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Medvedev KE, Schaeffer RD, Grishin NV. DrugDomain: The evolutionary context of drugs and small molecules bound to domains. Protein Sci 2024; 33:e5116. [PMID: 38979784 PMCID: PMC11231930 DOI: 10.1002/pro.5116] [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: 03/22/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity. Therefore, many drugs available on the market today are small molecules (72% of all approved drugs in the last 5 years). Proteins are composed of one or more domains: evolutionary units that convey function or fitness either singly or in concert with others. Understanding which domain(s) of the target protein binds to a drug can lead to additional opportunities for discovering novel targets. The evolutionary classification of protein domains (ECOD) classifies domains into an evolutionary hierarchy that focuses on distant homology. Previously, no structure-based protein domain classification existed that included information about both the interaction between small molecules or drugs and the structural domains of a target protein. This data is especially important for multidomain proteins and large complexes. Here, we present the DrugDomain database that reports the interaction between ECOD of human target proteins and DrugBank molecules and drugs. The pilot version of DrugDomain describes the interaction of 5160 DrugBank molecules associated with 2573 human proteins. It describes domains for all experimentally determined structures of these proteins and incorporates AlphaFold models when such structures are unavailable. The DrugDomain database is available online: http://prodata.swmed.edu/DrugDomain/.
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Affiliation(s)
- Kirill E. Medvedev
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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Identification of potential inhibitors for Hematopoietic Prostaglandin D2 synthase: Computational modeling and molecular dynamics simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The mercapturic acid pathway is a major route for the biotransformation of xenobiotic and endobiotic electrophilic compounds and their metabolites. Mercapturic acids (N-acetyl-l-cysteine S-conjugates) are formed by the sequential action of the glutathione transferases, γ-glutamyltransferases, dipeptidases, and cysteine S-conjugate N-acetyltransferase to yield glutathione S-conjugates, l-cysteinylglycine S-conjugates, l-cysteine S-conjugates, and mercapturic acids; these metabolites constitute a "mercapturomic" profile. Aminoacylases catalyze the hydrolysis of mercapturic acids to form cysteine S-conjugates. Several renal transport systems facilitate the urinary elimination of mercapturic acids; urinary mercapturic acids may serve as biomarkers for exposure to chemicals. Although mercapturic acid formation and elimination is a detoxication reaction, l-cysteine S-conjugates may undergo bioactivation by cysteine S-conjugate β-lyase. Moreover, some l-cysteine S-conjugates, particularly l-cysteinyl-leukotrienes, exert significant pathophysiological effects. Finally, some enzymes of the mercapturic acid pathway are described as the so-called "moonlighting proteins," catalytic proteins that exert multiple biochemical or biophysical functions apart from catalysis.
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Affiliation(s)
- Patrick E Hanna
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
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Meleza C, Thomasson B, Ramachandran C, O'Neill JW, Michelsen K, Lo MC. Development of a scintillation proximity binding assay for high-throughput screening of hematopoietic prostaglandin D2 synthase. Anal Biochem 2016; 511:17-23. [PMID: 27485270 DOI: 10.1016/j.ab.2016.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 01/22/2023]
Abstract
Prostaglandin D2 synthase (PGDS) catalyzes the isomerization of prostaglandin H2 (PGH2) to prostaglandin D2 (PGD2). PGD2 produced by hematopoietic prostaglandin D2 synthase (H-PGDS) in mast cells and Th2 cells is proposed to be a mediator of allergic and inflammatory responses. Consequently, inhibitors of H-PGDS represent potential therapeutic agents for the treatment of inflammatory diseases such as asthma. Due to the instability of the PGDS substrate PGH2, an in-vitro enzymatic assay is not feasible for large-scale screening of H-PGDS inhibitors. Herein, we report the development of a competition binding assay amenable to high-throughput screening (HTS) in a scintillation proximity assay (SPA) format. This assay was used to screen an in-house compound library of approximately 280,000 compounds for novel H-PGDS inhibitors. The hit rate of the H-PGDS primary screen was found to be 4%. This high hit rate suggests that the active site of H-PGDS can accommodate a large diversity of chemical scaffolds. For hit prioritization, these initial hits were rescreened at a lower concentration in SPA and tested in the LAD2 cell assay. 116 compounds were active in both assays with IC50s ranging from 6 to 807 nM in SPA and 82 nM to 10 μM in the LAD2 cell assay.
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Affiliation(s)
- Cesar Meleza
- Discovery Technologies, Amgen Inc., South San Francisco, CA 94080, USA
| | | | | | | | - Klaus Michelsen
- Discovery Attribute Sciences, Amgen Inc., Cambridge, MA 02141, USA
| | - Mei-Chu Lo
- Discovery Technologies, Amgen Inc., South San Francisco, CA 94080, USA.
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Gweshelo D, Muswe R, Mukanganyama S. In vivo and in vitro inhibition of rat liver glutathione transferases activity by extracts from Combretum zeyheri (Combretaceae) and Parinari curatellifolia (Chrysobalanaceae). Altern Ther Health Med 2016; 16:238. [PMID: 27457758 PMCID: PMC4960700 DOI: 10.1186/s12906-016-1235-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023]
Abstract
Background Parinari curatellifolia and Combretum zeyheri are medicinal plants used in Zimbabwe and other Southern African countries for stomach ailments, fever, body aches, wound healing, cancer and tuberculosis. Glutathione transferases (GSTs) are mammalian enzymes that play a significant role in the detoxification and metabolism of many xenobiotic and endogenous compounds and as such can interact with many exogenous compounds including herbal medicines. The effects of Parinari curatellifolia and Combretum zeyheri leaf extracts on glutathione transferases of male Sprague–Dawley rats were investigated in vivo and in vitro after oral administration of either leaf ethanol or water extracts of each plant. Methods For Parinari curatellifolia, 18 male Sprague-Dawley rats were administered with 0, 500 and 1000 mg/kg body weight of the leaf extracts in corn oil or saline. Animals were sacrificed after 96 h and the kidney and liver samples were removed and used to prepare the cytosolic fractions. GST activity was determined using 1-chloro-2, 4-dinitrobezene. For Combretum zeyheri, twenty four male Sprague–Dawley rats were randomly divided into two groups. These two groups were further divided into three groups of four animals each. They were given either the aqueous or ethanol extract at doses of C. zeyheri at 0, 50 mg/kg body weight and 200 mg/kg body weight. The extracts were administered orally by oral gavage for four consecutive days and the rats were sacrificed by cervical dislocation on the fifth day. Results In animals administered with C. zeyheri, GST activity was significantly increased by the 200 mg/kg aqueous extract in the kidneys and livers in vivo whilst the ethanolic extract at 200 mg/kg decreased enzyme activity significantly both organs. Both the ethanol and aqueous extracts inhibited GST activity in vitro with the ethanol extract being more potent inhibitor than ethacrynic acid, a standard GST inhibitor. The increased GST activity in vivo and versus inhibition in vitro suggests that metabolites may be responsible for the effects observed in vivo. For P. curatellifolia, a dose-dependent decrease in GST activity was observed in vivo for the animals given the aqueous extract but no changes were observed with the ethanol extract. There was a concentration-dependent inhibition of cytosolic GSTs when P. curatellifolia leaf extracts in vitro. The ethanol extract of P. curatellifolia exhibited GST-inhibitory activity in the liver with an IC50 value of 12 μg/mL and for ethacrynic acid, the IC50 was found to be 10 μg/mL. This showed that this extract was a potent inhibitor of GSTs in vitro. Conclusions C. zeyheri had an inductive effect on GST activity when administered in aqueous solution but inhibited GST in vitro whilst P. curatellifolia inhibited GST activity in vivo. Induction of GSTs would be cytoprotective against the toxic effects electrophilic chemicals. Since GSTs are responsible for the synthesis of prostaglandins, the inhibition of GST activity of by these two plants in vivo maybe one of the reasons that makes the plants important for use in the treatment pain and fever in ethnopharmacology.
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Buonfiglio R, Engkvist O, Várkonyi P, Henz A, Vikeved E, Backlund A, Kogej T. Investigating Pharmacological Similarity by Charting Chemical Space. J Chem Inf Model 2015; 55:2375-90. [DOI: 10.1021/acs.jcim.5b00375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Rosa Buonfiglio
- Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Ola Engkvist
- Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Péter Várkonyi
- Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Astrid Henz
- Division
of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC box 574, S-751 23 Uppsala, Sweden
| | - Elisabet Vikeved
- Division
of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC box 574, S-751 23 Uppsala, Sweden
| | - Anders Backlund
- Division
of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC box 574, S-751 23 Uppsala, Sweden
| | - Thierry Kogej
- Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
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Chimponda T, Mukanganyama S. Evaluation of Selected Zimbabwean Plant Extracts as Inhibitors of Hematopoietic Prostaglandin D2Synthase. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/10496475.2014.954073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Human cytosolic glutathione transferases: structure, function, and drug discovery. Trends Pharmacol Sci 2012; 33:656-68. [DOI: 10.1016/j.tips.2012.09.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/19/2022]
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Hematopoietic prostaglandin D synthase inhibitors. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:97-133. [PMID: 22520473 DOI: 10.1016/b978-0-12-396493-9.00004-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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PGD synthase and PGD2 in immune resposne. Mediators Inflamm 2012; 2012:503128. [PMID: 22791937 PMCID: PMC3389719 DOI: 10.1155/2012/503128] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 11/17/2022] Open
Abstract
PGD2 is formed from arachidonic acid by successive enzyme reactions: oxygenation of arachidonic acid to PGH2, a common precursor of various prostanoids, catalyzed by cyclooxygenase, and isomerization of PGH2 to PGD2 by PGD synthases (PGDSs). PGD2 can be either pro- or anti-inflammatory depending on disease process and etiology. The anti-inflammatory and immunomodulatory attributes of PGDS/PGD2 provide opportunities for development of novel therapeutic approaches for resistant infections and refractory inflammatory diseases. This paper highlights the role of PGD synthases and PGD2 in immune inflammatory response.
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Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): A tale of two waters. Bioorg Med Chem Lett 2012; 22:3795-9. [DOI: 10.1016/j.bmcl.2012.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/29/2012] [Accepted: 04/02/2012] [Indexed: 12/31/2022]
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Bhakta NR, Woodruff PG. Human asthma phenotypes: from the clinic, to cytokines, and back again. Immunol Rev 2011; 242:220-32. [PMID: 21682748 DOI: 10.1111/j.1600-065x.2011.01032.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A large body of experimental evidence supports the hypothesis that T-helper 2 (Th2) cytokines orchestrate allergic airway inflammation in animal models. However, human asthma is heterogeneous with respect to clinical features, cellular sources of inflammation, and response to common therapies. This disease heterogeneity has been investigated using sputum cytology as well as unbiased clustering approaches using cellular and clinical data. Important differences in cytokine-driven inflammation may underlie this heterogeneity, and studies in human subjects with asthma have begun to elucidate these molecular differences. This molecular heterogeneity may be assessed by existing biomarkers (induced sputum evaluation or exhaled nitric oxide testing) or may require novel biomarkers. Effective testing and application of emerging therapies that target Th2 cytokines will depend on accurate and easily obtained biomarkers of this molecular heterogeneity in asthma. Furthermore, whether other non-Th2 cytokine pathways underlie airway inflammation in specific subsets of patients with asthma is an unresolved question and an important goal of future research using both mouse models and human studies.
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Affiliation(s)
- Nirav R Bhakta
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
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Abstract
The glutathione transferases (GSTs) are one of the most important families of detoxifying enzymes in nature. The classic activity of the GSTs is conjugation of compounds with electrophilic centers to the tripeptide glutathione (GSH), but many other activities are now associated with GSTs, including steroid and leukotriene biosynthesis, peroxide degradation, double-bond cis-trans isomerization, dehydroascorbate reduction, Michael addition, and noncatalytic "ligandin" activity (ligand binding and transport). Since the first GST structure was determined in 1991, there has been an explosion in structural data across GSTs of all three families: the cytosolic GSTs, the mitochondrial GSTs, and the membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG family). In this review, the major insights into GST structure and function will be discussed.
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Affiliation(s)
- Aaron Oakley
- School of Chemistry, University of Wollongong, Wollongong, Australia.
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Christ AN, Labzin L, Bourne GT, Fukunishi H, Weber JE, Sweet MJ, Smythe ML, Flanagan JU. Development and characterization of new inhibitors of the human and mouse hematopoietic prostaglandin D(2) synthases. J Med Chem 2010; 53:5536-48. [PMID: 20684598 DOI: 10.1021/jm100194a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The hematopoietic prostaglandin D(2) synthase has a proinflammatory effect in a range of diseases, including allergic asthma, where its product prostaglandin D(2) (PGD(2)) has a role in regulating many of the hallmark disease characteristics. Here we describe the development and characterization of a novel series of hematopoietic prostaglandin D(2) synthase inhibitors with potency similar to that of known inhibitors. Compounds N-benzhydryl-5-(3-hydroxyphenyl)thiophene-2-carboxamide (compound 8) and N-(1-amino-1-oxo-3-phenylpropan-2-yl)-6-(thiophen-2-yl)nicotinamide (compound 34) demonstrated low micromolar potency in the inhibition of the purified enzyme, while only 34 reduced Toll-like receptor (TLR) inducible PGD(2) production in both mouse primary bone marrow-derived macrophages and the human megakaryocytic cell line MEG-01S. Importantly, 34 demonstrated a greater selectivity for inhibition of PGD(2) synthesis versus other eicosanoids that lie downstream of PGH(2) (PGE(2) and markers of prostacyclin (6-keto PGF(1alpha)) and thromboxane (TXB(2))) when compared to the known inhibitors HQL-79 (compound 1) and 2-phenyl-5-(1H-pyrazol-3-yl)thiazole (compound 2). Compound 34 therefore represents a selective hematopoietic prostaglandin D(2) synthase inhibitor.
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Affiliation(s)
- Angelika N Christ
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
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