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Leyden MR, Gowen B, Gonzalez-Romero R, Eirin-Lopez JM, Kim BH, Hayashi F, McCartney J, Zhang PC, Kubo-Irie M, Shabanowitz J, Hunt DF, Ferree P, Kasinsky H, Ausió J. Protamines and the sperm nuclear basic proteins Pandora's Box of insects. Biochem Cell Biol 2024; 102:238-251. [PMID: 38408323 DOI: 10.1139/bcb-2023-0363] [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] [Indexed: 02/28/2024] Open
Abstract
Insects are the largest group of animals when it comes to the number and diversity of species. Yet, with the exception of Drosophila, no information is currently available on the primary structure of their sperm nuclear basic proteins (SNBPs). This paper represents the first attempt in this regard and provides information about six species of Neoptera: Poecillimon thessalicus, Graptosaltria nigrofuscata, Apis mellifera, Nasonia vitripennis, Parachauliodes continentalis, and Tribolium castaneum. The SNBPs of these species were characterized by acetic acid urea gel electrophoresis (AU-PAGE) and high-performance liquid chromatography fractionated. Protein sequencing was obtained using a combination of mass spectrometry sequencing, Edman N-terminal degradation sequencing and genome mining. While the SNBPs of several of these species exhibit a canonical arginine-rich protamine nature, a few of them exhibit a protamine-like composition. They appear to be the products of extensive cleavage processing from a precursor protein which are sometimes further processed by other post-translational modifications that are likely involved in the chromatin transitions observed during spermiogenesis in these organisms.
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Affiliation(s)
- Melissa R Leyden
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Brent Gowen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Rodrigo Gonzalez-Romero
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jose Maria Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, USA
- Florida International University, Miami, FL, USA
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Fumio Hayashi
- Department of Biology, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | - Jay McCartney
- Institute of Natural Sciences, Massey University, Palmerston North, Manawatu, New Zealand
| | - Patrick C Zhang
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Miyoko Kubo-Irie
- Biological Laboratory, The Open University of Japan, Wakaba, Mihama-ku, Chiba, 261-8506, Japan
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
| | - Patrick Ferree
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Harold Kasinsky
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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2
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Chen D, Chen Q, Qin X, Tong P, Peng L, Zhang T, Xia C. Development and evolution of human glutaminyl cyclase inhibitors (QCIs): an alternative promising approach for disease-modifying treatment of Alzheimer's disease. Front Aging Neurosci 2023; 15:1209863. [PMID: 37600512 PMCID: PMC10435661 DOI: 10.3389/fnagi.2023.1209863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Human glutaminyl cyclase (hQC) is drawing considerable attention and emerging as a potential druggable target for Alzheimer's disease (AD) due to its close involvement in the pathology of AD via the post-translational pyroglutamate modification of amyloid-β. A recent phase 2a study has shown promising early evidence of efficacy for AD with a competitive benzimidazole-based QC inhibitor, PQ912, which also demonstrated favorable safety profiles. This finding has sparked new hope for the treatment of AD. In this review, we briefly summarize the discovery and evolution of hQC inhibitors, with a particular interest in classic Zinc binding group (ZBG)-containing chemicals reported in recent years. Additionally, we highlight several high-potency inhibitors and discuss new trends and challenges in the development of QC inhibitors as an alternative and promising disease-modifying therapy for AD.
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Affiliation(s)
- Daoyuan Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Qingxiu Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Xiaofei Qin
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Peipei Tong
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Liping Peng
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Institute of Basic Medicine, Fujian Medical University, Fuzhou, China
| | - Chunli Xia
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
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3
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Oaks Z, Patel A, Huang N, Choudhary G, Winans T, Faludi T, Krakko D, Duarte M, Lewis J, Beckford M, Blair S, Kelly R, Landas SK, Middleton FA, Asara JM, Chung SK, Fernandez DR, Banki K, Perl A. Cytosolic aldose metabolism contributes to progression from cirrhosis to hepatocarcinogenesis. Nat Metab 2023; 5:41-60. [PMID: 36658399 PMCID: PMC9892301 DOI: 10.1038/s42255-022-00711-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2022] [Indexed: 01/21/2023]
Abstract
Oxidative stress modulates carcinogenesis in the liver; however, direct evidence for metabolic control of oxidative stress during pathogenesis, particularly, of progression from cirrhosis to hepatocellular carcinoma (HCC), has been lacking. Deficiency of transaldolase (TAL), a rate-limiting enzyme of the non-oxidative branch of the pentose phosphate pathway (PPP), restricts growth and predisposes to cirrhosis and HCC in mice and humans. Here, we show that mitochondrial oxidative stress and progression from cirrhosis to HCC and acetaminophen-induced liver necrosis are critically dependent on NADPH depletion and polyol buildup by aldose reductase (AR), while this enzyme protects from carbon trapping in the PPP and growth restriction in TAL deficiency. Both TAL and AR are confined to the cytosol; however, their inactivation distorts mitochondrial redox homeostasis in opposite directions. The results suggest that AR acts as a rheostat of carbon recycling and NADPH output of the PPP with broad implications for disease progression from cirrhosis to HCC.
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Affiliation(s)
- Z Oaks
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - A Patel
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - N Huang
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - G Choudhary
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - T Winans
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - T Faludi
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - D Krakko
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - M Duarte
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - J Lewis
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - M Beckford
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - S Blair
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - R Kelly
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - S K Landas
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - F A Middleton
- Departments of Neuroscience, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - J M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - S K Chung
- Faculty of Medicine, Macau University of Science and Technology, Taipa, China
| | - D R Fernandez
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - K Banki
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, USA
| | - A Perl
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, USA.
- Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, USA.
- Departments of Microbiology and Immunology, State University of New York, Norton College of Medicine, Syracuse, NY, USA.
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Functional Analysis of the GPI Transamidase Complex by Screening for Amino Acid Mutations in Each Subunit. Molecules 2021; 26:molecules26185462. [PMID: 34576938 PMCID: PMC8465894 DOI: 10.3390/molecules26185462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/20/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) anchor modification is a posttranslational modification of proteins that has been conserved in eukaryotes. The biosynthesis and transfer of GPI to proteins are carried out in the endoplasmic reticulum. Attachment of GPI to proteins is mediated by the GPI-transamidase (GPI-TA) complex, which recognizes and cleaves the C-terminal GPI attachment signal of precursor proteins. Then, GPI is transferred to the newly exposed C-terminus of the proteins. GPI-TA consists of five subunits: PIGK, GPAA1, PIGT, PIGS, and PIGU, and the absence of any subunit leads to the loss of activity. Here, we analyzed functionally important residues of the five subunits of GPI-TA by comparing conserved sequences among homologous proteins. In addition, we optimized the purification method for analyzing the structure of GPI-TA. Using purified GPI-TA, preliminary single particle images were obtained. Our results provide guidance for the structural and functional analysis of GPI-TA.
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Xu C, Wang YN, Wu H. Glutaminyl Cyclase, Diseases, and Development of Glutaminyl Cyclase Inhibitors. J Med Chem 2021; 64:6549-6565. [PMID: 34000808 DOI: 10.1021/acs.jmedchem.1c00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyroglutamate (pE) modification, catalyzed mainly by glutaminyl cyclase (QC), is prevalent throughout nature and is particularly important in mammals including humans for the maturation of hormones, peptides, and proteins. In humans, the upregulation of QC is involved in multiple diseases and conditions including Alzheimer's disease, Huntington's disease, melanomas, thyroid carcinomas, accelerated atherosclerosis, septic arthritics, etc. This upregulation catalyzes the generation of modified mediators such as pE-amyloid beta (Aß) and pE-chemokine ligand 2 (CCL2) peptides. Not surprisingly, QC has emerged as a reasonable target for the development of therapeutics to combat these diseases and conditions. In this manuscript the deleterious effects of upregulated QC resulting in disease manifestation are reviewed, along with progress on the development of QC inhibitors.
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Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yi-Nan Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
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A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. J Mol Biol 2021; 433:166960. [PMID: 33774034 DOI: 10.1016/j.jmb.2021.166960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/21/2021] [Accepted: 03/15/2021] [Indexed: 11/21/2022]
Abstract
Proteins with sequence or structure similar to those of di-Zn exopeptidases are usually classified as the M28-family enzymes, including the mammalian-type glutaminyl cyclases (QCs). QC catalyzes protein N-terminal pyroglutamate formation, a posttranslational modification important under many physiological and pathological conditions, and is a drug target for treating neurodegenerative diseases, cancers and inflammatory disorders. Without functional characterization, mammalian QCs and their orthologs remain indistinguishable at the sequence and structure levels from other M28-family proteins, leading to few reported QCs. Here, we show that a low-barrier carboxylic-acid hydrogen-bond network (CAHBN) is required for QC activity and discriminates QCs from M28-family peptidases. We demonstrate that the CAHBN-containing M28 peptidases deposited in the PDB are indeed QCs. Our analyses identify several thousands of QCs from the three domains of life, and we enzymatically and structurally characterize several. For the first time, the interplay between a CAHBN and the binuclear metal-binding center of mammalian QCs is made clear. We found that the presence or absence of CAHBN is a key discriminator for the formation of either the mono-Zn QCs or the di-Zn exopeptidases. Our study helps explain the possible roles of QCs in life.
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Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT. Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J Biol Chem 2021; 296:100263. [PMID: 33837744 PMCID: PMC7948796 DOI: 10.1016/j.jbc.2021.100263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
The development of a targeted therapy would significantly improve the treatment of periodontitis and its associated diseases including Alzheimer’s disease, rheumatoid arthritis, and cardiovascular diseases. Glutaminyl cyclases (QCs) from the oral pathogens Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia represent attractive target enzymes for small-molecule inhibitor development, as their action is likely to stabilize essential periplasmic and outer membrane proteins by N-terminal pyroglutamination. In contrast to other microbial QCs that utilize the so-called type I enzymes, these oral pathogens possess sequences corresponding to type II QCs, observed hitherto only in animals. However, whether differences between these bacteroidal QCs and animal QCs are sufficient to enable development of selective inhibitors is not clear. To learn more, we recombinantly expressed all three QCs. They exhibit comparable catalytic efficiencies and are inhibited by metal chelators. Crystal structures of the enzymes from P. gingivalis (PgQC) and T. forsythia (TfQC) reveal a tertiary structure composed of an eight-stranded β-sheet surrounded by seven α-helices, typical of animal type II QCs. In each case, an active site Zn ion is tetrahedrally coordinated by conserved residues. Nevertheless, significant differences to mammalian enzymes are found around the active site of the bacteroidal enzymes. Application of a PgQC-selective inhibitor described here for the first time results in growth inhibition of two P. gingivalis clinical isolates in a dose-dependent manner. The insights gained by these studies will assist in the development of highly specific small-molecule bacteroidal QC inhibitors, paving the way for alternative therapies against periodontitis and associated diseases.
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Affiliation(s)
- Nadine Taudte
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany
| | - Miriam Linnert
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Jens-Ulrich Rahfeld
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.
| | - Anke Piechotta
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Mirko Buchholz
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany; Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Petr Kolenko
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - John A Houston
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - Florian Veillard
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sigrun Eick
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stephan Schilling
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany; Angewandte Biowissenschaften und Prozesstechnik, Hochschule Anhalt, Köthen, Germany
| | - Hans-Ulrich Demuth
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Milton T Stubbs
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany; ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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8
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Su CTT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct 2020; 15:14. [PMID: 32993792 PMCID: PMC7522609 DOI: 10.1186/s13062-020-00266-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defined sequence signal. Its five subunits are very hydrophobic; thus, solubility, heterologous expression and complex reconstruction are difficult. Therefore, theoretical approaches are currently the main source of insight into details of 3D structure and of the catalytic process. Results In this work, we generated model 3D structures of the lumenal domain of human GPAA1, the M28-type metallo-peptide-synthetase subunit of the transamidase, including zinc ion and model substrate positions. In comparative molecular dynamics (MD) simulations of M28-type structures and our GPAA1 models, we estimated the metal ion binding energies with evolutionary conserved amino acid residues in the catalytic cleft. We find that canonical zinc binding sites 2 and 3 are strongest binders for Zn1 and, where a second zinc is available, sites 2 and 4 for Zn2. Zinc interaction of site 5 with Zn1 enhances upon substrate binding in structures with only one zinc. Whereas a previously studied glutaminyl cyclase structure, the best known homologue to GPAA1, binds only one zinc ion at the catalytic site, GPAA1 can sterically accommodate two. The M28-type metallopeptidases segregate into two independent branches with regard to one/two zinc ion binding modality in a phylogenetic tree where the GPAA1 family is closer to the joint origin of both groups. For GPAA1 models, MD studies revealed two large loops (flaps) surrounding the active site being involved in an anti-correlated, breathing-like dynamics. Conclusions In the light of combined sequence-analytic and phylogenetic arguments as well as 3D structural modelling results, GPAA1 is most likely a single zinc ion metallopeptidase. Two large flaps environ the catalytic site restricting access to large substrates. Reviewers This article was reviewed by Thomas Dandekar (MD) and Michael Gromiha.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Lin W, Zheng X, Fang D, Zhou S, Wu W, Zheng K. Identifying hQC Inhibitors of Alzheimer's Disease by Effective Customized Pharmacophore-Based Virtual Screening, Molecular Dynamic Simulation, and Binding Free Energy Analysis. Appl Biochem Biotechnol 2018; 187:1173-1192. [PMID: 30187344 DOI: 10.1007/s12010-018-2780-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/06/2018] [Indexed: 01/14/2023]
Abstract
Human glutaminyl cyclase (hQC) appeared as a promising new target with its inhibitors attracted much attention for the treatment of Alzheimer's disease (AD) in recent years. But so far, only a few compounds have been reported as hQC inhibitors. To find novel and potent hQC inhibitors, a high-specificity ZBG (zinc-binding groups)-based pharmacophore model comprising customized ZBG feature was first generated using HipHop algorithm in Discovery Studio software for screening out hQC inhibitors from the SPECS database. After purification by docking studies and drug-like ADMET properties filters, four potential hit compounds were retrieved. Subsequently, these hit compounds were subjected to 30-ns molecular dynamic (MD) simulations to explore their binding modes at the active side of hQC. MD simulations demonstrated that these hit compounds formed a chelating interaction with the zinc ion, which was consistent with the finding that the electrostatic interaction was the major driving force for binding to hQC confirmed with MMPBSA energy decomposition. Higher binding affinities of these compounds were also verified by the binding free energy calculations comparing with the references. Thus, these identified compounds might be potential hQC candidates and could be used for further investigation.
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Affiliation(s)
- Weicong Lin
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaojie Zheng
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Danqing Fang
- Department of Cardiothoracic Surgery, Affiliated Second Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Shengfu Zhou
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Wenjuan Wu
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Kangcheng Zheng
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, China
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Eisenhaber B, Eisenhaber S, Kwang TY, Grüber G, Eisenhaber F. Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine. Cell Cycle 2014; 13:1912-7. [PMID: 24743167 PMCID: PMC4111754 DOI: 10.4161/cc.28761] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The transamidase subunit GAA1/GPAA1 is predicted to be the enzyme that catalyzes the attachment of the glycosylphosphatidyl (GPI) lipid anchor to the carbonyl intermediate of the substrate protein at the ω-site. Its ~300-amino acid residue lumenal domain is a M28 family metallo-peptide-synthetase with an α/β hydrolase fold, including a central 8-strand β-sheet and a single metal (most likely zinc) ion coordinated by 3 conserved polar residues. Phosphoethanolamine is used as an adaptor to make the non-peptide GPI lipid anchor look chemically similar to the N terminus of a peptide.
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Affiliation(s)
- Birgit Eisenhaber
- Bioinformatics Institute (BII); A*STAR; Singapore, Republic of Singapore
| | - Stephan Eisenhaber
- Department of Physical Chemistry; University of Vienna; Wien/Vienna, Republic of Austria
| | - Toh Yew Kwang
- Bioinformatics Institute (BII); A*STAR; Singapore, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute (BII); A*STAR; Singapore, Republic of Singapore; Nanyang Technological University; School of Biological Sciences; Singapore, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII); A*STAR; Singapore, Republic of Singapore; Department of Biological Sciences (DBS); National University of Singapore (NUS); Singapore, Republic of Singapore; School of Computer Engineering (SCE); Nanyang Technological University (NTU); Singapore, Republic of Singapore
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11
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Huang KF, Hsu HL, Karim S, Wang AHJ. Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:789-801. [PMID: 24598748 PMCID: PMC8494195 DOI: 10.1107/s1399004713033488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022]
Abstract
Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10-1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-sheet, resulting in an increased thermal stability. Is-QC contains ~0.5 stoichiometric zinc ions, which could be removed by 1 mM EDTA. Compared with the Zn-bound form, apo-Is-QC has a nearly identical active-site structure and stability, but unexpectedly possesses significantly increased QC activities towards both synthetic and physiological substrates. Enzyme-kinetic analysis revealed that apo-Is-QC has a stronger substrate-binding affinity, suggesting that bound zinc interferes with substrate binding during catalysis. The structures of Is-QC bound to the inhibitor PBD150 revealed similar binding modes to both forms of Is-QC, with the exception of the inhibitor imidazole ring, which is consistent with the comparable inhibition activities of the inhibitor towards both forms of Is-QC. These findings have implications for the design of new QC inhibitors.
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Affiliation(s)
- Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
| | - Hui-Ling Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
| | - Shahid Karim
- Department of Biological Sciences, The University of Southern Mississippi, 18 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
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Ramsbeck D, Buchholz M, Koch B, Böhme L, Hoffmann T, Demuth HU, Heiser U. Structure–Activity Relationships of Benzimidazole-Based Glutaminyl Cyclase Inhibitors Featuring a Heteroaryl Scaffold. J Med Chem 2013; 56:6613-25. [DOI: 10.1021/jm4001709] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Ramsbeck
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Mirko Buchholz
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Birgit Koch
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Livia Böhme
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Torsten Hoffmann
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Hans-Ulrich Demuth
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
| | - Ulrich Heiser
- Department
of Medicinal Chemistry, ‡Department of Enzymology §Department of Preclinical Pharmacology, Probiodrug AG, Weinbergweg 22, 06120
Halle, Germany
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13
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Kolenko P, Koch B, Rahfeld JU, Schilling S, Demuth HU, Stubbs MT. Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:358-61. [PMID: 23545638 PMCID: PMC3614157 DOI: 10.1107/s1744309113005575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/26/2013] [Indexed: 05/06/2024]
Abstract
The structure of ligand-free glutaminyl cyclase (QC) from Drosophila melanogaster (DmQC) has been determined in a novel crystal form. The protein crystallized in space group I4, with unit-cell parameters a = b = 122.3, c = 72.7 Å. The crystal diffracted to a resolution of 2 Å at the home source. The structure was solved by molecular replacement and was refined to an R factor of 0.169. DmQC exhibits a typical α/β-hydrolase fold. The electron density of three monosaccharides could be localized. The accessibility of the active site will facilitate structural studies of novel inhibitor-binding modes.
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Affiliation(s)
- Petr Kolenko
- Department of Physical Biochemistry, Institute of Biochemistry and Biotechnology, MLU, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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