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González A, Casado J, Chueca E, Salillas S, Velázquez-Campoy A, Sancho J, Lanas Á. Small Molecule Inhibitors of the Response Regulator ArsR Exhibit Bactericidal Activity against Helicobacter pylori. Microorganisms 2020; 8:microorganisms8040503. [PMID: 32244717 PMCID: PMC7232201 DOI: 10.3390/microorganisms8040503] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is considered the most prevalent bacterial pathogen in humans. The increasing antibiotic resistance evolved by this microorganism has raised alarm bells worldwide due to the significant reduction in the eradication rates of traditional standard therapies. A major challenge in this antibiotic resistance crisis is the identification of novel microbial targets whose inhibitors can overcome the currently circulating resistome. In the present study, we have validated the use of the essential response regulator ArsR as a novel and promising therapeutic target against H. pylori infections. A high-throughput screening of a repurposing chemical library using a fluorescence-based thermal shift assay identified several ArsR binders. At least four of these low-molecular weight compounds noticeably inhibited the DNA binding activity of ArsR and showed bactericidal effects against antibiotic-resistant strains of H. pylori. Among the ArsR inhibitors, a human secondary bile acid, lithocholic acid, quickly destroyed H. pylori cells and exhibited partial synergistic action in combination with clarithromycin or levofloxacin, while the antimicrobial effect of this compound against representative members of the normal human microbiota such as Escherichia coli and Staphylococcus epidermidis appeared irrelevant. Our results enhance the battery of novel therapeutic tools against refractory infections caused by multidrug-resistant H. pylori strains.
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Affiliation(s)
- Andrés González
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-976-762807
| | - Javier Casado
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Eduardo Chueca
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Sandra Salillas
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Government of Aragon, Ranillas 1-D, 50018 Zaragoza, Spain
| | - Javier Sancho
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Ángel Lanas
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, San Juan Bosco 15, 50009 Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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102
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Glöckner S, Ngo K, Wagner B, Heine A, Klebe G. The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II. Biomolecules 2020; 10:E509. [PMID: 32230853 PMCID: PMC7226267 DOI: 10.3390/biom10040509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022] Open
Abstract
The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.
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Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Björn Wagner
- F. Hoffmann-La Roche AG, Pharmaceutical Research & Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland;
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
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103
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Khowsathit J, Bazzoli A, Cheng H, Karanicolas J. Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation. ACS CENTRAL SCIENCE 2020; 6:390-403. [PMID: 32232139 PMCID: PMC7099597 DOI: 10.1021/acscentsci.9b01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.
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Affiliation(s)
- Jittasak Khowsathit
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Andrea Bazzoli
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Hong Cheng
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
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104
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Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors. ACS Chem Biol 2020; 15:675-685. [PMID: 32027480 DOI: 10.1021/acschembio.9b00895] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thermodynamics and kinetics of protein-ligand binding are both important aspects for the design of novel drug molecules. Presently, thermodynamic data are collected with isothermal titration calorimetry, while kinetic data are mostly derived from surface plasmon resonance. The new method of kinITC provides both thermodynamic and kinetic data from calorimetric titration measurements. The present study demonstrates the convenient collection of calorimetric data suitable for both thermodynamic and kinetic analysis for two series of congeneric ligands of human carbonic anhydrase II and correlates these findings with structural data obtained by macromolecular crystallography to shed light on the importance of shape complementarity for thermodynamics and kinetics governing a protein-ligand binding event. The study shows how minute chemical alterations change preferred ligand conformation and can be used to manipulate thermodynamic and kinetic signatures of binding. They give rise to the observation that analogous n-alkyl and n-alkyloxy derivatives of identical chain length swap their binding kinetic properties at unchanged binding affinity.
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Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph P Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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105
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Brown JI, Page BDG, Frankel A. The application of differential scanning fluorimetry in exploring bisubstrate binding to protein arginine N-methyltransferase 1. Methods 2020; 175:10-23. [PMID: 31726226 DOI: 10.1016/j.ymeth.2019.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022] Open
Abstract
Protein arginine N-methyltransferases (PRMTs) are a family of 9 enzymes that catalyze mono- or di-methylation of arginine residues using S-adenosyl-l-methionine (SAM). Arginine methylation is an important post-translational modification that can regulate the activity and structure of target proteins. Altered PRMT activity can lead to a variety of health issues including neurodevelopmental disease, autoimmune disorders, cancer, and cardiovascular disease. Thus, developing a robust mechanistic understanding of PRMT function may provide insight into these various disease states and enable the development of potential therapeutic agents. Although PRMTs have been studied for nearly two decades, a consensus regarding the mechanism of action for this class of enzymes has remained noticeably elusive. To address this shortcoming, differential scanning fluorimetry (DSF) was used to gain mechanistic insight into the order of PRMT substrate and cofactor binding. This methodology confirms that PRMT cofactor binding precedes target substrate binding and supports the use of DSF to study bisubstrate enzymatic reaction mechanisms.
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Affiliation(s)
- Jennifer I Brown
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada; Department of Oncology and Pathology, Karolinska Institutet, Tomtebodavagen 23A, Stockholm, Sweden.
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada.
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106
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Yamanaka K, Takahashi Y, Azuma Y, Hantani Y. Assay Development and Screening for the Identification of Ganglioside GM3 Synthase Inhibitors. Biochemistry 2020; 59:1242-1251. [DOI: 10.1021/acs.biochem.0c00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kenji Yamanaka
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yu Takahashi
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yuya Azuma
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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107
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Tian W, Trader DJ. Discovery of a Small Molecule Probe of Rpn-6, an Essential Subunit of the 26S Proteasome. ACS Chem Biol 2020; 15:554-561. [PMID: 31877015 DOI: 10.1021/acschembio.9b01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A considerable number of essential cellular proteins have no catalytic activity and serve instead as structural components to aid in assembling protein complexes. For example, the assembly and function of the 26S proteasome, the major enzymatic complex necessary for ubiquitin-dependent protein degradation, require a number of essential protein contacts to associate the 19S regulatory particle with the 20S core particle. Previously, small molecule inhibitors of the active sites of the 20S core particle have been developed, but the activity of the 26S proteasome could also be altered via the disruption of its assembly. We were interested in discovering a small molecule binder of Rpn-6, as it is among several essential proteins that facilitate 26S assembly, which could be used to further our understanding of the association of the 19S regulatory particle with the 20S core particle. Additionally, we were interested in whether a small molecule-Rpn-6 interaction could potentially be cytotoxic to cancer cells that rely heavily on proteasome activity for survival. A workflow for utilizing a one-bead, one-compound library and a thermal shift assay was developed to discover such a molecule. TXS-8, our lead hit, was discovered to have a low micromolar binding affinity for Rpn-6 as well as very limited binding to other proteins. The cytotoxicity of TXS-8 was evaluated in several cell lines, revealing increased cytotoxicity to hematological cancers. Discovery of this peptoid binder of Rpn-6 provides the initial evidence that Rpn-6 could be a druggable target to affect protein degradation and serves as a primary scaffold from which to design more potent binders. We suspect that Rpn-6 could have additional essential roles beyond that of a molecular clamp of the proteasome to help hematological cancer cells survive and that TXS-8 can serve as a useful tool for further elucidating its roles.
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Affiliation(s)
- Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Darci J. Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
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108
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Tetley GJN, Murphy NP, Bonetto S, Ivanova-Berndt G, Revell J, Mott HR, Cooley RN, Owen D. The discovery and maturation of peptide biologics targeting the small G-protein Cdc42: A bioblockade for Ras-driven signaling. J Biol Chem 2020; 295:2866-2884. [PMID: 31959628 DOI: 10.1074/jbc.ra119.010077] [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: 07/04/2019] [Revised: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Aberrant Ras signaling drives 30% of cancers, and inhibition of the Rho family small GTPase signaling has been shown to combat Ras-driven cancers. Here, we present the discovery of a 16-mer cyclic peptide that binds to Cdc42 with nanomolar affinity. Affinity maturation of this sequence has produced a panel of derived candidates with increased affinity and modulated specificity for other closely-related small GTPases. The structure of the tightest binding peptide was solved by NMR, and its binding site on Cdc42 was determined. Addition of a cell-penetrating sequence allowed the peptides to access the cell interior and engage with their target(s), modulating signaling pathways. In Ras-driven cancer cell models, the peptides have an inhibitory effect on proliferation and show suppression of both invasion and motility. As such, they represent promising candidates for Rho-family small GTPase inhibitors and therapeutics targeting Ras-driven cancers. Our data add to the growing literature demonstrating that peptides are establishing their place in the biologics arm of drug discovery.
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Affiliation(s)
- George J N Tetley
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Natasha P Murphy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Stephane Bonetto
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Gabriela Ivanova-Berndt
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jefferson Revell
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
| | - R Neil Cooley
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
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109
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Huang X, Slavkovic S, Song E, Botta A, Mehrazma B, Lento C, Johnson PE, Sweeney G, Wilson DJ. A Unique Conformational Distortion Mechanism Drives Lipocalin 2 Binding to Bacterial Siderophores. ACS Chem Biol 2020; 15:234-242. [PMID: 31613081 DOI: 10.1021/acschembio.9b00820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Lcn2 is a host defense protein induced via the innate immune response to sequester iron-loaded bacterial siderophores. However, excess or prolonged elevation of Lcn2 levels can induce adverse cellular effects, including oxidative stress and inflammation. In this work, we use Hydrogen-Deuterium eXchange (HDX) and Isothermal Titration Calorimetry (ITC) to characterize the binding interaction between Lcn2 and siderophores enterobactin and 2,3-DHBA, in the presence and absence of iron. Our results indicate a rare "Type II" interaction in which binding of siderophores drives the protein conformational equilibrium toward an unfolded state. Linking our molecular model to cellular assays, we demonstrate that this "distorted binding mode" facilitates a deleterious cellular accumulation of reactive oxygen species that could represent the molecular origin of Lcn2 pathology. These results add important insights into mechanisms of Lcn2 action and have implications in Lcn2-mediated effects including inflammation.
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110
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Seebald L, Madec AGE, Imperiali B. Deploying Fluorescent Nucleoside Analogues for High-Throughput Inhibitor Screening. Chembiochem 2020; 21:108-112. [PMID: 31709708 PMCID: PMC6980326 DOI: 10.1002/cbic.201900671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Indexed: 12/27/2022]
Abstract
High-throughput small-molecule screening in drug discovery processes commonly rely on fluorescence-based methods including fluorescent polarization and fluorescence/Förster resonance energy transfer. These techniques use highly accessible instrumentation; however, they can suffer from high false-negative rates and background signals, or might involve complex schemes for the introduction of fluorophore pairs. Herein we present the synthesis and application of fluorescent nucleoside analogues as the foundation for directed approaches for competitive binding analyses. The general approach describes selective fluorescent environment-sensitive (ES) nucleoside analogues that are adaptable to diverse enzymes that act on nucleoside-based substrates. We demonstrate screening a set of uridine analogues and development of an assay for fragment-based lead discovery with the TcdB glycosyltransferase (GT), an enzyme associated with virulence in Clostridium difficile. The uridine-based probe used for this high-throughput screen has a KD value of 7.2 μm with the TcdB GT and shows a >30-fold increase in fluorescence intensity upon binding. The ES-based probe assay is benchmarked against two other screening approaches.
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Affiliation(s)
- Leah Seebald
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amaël G E Madec
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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111
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Zakšauskas A, Čapkauskaitė E, Jezepčikas L, Linkuvienė V, Paketurytė V, Smirnov A, Leitans J, Kazaks A, Dvinskis E, Manakova E, Gražulis S, Tars K, Matulis D. Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Eur J Med Chem 2020; 185:111825. [PMID: 31740053 DOI: 10.1016/j.ejmech.2019.111825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
By applying an approach of a "ring with two tails", a series of novel inhibitors possessing high-affinity and significant selectivity towards selected carbonic anhydrase (CA) isoforms has been designed. The "ring" consists of 2-chloro/bromo-benzenesulfonamide, where the sulfonamide group is as an anchor coordinating the Zn(II) in the active site of CAs, and halogen atom orients the ring affecting the affinity and selectivity. First "tail" is a substituent containing carbonyl, carboxyl, hydroxyl, ether groups or hydrophilic amide linkage. The second "tail" contains aryl- or alkyl-substituents attached through a sulfanyl or sulfonyl group. Both "tails" are connected to the benzene ring and play a crucial role in selectivity. Varying the substituents, we designed compounds selective for CA VII, CA IX, CA XII, or CA XIV. Since due to binding-linked protonation reactions the binding-ready fractions of the compound and protein are much lower than one, the "intrinsic" affinities were calculated that should be used to study correlations between crystal structures and the thermodynamics of binding for rational drug design. The "intrinsic" affinities together with the intrinsic enthalpies and entropies of binding together with co-crystal structures were used demonstrate structural factors determining major contributions for compound affinity and selectivity.
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Affiliation(s)
- Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Linas Jezepčikas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elviss Dvinskis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Saulius Gražulis
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania.
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112
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Sindrewicz P, Yates EA, Turnbull JE, Lian LY, Yu LG. Interaction with the heparin-derived binding inhibitors destabilizes galectin-3 protein structure. Biochem Biophys Res Commun 2019; 523:336-341. [PMID: 31866013 DOI: 10.1016/j.bbrc.2019.12.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/22/2022]
Abstract
The β-galactoside-binding protein, galectin-3, is extensively involved in cancer development, progression and metastasis through multiple mechanisms. Inhibition of the galectin-3-mediated actions is increasingly considered as a promising therapeutic approach for cancer treatment. Our early studies have identified several novel galectin-3 binding inhibitors from chemical modification of the anticoagulant drug heparin. These heparin-derived galectin-3 binding inhibitors, which show no anticoagulant activity and bind to the galectin-3 canonical carbohydrate-binding site, induce galectin-3 conformational changes and inhibit galectin-3-mediated cancer cell adhesion, invasion and angiogenesis in vitro and reduce metastasis in mice. In this study, we determined the binding affinities of these heparin-derived ligands to galectin-3 using an isothermal titration calorimetry (ITC) ligand displacement approach. Such ITC experiments showed that the 2-de-O-sulphated, N-acetylated (compound E) and 6-de-O-sulphated, N-acetylated (F) heparin-derived ligands and their ultra-low molecular weight sub-fractions (E3 and F3) bind to galectin-3 with KD ranging from 0.96 to 1.32 mM.Differential scanning fluorimetry analysis revealed that, in contrast to the disaccharide ligand, N-acetyl-lactosamine, which binds to the fully folded form of galectin-3 and promotes galectin-3 thermal stability, the heparin-derived ligands preferentially bind to the unfolded state of galectin-3 and cause destabilization of the galectin-3 protein structure. These results provide molecular insights into the interaction of galectin-3 with the heparin-derived ligands and explain the previously demonstrated in vitro and in vivo effects of these binding inhibitors on galectin-3-mediated cancer cell behaviours.
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Affiliation(s)
- Paulina Sindrewicz
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jeremy E Turnbull
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Lu-Yun Lian
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Lu-Gang Yu
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GE, UK.
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113
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Pollock K, Liu M, Zaleska M, Meniconi M, Pfuhl M, Collins I, Guettler S. Fragment-based screening identifies molecules targeting the substrate-binding ankyrin repeat domains of tankyrase. Sci Rep 2019; 9:19130. [PMID: 31836723 PMCID: PMC6911004 DOI: 10.1038/s41598-019-55240-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
The PARP enzyme and scaffolding protein tankyrase (TNKS, TNKS2) uses its ankyrin repeat clusters (ARCs) to bind a wide range of proteins and thereby controls diverse cellular functions. A number of these are implicated in cancer-relevant processes, including Wnt/β-catenin signalling, Hippo signalling and telomere maintenance. The ARCs recognise a conserved tankyrase-binding peptide motif (TBM). All currently available tankyrase inhibitors target the catalytic domain and inhibit tankyrase's poly(ADP-ribosyl)ation function. However, there is emerging evidence that catalysis-independent "scaffolding" mechanisms contribute to tankyrase function. Here we report a fragment-based screening programme against tankyrase ARC domains, using a combination of biophysical assays, including differential scanning fluorimetry (DSF) and nuclear magnetic resonance (NMR) spectroscopy. We identify fragment molecules that will serve as starting points for the development of tankyrase substrate binding antagonists. Such compounds will enable probing the scaffolding functions of tankyrase, and may, in the future, provide potential alternative therapeutic approaches to inhibiting tankyrase activity in cancer and other conditions.
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Affiliation(s)
- Katie Pollock
- Divisions of Structural Biology & Cancer Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom
- Cancer Research UK Beatson Institute, Drug Discovery Programme, Glasgow, G61 1BD, United Kingdom
| | - Manjuan Liu
- Division of Cancer Therapeutics, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom
| | - Mariola Zaleska
- Divisions of Structural Biology & Cancer Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom
| | - Mirco Meniconi
- Division of Cancer Therapeutics, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom
| | - Mark Pfuhl
- School of Cardiovascular Medicine and Sciences and Randall Centre, King's College London, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom.
| | - Sebastian Guettler
- Divisions of Structural Biology & Cancer Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, United Kingdom.
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114
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Sorenson AE, Schaeffer PM. A new bivalent fluorescent fusion protein for differential Cu(II) and Zn(II) ion detection in aqueous solution. Anal Chim Acta 2019; 1101:120-128. [PMID: 32029102 DOI: 10.1016/j.aca.2019.12.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 12/15/2022]
Abstract
Simple and easy to engineer metal-sensing molecules that are capable of differentiating metal ions and producing metal-specific signals are highly desirable. Metal ions affect the thermal stability of proteins by increasing or decreasing their resistance to unfolding. This work illustrates a new strategy for designing bivalent fluorescent fusion proteins capable of differentiating metal ions in solution through their distinct effects on a protein's thermal stability. A new dual purpose metal sensor was developed consisting of biotin protein ligase (BirA) from B. pseudomallei (Bp) fused to green fluorescent protein (GFP). When coupled with differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) for signal-transduction detection, Bp BirA-GFP yields distinct protein unfolding signatures with Zn(II) and Cu(II) ions in aqueous solutions. The limit of detection of the system is ∼1 μM for both metal species. The system can be used in a variety of high-throughput assay formats including for the screening of metal-binding proteins and chelators. Bp BirA-GFP has also the additional benefit of being useful in Cu(II) ion field-testing applications through simple visual observation of a temperature-dependent loss of fluorescence. Bp BirA-GFP is the first example of a 2protein-based dual purpose Cu(II) and Zn(II) ion sensor compatible with two different yet complementary signal-transduction detection systems.
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Affiliation(s)
- A E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD, 4811, Australia
| | - P M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD, 4811, Australia.
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115
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Han H, Jain AD, Truica MI, Izquierdo-Ferrer J, Anker JF, Lysy B, Sagar V, Luan Y, Chalmers ZR, Unno K, Mok H, Vatapalli R, Yoo YA, Rodriguez Y, Kandela I, Parker JB, Chakravarti D, Mishra RK, Schiltz GE, Abdulkadir SA. Small-Molecule MYC Inhibitors Suppress Tumor Growth and Enhance Immunotherapy. Cancer Cell 2019; 36:483-497.e15. [PMID: 31679823 PMCID: PMC6939458 DOI: 10.1016/j.ccell.2019.10.001] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/19/2019] [Accepted: 09/30/2019] [Indexed: 01/16/2023]
Abstract
Small molecules that directly target MYC and are also well tolerated in vivo will provide invaluable chemical probes and potential anti-cancer therapeutic agents. We developed a series of small-molecule MYC inhibitors that engage MYC inside cells, disrupt MYC/MAX dimers, and impair MYC-driven gene expression. The compounds enhance MYC phosphorylation on threonine-58, consequently increasing proteasome-mediated MYC degradation. The initial lead, MYC inhibitor 361 (MYCi361), suppressed in vivo tumor growth in mice, increased tumor immune cell infiltration, upregulated PD-L1 on tumors, and sensitized tumors to anti-PD1 immunotherapy. However, 361 demonstrated a narrow therapeutic index. An improved analog, MYCi975 showed better tolerability. These findings suggest the potential of small-molecule MYC inhibitors as chemical probes and possible anti-cancer therapeutic agents.
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Affiliation(s)
- Huiying Han
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Atul D Jain
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208, USA
| | - Mihai I Truica
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Javier Izquierdo-Ferrer
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208, USA
| | - Jonathan F Anker
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Barbara Lysy
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vinay Sagar
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yi Luan
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zachary R Chalmers
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kenji Unno
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hanlin Mok
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rajita Vatapalli
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Young A Yoo
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yara Rodriguez
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - J Brandon Parker
- Division of Reproductive Science in Medicine, Department of OB/GYN, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Debabrata Chakravarti
- Division of Reproductive Science in Medicine, Department of OB/GYN, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago IL 60611, USA
| | - Rama K Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208, USA; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago IL 60611, USA
| | - Gary E Schiltz
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208, USA; The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago IL 60611, USA
| | - Sarki A Abdulkadir
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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116
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Choi HW, Wang L, Powell AF, Strickler SR, Wang D, Dempsey DA, Schroeder FC, Klessig DF. A genome-wide screen for human salicylic acid (SA)-binding proteins reveals targets through which SA may influence development of various diseases. Sci Rep 2019; 9:13084. [PMID: 31511554 PMCID: PMC6739329 DOI: 10.1038/s41598-019-49234-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/19/2019] [Indexed: 12/25/2022] Open
Abstract
Salicylic acid (SA) is the major metabolite and active ingredient of aspirin; both compounds reduce pain, fever, and inflammation. Despite over a century of research, aspirin/SA’s mechanism(s) of action is still only partially understood. Here we report the results of a genome-wide, high-throughput screen to identify potential SA-binding proteins (SABPs) in human HEK293 cells. Following photo-affinity crosslinking to 4-azidoSA and immuno-selection with an anti-SA antibody, approximately 2,000 proteins were identified. Among these, 95 were enriched more than 10-fold. Pathway enrichment analysis with these 95 candidate SABPs (cSABPs) revealed possible involvement of SA in multiple biological pathways, including (i) glycolysis, (ii) cytoskeletal assembly and/or signaling, and (iii) NF-κB-mediated immune signaling. The two most enriched cSABPs, which corresponded to the glycolytic enzymes alpha-enolase (ENO1) and pyruvate kinase isozyme M2 (PKM2), were assessed for their ability to bind SA and SA’s more potent derivative amorfrutin B1 (amoB1). SA and amoB1 bound recombinant ENO1 and PKM2 at low millimolar and micromolar concentrations, respectively, and inhibited their enzymatic activities in vitro. Consistent with these results, low millimolar concentrations of SA suppressed glycolytic activity in HEK293 cells. To provide insights into how SA might affect various human diseases, a cSABP-human disorder/disease network map was also generated.
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Affiliation(s)
- Hyong Woo Choi
- Boyce Thompson Institute, Ithaca, New York, 14853, USA.,Department of Plant Medicals, Andong National University, Andong, 36729, Korea
| | - Lei Wang
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | | | | | - Dekai Wang
- Boyce Thompson Institute, Ithaca, New York, 14853, USA.,College of life sciences and medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
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117
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Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors. Sci Rep 2019; 9:12710. [PMID: 31481705 PMCID: PMC6722136 DOI: 10.1038/s41598-019-49094-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 08/15/2019] [Indexed: 01/25/2023] Open
Abstract
Secretory human carbonic anhydrase VI (CA VI) has emerged as a potential drug target due to its role in pathological states, such as excess acidity-caused dental caries and injuries of gastric epithelium. Currently, there are no available CA VI-selective inhibitors or crystallographic structures of inhibitors bound to CA VI. The present study focuses on the site-directed CA II mutant mimicking the active site of CA VI for inhibitor screening. The interactions between CA VI-mimic and a series of benzenesulfonamides were evaluated by fluorescent thermal shift assay, stopped-flow CO2 hydration assay, isothermal titration calorimetry, and X-ray crystallography. Kinetic parameters showed that A65T, N67Q, F130Y, V134Q, L203T mutations did not influence catalytic properties of CA II, but inhibitor affinities resembled CA VI, exhibiting up to 0.16 nM intrinsic affinity for CA VI-mimic. Structurally, binding site of CA VI-mimic was found to be similar to CA VI. The ligand interactions with mutated side chains observed in three crystallographic structures allowed to rationalize observed variation of binding modes and experimental binding affinities to CA VI. This integrative set of kinetic, thermodynamic, and structural data revealed CA VI-mimic as a useful model to design CA VI-specific inhibitors which could be beneficial for novel therapeutic applications.
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118
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Expression, purification and stabilization of human serotonin transporter from E. coli. Protein Expr Purif 2019; 164:105479. [PMID: 31442583 DOI: 10.1016/j.pep.2019.105479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/31/2019] [Accepted: 08/15/2019] [Indexed: 11/21/2022]
Abstract
The serotonin transporter belongs to the family of sodium-chloride coupled neurotransmitter transporter and is related to depression in humans. It is therefore an important drug target to support treatment of depression. Recently, structures of human serotonin transporter in complex with inhibitor molecules have been published. However, the production of large protein amounts for crystallization experiments remains a bottleneck. Here we present the possibility to obtain purified serotonin transporter from E. coli. Fos-choline 12 solubilized target protein was obtained with a purity of >95% and a yield of 1.2 mg L-1 culture in autoinduction medium. CD spectroscopic analysis of protein stability allowed identifying CHS and POPX as stabilizing components, which increased hSERT thermostability by 7 °C. The kinetic dissociation constant KD of 2.8 μM (±0.05) for of the inhibitor Desipramine was determined with a ka of 10,848 M - 1 s-1 (±220) and a kd of 0.03 s-1 (±4.7 × 10-5).
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119
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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120
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Hall J. A simple model for determining affinity from irreversible thermal shifts. Protein Sci 2019; 28:1880-1887. [PMID: 31361943 PMCID: PMC6739816 DOI: 10.1002/pro.3701] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 11/23/2022]
Abstract
Thermal denaturation (Tm) data are easy to obtain; it is a technique that is used by both small labs and large‐scale industrial organizations. The link between ligand affinity (KD) and ΔTm is understood for reversible denaturation; however, there is a gap in our understanding of how to quantitatively interpret ΔTm for the many proteins that irreversibly denature. To better understand the origin, and extent of applicability, of a KD to ΔTm correlate, we define equations relating KD and ΔTm for irreversible protein unfolding, which we test with computational models and experimental data. These results suggest a general relationship exists between KD and ΔTm for irreversible denaturation.
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Affiliation(s)
- Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Groton, Connecticut
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121
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Syed MM, Doshi PJ, Dhavale DD, Doshi JB, Kate SL, Kulkarni G, Sharma N, Uppuladinne M, Sonavane U, Joshi R, Kulkarni MV. Potential of isoquercitrin as antisickling agent: a multi-spectroscopic, thermophoresis and molecular modeling approach. J Biomol Struct Dyn 2019; 38:2717-2736. [PMID: 31315526 DOI: 10.1080/07391102.2019.1645735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sickle cell disease is an inherited disease caused by point mutation in hemoglobin (β-globin gene). Under oxygen saturation, sickle hemoglobin form polymers, leading to rigid erythrocytes. The transition of the blood vessels is altered and initiated by the adhesion of erythrocytes, neutrophils and endothelial cells. Sickle Hemoglobin (HbS) polymerization is a major cause in red blood cells (RBC), promoting sickling and destruction of RBCs. Isoquercitrin, a medicinal bioactive compound found in various medicinal plants, has multiple health benefits. The present study examines the potential of isoquercitrin as an anti-sickle agent, showing a significant decrease in the rate of polymerization as well as sickling of RBCs. Isoquercitrin-induced graded alteration in absorbance and fluorescence of HbS, confirmed their interaction. A negative value of ΔG° strongly suggests that it is a spontaneous exothermic reaction induced by entropy. Negative ΔH° and positive ΔS° predicted that hydrogen and hydrophobic binding forces interfered with a hydrophobic microenvironment of β6Val leading to polymerization inhibition of HbS. HbS-Isoquercitrin complex exhibits helical structural changes leading to destabilization of the HbS polymer as confirmed by CD spectroscopy. MST and DSC results indicate greater changes in thermophoretic mobility and thermal stability of sickle hemoglobin in the presence of isoquercitrin, respectively. These findings were also supported by molecular simulation studies using DOCK6 and GROMACS. Hence, we can conclude that isoquercitrin interacts with HbS through hydrogen bonding, which leads to polymerization inhibition. Consequently, isoquercitrin could potentially be used as a medication for the treatment of sickle cell disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muntjeeb M Syed
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | - Pooja J Doshi
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | - Dilip D Dhavale
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
| | | | - Sudam L Kate
- College of Ayurveda and Research Centre Hadapsar, Maharashtra Arogya Mandal's Sumatibhai Shah Ayurved Mahavidyalaya, Pune, India
| | - Girish Kulkarni
- College of Ayurveda and Research Centre Hadapsar, Maharashtra Arogya Mandal's Sumatibhai Shah Ayurved Mahavidyalaya, Pune, India
| | - Neeru Sharma
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Mallikarjunachari Uppuladinne
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Uddhavesh Sonavane
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Rajendra Joshi
- HPC Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, India
| | - Mohan V Kulkarni
- Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Pune, India
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122
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Structural characterization of life-extending Caenorhabditis elegans Lipid Binding Protein 8. Sci Rep 2019; 9:9966. [PMID: 31292465 PMCID: PMC6620326 DOI: 10.1038/s41598-019-46230-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/24/2019] [Indexed: 01/07/2023] Open
Abstract
The lysosome plays a crucial role in the regulation of longevity. Lysosomal degradation is tightly coupled with autophagy that is induced by many longevity paradigms and required for lifespan extension. The lysosome also serves as a hub for signal transduction and regulates longevity via affecting nuclear transcription. One lysosome-to-nucleus retrograde signaling pathway is mediated by a lysosome-associated fatty acid binding protein LBP-8 in Caenorhabditis elegans. LBP-8 shuttles lysosomal lipids into the nucleus to activate lipid regulated nuclear receptors NHR-49 and NHR-80 and consequently promote longevity. However, the structural basis of LBP-8 action remains unclear. Here, we determined the first 1.3 Å high-resolution structure of this life-extending protein LBP-8, which allowed us to identify a structurally conserved nuclear localization signal and amino acids involved in lipid binding. Additionally, we described the range of fatty acids LBP-8 is capable of binding and show that it binds to life-extending ligands in worms such as oleic acid and oleoylethanolamide with high affinity.
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123
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Zhang H, Jiang JM, Han L, Lao YZ, Zheng D, Chen YY, Wan SJ, Zheng CW, Tan HS, Li ZG, Xu HX. Uncariitannin, a polyphenolic polymer from Uncaria gambier, attenuates Staphylococcus aureus virulence through an MgrA-mediated regulation of α-hemolysin. Pharmacol Res 2019; 147:104328. [PMID: 31288080 DOI: 10.1016/j.phrs.2019.104328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
Abstract
A global transcriptional regulator, MgrA, was previously identified as a key determinant of virulence in Staphylococcus aureus. An 80% EtOH extract of Uncaria gambier was found to attenuate the virulence of S. aureus via its effects on MgrA. Using bioassay-guided fractionation, a polyphenolic polymer, uncariitannin, was found to be the main bioactive constituent of the extract, and its structure was characterized using spectral and chemical analysis. The molecular weight and polydispersity of uncariitannin were determined by gel permeation chromatography-refractive index-light scattering analysis. An electrophoretic mobility shift assay showed that uncariitannin could effectively inhibit the interaction of MgrA with DNA in a dose-dependent manner. Treatment with uncariitannin could decrease the mRNA and protein levels of Hla in both the S. aureus Newman and USA300 LAC strains. Further analysis of Hla expression levels in the Newman ΔmgrA and Newman ΔmgrA/pYJ335-mgrA strains indicated that uncariitannin altered Hla expression primarily in an MgrA-dependent manner. A mouse model of infection indicated that uncariitannin could attenuate MRSA virulence. In conclusion, uncariitannin may be a potential candidate for further development as an antivirulence agent for the treatment of S. aureus infection.
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Affiliation(s)
- Hong Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Jia-Ming Jiang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Li Han
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Yuan-Zhi Lao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Dan Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Yu-Yu Chen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Shi-Jie Wan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Chang-Wu Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Hong-Sheng Tan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China
| | - Zi-Gang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, PR China.
| | - Hong-Xi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Shanghai, 201203, PR China.
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124
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Prevet H, Collins I. Labelled chemical probes for demonstrating direct target engagement in living systems. Future Med Chem 2019; 11:1195-1224. [PMID: 31280668 DOI: 10.4155/fmc-2018-0370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between in vitro pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology.
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Affiliation(s)
- Hugues Prevet
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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125
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Kirsch P, Jakob V, Oberhausen K, Stein SC, Cucarro I, Schulz TF, Empting M. Fragment-Based Discovery of a Qualified Hit Targeting the Latency-Associated Nuclear Antigen of the Oncogenic Kaposi's Sarcoma-Associated Herpesvirus/Human Herpesvirus 8. J Med Chem 2019; 62:3924-3939. [PMID: 30888817 DOI: 10.1021/acs.jmedchem.8b01827] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The latency-associated nuclear antigen (LANA) is required for latent replication and persistence of Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8. It acts via replicating and tethering the virus episome to the host chromatin and exerts other functions. We conceived a new approach for the discovery of antiviral drugs to inhibit the interaction between LANA and the viral genome. We applied a biophysical screening cascade and identified the first LANA binders from small, structurally diverse compound libraries. Starting from a fragment-sized scaffold, we generated optimized hits via fragment growing using a dedicated fluorescence-polarization-based assay as the structure-activity-relationship driver. We improved compound potency to the double-digit micromolar range. Importantly, we qualified the resulting hit through orthogonal methods employing EMSA, STD-NMR, and MST methodologies. This optimized hit provides an ideal starting point for subsequent hit-to-lead campaigns providing evident target-binding, suitable ligand efficiencies, and favorable physicochemical properties.
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Affiliation(s)
- Philine Kirsch
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany
| | - Valentin Jakob
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Kevin Oberhausen
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Saskia C Stein
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Strasse 1 , 30625 Hannover , Germany
| | - Ivano Cucarro
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Thomas F Schulz
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Strasse 1 , 30625 Hannover , Germany
| | - Martin Empting
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany
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126
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Seal S, Polley S, Sau S. A staphylococcal cyclophilin carries a single domain and unfolds via the formation of an intermediate that preserves cyclosporin A binding activity. PLoS One 2019; 14:e0210771. [PMID: 30925148 PMCID: PMC6440624 DOI: 10.1371/journal.pone.0210771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
Cyclophilin (Cyp), a peptidyl-prolyl cis-trans isomerase (PPIase), acts as a virulence factor in many bacteria including Staphylococcus aureus. The enzymatic activity of Cyp is inhibited by cyclosporin A (CsA), an immunosuppressive drug. To precisely determine the unfolding mechanism and the domain structure of Cyp, we have investigated a chimeric S. aureus Cyp (rCyp) using various probes. Our limited proteolysis and the consequent analysis of the proteolytic fragments indicate that rCyp is composed of one domain with a short flexible tail at the C-terminal end. We also show that the urea-induced unfolding of both rCyp and rCyp-CsA is completely reversible and proceeds via the synthesis of at least one stable intermediate. Both the secondary structure and the tertiary structure of each intermediate appears very similar to those of the corresponding native protein. Conversely, the hydrophobic surface areas of the intermediates are comparatively less. Further analyses reveal no loss of CsA binding activity in rCyp intermediate. The thermodynamic stability of rCyp was also significantly increased in the presence of CsA, recommending that this protein could be employed to screen new CsA derivatives in the future.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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127
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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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128
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Libreros-Zúñiga GA, dos Santos Silva C, Salgado Ferreira R, Dias MVB. Structural Basis for the Interaction and Processing of β-Lactam Antibiotics by l,d-Transpeptidase 3 (Ldt Mt3) from Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:260-271. [PMID: 30556998 DOI: 10.1021/acsinfecdis.8b00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting Mycobacterium tuberculosis peptidoglycans with β-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. β-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 → 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (LdtMt1-5), of which LdtMt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of LdtMt3 at 1.3 and 1.8 Å resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other LdtsMt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The LdtMt3-faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a β-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that LdtMt3 is inactivated by β-lactams. Docking simulations with intact β-lactams predicted key LdtMt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of LdtMt3 for ten β-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of β-lactams by LdtMt3, which may be useful for the development of additional β-lactams with potential antitubercular activity.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
- Departamento de Microbiología, Facultad de Salud, Universidad del Valle, Calle 4B No. 36-00 Cali, Colombia
| | - Catharina dos Santos Silva
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Belo Horizonte, Brazil
| | - Marcio Vinicius Bertacine Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
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129
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Deore PS, Manderville RA. Aptamer-induced thermofluorimetric protein stabilization and G-quadruplex nucleic acid staining by SYPRO orange dye. NEW J CHEM 2019. [DOI: 10.1039/c9nj00188c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Serendipitously discovered nucleic acid staining by SYPRO Orange dye utilized to demonstrate proteins thermal stabilization (increase in melting temperature,Tm) as a function of increased DNA aptamer binding affinity (decrease in dissociation constant,Kd).
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Affiliation(s)
- Prashant S. Deore
- Departments of Chemistry & Toxicology
- University of Guelph
- Guelph
- Canada
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130
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Nuth M, Guan H, Xiao Y, Kulp JL, Parker MH, Strobel ED, Isaacs SN, Scott RW, Reitz AB, Ricciardi RP. Mutation and structure guided discovery of an antiviral small molecule that mimics an essential C-Terminal tripeptide of the vaccinia D4 processivity factor. Antiviral Res 2018; 162:178-185. [PMID: 30578797 PMCID: PMC10124107 DOI: 10.1016/j.antiviral.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022]
Abstract
The smallpox virus (variola) remains a bioterrorism threat since a majority of the human population has never been vaccinated. In the event of an outbreak, at least two drugs against different targets of variola are critical to circumvent potential viral mutants that acquire resistance. Vaccinia virus (VACV) is the model virus used in the laboratory for studying smallpox. The VACV processivity factor D4 is an ideal therapeutic target since it is both essential and specific for poxvirus replication. Recently, we identified a tripeptide (Gly-Phe-Ile) motif at the C-terminus of D4 that is conserved among poxviruses and is necessary for maintaining protein function. In the current work, a virtual screening for small molecule mimics of the tripeptide identified a thiophene lead that effectively inhibited VACV, cowpox virus, and rabbitpox virus in cell culture (EC50 = 8.4-19.7 μM) and blocked in vitro processive DNA synthesis (IC50 = 13.4 μM). Compound-binding to D4 was demonstrated through various biophysical methods and a dose-dependent retardation of the proteolysis of D4 proteins. This study highlights an inhibitor design strategy that exploits a susceptible region of the protein and identifies a novel scaffold for a broad-spectrum poxvirus inhibitor.
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Affiliation(s)
- Manunya Nuth
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hancheng Guan
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhong Xiao
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John L Kulp
- Conifer Point Pharmaceuticals, Doylestown, PA, USA
| | | | - Eric D Strobel
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Stuart N Isaacs
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard W Scott
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Robert P Ricciardi
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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131
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Paketurytė V, Linkuvienė V, Krainer G, Chen WY, Matulis D. Repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein–ligand binding reaction measured by isothermal titration calorimetry. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 48:139-152. [DOI: 10.1007/s00249-018-1341-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 10/18/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022]
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132
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Liu LK, Tanner JJ. Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer. J Mol Biol 2018; 431:524-541. [PMID: 30529746 DOI: 10.1016/j.jmb.2018.11.030] [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: 11/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022]
Abstract
The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD+-dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the superfamily, owing to its extra C-terminal domain of unknown function and the absence of the essential catalytic cysteine residue in certain non-bacterial ALDH16 sequences. Herein we report the first production of recombinant ALDH16, the first biochemical characterization of ALDH16, and the first crystal structure of ALDH16. Recombinant expression systems were generated for the bacterial ALDH16 from Loktanella sp. and human ALDH16A1. Four high-resolution crystal structures of Loktanella ALDH16 were determined. Loktanella ALDH16 is found to be a bona fide enzyme, exhibiting NAD+-binding, ALDH activity, and esterase activity. In contrast, human ALDH16A1 apparently lacks measurable aldehyde oxidation activity, suggesting that it is a pseudoenzyme, consistent with the absence of the catalytic Cys in its sequence. The fold of ALDH16 comprises three domains: NAD+-binding, catalytic, and C-terminal. The latter is unique to ALDH16 and features a Rossmann fold connected to a protruding β-flap. The tertiary structural interactions of the C-terminal domain mimic the quaternary structural interactions of the classic ALDH superfamily dimer, a phenomenon we call "trans-hierarchical structural similarity." ALDH16 forms a unique dimer in solution, which mimics the classic ALDH superfamily dimer-of-dimer tetramer. Small-angle X-ray scattering shows that human ALDH16A1 has the same dimeric structure and fold as Loktanella ALDH16. We suggest that the Loktanella ALDH16 structure may be considered to be the archetype of the ALDH16 family.
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Affiliation(s)
- Li-Kai Liu
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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133
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Martín-Mora D, Fernández M, Velando F, Ortega Á, Gavira JA, Matilla MA, Krell T. Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges. Int J Mol Sci 2018; 19:ijms19123755. [PMID: 30486299 PMCID: PMC6321045 DOI: 10.3390/ijms19123755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.
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Affiliation(s)
- David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Murcia, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, (CSIC-UGR), Avenida las Palmeras 4, 18100 Armilla, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
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134
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Seashore-Ludlow B, Axelsson H, Almqvist H, Dahlgren B, Jonsson M, Lundbäck T. Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay. Biochemistry 2018; 57:6715-6725. [PMID: 30418016 DOI: 10.1021/acs.biochem.8b01057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Evidence of physical interaction with the target protein is essential in the development of chemical probes and drugs. The cellular thermal shift assay (CETSA) allows evaluation of drug binding in live cells but lacks a framework to support quantitative interpretations and comparisons with functional data. We outline an experimental platform for such analysis using human kinase p38α. Systematic variations to the assay's characteristic heat challenge demonstrate an apparent loss of compound potency with an increase in duration or temperature, in line with expectations from the literature for thermal shift assays. Importantly, data for five structurally diverse inhibitors can be quantitatively explained using a simple model of linked equilibria and published binding parameters. The platform further distinguishes between ligand mechanisms and allows for quantitative comparisons of drug binding affinities and kinetics in live cells and lysates. We believe this work has broad implications in the appropriate use of the CETSA for target and compound validation.
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Affiliation(s)
- Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Helena Almqvist
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Björn Dahlgren
- Department of Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Mats Jonsson
- Department of Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden.,Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg, SE-431 83 Mölndal , Sweden
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135
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Tolmachova KA, Moroz YS, Konovets A, Platonov MO, Vasylchenko OV, Borysko P, Zozulya S, Gryniukova A, Bogolubsky AV, Pipko S, Mykhailiuk PK, Brovarets VS, Grygorenko OO. (Chlorosulfonyl)benzenesulfonyl Fluorides-Versatile Building Blocks for Combinatorial Chemistry: Design, Synthesis and Evaluation of a Covalent Inhibitor Library. ACS COMBINATORIAL SCIENCE 2018; 20:672-680. [PMID: 30354064 DOI: 10.1021/acscombsci.8b00130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multigram synthesis of (chlorosulfonyl)benzenesulfonyl fluorides is described. Selective modification of these building blocks at the sulfonyl chloride function under parallel synthesis conditions is achieved. It is shown that the reaction scope includes the use of (hetero)aromatic and electron-poor aliphatic amines (e.g., amino nitriles). Utility of the method is demonstrated by preparation of the sulfonyl fluoride library for potential use as covalent fragments, which is demonstrated by a combination of in silico and in vitro screening against trypsin as a model enzyme. As a result, several inhibitors were identified with activity on par with that of the known inhibitor.
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Affiliation(s)
- Kateryna A. Tolmachova
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Yurii S. Moroz
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Chemspace, Ilukstes iela 38-5, Riga, LV-1082, Latvia
| | - Angelika Konovets
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | | | | | - Petro Borysko
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | | | | | - Sergey Pipko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Pavel K. Mykhailiuk
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Volodymyr S. Brovarets
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Oleksandr O. Grygorenko
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
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136
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Zakšauskas A, Čapkauskaitė E, Jezepčikas L, Linkuvienė V, Kišonaitė M, Smirnov A, Manakova E, Gražulis S, Matulis D. Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases. Eur J Med Chem 2018; 156:61-78. [PMID: 30006175 DOI: 10.1016/j.ejmech.2018.06.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/11/2018] [Accepted: 06/23/2018] [Indexed: 01/08/2023]
Abstract
Rational design of compounds that would bind specific pockets of the target proteins is a difficult task in drug design. The 12 isoforms of catalytically active human carbonic anhydrases (CAs) have highly similar active sites that make it difficult to design inhibitors selective for one or several CA isoforms. A series of CA inhibitors based on 2-chloro/bromo-benzenesulfonamide that is largely fixed in the CA active site together with one or two tails yielded compounds that were synthesized and evaluated as inhibitors of CA isoforms. Introduction of a second tail had significant influence on the binding affinity and two-tailed compounds in most cases provided high affinity and selectivity for CA IX and CA XIV. The contacts between several compounds and CA amino acids were determined by X-ray crystallography. Together with the intrinsic enthalpy and entropy of binding they provided the structure-thermodynamics correlations for this series of compounds with the insight how to rationally build compounds with desired CA isoform as a target.
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Affiliation(s)
- Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Linas Jezepčikas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Miglė Kišonaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Alexey Smirnov
- Department of Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Saulius Gražulis
- Department of Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.
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137
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Rauh O, Hansen UP, Scheub DD, Thiel G, Schroeder I. Site-specific ion occupation in the selectivity filter causes voltage-dependent gating in a viral K + channel. Sci Rep 2018; 8:10406. [PMID: 29991721 PMCID: PMC6039446 DOI: 10.1038/s41598-018-28751-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/28/2018] [Indexed: 12/24/2022] Open
Abstract
Many potassium channels show voltage-dependent gating without a dedicated voltage sensor domain. This is not fully understood yet, but often explained by voltage-induced changes of ion occupation in the five distinct K+ binding sites in the selectivity filter. To better understand this mechanism of filter gating we measured the single-channel current and the rate constant of sub-millisecond channel closure of the viral K+ channel KcvNTS for a wide range of voltages and symmetric and asymmetric K+ concentrations in planar lipid membranes. A model-based analysis employed a global fit of all experimental data, i.e., using a common set of parameters for current and channel closure under all conditions. Three different established models of ion permeation and various relationships between ion occupation and gating were tested. Only one of the models described the data adequately. It revealed that the most extracellular binding site (S0) in the selectivity filter functions as the voltage sensor for the rate constant of channel closure. The ion occupation outside of S0 modulates its dependence on K+ concentration. The analysis uncovers an important role of changes in protein flexibility in mediating the effect from the sensor to the gate.
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Affiliation(s)
- O Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - U P Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - D D Scheub
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - G Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - I Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.
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138
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Borysko P, Moroz YS, Vasylchenko OV, Hurmach VV, Starodubtseva A, Stefanishena N, Nesteruk K, Zozulya S, Kondratov IS, Grygorenko OO. Straightforward hit identification approach in fragment-based discovery of bromodomain-containing protein 4 (BRD4) inhibitors. Bioorg Med Chem 2018; 26:3399-3405. [DOI: 10.1016/j.bmc.2018.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
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139
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A widely-applicable high-throughput cellular thermal shift assay (CETSA) using split Nano Luciferase. Sci Rep 2018; 8:9472. [PMID: 29930256 PMCID: PMC6013488 DOI: 10.1038/s41598-018-27834-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022] Open
Abstract
Assessment of the interactions between a drug and its protein target in a physiologically relevant cellular environment constitutes a major challenge in the pre-clinical drug discovery space. The Cellular Thermal Shift Assay (CETSA) enables such an assessment by quantifying the changes in the thermal stability of proteins upon ligand binding in intact cells. Here, we present the development and validation of a homogeneous, standardized, target-independent, and high-throughput (384- and 1536-well formats) CETSA platform that uses a split Nano Luciferase approach (SplitLuc CETSA). The broad applicability of the assay was demonstrated for diverse targets, and its performance was compared with independent biochemical and cell-based readouts using a set of well-characterized inhibitors. Moreover, we investigated the utility of the platform as a primary assay for high-throughput screening. The SplitLuc CETSA presented here enables target engagement studies for medium and high-throughput applications. Additionally, it provides a rapid assay development and screening platform for targets where phenotypic or other cell-based assays are not readily available.
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140
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Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells. Oncotarget 2018; 9:26800-26816. [PMID: 29928486 PMCID: PMC6003569 DOI: 10.18632/oncotarget.25508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/14/2018] [Indexed: 12/11/2022] Open
Abstract
Human carbonic anhydrase (CA) IX has emerged as a promising anticancer target and a diagnostic biomarker for solid hypoxic tumors. Novel fluorinated CA IX inhibitors exhibited up to 50 pM affinity towards the recombinant human CA IX, selectivity over other CAs, and direct binding to Zn(II) in the active site of CA IX inducing novel conformational changes as determined by X-ray crystallography. Mass spectrometric gas-analysis confirmed the CA IX-based mechanism of the inhibitors in a CRISPR/Cas9-mediated CA IX knockout in HeLa cells. Hypoxia-induced extracellular acidification was significantly reduced in HeLa, H460, MDA-MB-231, and A549 cells exposed to the compounds, with the IC50 values up to 1.29 nM. A decreased clonogenic survival was observed when hypoxic H460 3D spheroids were incubated with our lead compound. These novel compounds are therefore promising agents for CA IX-specific therapy.
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141
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Miettinen TP, Peltier J, Härtlova A, Gierliński M, Jansen VM, Trost M, Björklund M. Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib. EMBO J 2018; 37:e98359. [PMID: 29669860 PMCID: PMC5978322 DOI: 10.15252/embj.201798359] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 11/24/2022] Open
Abstract
Palbociclib is a CDK4/6 inhibitor approved for metastatic estrogen receptor-positive breast cancer. In addition to G1 cell cycle arrest, palbociclib treatment results in cell senescence, a phenotype that is not readily explained by CDK4/6 inhibition. In order to identify a molecular mechanism responsible for palbociclib-induced senescence, we performed thermal proteome profiling of MCF7 breast cancer cells. In addition to affecting known CDK4/6 targets, palbociclib induces a thermal stabilization of the 20S proteasome, despite not directly binding to it. We further show that palbociclib treatment increases proteasome activity independently of the ubiquitin pathway. This leads to cellular senescence, which can be counteracted by proteasome inhibitors. Palbociclib-induced proteasome activation and senescence is mediated by reduced proteasomal association of ECM29. Loss of ECM29 activates the proteasome, blocks cell proliferation, and induces a senescence-like phenotype. Finally, we find that ECM29 mRNA levels are predictive of relapse-free survival in breast cancer patients treated with endocrine therapy. In conclusion, thermal proteome profiling identifies the proteasome and ECM29 protein as mediators of palbociclib activity in breast cancer cells.
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Affiliation(s)
- Teemu P Miettinen
- Division of Cell and Developmental Biology, University of Dundee, Dundee, UK
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Anetta Härtlova
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marek Gierliński
- Division of Computational Biology, University of Dundee, Dundee, UK
| | - Valerie M Jansen
- Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mikael Björklund
- Division of Cell and Developmental Biology, University of Dundee, Dundee, UK
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142
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Cellular and Biophysical Pipeline for the Screening of Peroxisome Proliferator-Activated Receptor Beta/Delta Agonists: Avoiding False Positives. PPAR Res 2018; 2018:3681590. [PMID: 29849537 PMCID: PMC5924986 DOI: 10.1155/2018/3681590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/22/2018] [Accepted: 02/05/2018] [Indexed: 02/06/2023] Open
Abstract
Peroxisome proliferator-activated receptor beta/delta (PPARß/δ) is considered a therapeutic target for metabolic disorders, cancer, and cardiovascular diseases. Here, we developed one pipeline for the screening of PPARß/δ agonists, which reduces the cost, time, and false-positive hits. The first step is an optimized 3-day long cellular transactivation assay based on reporter-gene technology, which is supported by automated liquid-handlers. This primary screening is followed by a confirmatory transactivation assay and by two biophysical validation methods (thermal shift assay (TSA) and (ANS) fluorescence quenching), which allow the calculation of the affinity constant, giving more information about the selected hits. All of the assays were validated using well-known commercial agonists providing trustworthy data. Furthermore, to validate and test this pipeline, we screened a natural extract library (560 extracts), and we found one plant extract that might be interesting for PPARß/δ modulation. In conclusion, our results suggested that we developed a cheaper and more robust pipeline that goes beyond the single activation screening, as it also evaluates PPARß/δ tertiary structure stabilization and the ligand affinity constant, selecting only molecules that directly bind to the receptor. Moreover, this approach might improve the effectiveness of the screening for agonists that target PPARß/δ for drug development.
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143
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Čapkauskaitė E, Zubrienė A, Paketurytė V, Timm DD, Tumkevičius S, Matulis D. Thiazole-substituted benzenesulfonamides as inhibitors of 12 human carbonic anhydrases. Bioorg Chem 2018; 77:534-541. [PMID: 29459130 DOI: 10.1016/j.bioorg.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 12/26/2022]
Abstract
Four series of para or meta - substituted thiazolylbenzenesulfonamides bearing Cl substituents were designed, synthesized, and evaluated as inhibitors of all 12 catalytically active recombinant human carbonic anhydrase (CA) isoforms. Observed affinities were determined by the fluorescent thermal shift assay and the intrinsic affinities were calculated based on the fractions of binding-ready deprotonated sulfonamide and CA bearing protonated hydroxide bound to the catalytic Zn(II) in the active site. Several compounds exhibited selectivity towards CA IX, an anticancer target. Intrinsic affinities reached 30 pM, while the observed affinities - 70 nM. The structure-intrinsic affinity relationship map of the compounds showed the energetic contributions of the thiazole ring and its substituents.
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Affiliation(s)
- Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - David D Timm
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Sigitas Tumkevičius
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.
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144
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Sites associated with Kalydeco binding on human Cystic Fibrosis Transmembrane Conductance Regulator revealed by Hydrogen/Deuterium Exchange. Sci Rep 2018; 8:4664. [PMID: 29549268 PMCID: PMC5856801 DOI: 10.1038/s41598-018-22959-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Cystic Fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Mutations associated with CF cause loss-of-function in CFTR leading to salt imbalance in epithelial tissues. Kalydeco (also called VX-770 or ivacaftor) was approved for CF treatment in 2012 but little is known regarding the compound’s interactions with CFTR including the site of binding or mechanisms of action. In this study we use hydrogen/deuterium exchange (HDX) coupled with mass spectrometry to assess the conformational dynamics of a thermostabilized form of CFTR in apo and ligand-bound states. We observe HDX protection at a known binding site for AMPPNP and significant protection for several regions of CFTR in the presence of Kalydeco. The ligand-induced changes of CFTR in the presence of Kalydeco suggest a potential binding site.
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145
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Mazal H, Aviram H, Riven I, Haran G. Effect of ligand binding on a protein with a complex folding landscape. Phys Chem Chem Phys 2018; 20:3054-3062. [PMID: 28721412 DOI: 10.1039/c7cp03327c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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146
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Linkuvienė V, Talibov VO, Danielson UH, Matulis D. Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design. J Med Chem 2018; 61:2292-2302. [DOI: 10.1021/acs.jmedchem.7b01408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
| | - Vladimir O. Talibov
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
| | - U. Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
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147
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McQueeney KE, Salamoun JM, Burnett JC, Barabutis N, Pekic P, Lewandowski SL, Llaneza DC, Cornelison R, Bai Y, Zhang ZY, Catravas JD, Landen CN, Wipf P, Lazo JS, Sharlow ER. Targeting ovarian cancer and endothelium with an allosteric PTP4A3 phosphatase inhibitor. Oncotarget 2018; 9:8223-8240. [PMID: 29492190 PMCID: PMC5823565 DOI: 10.18632/oncotarget.23787] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/25/2017] [Indexed: 12/16/2022] Open
Abstract
Overexpression of protein tyrosine phosphatase PTP4A oncoproteins is common in many human cancers and is associated with poor patient prognosis and survival. We observed elevated levels of PTP4A3 phosphatase in 79% of human ovarian tumor samples, with significant overexpression in tumor endothelium and pericytes. Furthermore, PTP4A phosphatases appear to regulate several key malignant processes, such as invasion, migration, and angiogenesis, suggesting a pivotal regulatory role in cancer and endothelial signaling pathways. While phosphatases are attractive therapeutic targets, they have been poorly investigated because of a lack of potent and selective chemical probes. In this study, we disclose that a potent, selective, reversible, and noncompetitive PTP4A inhibitor, JMS-053, markedly enhanced microvascular barrier function after exposure of endothelial cells to vascular endothelial growth factor or lipopolysaccharide. JMS-053 also blocked the concomitant increase in RhoA activation and loss of Rac1. In human ovarian cancer cells, JMS-053 impeded migration, disrupted spheroid growth, and decreased RhoA activity. Importantly, JMS-053 displayed anticancer activity in a murine xenograft model of drug resistant human ovarian cancer. These data demonstrate that PTP4A phosphatases can be targeted in both endothelial and ovarian cancer cells, and confirm that RhoA signaling cascades are regulated by the PTP4A family.
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Affiliation(s)
- Kelley E. McQueeney
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | | | - James C. Burnett
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nektarios Barabutis
- Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA
| | - Paula Pekic
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | | | - Danielle C. Llaneza
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA, USA
| | - Robert Cornelison
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA, USA
| | - Yunpeng Bai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - John D. Catravas
- Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA
| | - Charles N. Landen
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, VA, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - John S. Lazo
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
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148
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Kyani A, Tamura S, Yang S, Shergalis A, Samanta S, Kuang Y, Ljungman M, Neamati N. Discovery and Mechanistic Elucidation of a Class of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma. ChemMedChem 2018; 13:164-177. [PMID: 29235250 DOI: 10.1002/cmdc.201700629] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/10/2017] [Indexed: 12/14/2022]
Abstract
Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein we describe a novel nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblastoma cell lines. We performed a medium-throughput 20 000-compound screen of a diverse subset of 1 000 000 compounds to identify cytotoxic small molecules. Cytotoxic compounds were screened for PDI inhibition, and, from the screen, 35G8 emerged as the most cytotoxic inhibitor of PDI. Bromouridine labeling and sequencing (Bru-seq) of nascent RNA revealed that 35G8 induces nuclear factor-like 2 (Nrf2) antioxidant response, endoplasmic reticulum (ER) stress response, and autophagy. Specifically, 35G8 upregulated heme oxygenase 1 and solute carrier family 7 member 11 (SLC7A11) transcription and protein expression and repressed PDI target genes such as thioredoxin-interacting protein 1 (TXNIP) and early growth response 1 (EGR1). Interestingly, 35G8-induced cell death did not proceed via apoptosis or necrosis, but by a mixture of autophagy and ferroptosis. Cumulatively, our data demonstrate a mechanism for a novel PDI inhibitor as a chemical probe to validate PDI as a target for brain cancer.
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Affiliation(s)
- Anahita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Shuzo Tamura
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Soma Samanta
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Yuting Kuang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, North Campus Research Complex, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
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149
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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150
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Ehrhardt MKG, Warring SL, Gerth ML. Screening Chemoreceptor-Ligand Interactions by High-Throughput Thermal-Shift Assays. Methods Mol Biol 2018; 1729:281-290. [PMID: 29429098 DOI: 10.1007/978-1-4939-7577-8_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identifying the ligands sensed by chemoreceptors remains challenging, in part because current screening methods are low-throughput, costly, and/or time-consuming. In contrast, fluorescence thermal shift (FTS) assays provide a fast and inexpensive approach to chemoreceptor-ligand screening. In FTS assays, the temperature at which a protein denatures is measured by monitoring the fluorescence of a dye with affinity for hydrophobic regions of the protein, which are exposed as the protein unfolds. A detectable increase (or "shift") in the melting temperature (T m ) of the protein in the presence of a potential ligand indicates binding. Here, we present our protocol for using FTS assays for the screening of chemoreceptor ligands in a high-throughput, 96-well plate format. We have also included details on the use of Biolog Phenotype Microarray plates as a convenient ligand library, although the methods described should be generally applicable to other library formats as well.
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Affiliation(s)
| | - Suzanne L Warring
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Monica L Gerth
- Department of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
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