. Formation of activity cliffs is accompanied by systematic increases in ligand efficiency from lowly to highly potent compounds. AAPS JOURNAL 2014; 16:335-41. [PMID: 24477941 DOI: 10.1208/s12248-014-9567-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/09/2014] [Indexed: 11/30/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds sharing the same biological activity but having a large difference in potency. Therefore, ACs are often studied to rationalize structure-activity relationships (SARs) and aid in lead optimization. Hence, the AC concept plays an important role in compound development. For compound optimization, ligand efficiency (LE) represents another key concept. LE accounts for the relation between compound potency and mass. A major goal of lead optimization is to increase potency and also LE. Despite their high relevance for drug development, the AC and LE concepts have thus far not been considered in combination. It is currently unknown how compounds forming ACs might be related in terms of LE. To explore this question, ACs were systematically identified on the basis of high-confidence activity data and LE values for cliff partners were determined. Surprisingly, a significant increase in LE was generally detected for highly potent cliff partners compared to their lowly potent counterparts, regardless of the compound classes and their targets. Hence, ACs reveal chemical modifications that determine SARs and improve LE. These findings further increase the attractiveness of AC information for compound optimization and development.
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Affiliation(s)
- Antonio de la Vega de León
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, 53113, Bonn, Germany
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Mohammadi MK, Firuzi O, Khoshneviszadeh M, Razzaghi-Asl N, Sepehri S, Miri R. Novel 9-(alkylthio)-Acenaphtho[1,2-e]-1,2,4-triazine derivatives: synthesis, cytotoxic activity and molecular docking studies on B-cell lymphoma 2 (Bcl-2). ACTA ACUST UNITED AC 2014; 22:2. [PMID: 24393539 PMCID: PMC3917598 DOI: 10.1186/2008-2231-22-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/08/2013] [Indexed: 11/16/2022]
Abstract
Background and purpose of the study Acenaphtho derivatives have been reported as antitumor agents. Due to this fact and also with the aim of developing the chemistry of potentially bioactive heterocyclic compounds via efficient reactions, a facile procedure for the synthesis of 9-(alkylthio)-acenaphtho[1,2-e]-1,2,4-triazines via two step condensation of thiosemicarbazide and acenaphtylene-9,10-quinone to form acenaphtho[1,2-e]-1,2,4-triazine-9(8H)-thiones and subsequent reaction with benzyl chloride derivatives is reported. Methods 9-(alkylthio) acenaphtho[1,2-e]-1,2,4-triazines were synthesized via the reaction of acenaphtho-9,10-quinone with thiosemicarbazide, and then with the benzyl chloride derivatives. Cytotoxicity of some prepared compounds was assessed through MTT assay on three different human cancerous cell lines (HL-60, MCF7, and MOLT-4 cells). Molecular docking studies were performed via AutoDock4.2 software in order to confirm an apoptosis-inducing activity of acenaphtho scaffolds via the Bcl-2 protein. Results Excellent yields of the products, short reaction times and simple work-up are attractive features of this synthetic protocol. The evaluated compounds exhibited moderate to good cytotoxic activities. Docking results on the active site of B-cell lymphoma 2 (Bcl-2) supported the experimental biological data and agreed well with previous in silico data for commonly used anti-cancer drugs. Moreover; results were analyzed considering binding efficiency indices. Conclusions The outcomes of the present study may be helpful in future targeting of Bcl-2 with the aim of developing apoptosis-inducing agents.
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Affiliation(s)
| | | | | | | | | | - Ramin Miri
- Medicinal and Natural Products Chemistry Research Center, Shiraz, University of Medical Sciences, PO Box 3288-71345, Shiraz, Iran.
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Zhu T, Lee H, Lei H, Jones C, Patel K, Johnson ME, Hevener KE. Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol. J Chem Inf Model 2013; 53:560-72. [PMID: 23432621 PMCID: PMC3752004 DOI: 10.1021/ci300502h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have developed a rigorous computational screening protocol to identify novel fragment-like inhibitors of N(5)-CAIR mutase (PurE), a key enzyme involved in de novo purine synthesis that represents a novel target for the design of antibacterial agents. This computational screening protocol utilizes molecular docking, graphics processing unit (GPU)-accelerated molecular dynamics, and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) free energy estimations to investigate the binding modes and energies of fragments in the active sites of PurE. PurE is a functional octamer comprised of identical subunits. The octameric structure, with its eight active sites, provided a distinct advantage in these studies because, for a given simulation length, we were able to place eight separate fragment compounds in the active sites to increase the throughput of the MM/PBSA analysis. To validate this protocol, we have screened an in-house fragment library consisting of 352 compounds. The theoretical results were then compared with the results of two experimental fragment screens, Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) binding analyses. In these validation studies, the protocol was able to effectively identify the competitive binders that had been independently identified by experimental testing, suggesting the potential utility of this method for the identification of novel fragments for future development as PurE inhibitors.
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Affiliation(s)
- Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Hyun Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Hao Lei
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Christopher Jones
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S Ashland Ave., Suite 3100, Chicago, IL 60607-7173 (USA)
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Zhang Z, Song T, Li X, Wu Z, Feng Y, Xie F, Liu C, Qin J, Chen H. Novel soluble myeloid cell leukemia sequence 1 (Mcl-1) inhibitor (E,E)-2-(benzylaminocarbonyl)-3-styrylacrylonitrile (4g) developed using a fragment-based approach. Eur J Med Chem 2012; 59:141-9. [PMID: 23220642 DOI: 10.1016/j.ejmech.2012.10.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 02/08/2023]
Abstract
Based on a known nanomolar Bcl-2 homology domain 3 (BH3) mimetic 3-thiomorpholin-8-oxo-8H-acenaphtho[1,2-b] pyrrole-9-carbonitrile (S1, MW: 331), we applied a fragment-based approach to obtain BH3 mimetics with improved affinity and improved solubility in a water-ethanol (9:1) cosolvent. After the deconstruction of 1 (S1), we obtained fragment cyanoacetamide (4), which was determined to be a ligand efficiency (LE) hot part. After a rational optimization through fragment evolution beginning with fragment 4, a smaller Mcl-1 inhibitor (E,E)-2-(benzylaminocarbonyl)-3-styrylacrylonitrile (4g, MW: 288) with a 6-fold increase in affinity compared to 1 was obtained, as predicted by our optimization curve and identified by Mcl-1 protein nuclear magnetic resonance (NMR).
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Affiliation(s)
- Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, No. 2, Linggong Road, Dalian 116012, People's Republic of China.
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Khan MNA, Suzuki T, Miyata N. An overview of phenylcyclopropylamine derivatives: biochemical and biological significance and recent developments. Med Res Rev 2012; 33:873-910. [PMID: 22893613 DOI: 10.1002/med.21269] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
trans-2-Phencylcyclopropylamine (2-PCPA), a potent, clinically used antidepressant, affects monoamine neurotransmitter levels by inhibiting the main metabolizing enzymes, monoamine oxidases (MAOs). However, the antidepressant action of this compound was not fully explained by its effects on MAOs due to its wide variety of biological effects. 2-PCPA also affects depression-associated pathophysiological pathways, and linked with increased levels of trace amines in brain, upregulation of GABAB receptors (where GABA is gamma amino butyric acid), modulation of phospholipid metabolism, and interference with various cytochrome P450 (CYP) enzymes. Consequently, despite its adverse effects and limited clinical applicability, 2-PCPA has attracted interest as a structural scaffold for the development of mechanism-based inhibitors of various enzymes, including lysine-specific demethylase 1 (LSD1), which is a possible target for cancer chemotherapy. In the recent years, many reports have appeared in the literature based on 2-PCPA scaffold and their potential medicinal implications. This review mainly focuses on the medicinal chemistry aspects including drug design, structure-activity relationships (SAR), biological and biochemical properties, and mechanism of actions of 2-PCPA and its derivatives. Furthermore, we also highlight recent advance in this area and discuss their future applications for beneficial therapeutic effects.
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van Westen GJP, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HWT, Bender A. Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data. J Med Chem 2012; 55:7010-20. [PMID: 22827545 DOI: 10.1021/jm3003069] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The four subtypes of adenosine receptors form relevant drug targets in the treatment of, e.g., diabetes and Parkinson's disease. In the present study, we aimed at finding novel small molecule ligands for these receptors using virtual screening approaches based on proteochemometric (PCM) modeling. We combined bioactivity data from all human and rat receptors in order to widen available chemical space. After training and validating a proteochemometric model on this combined data set (Q(2) of 0.73, RMSE of 0.61), we virtually screened a vendor database of 100910 compounds. Of 54 compounds purchased, six novel high affinity adenosine receptor ligands were confirmed experimentally, one of which displayed an affinity of 7 nM on the human adenosine A(1) receptor. We conclude that the combination of rat and human data performs better than human data only. Furthermore, we conclude that proteochemometric modeling is an efficient method to quickly screen for novel bioactive compounds.
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Affiliation(s)
- Gerard J P van Westen
- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Chatterjee AK, Yeung BKS. Back to the future: lessons learned in modern target-based and whole-cell lead optimization of antimalarials. Curr Top Med Chem 2012; 12:473-83. [PMID: 22242845 PMCID: PMC3355380 DOI: 10.2174/156802612799362977] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/09/2011] [Accepted: 11/17/2011] [Indexed: 11/22/2022]
Abstract
Antimalarial drug discovery has historically benefited from the whole-cell (phenotypic) screening approach to identify lead molecules in the search for new drugs. However over the past two decades there has been a shift in the pharmaceutical industry to move away from whole-cell screening to target-based approaches. As part of a Wellcome Trust and Medicines for Malaria Venture (MMV) funded consortium to discover new blood-stage antimalarials, we used both approaches to identify new antimalarial chemotypes, two of which have progressed beyond the lead optimization phase and display excellent in vivo efficacy in mice. These two advanced series were identified through a cell-based optimization devoid of target information and in this review we summarize the advantages of this approach versus a target-based optimization. Although the each lead optimization required slightly different medicinal chemistry strategies, we observed some common issues across the different the scaffolds which could be applied to other cell based lead optimization programs.
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Affiliation(s)
- Arnab K Chatterjee
- Genomics Institute, Novartis Research Foundation, San Diego, CA 92121, USA.
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Shen HC, Hammock BD. Discovery of inhibitors of soluble epoxide hydrolase: a target with multiple potential therapeutic indications. J Med Chem 2012; 55:1789-808. [PMID: 22168898 PMCID: PMC3420824 DOI: 10.1021/jm201468j] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hong C. Shen
- RY800-C114, Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ07065, 609-716-9647
| | - Bruce D. Hammock
- Department of Entomology &Cancer Center, University of California, Davis, CA 95616 USA, 530-752-7519
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Design and combinatorial synthesis of a novel kinase-focused library using click chemistry-based fragment assembly. Bioorg Med Chem Lett 2011; 22:591-6. [PMID: 22104147 DOI: 10.1016/j.bmcl.2011.10.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/02/2011] [Accepted: 10/22/2011] [Indexed: 11/24/2022]
Abstract
Fragment-based lead discovery is a new approach for lead generation that has emerged in the past decade. Because the initial fragments identified in the fragment screening typically show weak binding affinity, an intensive medicinal chemistry effort would be required to grow initial fragments into a potential lead compound. Here we demonstrate a kinase focused evolved fragment (KFEF) library, constructed by click chemistry-based fragment assembly, that is a valuable source of kinase inhibitors. This combinatorial assembly of two fragments, kinase-privileged alkyne fragments and diversified azide fragments, by two cycloaddition reactions shows a unique potential for the one-step synthesis of structurally diverse evolved fragments. The screening of this triazole-based KFEF library allowed the rapid identification of potent lead candidates for FLT3 and GSK3β kinase.
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Meanwell NA. Improving Drug Candidates by Design: A Focus on Physicochemical Properties As a Means of Improving Compound Disposition and Safety. Chem Res Toxicol 2011; 24:1420-56. [DOI: 10.1021/tx200211v] [Citation(s) in RCA: 373] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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