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Wang TY, Krylov SN. Deterministic error propagation in ITC: Revealing multi-fold errors in K d values under standard conditions. Biophys Chem 2025; 323:107455. [PMID: 40349382 DOI: 10.1016/j.bpc.2025.107455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Revised: 05/05/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
Abstract
Accurate determination of the equilibrium dissociation constant (Kd) is essential in fields such as drug discovery and molecular diagnostics, where a rigorous understanding of molecular interactions drives critical decisions. Among established techniques, isothermal titration calorimetry (ITC) is highly valued for its ability to directly capture binding thermodynamics without the need for labeling or immobilization. However, while ITC is often praised for its precision, potential inaccuracies due to the systematic errors in experimental variables (analyte concentrations and measured heat) are frequently overlooked. One key reason for this oversight is the lack of a deterministic framework that explicitly demonstrates how ITC-derived Kd values can be affected by these errors. To address this gap, we derived a closed-form mathematical model for error propagation in ITC-based Kd determination, quantifying the impact of inaccuracies in analyte concentrations and measured heat on the resulting Kd. This framework provides a robust foundation for understanding and predicting the influence of these systematic errors on Kd accuracy. Using this solution, we demonstrate that even within the conventionally recommended c-value range of 10-100, expected systematic errors in concentrations and heat can potentially lead to significant multi-fold deviations in Kd. These findings underscore the need for quantitative accuracy assessments in ITC experiments and highlight the importance of developing practical tools to support such evaluations.
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Affiliation(s)
- Tong Ye Wang
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada; Centre for Research on Biomolecular Interactions, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada; Centre for Research on Biomolecular Interactions, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada.
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2
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Dashevskii D, Luginina A, Maslov I, Shevelyova M, Khorn P, Dmitrieva D, Kapranov I, Belousov A, Permyakov S, Cherezov V, Borshchevskiy V, Mishin A. Unlocking GPCR-ligand interactions: Measuring binding affinities with thermal shift assay. Protein Sci 2025; 34:e70120. [PMID: 40247825 PMCID: PMC12006757 DOI: 10.1002/pro.70120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 03/18/2025] [Accepted: 03/20/2025] [Indexed: 04/19/2025]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest transmembrane protein superfamily, with over 800 representatives in the human genome. Recognized as pivotal targets in pharmacological research and drug discovery, these receptors play a crucial role in advancing therapeutics. Understanding the molecular mechanisms of receptor-ligand interactions is imperative for drug discovery applications. However, experimental procedures for measuring ligand binding are complicated by various factors, including the transmembrane nature of the receptors and the high cost associated with specialized instruments and consumables. Here we introduce an application of the thermal shift assay (TSA) to measuring ligand binding affinities for GPCRs. TSA is a cost-effective and user-friendly method that detects changes in protein stability induced by alterations in environmental conditions. Employing the human A2A adenosine receptor as a representative GPCR, we determined binding constants for four orthosteric ligands and allosteric sodium using three mathematical models for TSA data approximation and analysis. Models were additionally validated by two antagonists of cysteinyl leukotriene GPCR (CysLT1R), used as antiasthmatic drugs. Our results suggest that the TSA approach demonstrates a high degree of reproducibility and agreement with existing literature data, thereby affirming its suitability for investigating GPCR interactions with various types of ligands.
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Affiliation(s)
- Dmitrii Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Marina Shevelyova
- Pushchino Scientific Center for Biological Research of the Russian Academy of ScienceInstitute for Biological InstrumentationPushchinoRussia
| | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Daria Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
| | - Anatolii Belousov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
- Sao Carlos Institute of PhysicsUniversity of Sao PauloSao CarlosSão PaoloBrazil
| | - Sergei Permyakov
- Pushchino Scientific Center for Biological Research of the Russian Academy of ScienceInstitute for Biological InstrumentationPushchinoRussia
| | - Vadim Cherezov
- Bridge Institute, Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
- Frank Laboratory of Neutron PhysicsDubnaRussia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyMoscowRussia
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3
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Saxena R, Wright MM, Rathman BM, Karki U, Chapagain PP, Del Valle JR, Stahelin RV. Design of a stapled peptide that binds to the Ebola virus matrix protein dimer interface. RSC Chem Biol 2025:d5cb00048c. [PMID: 40343175 PMCID: PMC12057636 DOI: 10.1039/d5cb00048c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2025] [Accepted: 04/22/2025] [Indexed: 05/11/2025] Open
Abstract
The Ebola virus (EBOV) is a filamentous lipid-enveloped RNA virus that can cause viral hemmorhagic fever and has a high fatility rate. EBOV encodes seven genes including the lipid-binding matrix protein, VP40, which lies beneath the lipid-envelope. VP40 is a 326 amino acid protein with a N-terminal domain (NTD) harboring a high affinity dimer interface and a C-terminal domain (CTD) critical to plasma membrane lipid interactions. Disruption of VP40 dimer formation via mutagenesis inhibits assembly and budding of VP40. A series of conformationally constrained mimics of the VP40 α2 helix were designed based on the crystal structures of the VP40 dimer. A thermal shift assay was used to screen constrained and native peptides for significant alterations in VP40 stability. The most meritorious peptides were then confirmed to directly bind VP40 using microscale thermophoresis and isothermal titration calorimetry. A constrained VP40 peptide mimetic with a di-cysteine staple emerged with micromolar affinity for the VP40 dimer. This peptide was able to shift the VP40 dimer-monomer equilibrium as evidenced by size exclusion chromatography and bound near the NTD α-helix dimer interface. This study provides the first evidence of a designed small molecule induced disruption of VP40 dimer-monomer equilibrium.
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Affiliation(s)
- Roopashi Saxena
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University West Lafayette IN 47907 USA
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Benjamin M Rathman
- Department of Chemistry & Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Ukesh Karki
- Department of Physics, Florida International University Miami FL 33199 USA
| | - Prem P Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Robert V Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University West Lafayette IN 47907 USA
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4
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Baxter CE, Khan AN, Starcevic CM, Shkolnik N, Zimmermann J. The Photophysical Properties of the Protonation States of SYPRO ® Orange in Aqueous Solution. Molecules 2025; 30:1691. [PMID: 40333691 PMCID: PMC12029588 DOI: 10.3390/molecules30081691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 03/31/2025] [Accepted: 04/03/2025] [Indexed: 05/09/2025] Open
Abstract
SYPRO® Orange (SyO) is a zwitterionic dye that is used for protein gel staining, for thermal melt assays of proteins, and as a marker for misfolded proteins. However, while widely utilized, much of SyOs' photophysics remains unexplored. We studied the effect of pH on the photophysical properties of SyO in aqueous solution and found two well-defined transitions in the 0 to 10 pH range between three SyO species with distinct absorption and fluorescence properties. The first transition occurs around pH 1.5 and appears to be a coupled deprotonation-aggregation event. The second transition occurs between pH 4 and 5, and its pKa depends on the concentration of SyO. A link between the concentration dependence of the pKa of the second pH transition and the aggregation behavior of SyO at neutral pH is discussed, and aggregation equilibrium titrations are presented that suggest that SyO forms multimeric aggregates at neutral pH containing ten or more SyO molecules.
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Affiliation(s)
| | | | | | | | - Jörg Zimmermann
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA; (C.E.B.)
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5
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Ardini M, Angelucci F, Rea F, Paluzzi L, Gabriele F, Palerma M, Di Leandro L, Ippoliti R, Pitari G. Functional and structural characterization of the human indolethylamine N-methyltransferase through fluorometric, thermal and computational docking analyses. Biol Direct 2025; 20:50. [PMID: 40211327 PMCID: PMC11987180 DOI: 10.1186/s13062-025-00632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 03/13/2025] [Indexed: 04/13/2025] Open
Abstract
BACKGROUND The "psychedelic renaissance" is sparking growing interest in clinical research, along with a rise in clinical trials. Substances such as 3,4-methylenedioxymethamphetamine (MDMA), psilocybin and N,N-dimethyltryptamine (DMT) are involved. The focus of this paper is on indolethylamine N-methyltransferase (INMT), a crucial enzyme in the biosynthesis of key compounds, including DMT, which meets science, medicine and spirituality. The presence of DMT in animals and plants raises many questions about its biological role. Meanwhile, the distribution of INMT in various organs and its involvement in diseases like cancer and mental disorders also fuel investigations worldwide. However, INMT remains largely unexplored, particularly its enzymatic mechanism and structural properties, leaving a significant gap in potential applications. RESULTS This study examines for the first time the catalytic activity of the human INMT (hINMT) using a simple fluorometric steady-state assay employing the substrate quinoline. The findings are supported by thermal shift and docking analyses, providing valuable information about optimal chemical conditions and potential binding sites for substrates. The thermal shift assays indicate that recombinant hINMT is unstable and requires acidic or near-neutral pH and low salt levels. These experiments also allow for the estimation of dissociation constants for its natural coenzymes SAM and SAH, helping to determine the appropriate setup for the fluorometric assays and calculate kinetic constants, which are comparable to other methyltransferases. The docking indicates that quinoline occupies the same site as the natural substrate tryptamine, further validating the fluorometric approach. CONCLUSIONS The paper provides a foundation for thoroughly studying hINMT under consistent conditions, which is crucial for obtaining reliable kinetic data and maintaining molecular stability for future structural analysis. This represents a valid alternative over previous endpoint radioactive-based and chromatography-mass spectrometry assays, which can provide only apparent steady-state parameters. Given the polymorphisms observed in hINMT and their potential association with psychiatric disorders, e.g., schizophrenia, and cancer, this strategy could serve as an invaluable tool for understanding the structure-function relationship of enzyme mutants and their role in diseases. Furthermore, these findings for the first time provide insights into the interaction modalities of hINMT with its substrates and lay the groundwork for inhibition experiments aimed at practical applications.
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Affiliation(s)
- Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Rea
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Luca Paluzzi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Department of Science, Technology and Society, University School for Advanced Studies of Pavia, Pavia, Italy
| | - Federica Gabriele
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Marta Palerma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Department of Science, Technology and Society, University School for Advanced Studies of Pavia, Pavia, Italy
| | - Luana Di Leandro
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Giuseppina Pitari
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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6
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Bates TA, Gurmessa SK, Weinstein JB, Trank-Greene M, Wrynla XH, Anastas A, Anley TW, Hinchliff A, Shinde U, Burke JE, Tafesse FG. Biolayer interferometry for measuring the kinetics of protein-protein interactions and nanobody binding. Nat Protoc 2025; 20:861-883. [PMID: 39572731 DOI: 10.1038/s41596-024-01079-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 09/24/2024] [Indexed: 04/10/2025]
Abstract
Protein-protein interactions underpin nearly all biological processes, and understanding the molecular mechanisms that govern these interactions is crucial for the progress of biomedical sciences. The emergence of artificial intelligence-driven computational tools can help reshape the methods of structural biology; however, model data often require empirical validation. The large scale of predictive modeling data will therefore benefit from optimized methodologies for the high-throughput biochemical characterization of protein-protein interactions. Biolayer interferometry is one of very few approaches that can determine the rate of biomolecular interactions, called kinetics, and, of the commonly available kinetic measurement techniques, it is the most suitable for high-throughput experimental designs. Here we provide step-by-step instructions on how to perform kinetics experiments using biolayer interferometry. We further describe the basis and execution of competition and epitope binning experiments, which are particularly useful for antibody and nanobody screening applications. The procedure requires 3 h to complete and is suitable for users with minimal experience with biochemical techniques.
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Affiliation(s)
- Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA.
| | - Sintayehu K Gurmessa
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Jules B Weinstein
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Mila Trank-Greene
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Xammy Huu Wrynla
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Aidan Anastas
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Teketay Wassie Anley
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Audrey Hinchliff
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Ujwal Shinde
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA.
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7
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Faustino M, Strobbe S, Sanchez-Muñoz R, Cao D, Mishra RC, Lourenço T, Oliveira MM, Van Der Straeten D. In silico, in vitro, and in vivo characterization of thiamin-binding proteins from plant seeds. Biochem J 2025; 482:BCJ20240429. [PMID: 39831786 DOI: 10.1042/bcj20240429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 01/14/2025] [Accepted: 01/20/2025] [Indexed: 01/22/2025]
Abstract
Thiamin, an essential micronutrient, is a cofactor for enzymes involved in the central carbon metabolism and amino acid pathways. Despite efforts to enhance thiamin content in rice by incorporating thiamin biosynthetic genes, increasing thiamin content in the endosperm remains challenging, possibly due to a lack of thiamin stability and/or a local sink. The introduction of storage proteins has been successful in several biofortification strategies, and similar efforts targeting thiamin have been performed, leading to a 3-4-fold increase in white rice. However, only one thiamin-binding protein (TBP) sequence has been described in plants, more specifically from sesame seeds. Therefore, we aimed to identify and characterize TBPs, as well as to evaluate the effect of their expression on thiamin concentration, using a comprehensive approach integrating in silico, in vitro, and in vivo methods. We identified the sequences of putative TBPs from Oryza sativa (Os, rice), Fagopyrum esculentum (Fe, buckwheat), and Zea mays (Zm, maize) and pinpointed the thiamin-binding pockets through molecular docking. FeTBP and OsTBP contained one pocket with binding affinities similar to the Escherichia coli TBP, a well-characterized TBP, supporting their function as TBPs. In vivo expression studies of TBPs in tobacco leaves and rice callus resulted in increased thiamin levels, with FeTBP and OsTBP showing the most pronounced effects. Additionally, thermal shift assays confirmed the thiamin-binding capabilities of FeTBP and OsTBP, as observed by the significant increases in melting temperatures upon thiamin binding, indicating protein stabilization. These findings offer new insights into the diversity and function of plant TBPs and highlight the potential of FeTBP and OsTBP to modulate thiamin levels in crop plants.
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Affiliation(s)
- Maria Faustino
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
- Laboratory of Plant Functional Genomics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Raul Sanchez-Muñoz
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Da Cao
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Ratnesh C Mishra
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Tiago Lourenço
- Laboratory of Plant Functional Genomics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Laboratory of Plant Functional Genomics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
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8
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DiPuma T, Kelley EH, Thabthimthong T, Bland A, Konczak K, Torma KJ, Mohammad TSH, Olsen KW, Becker DP. Synthesis of Pyrazole-Based Inhibitors of the Bacterial Enzyme N-Succinyl-l,l-2,6-Diaminopimelic Acid Desuccinylase (DapE) as Potential Antibiotics. Int J Mol Sci 2024; 26:22. [PMID: 39795881 PMCID: PMC11720106 DOI: 10.3390/ijms26010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 12/21/2024] [Accepted: 12/22/2024] [Indexed: 01/13/2025] Open
Abstract
Based on the inhibitory potencies from earlier reported tetrazole thioether analogs, we now describe the synthesis and inhibition of pyrazole-based inhibitors of N-succinyl-l,l-2,6-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae (HiDapE). The most potent pyrazole analog 7d bears an aminopyridine amide with an IC50 of 17.9 ± 8.0 μM, and the single enantiomer of ɑ-methyl analog 7q has an IC50 of 18.8 µM, with potency residing in the (R)-enantiomer. Thermal shift revealed strong stabilization upon binding inhibitor (R)-7q with Tm = 50.2 °C and a Ki of 17.3 ± 2.8 μM. Enzyme kinetic experiments confirm competitive inhibition, and docking reveals key active site interactions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA; (T.D.J.); (E.H.K.); (T.T.); (A.B.); (K.K.); (K.J.T.); (T.S.H.M.); (K.W.O.)
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9
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Kelley EH, Osipiuk J, Korbas M, Endres M, Bland A, Ehrman V, Joachimiak A, Olsen KW, Becker DP. N α -acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification. Front Chem 2024; 12:1415644. [PMID: 39055043 PMCID: PMC11270798 DOI: 10.3389/fchem.2024.1415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 07/27/2024] Open
Abstract
Bacteria are becoming increasingly resistant to antibiotics, therefore there is an urgent need for new classes of antibiotics to fight antibiotic resistance. Mammals do not express N ɑ -acetyl-L-ornithine deacetylase (ArgE), an enzyme that is critical for bacterial survival and growth, thus ArgE represents a promising new antibiotic drug target, as inhibitors would not suffer from mechanism-based toxicity. A new ninhydrin-based assay was designed and validated that included the synthesis of the substrate analog N 5, N 5-di-methyl N α-acetyl-L-ornithine (kcat/Km = 7.32 ± 0.94 × 104 M-1s-1). This new assay enabled the screening of potential inhibitors that absorb in the UV region, and thus is superior to the established 214 nm assay. Using this new ninhydrin-based assay, captopril was confirmed as an ArgE inhibitor (IC50 = 58.7 μM; Ki = 37.1 ± 0.85 μM), and a number of phenylboronic acid derivatives were identified as inhibitors, including 4-(diethylamino)phenylboronic acid (IC50 = 50.1 μM). Selected inhibitors were also tested in a thermal shift assay with ArgE using SYPRO Orange dye against Escherichia coli ArgE to observe the stability of the enzyme in the presence of inhibitors (captopril Ki = 35.9 ± 5.1 μM). The active site structure of di-Zn EcArgE was confirmed using X-ray absorption spectroscopy, and we reported two X-ray crystal structures of E. coli ArgE. In summary, we describe the development of a new ninhydrin-based assay for ArgE, the identification of captopril and phenylboronic acids as ArgE inhibitors, thermal shift studies with ArgE + captopril, and the first two published crystal structures of ArgE (mono-Zn and di-Zn).
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Affiliation(s)
- Emma H. Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Jerzy Osipiuk
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- eBERlight, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | | | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Alayna Bland
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Victoria Ehrman
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Andrzej Joachimiak
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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10
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Bütikofer M, Stadler GR, Kadavath H, Cadalbert R, Torres F, Riek R. Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR. J Am Chem Soc 2024; 146:17974-17985. [PMID: 38957136 PMCID: PMC11228983 DOI: 10.1021/jacs.4c04000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of peptides binding to a PDZ domain and fragment ligands binding to the protein PIN1. The method can also be extended to measure the affinity of nonphoto-CIDNP-polarizable ligands in competition binding experiments. Finally, we demonstrate a strong correlation between the ligand-reduced signals in photo-CIDNP-based NMR fragment screening and the well-established saturation transfer difference (STD) NMR. Thus, our methodology measures protein-ligand affinities in the micro- to millimolar range in only a few minutes and informs on the binding epitope in a single-scan experiment, opening new avenues for early stage drug discovery approaches.
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Affiliation(s)
- Matthias Bütikofer
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Gabriela R Stadler
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Felix Torres
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
- NexMR AG, Wiesenstrasse 10A, 8952 Schlieren, Switzerland
| | - Roland Riek
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
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11
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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12
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Kelley EH, Minasov G, Konczak K, Shuvalova L, Brunzelle JS, Shukla S, Beulke M, Thabthimthong T, Olsen KW, Inniss NL, Satchell KJF, Becker DP. Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii. ACS OMEGA 2024; 9:3905-3915. [PMID: 38284080 PMCID: PMC10809365 DOI: 10.1021/acsomega.3c08231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from Haemophilus influenzae (HiDapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen Acinetobacter baumannii (AbDapE) and studied inhibition by known inhibitors of HiDapE. AbDapE is inhibited by captopril and sulfate comparable to HiDapE, but AbDapE was not significantly inhibited by a known indoline sulfonamide HiDapE inhibitor. Captopril and sulfate both stabilize HiDapE by increasing the thermal melting temperature (Tm) in thermal shift assays. By contrast, sulfate decreases the stability of the AbDapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted AbDapE in the closed conformation, one with AbDapE in complex with succinate derived from enzymatic hydrolysis of N6-methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of AbDapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).
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Affiliation(s)
- Emma H. Kelley
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - George Minasov
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Katherine Konczak
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Ludmilla Shuvalova
- Department
of Pharmacology, Northwestern University,
Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Joseph S. Brunzelle
- Northwestern
Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Shantanu Shukla
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Megan Beulke
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Teerana Thabthimthong
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Kenneth W. Olsen
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Nicole L. Inniss
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Karla J. F. Satchell
- Department
of Microbiology-Immunology, Northwestern
University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center
for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Daniel P. Becker
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
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13
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Habeeb Mohammad TS, Kelley EH, Reidl CT, Konczak K, Beulke M, Javier J, Olsen KW, Becker DP. Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics. Int J Mol Sci 2024; 25:1339. [PMID: 38279338 PMCID: PMC10815964 DOI: 10.3390/ijms25021339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/- 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE).
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Affiliation(s)
| | | | | | | | | | | | | | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA; (T.S.H.M.); (E.H.K.); (K.K.); (M.B.); (J.J.); (K.W.O.)
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14
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Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Commun Biol 2023; 6:1214. [PMID: 38030679 PMCID: PMC10687169 DOI: 10.1038/s42003-023-05602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
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Affiliation(s)
- Da Eun Jeong
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Jun Kim
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Ho-Chul Shin
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
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15
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Patel HP, Martinez‐Ramirez G, Dobrzynski E, Iglesias AA, Liu D, Ballicora MA. A critical inter-subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2023; 32:e4747. [PMID: 37551561 PMCID: PMC10461462 DOI: 10.1002/pro.4747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat , but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.
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Affiliation(s)
- Hiral P. Patel
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Emily Dobrzynski
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Dali Liu
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | - Miguel A. Ballicora
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
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16
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Liveris ZJ, Kelley EH, Simmons E, Konczak K, Lutz MR, Ballicora M, Olsen KW, Becker DP. Synthesis and characterization of the N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) alternate substrate analog N,N-dimethyl-l,l-SDAP. Bioorg Med Chem 2023; 91:117415. [PMID: 37459673 DOI: 10.1016/j.bmc.2023.117415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.
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Affiliation(s)
- Zachary J Liveris
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma H Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma Simmons
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Katherine Konczak
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Marlon R Lutz
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Miguel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States.
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17
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Machera SJ, Niedziółka-Jönsson J, Jönsson-Niedziółka M, Szot-Karpińska K. Determination of the Dissociation Constant for Polyvalent Receptors Using ELISA: A Case of M13 Phages Displaying Troponin T-Specific Peptides. ACS OMEGA 2023; 8:26253-26262. [PMID: 37521637 PMCID: PMC10373194 DOI: 10.1021/acsomega.3c02551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (Kd). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to five copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating Kd values from ELISA experiments was developed and is presented. The determined Kd values are in the picomolar range.
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18
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Khan AM, Atia-Tul-Wahab, Farooq S, Ullah A, Choudhary MI. Repurposing of US-FDA approved drugs against SARS-CoV-2 main protease (M pro) by using STD-NMR spectroscopy, in silico studies and antiviral assays. Int J Biol Macromol 2023; 234:123540. [PMID: 36740128 PMCID: PMC9896891 DOI: 10.1016/j.ijbiomac.2023.123540] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
SARS-CoV-2 Main protease (Mpro) is a well-known drug target against SARS-CoV-2 infection. Identification of Mpro inhibitors is vigorously pursued due to its crucial role in viral replication. The present study was aimed to identify Mpro inhibitors via repurposing of US-FDA approved drugs by STD-NMR spectroscopy. In this study, 156 drugs and natural compounds were evaluated against Mpro. Among them, 10 drugs were found to be interacting with Mpro, including diltiazem HCl (1), mefenamic acid (2), losartan potassium (3), mexiletine HCl (4), glaucine HBr (5), trimebutine maleate (6), flurbiprofen (7), amantadine HCl (8), dextromethorphan (9), and lobeline HCl (10) in STD-NMR spectroscopy. Their interactions were compared with three standards (Repurposed anti-viral drugs), dexamethasone, chloroquine phosphate, and remdesivir. Thermal stability of Mpro and dissociation constant (Kd) of six interacting drugs were also determined using DSF. RMSD plots in MD simulation studies showed the formation of stable protein-ligand complexes. They were further examined for their antiviral activity by plaque reduction assay against SARS-CoV-2, which showed 55-100% reduction in viral plaques. This study demonstrates the importance of drug repurposing against emerging and neglected diseases. This study also exhibits successful application of STD-NMR spectroscopy combined with plaque reduction assay in rapid identification of potential anti-viral agents.
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Affiliation(s)
- Abdul Mateen Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Saba Farooq
- National Institute of Virology, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Asmat Ullah
- Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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19
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Production of a halotolerant endo-1,4-β-glucanase by a newly isolated Bacillus velezensis H1 on olive mill wastes without pretreatment: purification and characterization of the enzyme. Arch Microbiol 2022; 204:681. [DOI: 10.1007/s00203-022-03300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/07/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
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