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De Rose SA, Isupov MN, Worthy HL, Stracke C, Harmer NJ, Siebers B, Littlechild JA. Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus. Front Microbiol 2023; 14:1267570. [PMID: 38045033 PMCID: PMC10690619 DOI: 10.3389/fmicb.2023.1267570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 12/05/2023] Open
Abstract
The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as Methanothermus fervidus, Methanopyrus kandleri, and Methanothermobacter thermoautotrophicus. Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent SN2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.
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Affiliation(s)
- Simone A. De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Harley L. Worthy
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Christina Stracke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Nicholas J. Harmer
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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2
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Starnes HM, Jackson TW, Rock KD, Belcher SM. Quantitative Cross-Species Comparison of Serum Albumin Binding of Per- and Polyfluoroalkyl Substances from Five Structural Classes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566613. [PMID: 38014292 PMCID: PMC10680784 DOI: 10.1101/2023.11.10.566613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a class of over 8,000 chemicals that are persistent, bioaccumulative, and toxic to humans, livestock, and wildlife. Serum protein binding affinity is instrumental in understanding PFAS toxicity, yet experimental binding data is limited to only a few PFAS congeners. Previously, we demonstrated the usefulness of a high-throughput, in vitro differential scanning fluorimetry assay for determination of relative binding affinities of human serum albumin for 24 PFAS congeners from 6 chemical classes. In the current study, we used this differential scanning fluorimetry assay to comparatively examine differences in human, bovine, porcine, and rat serum albumin binding of 8 structurally informative PFAS congeners from 5 chemical classes. With the exception of the fluorotelomer alcohol 1H,1H,2H,2H-perfluorooctanol (6:2 FTOH), each PFAS congener bound by human serum albumin was also bound by bovine, porcine, and rat serum albumin. The critical role of the charged functional headgroup in albumin binding was supported by the inability of serum albumin of each species tested to bind 6:2 FTOH. Significant interspecies differences in serum albumin binding affinities were identified for each of the bound PFAS congeners. Relative to human albumin, perfluoroalkyl carboxylic and sulfonic acids were bound with greater affinity by porcine and rat serum albumin, and perfluoroalkyl ether congeners bound with lower affinity to porcine and bovine serum albumin. These comparative affinity data for PFAS binding by serum albumin from human, experimental model and livestock species reduce critical interspecies uncertainty and improve accuracy of predictive toxicity assessments for PFAS.
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Affiliation(s)
- Hannah M. Starnes
- Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus Box 7617, Raleigh, NC 27607, USA
| | - Thomas W. Jackson
- Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus Box 7617, Raleigh, NC 27607, USA
- Current address: Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Kylie D. Rock
- Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus Box 7617, Raleigh, NC 27607, USA
- Current address: Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Scott M. Belcher
- Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus Box 7617, Raleigh, NC 27607, USA
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3
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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4
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Ordonez-Rubiano SC, Maschinot CA, Wang S, Sood S, Baracaldo-Lancheros LF, Strohmier BP, McQuade AJ, Smith BC, Dykhuizen EC. Rational Design and Development of Selective BRD7 Bromodomain Inhibitors and Their Activity in Prostate Cancer. J Med Chem 2023; 66:11250-11270. [PMID: 37552884 PMCID: PMC10641717 DOI: 10.1021/acs.jmedchem.3c00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer. Bromodomain-containing protein 7 (BRD7) is implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease. Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a binding pocket exclusive to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two inhibitors with increased selectivity toward BRD7, 1-78 and 2-77, which bind with submicromolar affinity to the BRD7 BD. Our binding mode analyses indicate that these ligands occupy a uniquely accessible binding cleft in BRD7 and maintain key interactions with the asparagine and tyrosine residues critical for acetylated lysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.
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Affiliation(s)
- Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chad A Maschinot
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Luisa F Baracaldo-Lancheros
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Alexander J McQuade
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brian C Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, College of Pharmacy, Purdue University, 201 S University St., West Lafayette, Indiana 47907, United States
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5
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Premageetha GTR, Dhanabalan K, Bose S, Manjunath L, Joseph D, Paz A, Grandfield S, Nayak V, Bredeston LM, Abramson J, Ramaswamy S. Biochemical characterization of a GDP-mannose transporter from Chaetomium thermophilum. PLoS One 2023; 18:e0280975. [PMID: 37079572 PMCID: PMC10118193 DOI: 10.1371/journal.pone.0280975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
Nucleotide Sugar Transporters (NSTs) belong to the SLC35 family (human solute carrier) of membrane transport proteins and are crucial components of the glycosylation machinery. NSTs are localized in the ER and Golgi apparatus membranes, where they accumulate nucleotide sugars from the cytosol for subsequent polysaccharide biosynthesis. Loss of NST function impacts the glycosylation of cell surface molecules. Mutations in NSTs cause several developmental disorders, immune disorders, and increased susceptibility to infection. Atomic resolution structures of three NSTs have provided a blueprint for a detailed molecular interpretation of their biochemical properties. In this work, we have identified, cloned, and expressed 18 members of the SLC35 family from various eukaryotic organisms in Saccharomyces cerevisiae. Out of 18 clones, we determined Vrg4 from Chaetomium thermophilum (CtVrg4) is a GDP-mannose transporter with an enhanced melting point temperature (Tm) of 56.9°C, which increases with the addition of substrates, GMP and GDP-mannose. In addition, we report-for the first time-that the CtVrg4 shows an affinity to bind to phosphatidylinositol lipids.
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Affiliation(s)
- Gowtham Thambra Rajan Premageetha
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - KanagaVijayan Dhanabalan
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Lavanyaa Manjunath
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Deepthi Joseph
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Aviv Paz
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Samuel Grandfield
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Vinod Nayak
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Luis M. Bredeston
- Departamento de Química Biológica-IQUIFIB, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Ciudad Autónoma de Buenos Aires, Junín, Argentina
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Subramanian Ramaswamy
- Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
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6
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Grzela R, Piecyk K, Stankiewicz-Drogon A, Pietrow P, Lukaszewicz M, Kurpiejewski K, Darzynkiewicz E, Jankowska-Anyszka M. N2 modified dinucleotide cap analogs as a potent tool for mRNA engineering. RNA (NEW YORK, N.Y.) 2023; 29:200-216. [PMID: 36418172 PMCID: PMC9891257 DOI: 10.1261/rna.079460.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
mRNA-based vaccines are relatively new technologies that have been in the field of interest of research centers and pharmaceutical companies in recent years. Such therapeutics are an attractive alternative for DNA-based vaccines since they provide material that can be used with no risk of genomic integration. Additionally, mRNA can be quite easily engineered to introduce modifications for different applications or to modulate its properties, for example, to increase translational efficiency or stability, which is not available for DNA vectors. Here, we describe the use of N2 modified dinucleotide cap analogs as components of mRNA transcripts. The compounds obtained showed very promising biological properties while incorporated into mRNA. The presented N2-guanine modifications within the cap structure ensure proper attachment of the dinucleotide to the transcripts in the IVT reaction, guarantees their incorporation only in the correct orientation, and enables highly efficient translation of mRNA both in the in vitro translation system and in human HEK293 cells.
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Affiliation(s)
- Renata Grzela
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Karolina Piecyk
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Anna Stankiewicz-Drogon
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Paulina Pietrow
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
- Center of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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7
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Sanders J, Castiglione M, Shun T, Vollmer LL, Schurdak ME, Vogt A, Schwacha A. Validation of a high throughput screening assay to identify small molecules that target the eukaryotic replicative helicase. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:229-241. [PMID: 35058181 PMCID: PMC9196137 DOI: 10.1016/j.slasd.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mcm2-7 is the catalytic core of the eukaryotic replicative helicase, which together with CDC45 and the GINS complex unwind parental DNA to generate templates for DNA polymerase. Being a highly regulated and complex enzyme that operates via an incompletely understood multi-step mechanism, molecular probes of Mcm2-7 that interrogate specific mechanistic steps would be useful tools for research and potential future chemotherapy. Based upon a synthetic lethal approach, we previously developed a budding yeast multivariate cell-based high throughput screening (HTS) assay to identify putative Mcm inhibitors by their ability to specifically cause a growth defect in an mcm mutant relative to a wild-type strain[1]. Here, as proof of concept, we used this assay to screen a 1280-member compound library (LOPAC) for potential Mcm2-7 inhibitors. Primary screening and dose-dependent retesting identified twelve compounds from this library that specifically inhibited the growth of the Mcm mutant relative to the corresponding wild-type strain (0.9 % hit rate). Secondary assays were employed to rule out non-specific DNA damaging agents, establish direct protein-ligand interaction via biophysical methods, and verify in vivo DNA replication inhibition via fluorescence activated cell sorter analysis (FACS). We identified one agent (β-carboline-3-carboxylic acid N-methylamide, CMA) that physically bound to the purified Mcm2-7 complex (Kdapp119 µM), and at slightly higher concentrations specifically blocked S-phase cell cycle progression of the wild-type strain. In total, identification of Mcm2-7 as a CMA target validates our synthetic lethal HTS assay paradigm as a tool to identify chemical probes for the Mcm2-7 replicative helicase.
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Affiliation(s)
- Jordan Sanders
- The Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260
| | - Michael Castiglione
- Drug Discovery Institute, University of Pittsburgh Medical School, Pittsburgh PA 15260
| | - Tongying Shun
- Drug Discovery Institute, University of Pittsburgh Medical School, Pittsburgh PA 15260
| | - Laura L Vollmer
- Drug Discovery Institute, University of Pittsburgh Medical School, Pittsburgh PA 15260
| | - Mark E Schurdak
- Drug Discovery Institute, University of Pittsburgh Medical School, Pittsburgh PA 15260; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh PA 15260
| | - Andreas Vogt
- Drug Discovery Institute, University of Pittsburgh Medical School, Pittsburgh PA 15260; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh PA 15260.
| | - Anthony Schwacha
- The Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260.
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8
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Barthels F, Hammerschmidt SJ, Fischer TR, Zimmer C, Kallert E, Helm M, Kersten C, Schirmeister T. A low-cost 3D-printable differential scanning fluorometer for protein and RNA melting experiments. HARDWAREX 2022; 11:e00256. [PMID: 35509940 PMCID: PMC9058602 DOI: 10.1016/j.ohx.2022.e00256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/02/2021] [Accepted: 01/01/2022] [Indexed: 06/14/2023]
Abstract
Differential scanning fluorimetry (DSF) is a widely used biophysical technique with applications to drug discovery and protein biochemistry. DSF experiments are commonly performed in commercial real-time polymerase chain reaction (qPCR) thermal cyclers or nanoDSF instruments. Here, we report the construction, validation, and example applications of an open-source DSF system for 176 €, which, in addition to protein-DSF experiments, also proved to be a versatile biophysical instrument for less conventional RNA-DSF experiments. Using 3D-printed parts made of polyoxymethylene, we were able to fabricate a thermostable machine chassis for protein-melting experiments. The combination of blue high-power LEDs as the light source and stage light foil as filter components was proven to be a reliable and affordable alternative to conventional optics equipment for the detection of SYPRO Orange or Sybr Gold fluorescence. The ESP32 microcontroller is the core piece of this openDSF instrument, while the in-built I2S interface was found to be a powerful analog-to-digital converter for fast acquisition of fluorescence and temperature data. Airflow heating and inline temperature control by thermistors enabled high-accuracy temperature management in PCR tubes (±0.1 °C) allowing us to perform high-resolution thermal shift assays (TSA) from exemplary biological applications.
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9
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Guzman KM, Khosla C. Fragment antigen binding domains (F abs) as tools to study assembly-line polyketide synthases. Synth Syst Biotechnol 2022; 7:506-512. [PMID: 34977395 PMCID: PMC8683866 DOI: 10.1016/j.synbio.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022] Open
Abstract
The crystallization of proteins remains a bottleneck in our fundamental understanding of their functions. Therefore, discovering tools that aid crystallization is crucial. In this review, the versatility of fragment-antigen binding domains (Fabs) as protein crystallization chaperones is discussed. Fabs have aided the crystallization of membrane-bound and soluble proteins as well as RNA. The ability to bind three Fabs onto a single protein target has demonstrated their potential for crystallization of challenging proteins. We describe a high-throughput workflow for identifying Fabs to aid the crystallization of a protein of interest (POI) by leveraging phage display technologies and differential scanning fluorimetry (DSF). This workflow has proven to be especially effective in our structural studies of assembly-line polyketide synthases (PKSs), which harbor flexible domains and assume transient conformations. PKSs are of interest to us due to their ability to synthesize an unusually broad range of medicinally relevant compounds. Despite years of research studying these megasynthases, their overall topology has remained elusive. One Fab in particular, 1B2, has successfully enabled X-ray crystallographic and single particle cryo-electron microscopic (cryoEM) analyses of multiple modules from distinct assembly-line PKSs. Its use has not only facilitated multidomain protein crystallization but has also enhanced particle quality via cryoEM, thereby enabling the visualization of intact PKS modules at near-atomic (3-5 Å) resolution. The identification of PKS-binding Fabs can be expected to continue playing a key role in furthering our knowledge of polyketide biosynthesis on assembly-line PKSs.
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Affiliation(s)
- Katarina M. Guzman
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
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10
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Watanabe M, Toyomura T, Wake H, Nishinaka T, Hatipoglu OF, Takahashi H, Nishibori M, Mori S. Identification of ribosomal protein L9 as a novel regulator of proinflammatory damage-associated molecular pattern molecules. Mol Biol Rep 2022; 49:2831-2838. [DOI: 10.1007/s11033-021-07096-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023]
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11
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Pinz S, Doskocil E, Seufert W. Thermofluor-Based Analysis of Protein Integrity and Ligand Interactions. Methods Mol Biol 2022; 2533:247-257. [PMID: 35796993 PMCID: PMC9761908 DOI: 10.1007/978-1-0716-2501-9_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Thermofluor is a fluorescence-based thermal shift assay, which measures temperature-induced protein unfolding and thereby yields valuable information about the integrity of a purified recombinant protein. Analysis of ligand binding to a protein is another popular application of this assay. Thermofluor requires neither protein labeling nor highly specialized equipment, and can be performed in a regular real-time PCR instrument. Thus, for a typical molecular biology laboratory, Thermofluor is a convenient method for the routine assessment of protein quality. Here, we provide Thermofluor protocols using the example of Cdc123. This ATP-grasp protein is an essential assembly chaperone of the eukaryotic translation initiation factor eIF2. We also report on a destabilized mutant protein version and on the ATP-mediated thermal stabilization of wild-type Cdc123 illustrating protein integrity assessment and ligand binding analysis as two major applications of the Thermofluor assay.
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Affiliation(s)
- Sophia Pinz
- Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
| | - Eva Doskocil
- Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Wolfgang Seufert
- Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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12
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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13
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Iacono R, Minopoli N, Ferrara MC, Tarallo A, Damiano C, Porto C, Strollo S, Roig-Zamboni V, Peluso G, Sulzenbacher G, Cobucci-Ponzano B, Parenti G, Moracci M. Carnitine is a pharmacological allosteric chaperone of the human lysosomal α-glucosidase. J Enzyme Inhib Med Chem 2021; 36:2068-2079. [PMID: 34565280 PMCID: PMC8477953 DOI: 10.1080/14756366.2021.1975694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/23/2021] [Accepted: 08/29/2021] [Indexed: 11/22/2022] Open
Abstract
Pompe disease is an inherited metabolic disorder due to the deficiency of the lysosomal acid α-glucosidase (GAA). The only approved treatment is enzyme replacement therapy with the recombinant enzyme (rhGAA). Further approaches like pharmacological chaperone therapy, based on the stabilising effect induced by small molecules on the target enzyme, could be a promising strategy. However, most known chaperones could be limited by their potential inhibitory effects on patient's enzymes. Here we report on the discovery of novel chaperones for rhGAA, L- and D-carnitine, and the related compound acetyl-D-carnitine. These drugs stabilise the enzyme at pH and temperature without inhibiting the activity and acted synergistically with active-site directed pharmacological chaperones. Remarkably, they enhanced by 4-fold the acid α-glucosidase activity in fibroblasts from three Pompe patients with added rhGAA. This synergistic effect of L-carnitine and rhGAA has the potential to be translated into improved therapeutic efficacy of ERT in Pompe disease.
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Affiliation(s)
- Roberta Iacono
- Department of Biology, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Naples, Italy
- Institute of Biosciences and Bioresources – CNR, Naples, Italy
| | - Nadia Minopoli
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | | | | | - Carla Damiano
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Caterina Porto
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Sandra Strollo
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
| | - Véronique Roig-Zamboni
- Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, AFMB, Marseille, France
| | - Gianfranco Peluso
- Research Institute on Terrestrial Ecosystems, UOS Naples-CNR, Naples, Italy
| | - Gerlind Sulzenbacher
- Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, AFMB, Marseille, France
| | | | - Giancarlo Parenti
- Telethon Institute of Genetics & Medicine, Pozzuoli, Italy
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Naples, Italy
- Institute of Biosciences and Bioresources – CNR, Naples, Italy
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14
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Froes TQ, Chaves BT, Mendes MS, Ximenes RM, da Silva IM, da Silva PBG, de Albuquerque JFC, Castilho MS. Synthesis and biological evaluation of thiazolidinedione derivatives with high ligand efficiency to P. aeruginosa PhzS. J Enzyme Inhib Med Chem 2021; 36:1217-1229. [PMID: 34080514 PMCID: PMC8186431 DOI: 10.1080/14756366.2021.1931165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
The thiazolidinone ring is found in compounds that have widespan biology activity and there is mechanism-based evidence that compounds bearing this moiety inhibit P. aeruginosa PhzS (PaPzhS), a key enzyme in the biosynthesis of the virulence factor named pyocyanin. Ten novel thiazolidinone derivatives were synthesised and screened against PaPhzS, using two orthogonal assays. The biological results provided by these and 28 other compounds, whose synthesis had been described, suggest that the dihydroquinazoline ring, found in the previous hit (A- Kd = 18 µM and LE = 0.20), is not required for PaPzhS inhibition, but unsubstituted nitrogen at the thiazolidinone ring is. The molecular simplification approach, pursued in this work, afforded an optimised lead compound (13- 5-(2,4-dimethoxyphenyl)thiazolidine-2,4-dione) with 10-fold improvement in affinity (Kd= 1.68 µM) and more than 100% increase in LE (0.45), which follows the same inhibition mode as the original hit compound (competitive to NADH).Executive summaryPhzS is a key enzyme in the pyocyanin biosynthesis pathway in P. aeruginosa.Orthogonal assays (TSA and FITC) show that fragment-like thiazolidinedione derivatives bind to PaPhzS with one-digit micromolar affinity.Fragment-like thiazolidinedione derivatives bind to the cofactor (NADH) binding site in PaPhzS.The molecular simplification optimised the ligand efficiency and affinity of the lead compound.
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Affiliation(s)
- Thamires Quadros Froes
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Marina Sena Mendes
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
| | - Rafael Matos Ximenes
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | - Ivanildo Mangueira da Silva
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | | | | | - Marcelo Santos Castilho
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
- Programa de Pós-Graduação em Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
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15
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Thermostability-based binding assays reveal complex interplay of cation, substrate and lipid binding in the bacterial DASS transporter, VcINDY. Biochem J 2021; 478:3847-3867. [PMID: 34643224 PMCID: PMC8652582 DOI: 10.1042/bcj20210061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022]
Abstract
The divalent anion sodium symporter (DASS) family of transporters (SLC13 family in humans) are key regulators of metabolic homeostasis, disruption of which results in protection from diabetes and obesity, and inhibition of liver cancer cell proliferation. Thus, DASS transporter inhibitors are attractive targets in the treatment of chronic, age-related metabolic diseases. The characterisation of several DASS transporters has revealed variation in the substrate selectivity and flexibility in the coupling ion used to power transport. Here, using the model DASS co-transporter, VcINDY from Vibrio cholerae, we have examined the interplay of the three major interactions that occur during transport: the coupling ion, the substrate, and the lipid environment. Using a series of high-throughput thermostability-based interaction assays, we have shown that substrate binding is Na+-dependent; a requirement that is orchestrated through a combination of electrostatic attraction and Na+-induced priming of the binding site architecture. We have identified novel DASS ligands and revealed that ligand binding is dominated by the requirement of two carboxylate groups in the ligand that are precisely distanced to satisfy carboxylate interaction regions of the substrate-binding site. We have also identified a complex relationship between substrate and lipid interactions, which suggests a dynamic, regulatory role for lipids in VcINDY's transport cycle.
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16
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Tarallo A, Damiano C, Strollo S, Minopoli N, Indrieri A, Polishchuk E, Zappa F, Nusco E, Fecarotta S, Porto C, Coletta M, Iacono R, Moracci M, Polishchuk R, Medina DL, Imbimbo P, Monti DM, De Matteis MA, Parenti G. Correction of oxidative stress enhances enzyme replacement therapy in Pompe disease. EMBO Mol Med 2021; 13:e14434. [PMID: 34606154 PMCID: PMC8573602 DOI: 10.15252/emmm.202114434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023] Open
Abstract
Pompe disease is a metabolic myopathy due to acid alpha-glucosidase deficiency. In addition to glycogen storage, secondary dysregulation of cellular functions, such as autophagy and oxidative stress, contributes to the disease pathophysiology. We have tested whether oxidative stress impacts on enzyme replacement therapy with recombinant human alpha-glucosidase (rhGAA), currently the standard of care for Pompe disease patients, and whether correction of oxidative stress may be beneficial for rhGAA therapy. We found elevated oxidative stress levels in tissues from the Pompe disease murine model and in patients' cells. In cells, stress levels inversely correlated with the ability of rhGAA to correct the enzymatic deficiency. Antioxidants (N-acetylcysteine, idebenone, resveratrol, edaravone) improved alpha-glucosidase activity in rhGAA-treated cells, enhanced enzyme processing, and improved mannose-6-phosphate receptor localization. When co-administered with rhGAA, antioxidants improved alpha-glucosidase activity in tissues from the Pompe disease mouse model. These results indicate that oxidative stress impacts on the efficacy of enzyme replacement therapy in Pompe disease and that manipulation of secondary abnormalities may represent a strategy to improve the efficacy of therapies for this disorder.
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Affiliation(s)
- Antonietta Tarallo
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Carla Damiano
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Sandra Strollo
- Telethon Institute of Genetics and MedicinePozzuoliItaly
| | - Nadia Minopoli
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Alessia Indrieri
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Institute for Genetic and Biomedical Research (IRGB)National Research Council (CNR)MilanItaly
| | | | - Francesca Zappa
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Present address:
Department of Molecular, Cellular, and Developmental BiologyUniversity of CaliforniaSanta BarbaraCAUSA
| | - Edoardo Nusco
- Telethon Institute of Genetics and MedicinePozzuoliItaly
| | - Simona Fecarotta
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Caterina Porto
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Marcella Coletta
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
- Present address:
IInd Division of NeurologyMultiple Sclerosis CenterUniversity of Campania "Luigi Vanvitelli"NaplesItaly
| | - Roberta Iacono
- Department of BiologyUniversity of Naples "Federico II", Complesso Universitario di Monte S. AngeloNaplesItaly
- Institute of Biosciences and BioResources ‐ National Research Council of ItalyNaplesItaly
| | - Marco Moracci
- Department of BiologyUniversity of Naples "Federico II", Complesso Universitario di Monte S. AngeloNaplesItaly
- Institute of Biosciences and BioResources ‐ National Research Council of ItalyNaplesItaly
| | | | - Diego Luis Medina
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Paola Imbimbo
- Department of Chemical SciencesFederico II UniversityNaplesItaly
| | | | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Molecular Medicine and Medical BiotechnologiesFederico II UniversityNaplesItaly
| | - Giancarlo Parenti
- Telethon Institute of Genetics and MedicinePozzuoliItaly
- Department of Translational Medical SciencesFederico II UniversityNaplesItaly
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17
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Cogan DP, Zhang K, Li X, Li S, Pintilie GD, Roh SH, Craik CS, Chiu W, Khosla C. Mapping the catalytic conformations of an assembly-line polyketide synthase module. Science 2021; 374:729-734. [PMID: 34735239 DOI: 10.1126/science.abi8358] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dillon P Cogan
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiuyuan Li
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 151-742, Korea
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford, CA 94305, USA
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18
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Jackson TW, Scheibly CM, Polera ME, Belcher SM. Rapid Characterization of Human Serum Albumin Binding for Per- and Polyfluoroalkyl Substances Using Differential Scanning Fluorimetry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12291-12301. [PMID: 34495656 PMCID: PMC8651256 DOI: 10.1021/acs.est.1c01200] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a diverse class of synthetic chemicals that accumulate in the environment. Many proteins, including the primary human serum transport protein albumin (HSA), bind PFAS. The predictive power of physiologically based pharmacokinetic modeling approaches is currently limited by a lack of experimental data defining albumin-binding properties for most PFAS. A novel thermal denaturation assay was optimized to evaluate changes in the thermal stability of HSA in the presence of increasing concentrations of known ligands and a structurally diverse set of PFAS. Assay performance was initially evaluated for fatty acids and HSA-binding drugs ibuprofen and warfarin. Concentration-response relationships were determined and dissociation constants (Kd) for each compound were calculated using regression analysis of the dose-dependent changes in HSA melting temperature. Estimated Kd values for HSA binding of octanoic acid, decanoic acid, hexadecenoic acid, ibuprofen, and warfarin agreed with established values. The binding affinities for 24 PFAS that included perfluoroalkyl carboxylic acids (C4-C12), perfluoroalkyl sulfonic acids (C4-C8), mono- and polyether perfluoroalkyl ether acids, and polyfluoroalkyl fluorotelomer substances were determined. These results demonstrate the utility of this differential scanning fluorimetry assay as a rapid high-throughput approach for determining the relative protein-binding properties and identification of chemical structures involved in binding for large numbers of structurally diverse PFAS.
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Affiliation(s)
- Thomas W Jackson
- Center for Human Health and The Environment Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus, P.O. Box 7617, Raleigh, North Carolina 27695, United States
| | - Chris M Scheibly
- Center for Human Health and The Environment Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus, P.O. Box 7617, Raleigh, North Carolina 27695, United States
| | - M E Polera
- Center for Human Health and The Environment Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus, P.O. Box 7617, Raleigh, North Carolina 27695, United States
| | - Scott M Belcher
- Center for Human Health and The Environment Department of Biological Sciences, North Carolina State University, 127 David Clark Labs Campus, P.O. Box 7617, Raleigh, North Carolina 27695, United States
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19
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Sharoyko VV, Iamalova NR, Ageev SV, Meshcheriakov AA, Iurev GO, Petrov AV, Nerukh DA, Farafonov VS, Vasina LV, Penkova AV, Semenov KN. In Vitro and In Silico Investigation of Water-Soluble Fullerenol C 60(OH) 24: Bioactivity and Biocompatibility. J Phys Chem B 2021; 125:9197-9212. [PMID: 34375109 DOI: 10.1021/acs.jpcb.1c03332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Light fullerenes, C60 and C70, have significant potential in biomedical applications due to their ability to absorb reactive oxygen species, inhibit the development of tumors, inactivate viruses and bacteria, and as the basis for developing systems for targeted drug delivery. However, the hydrophobicity of individual fullerenes complicates their practical use; therefore, creating water-soluble derivatives of fullerenes is increasingly important. Currently, the most studied soluble adducts of fullerenes are polyhydroxy fullerenes or fullerenols. Unfortunately, investigations of fullerenol biocompatibility are fragmental. They often lack reproducibility both in the synthesis of the compounds and their biological action. We here investigate the biocompatibility of a well-defined fullerenol C60(OH)24 obtained using methods that minimize the content of impurities and quantitatively characterize the product's composition. We carry out comprehensive biochemical and biophysical investigations of C60(OH)24 that include photodynamic properties, cyto- and genotoxicity, hemocompatibility (spontaneous and photo-induced hemolysis, platelet aggregation), and the thermodynamic characteristics of C60(OH)24 binding to human serum albumin and DNA. The performed studies show good biocompatibility of fullerenol C60(OH)24, which makes it a promising object for potential use in biomedicine.
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Affiliation(s)
- Vladimir V Sharoyko
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia.,A. M. Granov Russian Research Centre for Radiology and Surgical Technologies, 70 Leningradskaya Ulitsa, Saint Petersburg 197758, Russia
| | - Nailia R Iamalova
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Agrophysical Research Institute, 14 Grazhdanskii prospect, Saint Petersburg 195220, Russia
| | - Sergei V Ageev
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia
| | - Anatolii A Meshcheriakov
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia
| | - Gleb O Iurev
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Almazov National Medical Research Centre, 2 Akkuratova ulitsa, Saint Petersburg 197341, Russia
| | - Andrey V Petrov
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia
| | - Dmitry A Nerukh
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
| | - Vladimir S Farafonov
- V. N. Karazin Kharkiv National University, 4 Svobody ploshchad, Kharkiv 61022, Ukraine
| | - Lubov V Vasina
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia
| | - Anastasia V Penkova
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia
| | - Konstantin N Semenov
- Pavlov First Saint Petersburg State Medical University, 6-8 L'va Tolstogo ulitsa, Saint Petersburg 197022, Russia.,Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospekt, Saint Petersburg 198504, Russia.,A. M. Granov Russian Research Centre for Radiology and Surgical Technologies, 70 Leningradskaya Ulitsa, Saint Petersburg 197758, Russia
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20
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Abstract
Chemoreceptors enable the legume symbiont Sinorhizobium meliloti to detect and respond to specific chemicals released from their host plant alfalfa, which allows the establishment of a nitrogen-fixing symbiosis. The periplasmic region (PR) of transmembrane chemoreceptors act as the sensory input module for chemotaxis systems via binding of specific ligands, either directly or indirectly. S. meliloti has six transmembrane and two cytosolic chemoreceptors. However, the function of only three of the transmembrane receptors have been characterized so far, with McpU, McpV, and McpX serving as general amino acid, short-chain carboxylate, and quaternary ammonium compound sensors, respectively. In the present study, we analyzed the S. meliloti chemoreceptor McpT. High-throughput differential scanning fluorimetry assays, using Biolog phenotype microarray plates, identified 15 potential ligands for McpTPR, with the majority classified as mono-, di-, and tricarboxylates. S. meliloti exhibited positive chemotaxis toward seven selected carboxylates, namely, α-ketobutyrate, citrate, glyoxylate, malate, malonate, oxalate, and succinate. These carboxylates were detected in seed exudates of the alfalfa host. Deletion of mcpT resulted in a significant decrease of chemotaxis to all carboxylates except for citrate. Isothermal titration calorimetry revealed that McpTPR bound preferentially to the monocarboxylate glyoxylate and with lower affinity to the dicarboxylates malate, malonate, and oxalate. However, no direct binding was detected for the remaining three carboxylates that elicited an McpT-dependent chemotaxis response. Taken together, these results demonstrate that McpT is a broad-range carboxylate chemoreceptor that mediates chemotactic response via direct ligand binding and an indirect mechanism that needs to be identified. IMPORTANCE Nitrate pollution is one of the most widespread and challenging environmental problems that is mainly caused by the agricultural overapplication of nitrogen fertilizers. Biological nitrogen fixation by the endosymbiont Sinorhizobium meliloti enhances the growth of its host Medicago sativa (alfalfa), which also efficiently supplies the soil with nitrogen. Establishment of the S. meliloti-alfalfa symbiosis relies on the early exchange and recognition of chemical signals. The present study contributes to the disclosure of this complex molecular dialogue by investigating the underlying mechanisms of carboxylate sensing in S. meliloti. Understanding individual steps that govern the S. meliloti-alfalfa molecular cross talk helps in the development of efficient, commercial bacterial inoculants that promote the growth of alfalfa, which is the most cultivated forage legume in the world, and improves soil fertility.
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21
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Valentino H, Korasick DA, Bohac TJ, Shapiro JA, Wencewicz TA, Tanner JJ, Sobrado P. Structural and Biochemical Characterization of the Flavin-Dependent Siderophore-Interacting Protein from Acinetobacter baumannii. ACS OMEGA 2021; 6:18537-18547. [PMID: 34308084 PMCID: PMC8296543 DOI: 10.1021/acsomega.1c03047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/23/2021] [Indexed: 05/09/2023]
Abstract
Acinetobacter baumannii is an opportunistic pathogen with a high mortality rate due to multi-drug-resistant strains. The synthesis and uptake of the iron-chelating siderophores acinetobactin (Acb) and preacinetobactin (pre-Acb) have been shown to be essential for virulence. Here, we report the kinetic and structural characterization of BauF, a flavin-dependent siderophore-interacting protein (SIP) required for the reduction of Fe(III) bound to Acb/pre-Acb and release of Fe(II). Stopped-flow spectrophotometric studies of the reductive half-reaction show that BauF forms a stable neutral flavin semiquinone intermediate. Reduction with NAD(P)H is very slow (k obs, 0.001 s-1) and commensurate with the rate of reduction by photobleaching, suggesting that NAD(P)H are not the physiological partners of BauF. The reduced BauF was oxidized by Acb-Fe (k obs, 0.02 s-1) and oxazole pre-Acb-Fe (ox-pre-Acb-Fe) (k obs, 0.08 s-1), a rigid analogue of pre-Acb, at a rate 3-11 times faster than that with molecular oxygen alone. The structure of FAD-bound BauF was solved at 2.85 Å and was found to share a similarity to Shewanella SIPs. The biochemical and structural data presented here validate the role of BauF in A. baumannii iron assimilation and provide information important for drug design.
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Affiliation(s)
- Hannah Valentino
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David A. Korasick
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tabbetha J. Bohac
- Department
of Chemistry, Washington University in Saint
Louis, St. Louis, Missouri 63130, United States
| | - Justin A. Shapiro
- Department
of Chemistry, Washington University in Saint
Louis, St. Louis, Missouri 63130, United States
| | - Timothy A. Wencewicz
- Department
of Chemistry, Washington University in Saint
Louis, St. Louis, Missouri 63130, United States
| | - John J. Tanner
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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22
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Abstract
Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent Kds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (\documentclass[12pt]{minimal}
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\begin{document}$$\Delta {C}_{p}$$\end{document}ΔCp) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.
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23
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Reddy MV, Steinbüchel A. 3,3'-Thiodipropionic acid (TDP), a possible precursor for the synthesis of polythioesters: identification of TDP transport proteins in Variovorax paradoxus TBEA6. Appl Microbiol Biotechnol 2021; 105:3733-3743. [PMID: 33900422 PMCID: PMC8102459 DOI: 10.1007/s00253-021-11294-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/21/2021] [Accepted: 04/12/2021] [Indexed: 11/26/2022]
Abstract
3,3'-Thiodipropionic acid (TDP) is an antioxidant, which can be used as precursor carbon source to synthesize polythioesters. The bacterium Variovorax paradoxus TBEA6 strain can use TDP as a single source of carbon and energy. In the present study, experiments were carried out to identify proteins involved in the transport of TDP into the cells of strain TBEA6. Hence, eight putative tctC genes, which encode for the TctC proteins, were amplified from genomic DNA of TBEA6 strain using polymerase chain reaction and expressed in E. coli BL21 cells. Cells were grown in auto-induction medium, and protein purification was done using His Spin Trap affinity columns. Purity and molecular weight of each protein were confirmed by SDS-PAGE analysis. Protein-ligand interactions were monitored in thermoshift assays using the real-time PCR system. Two TctC proteins (locus tags VPARA-44430 and VPARA-01760) out of eight proteins showed a significant shift in their melting temperatures when they interact with the ligand (TDP or gluconate). The responsible genes were deleted in the genome of TBEA6 using suicide plasmid pJQ200mp18Tc, and single deletion mutants of the two candidate genes were subsequently generated. Finally, growth of the wild-type strain (TBEA6) and the two mutant strains (ΔVPARA-44430 and ΔVPARA-01760) were monitored and compared using TDP or gluconate as carbon sources. Wild type strains were successfully grown with TDP or gluconate. From the two mutant strains, one (ΔVPARA-44430) was unable to grow with TDP indicating that the tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP.Key Points• Putative tctC genes from V. paradoxus TBEA6 were heterologously expressed in E. coli.• Protein-ligand interactions monitored in thermoshift assays using the real-time PCR.• tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP.
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Affiliation(s)
- M Venkateswar Reddy
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany.
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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POT1 stability and binding measured by fluorescence thermal shift assays. PLoS One 2021; 16:e0245675. [PMID: 33784306 PMCID: PMC8009405 DOI: 10.1371/journal.pone.0245675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.
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25
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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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GigC, a LysR Family Transcription Regulator, Is Required for Cysteine Metabolism and Virulence in Acinetobacter baumannii. Infect Immun 2020; 89:IAI.00180-20. [PMID: 33077621 DOI: 10.1128/iai.00180-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/11/2020] [Indexed: 11/20/2022] Open
Abstract
A critical facet of mammalian innate immunity involves the hosts' attempts to sequester and/or limit the availability of key metabolic products from pathogens. For example, nutritional immunity encompasses host approaches to limit the availability of key heavy metal ions such as zinc and iron. Previously, we identified several hundred genes in a multidrug-resistant isolate of Acinetobacter baumannii that are required for growth and/or survival in the Galleria mellonella infection model. In the present study, we further characterize one of these genes, a LysR family transcription regulator that we previously named GigC. We show that mutant strains lacking gigC have impaired growth in the absence of the amino acid cysteine and that gigC regulates the expression of several genes involved in the sulfur assimilation and cysteine biosynthetic pathways. We further show that cells harboring a deletion of the gigC gene are attenuated in two murine infection models, suggesting that the GigC protein, likely through its regulation of the cysteine biosynthetic pathway, plays a key role in the virulence of A. baumannii.
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27
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Kim MS, Gernapudi R, Cedeño YC, Polster BM, Martinez R, Shapiro P, Kesari S, Nurmemmedov E, Passaniti A. Targeting breast cancer metabolism with a novel inhibitor of mitochondrial ATP synthesis. Oncotarget 2020; 11:3863-3885. [PMID: 33196708 PMCID: PMC7597410 DOI: 10.18632/oncotarget.27743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/24/2020] [Indexed: 01/17/2023] Open
Abstract
Inhibitors of mitochondrial respiration and ATP synthesis may promote the selective killing of respiration-competent cancer cells that are critical for tumor progression. We previously reported that CADD522, a small molecule inhibitor of the RUNX2 transcription factor, has potential for breast cancer treatment. In the current study, we show that CADD522 inhibits mitochondrial oxidative phosphorylation by decreasing the mitochondrial oxygen consumption rate (OCR) and ATP production in human breast cancer cells in a RUNX2-independent manner. The enzyme activity of mitochondrial ATP synthase was inhibited by CADD522 treatment. Importantly, results from cellular thermal shift assays that detect drug-induced protein stabilization revealed that CADD522 interacts with both α and β subunits of the F1-ATP synthase complex. Differential scanning fluorimetry also demonstrated interaction of α subunits of the F1-ATP synthase to CADD522. These results suggest that CADD522 might target the enzymatic F1 subunits in the ATP synthase complex. CADD522 increased the levels of intracellular reactive oxygen species (ROS), which was prevented by MitoQ, a mitochondria-targeted antioxidant, suggesting that cancer cells exposed to CADD522 may elevate ROS from mitochondria. CADD522-increased mitochondrial ROS levels were enhanced by exogenously added pro-oxidants such as hydrogen peroxide or tert-butyl hydroperoxide. Conversely, CADD522-mediated cell growth inhibition was blocked by N-acetyl-l-cysteine, a general ROS scavenger. Therefore, CADD522 may exert its antitumor activity by increasing mitochondrial driven cellular ROS levels. Collectively, our data suggest in vitro proof-of-concept that supports inhibition of mitochondrial ATP synthase and ROS generation as contributors to the effectiveness of CADD522 in suppression of tumor growth.
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Affiliation(s)
- Myoung Sook Kim
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Ramkishore Gernapudi
- Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Brian M. Polster
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Research Health Scientist, The Veteran's Health Administration Research & Development Service (VAMHCS), Baltimore, MD, USA
| | - Ramon Martinez
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Santosh Kesari
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Antonino Passaniti
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
- Research Health Scientist, The Veteran's Health Administration Research & Development Service (VAMHCS), Baltimore, MD, USA
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28
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Luti S, Bemporad F, Vivoli Vega M, Leri M, Musiani F, Baccelli I, Pazzagli L. Partitioning the structural features that underlie expansin-like and elicitor activities of cerato-platanin. Int J Biol Macromol 2020; 165:2845-2854. [PMID: 33736287 DOI: 10.1016/j.ijbiomac.2020.10.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
Cerato-platanin family (CPF) proteins are produced by fungi and elicit defences when applied to plants, behaving as PAMPs/MAMPs. CPF proteins share structural similarity to plant and bacterial expansins, and have been demonstrated, in some cases, to possess expansin-like loosening activity on cellulose. This is the case of cerato-platanin (CP), the founder of the CPF, which shows both eliciting and cellulose-loosening activities, raising the question as to whether the expansin-like activity may be responsible for defence activation. To pinpoint structural and thermodynamic features underlying eliciting and expansin-like activity of CP, we carried out site-directed mutagenesis targeting separately net charge (N84D mutation), conformational stability (V63A mutation), or conserved position previously shown to affect expansin-like activity in CP (D77A mutation), and characterized wild-type protein and its variants. Removing or adding negative charges on the protein surface led to reducing or increasing, respectively, the expansin-like activity. The activity was instead not affected by mutations affecting protein fold and stability. In contrast, all the mutants showed reduced capacity to elicit defences in plants. We conclude that the expansin-like activity of CP depends on net charge and ability to (weakly) bind cellulose, whereas the eliciting activity on plants does not depend on the cellulose-loosening activity.
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Affiliation(s)
- S Luti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy; Institute for Sustainable Plant Protection, National Research Council, via Madonna del piano 10, 50019 Sesto Fiorentino, Florence, Italy.
| | - F Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - M Vivoli Vega
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - M Leri
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - F Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - I Baccelli
- Institute for Sustainable Plant Protection, National Research Council, via Madonna del piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - L Pazzagli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
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29
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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30
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Karambelkar S, Udupa S, Gowthami VN, Ramachandra SG, Swapna G, Nagaraja V. Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu. Nucleic Acids Res 2020; 48:5294-5305. [PMID: 32369169 PMCID: PMC7261163 DOI: 10.1093/nar/gkaa319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023] Open
Abstract
The broad host range bacteriophage Mu employs a novel 'methylcarbamoyl' modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and metal-binding properties of Mom and provide a molecular mechanism to explain 'methylcarbamoyl'ation of DNA by Mom. Computational analyses revealed a conserved GNAT (GCN5-related N-acetyltransferase) fold in Mom. We demonstrate that Mom binds to acetyl CoA and identify the active site. We discovered that Mom is an iron-binding protein, with loss of Fe2+/3+-binding associated with loss of DNA modification activity. The importance of Fe2+/3+ is highlighted by the colocalization of Fe2+/3+ with acetyl CoA within the Mom active site. Puzzlingly, acid-base mechanisms employed by >309,000 GNAT members identified so far, fail to support methylcarbamoylation of adenine using acetyl CoA. In contrast, free-radical chemistry catalyzed by transition metals like Fe2+/3+ can explain the seemingly challenging reaction, accomplished by collaboration between acetyl CoA and Fe2+/3+. Thus, binding to Fe2+/3+, a small but unprecedented step in the evolution of Mom, allows a giant chemical leap from ordinary acetylation to a novel methylcarbamoylation function, while conserving the overall protein architecture.
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Affiliation(s)
- Shweta Karambelkar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Shubha Udupa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Vykuntham Naga Gowthami
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Ganduri Swapna
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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31
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Ganaie AA, Siddique HR, Sheikh IA, Parray A, Wang L, Panyam J, Villalta PW, Deng Y, Konety BR, Saleem M. A novel terpenoid class for prevention and treatment of KRAS-driven cancers: Comprehensive analysis using in situ, in vitro, and in vivo model systems. Mol Carcinog 2020; 59:886-896. [PMID: 32291806 PMCID: PMC7334075 DOI: 10.1002/mc.23200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
Inhibiting the disease progression in KRAS-driven cancers after diagnosis has been a difficult task for clinicians to manage due to the lack of effective intervention/preventive therapies. KRAS-driven cancers depend on sustained KRAS signaling. Although developing inhibitors of KRAS signaling has proven difficult in the past, the quest for identifying newer agents has not stopped. Based on studies showing terpenoids as modulators of KRAS-regulated downstream molecular pathways, we asked if this chemical family has an affinity of inhibiting KRAS protein activity. Using crystal structure as a bait in silico, we identified 20 terpenoids for their KRAS protein-binding affinity. We next carried out biological validation of in silico data by employing in situ, in vitro, patient-derived explant ex vivo, and KPC transgenic mouse models. In this report, we provide a comprehensive analysis of a lup-20(29)-en-3b-ol (lupeol) as a KRAS inhibitor. Using nucleotide exchange, isothermal titration calorimetry, differential scanning fluorimetry, and immunoprecipitation assays, we show that lupeol has the potential to reduce the guanosine diphosphate/guanosine triphosphate exchange of KRAS protein including mutant KRASG12V . Lupeol treatment inhibited the KRAS activation in KRAS-activated cell models (NIH-panel, colorectal, lung, and pancreatic intraepithelial neoplasia) and patient tumor explants ex vivo. Lupeol reduced the three-dimensional growth of KRAS-activated cells. The pharmacokinetic analysis showed the bioavailability of lupeol after consumption via oral and intraperitoneal routes in animals. Tested under prevention settings, the lupeol consumption inhibited the development of pancreatic intraepithelial neoplasia in LSL-KRASG12D/Pdx-cre mice (pancreatic ductal adenocarcinoma progression model). These data suggest that the selected members of the triterpene family (such as lupeol) could be exploited as clinical agents for preventing the disease progression in KRAS-driven cancers which however warrants further investigation.
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Affiliation(s)
- Arsheed A. Ganaie
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Hifzur R. Siddique
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
- Department of Zoology, Aligarh Muslim University, India
| | - Ishfaq A. Sheikh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aijaz Parray
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
- Academic Health Systems Hamad Medical Corporation, Doha, Qatar
| | | | - Jayanth Panyam
- School of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Peter W. Villalta
- Analytical Chemistry Core, Masonic Cancer Center, University of Minnesota, MN
| | - Yibin Deng
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Badrinath R. Konety
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Mohammad Saleem
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
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32
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Onwubiko NO, Borst A, Diaz SA, Passkowski K, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen interactions with ssDNA and replication protein A: a regulatory role of T antigen monomers in lagging strand DNA replication. Nucleic Acids Res 2020; 48:3657-3677. [PMID: 32128579 PMCID: PMC7144908 DOI: 10.1093/nar/gkaa138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
DNA replication is a central process in all living organisms. Polyomavirus DNA replication serves as a model system for eukaryotic DNA replication and has considerably contributed to our understanding of basic replication mechanisms. However, the details of the involved processes are still unclear, in particular regarding lagging strand synthesis. To delineate the complex mechanism of coordination of various cellular proteins binding simultaneously or consecutively to DNA to initiate replication, we investigated single-stranded DNA (ssDNA) interactions by the SV40 large T antigen (Tag). Using single molecule imaging by atomic force microscopy (AFM) combined with biochemical and spectroscopic analyses we reveal independent activity of monomeric and oligomeric Tag in high affinity binding to ssDNA. Depending on ssDNA length, we obtain dissociation constants for Tag-ssDNA interactions (KD values of 10–30 nM) that are in the same order of magnitude as ssDNA binding by human replication protein A (RPA). Furthermore, we observe the formation of RPA-Tag-ssDNA complexes containing hexameric as well as monomeric Tag forms. Importantly, our data clearly show stimulation of primase function in lagging strand Okazaki fragment synthesis by monomeric Tag whereas hexameric Tag inhibits the reaction, redefining DNA replication initiation on the lagging strand.
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Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Angela Borst
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Suraya A Diaz
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Katharina Passkowski
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Heinz P Nasheuer
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
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33
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Abstract
In an oxygenic environment, poorly soluble Fe3+ must be reduced to meet the cellular Fe2+ demand. This study demonstrates that elevated CO2/HCO3− levels accelerate chemical Fe3+ reduction through phenolic compounds, thus increasing intracellular Fe2+ availability. A number of biological environments are characterized by the presence of phenolic compounds and elevated HCO3− levels and include soil habitats and the human body. Fe2+ availability is of particular interest in the latter, as it controls the infectiousness of pathogens. Since the effect postulated here is abiotic, it generally affects the Fe2+ distribution in nature. Iron is a vital mineral for almost all living organisms and has a pivotal role in central metabolism. Despite its great abundance on earth, the accessibility for microorganisms is often limited, because poorly soluble ferric iron (Fe3+) is the predominant oxidation state in an aerobic environment. Hence, the reduction of Fe3+ is of essential importance to meet the cellular demand of ferrous iron (Fe2+) but might become detrimental as excessive amounts of intracellular Fe2+ tend to undergo the cytotoxic Fenton reaction in the presence of hydrogen peroxide. We demonstrate that the complex formation rate of Fe3+ and phenolic compounds like protocatechuic acid was increased by 46% in the presence of HCO3− and thus accelerated the subsequent redox reaction, yielding reduced Fe2+. Consequently, elevated CO2/HCO3− levels increased the intracellular Fe2+ availability, which resulted in at least 50% higher biomass-specific fluorescence of a DtxR-based Corynebacterium glutamicum reporter strain, and stimulated growth. Since the increased Fe2+ availability was attributed to the interaction of HCO3− and chemical iron reduction, the abiotic effect postulated in this study is of general relevance in geochemical and biological environments.
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34
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Wang S, Denton KE, Hobbs KF, Weaver T, McFarlane JMB, Connelly KE, Gignac MC, Milosevich N, Hof F, Paci I, Musselman CA, Dykhuizen EC, Krusemark CJ. Optimization of Ligands Using Focused DNA-Encoded Libraries To Develop a Selective, Cell-Permeable CBX8 Chromodomain Inhibitor. ACS Chem Biol 2020; 15:112-131. [PMID: 31755685 DOI: 10.1021/acschembio.9b00654] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2, CBX4, CBX6, CBX7, and CBX8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarities in sequence and structure among the CBX ChDs provide a major obstacle in developing selective CBX ChD inhibitors. Here we report the selection of small, focused, DNA-encoded libraries (DELs) against multiple homologous ChDs to identify modifications to a parental ligand that confer both selectivity and potency for the ChD of CBX8. This on-DNA, medicinal chemistry approach enabled the development of SW2_110A, a selective, cell-permeable inhibitor of the CBX8 ChD. SW2_110A binds CBX8 ChD with a Kd of 800 nM, with minimal 5-fold selectivity for CBX8 ChD over all other CBX paralogs in vitro. SW2_110A specifically inhibits the association of CBX8 with chromatin in cells and inhibits the proliferation of THP1 leukemia cells driven by the MLL-AF9 translocation. In THP1 cells, SW2_110A treatment results in a significant decrease in the expression of MLL-AF9 target genes, including HOXA9, validating the previously established role for CBX8 in MLL-AF9 transcriptional activation, and defining the ChD as necessary for this function. The success of SW2_110A provides great promise for the development of highly selective and cell-permeable probes for the full CBX family. In addition, the approach taken provides a proof-of-principle demonstration of how DELs can be used iteratively for optimization of both ligand potency and selectivity.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Kyle E. Denton
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Kathryn F. Hobbs
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, Iowa 52242, United States
| | - Tyler Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, Iowa 52242, United States
| | | | - Katelyn E. Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Michael C. Gignac
- Department of Chemistry, University of Victoria, Victoria V8W 3V6, Canada
| | - Natalia Milosevich
- Department of Chemistry, University of Victoria, Victoria V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria V8W 3V6, Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria, Victoria V8W 3V6, Canada
| | - Catherine A. Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, Iowa 52242, United States
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
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35
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Thomas A, Cutlan R, Finnigan W, van der Giezen M, Harmer N. Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction. Commun Biol 2019; 2:429. [PMID: 31799431 PMCID: PMC6874671 DOI: 10.1038/s42003-019-0677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022] Open
Abstract
Carboxylic acid reductases (CARs) are biocatalysts of industrial importance. Their properties, especially their poor stability, render them sub-optimal for use in a bioindustrial pipeline. Here, we employed ancestral sequence reconstruction (ASR) - a burgeoning engineering tool that can identify stabilizing but enzymatically neutral mutations throughout a protein. We used a three-algorithm approach to reconstruct functional ancestors of the Mycobacterial and Nocardial CAR1 orthologues. Ancestral CARs (AncCARs) were confirmed to be CAR enzymes with a preference for aromatic carboxylic acids. Ancestors also showed varied tolerances to solvents, pH and in vivo-like salt concentrations. Compared to well-studied extant CARs, AncCARs had a Tm up to 35 °C higher, with half-lives up to nine times longer than the greatest previously observed. Using ancestral reconstruction we have expanded the existing CAR toolbox with three new thermostable CAR enzymes, providing access to the high temperature biosynthesis of aldehydes to drive new applications in biocatalysis.
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Affiliation(s)
- Adam Thomas
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Rhys Cutlan
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - William Finnigan
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Mark van der Giezen
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
- Centre for Organelle Research, University of Stavanger, Richard Johnsens gate 4, Stavanger, 4021 Norway
| | - Nicholas Harmer
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
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36
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Sun C, Li Y, Yates EA, Fernig DG. SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions. Protein Sci 2019; 29:19-27. [PMID: 31394001 DOI: 10.1002/pro.3703] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/27/2019] [Accepted: 08/06/2019] [Indexed: 02/02/2023]
Abstract
Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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37
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Bradshaw WJ, Bruxelle JF, Kovacs-Simon A, Harmer NJ, Janoir C, Péchiné S, Acharya KR, Michell SL. Molecular features of lipoprotein CD0873: A potential vaccine against the human pathogen Clostridioides difficile. J Biol Chem 2019; 294:15850-15861. [PMID: 31420448 PMCID: PMC6816091 DOI: 10.1074/jbc.ra119.010120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/15/2019] [Indexed: 01/10/2023] Open
Abstract
Clostridioides difficile is the primary cause of antibiotic-associated diarrhea and colitis, a healthcare-associated intestinal disease resulting in a significant fatality rate. Colonization of the gut is critical for C. difficile pathogenesis. The bacterial molecules essential for efficient colonization therefore offer great potential as vaccine candidates. Here we present findings demonstrating that the C. difficile immunogenic lipoprotein CD0873 plays a critical role in pathogen success in vivo. We found that in a dixenic colonization model, a CD0873-positive strain of C. difficile significantly outcompeted a CD0873-negative strain. Immunization of mice with recombinant CD0873 prevented long-term gut colonization and was correlated with a strong secretory IgA immune response. We further present high-resolution crystal structures of CD0873, at 1.35–2.50 Å resolutions, offering a first view of the ligand-binding pocket of CD0873 and provide evidence that this lipoprotein adhesin is part of a tyrosine import system, an amino acid key in C. difficile infection. These findings suggest that CD0873 could serve as an effective component in a vaccine against C. difficile.
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Affiliation(s)
- William J Bradshaw
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Jean-François Bruxelle
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), University Paris-Sud, Université Paris-Saclay, Châtenay-Malabry Cedex, France
| | - Andrea Kovacs-Simon
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Nicholas J Harmer
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.,Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Claire Janoir
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), University Paris-Sud, Université Paris-Saclay, Châtenay-Malabry Cedex, France
| | - Severine Péchiné
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), University Paris-Sud, Université Paris-Saclay, Châtenay-Malabry Cedex, France
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Stephen L Michell
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
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38
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Bandla S, Diaz S, Nasheuer HP, FitzGerald U. ATPase activity of human binding immunoglobulin protein (BiP) variants is enhanced by signal sequence and physiological concentrations of Mn 2. FEBS Open Bio 2019; 9:1355-1369. [PMID: 31033254 PMCID: PMC6668376 DOI: 10.1002/2211-5463.12645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 11/30/2022] Open
Abstract
B‐cell immunoglobulin binding protein (BiP) is an essential endoplasmic reticulum (ER) chaperone normally found in the ER lumen. However, BiP also has other extracellular and intracellular functions. As it is unclear whether peripheral BiP has a signal and/or ER retention sequence, here we produced and biochemically characterised four variants of BiP. The variants differed depending on the presence or the absence of signal and ER retention peptides. Proteins were purified using nickel affinity chromatography, and variant size and quality were confirmed using SDS/PAGE gels. The thermal denaturing temperature of these proteins was found to be 46–47 °C. In addition, we characterised nucleotide binding properties in the absence and the presence of divalent cations. Interestingly, in the absence of cations, ADP has a higher binding affinity to BiP than ATP. The presence of divalent cations results in a decrease of the Kd values of both ADP and ATP, indicating higher affinities of both nucleotides for BiP. ATPase assays were carried out to study the enzyme activity of these variants and to characterise the kinetic parameters of BiP variants. Variants with the signal sequence had higher specific activities than those without. Both Mg2+ and Mn2+ efficiently stimulated the ATPase activity of these variants at low micromolar concentrations, whereas calcium failed to stimulate BiP ATPase. Our novel findings indicate the potential functionality of BiP variants that retain a signal sequence, and also reveal the effect of physiological concentrations of cations on the nucleotide binding properties and enzyme activities of all variants.
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Affiliation(s)
- Sravanthi Bandla
- School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
| | - Suraya Diaz
- School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Heinz Peter Nasheuer
- School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Una FitzGerald
- School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Galway Neuroscience Centre, National University of Ireland Galway, Galway, Ireland
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39
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Huang L, Li X, Li Y, Yin X, Li Y, Wu B, Mo H, Liao CJ, Mengiste T, Guo W, Dai M, Zhang C. Endosidin2-14 Targets the Exocyst Complex in Plants and Fungal Pathogens to Inhibit Exocytosis. PLANT PHYSIOLOGY 2019; 180:1756-1770. [PMID: 31072814 PMCID: PMC6752926 DOI: 10.1104/pp.18.01457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 05/29/2023]
Abstract
The evolutionarily conserved octameric exocyst complex tethers secretory vesicles to the site of membrane fusion during exocytosis. The plant exocyst complex functions in cell wall biosynthesis, polarized growth, stress responses, and hormone signaling. In fungal pathogens, the exocyst complex is required for growth, development, and pathogenesis. Endosidin2 (ES2) is known to inhibit exocytosis in plant and mammalian cells by targeting the EXO70 subunit of the exocyst complex. Here we show that an analog of ES2, ES2-14, targets plant and two fungal EXO70s. A lower dosage of ES2-14 than of ES2 is required to inhibit plant growth, plant exocytic trafficking, and fungal growth. ES2-14 treatments inhibit appressorium formation and reduce lesion sizes caused by Magnaporthe oryzae Inhibition of EXO70 by ES2-14 in Botrytis cinerea also reduces its virulence in Arabidopsis (Arabidopsis thaliana). Interestingly, ES2-14 did not affect EXO70 localization or transferrin recycling in mammalian cells. Overall, our results indicate that a minor change in ES2 affects its specificity in targeting EXO70s in different organisms and they demonstrate the potential of using ES2-14 to study the mechanisms of plant and fungal exocytosis and the roles of exocytosis in fungus-plant interactions.
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Affiliation(s)
- Lei Huang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Yang Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Xianglin Yin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Yong Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Bin Wu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Huaping Mo
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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40
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Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H, Moraes I. Selection of Biophysical Methods for Characterisation of Membrane Proteins. Int J Mol Sci 2019; 20:E2605. [PMID: 31137900 PMCID: PMC6566885 DOI: 10.3390/ijms20102605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/01/2023] Open
Abstract
Over the years, there have been many developments and advances in the field of integral membrane protein research. As important pharmaceutical targets, it is paramount to understand the mechanisms of action that govern their structure-function relationships. However, the study of integral membrane proteins is still incredibly challenging, mostly due to their low expression and instability once extracted from the native biological membrane. Nevertheless, milligrams of pure, stable, and functional protein are always required for biochemical and structural studies. Many modern biophysical tools are available today that provide critical information regarding to the characterisation and behaviour of integral membrane proteins in solution. These biophysical approaches play an important role in both basic research and in early-stage drug discovery processes. In this review, it is not our objective to present a comprehensive list of all existing biophysical methods, but a selection of the most useful and easily applied to basic integral membrane protein research.
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Affiliation(s)
- Tristan O C Kwan
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Rosana Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Harish Cheruvara
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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41
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Yang S, Shergalis A, Lu D, Kyani A, Liu Z, Ljungman M, Neamati N. Design, Synthesis, and Biological Evaluation of Novel Allosteric Protein Disulfide Isomerase Inhibitors. J Med Chem 2019; 62:3447-3474. [PMID: 30759340 DOI: 10.1021/acs.jmedchem.8b01951] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) is responsible for nascent protein folding in the endoplasmic reticulum (ER) and is critical for glioblastoma survival. To improve the potency of lead PDI inhibitor BAP2 (( E)-3-(3-(4-hydroxyphenyl)-3-oxoprop-1-en-1-yl)benzonitrile), we designed and synthesized 67 analogues. We determined that PDI inhibition relied on the A ring hydroxyl group of the chalcone scaffold and cLogP increase in the sulfonamide chain improved potency. Docking studies revealed that BAP2 and analogues bind to His256 in the b' domain of PDI, and mutation of His256 to Ala abolishes BAP2 analogue activity. BAP2 and optimized analogue 59 have modest thiol reactivity; however, we propose that PDI inhibition by BAP2 analogues depends on the b' domain. Importantly, analogues inhibit glioblastoma cell growth, induce ER stress, increase expression of G2M checkpoint proteins, and reduce expression of DNA repair proteins. Cumulatively, our results support inhibition of PDI as a novel strategy to treat glioblastoma.
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Affiliation(s)
- Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Dan Lu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Anahita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Ziwei Liu
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
| | - Mats Ljungman
- Department of Radiation Oncology Rogel Cancer Center , University of Michigan Medical School and Rogel Cancer Center, School of Public Health , Ann Arbor , Michigan 48109 , United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center , University of Michigan , North Campus Research Complex, 1600 Huron Parkway , Ann Arbor , Michigan 48109 , United States
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42
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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43
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Ramos J, Muthukumaran J, Freire F, Paquete-Ferreira J, Otrelo-Cardoso AR, Svergun D, Panjkovich A, Santos-Silva T. Shedding Light on the Interaction of Human Anti-Apoptotic Bcl-2 Protein with Ligands through Biophysical and in Silico Studies. Int J Mol Sci 2019; 20:E860. [PMID: 30781512 PMCID: PMC6413030 DOI: 10.3390/ijms20040860] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022] Open
Abstract
Bcl-2 protein is involved in cell apoptosis and is considered an interesting target for anti-cancer therapy. The present study aims to understand the stability and conformational changes of Bcl-2 upon interaction with the inhibitor venetoclax, and to explore other drug-target regions. We combined biophysical and in silico approaches to understand the mechanism of ligand binding to Bcl-2. Thermal shift assay (TSA) and urea electrophoresis showed a significant increase in protein stability upon venetoclax incubation, which is corroborated by molecular docking and molecular dynamics simulations. An 18 °C shift in Bcl-2 melting temperature was observed in the TSA, corresponding to a binding affinity multiple times higher than that of any other reported Bcl-2 inhibitor. This protein-ligand interaction does not implicate alternations in protein conformation, as suggested by SAXS. Additionally, bioinformatics approaches were used to identify deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) of Bcl-2 and their impact on venetoclax binding, suggesting that venetoclax interaction is generally favored against these deleterious nsSNPs. Apart from the BH3 binding groove of Bcl-2, the flexible loop domain (FLD) also plays an important role in regulating the apoptotic process. High-throughput virtual screening (HTVS) identified 5 putative FLD inhibitors from the Zinc database, showing nanomolar affinity toward the FLD of Bcl-2.
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Affiliation(s)
- Joao Ramos
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Jayaraman Muthukumaran
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Filipe Freire
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - João Paquete-Ferreira
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Ana Rita Otrelo-Cardoso
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, 22067 Hamburg, Germany.
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, 22067 Hamburg, Germany.
| | - Teresa Santos-Silva
- UCIBIO-NOVA, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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44
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Heine V, Meinert-Berning C, Lück J, Mikowsky N, Voigt B, Riedel K, Steinbüchel A. The catabolism of 3,3'-thiodipropionic acid in Variovorax paradoxus strain TBEA6: A proteomic analysis. PLoS One 2019; 14:e0211876. [PMID: 30742653 PMCID: PMC6370202 DOI: 10.1371/journal.pone.0211876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Variovorax paradoxus strain TBEA6 is one of the few organisms known to utilize 3,3'-thiodipropionate (TDP) as the only source of carbon and energy. It cleaves TDP to 3-mercaptopropionate (3MP), which is a direct precursor for polythioester synthesis. To establish this process in V. paradoxus TBEA6, it is crucial to unravel its TDP metabolism. Therefore, a proteomic approach with subsequent deletion of interesting genes in the bacterium was chosen. Cells were cultivated with D-gluconate, TDP or 3-sulfinopropionate as the only carbon sources. Proteins with high abundances in gels of cells cultivated with either of the organic sulfur compounds were analyzed further. Thereby, we did not only confirm parts of the already postulated TDP metabolism, but also eight new protein candidates for TDP degradation were detected. Deletions of the corresponding genes (two enoyl-CoA hydratases (Ech-20 and Ech-30), an FK506-binding protein, a putative acetolactate synthase, a carnitinyl-CoA dehydratase, and a putative crotonase family protein) were obtained. Only the deletions of both Ech-20 and Ech-30 led to a TDP negative phenotype. The deletion mutant of VPARA_05510, which encodes the putative crotonase family protein showed reduced growth with TDP. The three genes are located in one cluster with genes proven to be involved in TDP metabolism. Thermal shift assays showed an increased stability of Ech-20 with TDP-CoA but not with TDP. These results indicate that Ech-20 uses TDP-CoA as a substrate instead of TDP. Hence, we postulate a new putative pathway for TDP metabolism. Ech-30 interacts with neither TDP-CoA nor TDP but might interact with other CoA-activated intermediates of the proposed pathway. Further enzyme characterization is necessary to unravel the complete pathway from TDP to 3MP.
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Affiliation(s)
- Viktoria Heine
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Christina Meinert-Berning
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Janina Lück
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Nadine Mikowsky
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Katharina Riedel
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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45
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Rack JGM, Ariza A, Drown BS, Henfrey C, Bartlett E, Shirai T, Hergenrother PJ, Ahel I. (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell Chem Biol 2018; 25:1533-1546.e12. [PMID: 30472116 PMCID: PMC6309922 DOI: 10.1016/j.chembiol.2018.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/25/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023]
Abstract
Protein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors. Here we present a comprehensive structural analysis of the enzymatically active family members ARH1 and ARH3. These two enzymes have very distinct substrate requirements. Our data show that binding of the adenosine ribose moiety is highly diverged between the two enzymes, whereas the active sites harboring the distal ribose closely resemble each other. Despite this apparent similarity, we elucidate the structural basis for the selective inhibition of ARH3 by the ADP-ribose analogues ADP-HPD and arginine-ADP-ribose. Together, our biochemical and structural work provides important insights into the mode of enzyme-ligand interaction, helps to understand differences in their catalytic behavior, and provides useful tools for targeted drug design.
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Affiliation(s)
| | - Antonio Ariza
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
| | - Bryon S Drown
- University of Illinois, Department of Chemistry, Urbana, IL 61801, USA
| | - Callum Henfrey
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
| | - Edward Bartlett
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK; Kyoto Institute of Technology, Matsugasaki Hashikamicho, Sakyo Ward, Kyoto, Japan
| | - Tomohiro Shirai
- University of Illinois, Department of Chemistry, Urbana, IL 61801, USA
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK.
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46
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Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase. Biochem J 2018; 475:2457-2471. [DOI: 10.1042/bcj20180271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 11/17/2022]
Abstract
Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase (MtHIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of MtHIBADH show that the enzyme is a dimer. The enzyme preferentially uses NAD+ as the cofactor and is specific to S-hydroxyisobutyric acid (HIBA). It can also use R-HIBA, l-serine and 3-hydroxypropanoic acid (3-HP) as substrates, but with much less efficiency. The pH optimum for activity is ∼11. Structures of the native enzyme, the holoenzyme, binary complexes with NAD+, S-HIBA, R-HIBA, l-serine and 3-HP and ternary complexes involving the substrates and NAD+ have been determined. None of the already known structures of HIBADH contain a substrate molecule at the binding site. The structures reported here provide for the first time, among other things, a clear indication of the location and interactions of the substrates at the active site. They also define the entrance of the substrates to the active site region. The structures provide information on the role of specific residues at the active site and the entrance. The results obtained from crystal structures are consistent with solution studies including mutational analysis. They lead to the proposal of a plausible mechanism of the action of the enzyme.
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47
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de Castro E, Reus TL, de Aguiar AM, Ávila AR, de Arruda Campos Brasil de Souza T. Procaspase-activating compound-1 induces apoptosis in Trypanosoma cruzi. Apoptosis 2018; 22:1564-1577. [PMID: 29058102 DOI: 10.1007/s10495-017-1428-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Some therapeutics for parasitic, cardiac and neurological diseases activate apoptosis. Therefore, the study of apoptotic proteins in pathogenic organisms is relevant. However, the molecular mechanism of apoptosis in unicellular organisms remain elusive, despite morphological evidence of its occurrence. In Trypanosoma cruzi, the causative agent of Chagas disease, metacaspase 3 (TcMCA3), seems to have a key role in parasite apoptosis. Accordingly, this work provides data concerning TcMCA3 regulation through its interaction with procaspase-activating compound 1 (PAC-1), a procaspase 3 activator. Indeed, PAC-1 reduced T. cruzi epimastigote viability with an IC50 of 14.12 µM and induced loss of mitochondrial potential and exposure of phosphatidylserine, features of the apoptotic process. Notwithstanding, those PAC-1-inducible effects were not conserved in metacyclic trypomastigotes. Moreover, PAC-1 reduced the viability of mammalian cells with a greater IC50 (25.70 µM) compared to T. cruzi epimastigotes, indicating distinct modes of binding between caspases and metacaspases. To shed light on the selectivity of metacaspases and caspases, we determined the structural features related to the PAC-1 binding sites in both types of proteins. These data are important for improving the understanding of the apoptosis pathway in T. cruzi so that TcMCA3 could be better targeted with future pharmaceuticals.
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Affiliation(s)
- Emanuella de Castro
- Laboratório de Proteômica e Engenharia de Proteínas, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | - Thamile Luciane Reus
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brazil
| | - Alessandra Melo de Aguiar
- Laboratório de Biologia Básica de Células Tronco, Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brazil
| | - Andrea Rodrigues Ávila
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brazil
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48
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O'Reilly MC, Dong SH, Rossi FM, Karlen KM, Kumar RS, Nair SK, Blackwell HE. Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop "Out" Conformation for LasR. Cell Chem Biol 2018; 25:1128-1139.e3. [PMID: 30033130 DOI: 10.1016/j.chembiol.2018.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/27/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Chemical strategies to block quorum sensing (QS) could provide a route to attenuate virulence in bacterial pathogens. Considerable research has focused on this approach in Pseudomonas aeruginosa, which uses the LuxR-type receptor LasR to regulate much of its QS network. Non-native ligands that antagonize LasR have been developed, yet we have little understanding of the mode by which these compounds interact with LasR and alter its function, as the receptor is unstable in their presence. Herein, we report an approach to circumvent this challenge through the study of a series of synthetic LasR agonists with varying levels of potency. Structural investigations of these ligands with the LasR ligand-binding domain reveal that certain agonists can enforce a conformation that deviates from that observed for other, often more potent agonists. These results, when combined with cell-based and biophysical analyses, suggest a functional model for LasR that could guide future ligand design.
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Affiliation(s)
- Matthew C O'Reilly
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Francis M Rossi
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Kaleigh M Karlen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Rohan S Kumar
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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49
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Ortiz-Soto ME, Ertl J, Mut J, Adelmann J, Le TA, Shan J, Teßmar J, Schlosser A, Engels B, Seibel J. Product-oriented chemical surface modification of a levansucrase (SacB) via an ene-type reaction. Chem Sci 2018; 9:5312-5321. [PMID: 30009003 PMCID: PMC6009436 DOI: 10.1039/c8sc01244j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/18/2018] [Indexed: 12/29/2022] Open
Abstract
Carbohydrate processing enzymes are sophisticated tools of living systems that have evolved to execute specific reactions on sugars. Here we present for the first time the site-selective chemical modification of exposed tyrosine residues in SacB, a levansucrase from Bacillus megaterium (Bm-LS) for enzyme engineering purposes via an ene-type reaction. Bm-LS is unable to sustain the synthesis of high molecular weight (HMW) levan (a fructose polymer) due to protein-oligosaccharide dissociation events occurring at an early stage during polymer elongation. We switched the catalyst from levan-like oligosaccharide synthesis to the efficient production of a HMW fructan polymer through the covalent addition of a flexible chemical side-chain that fluctuates over the central binding cavity of the enzyme preventing premature oligosaccharide disengagement.
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Affiliation(s)
- Maria Elena Ortiz-Soto
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Julia Ertl
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Jürgen Mut
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Juliane Adelmann
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Thien Anh Le
- Institut für Physikalische und Theoretische Chemie , Universität Würzburg , Emil-Fischer Strasse 42 , 97074 Würzburg , Germany
| | - Junwen Shan
- Abteilung für Funktionswerkstoffe der Medizin und der Zahnheilkunde , Universitätsklinikum Würzburg , Pleicherwall 2 , D-97070 Würzburg , Germany
| | - Jörg Teßmar
- Abteilung für Funktionswerkstoffe der Medizin und der Zahnheilkunde , Universitätsklinikum Würzburg , Pleicherwall 2 , D-97070 Würzburg , Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin , Universität Würzburg , Josef-Schneider Str. 2, Haus D15 , 97080 Würzburg , Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie , Universität Würzburg , Emil-Fischer Strasse 42 , 97074 Würzburg , Germany
| | - Jürgen Seibel
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
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50
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Chen S, Campillo-Brocal JC, Berglund P, Humble MS. Characterization of the stability of Vibrio fluvialis JS17 amine transaminase. J Biotechnol 2018; 282:10-17. [PMID: 29906477 DOI: 10.1016/j.jbiotec.2018.06.309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 10/14/2022]
Abstract
The amine transaminase from Vibrio fluvialis (Vf-ATA) is an attractive enzyme with applications within Biocatalysis for the preparation of chiral amines. Various catalytic properties of Vf-ATA have been investigated, but a biophysical characterization of its stability has been lacking. Today, the industrial application of Vf-ATA is limited by its low operational stability. In order to enhance the knowledge regarding the structural stability of ATAs, general characterizations of different ATAs are required. In this work, the stability of Vf-ATA was explored. First, the affinity between enzyme and pyridoxal-5'-phosphate (PLP) (KD value of 7.9 μM) was determined. Addition of PLP to enzyme preparations significantly improved the enzyme thermal stability by preventing enzyme unfolding. With the aim to understand if this was due to the PLP phosphate group coordination into the phosphate group binding cup, the effect of phosphate buffer on the enzyme stability was compared to HEPES buffer. Low concentrations of phosphate buffer showed a positive effect on the enzyme initial activity, while higher phosphate buffer concentrations prevented cofactor dissociation. Additionally, the effects of various amine or ketone substrates on the enzyme stability were explored. All tested amines caused a concentration dependent enzyme inactivation, while the corresponding ketones showed no or stabilizing effects. The enzyme inactivation due to the presence of amine can be connected to the formation of PMP, which forms in the presence of amines in the absence of ketone. Since PMP is not covalently bound to the enzyme, it could readily leave the enzyme upon formation. Exploring the different stability effects of cofactor, substrates, additives and buffer system on ATAs seems to be important in order to understand and improve the general performance of ATAs.
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Affiliation(s)
- Shan Chen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial Biotechnology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Jonatan C Campillo-Brocal
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial Biotechnology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Per Berglund
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial Biotechnology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Maria Svedendahl Humble
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Department of Industrial Biotechnology, AlbaNova University Center, SE-106 91, Stockholm, Sweden; Pharem Biotech AB, Biovation Park, Forskargatan 20 J, SE-151 36, Södertälje, Sweden.
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