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Sokratous K, Cooper-Shepherd DA, Ujma J, Qu F, Giles K, Ben-Younis A, Hensen M, Langridge JI, Gault J, Jazayeri A, Liko I, Hopper JTS. Enhanced Declustering Enables Native Top-Down Analysis of Membrane Protein Complexes using Ion-Mobility Time-Aligned Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1891-1901. [PMID: 39007842 DOI: 10.1021/jasms.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Native mass spectrometry (MS) is proving to be a disruptive technique for studying the interactions of proteins, necessary for understanding the functional roles of these biomolecules. Recent research is expanding the application of native MS towards membrane proteins directly from isolated membrane preparations or from purified detergent micelles. The former results in complex spectra comprising several heterogeneous protein complexes; the latter enables therapeutic protein targets to be screened against multiplexed preparations of compound libraries. In both cases, the resulting spectra are increasingly complex to assign/interpret, and the key to these new directions of native MS research is the ability to perform native top-down analysis, which allows unambiguous peak assignment. To achieve this, detergent removal is necessary prior to MS analyzers, which allow selection of specific m/z values, representing the parent ion for downstream activation. Here, we describe a novel, enhanced declustering (ED) device installed into the first pumping region of a cyclic IMS-enabled mass spectrometry platform. The device enables declustering of ions prior to the quadrupole by imparting collisional activation through an oscillating electric field applied between two parallel plates. The positioning of the device enables liberation of membrane protein ions from detergent micelles. Quadrupole selection can now be utilized to isolate protein-ligand complexes, and downstream collision cells enable the dissociation and identification of binding partners. We demonstrate that ion mobility (IM) significantly aids in the assignment of top-down spectra, aligning fragments to their corresponding parent ions by means of IM drift time. Using this approach, we were able to confidently assign and identify a novel hit compound against PfMATE, obtained from multiplexed ligand libraries.
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Affiliation(s)
- Kleitos Sokratous
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | | | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Feng Qu
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Aisha Ben-Younis
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Mario Hensen
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph Gault
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Ali Jazayeri
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Idlir Liko
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Jonathan T S Hopper
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
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2
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Jayasekera HS, Mohona FA, Ewbank M, Marty MT. Simultaneous Native Mass Spectrometry Analysis of Single and Double Mutants To Probe Lipid Binding to Membrane Proteins. Anal Chem 2024; 96:10426-10433. [PMID: 38859611 PMCID: PMC11215972 DOI: 10.1021/acs.analchem.4c01704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Lipids are critical modulators of membrane protein structure and function. However, it is challenging to investigate the thermodynamics of protein-lipid interactions because lipids can simultaneously bind membrane proteins at different sites with different specificities. Here, we developed a native mass spectrometry (MS) approach using single and double mutants to measure the relative energetic contributions of specific residues on Aquaporin Z (AqpZ) toward cardiolipin (CL) binding. We first mutated potential lipid-binding residues on AqpZ, and mixed mutant and wild-type proteins together with CL. By using native MS to simultaneously resolve lipid binding to the mutant and wild-type proteins in a single spectrum, we directly determined the relative affinities of CL binding, thereby revealing the relative Gibbs free energy change for lipid binding caused by the mutation. Comparing different mutants revealed that W14 contributes to the tightest CL binding site, with R224 contributing to a lower affinity site. Using double mutant cycling, we investigated the synergy between W14 and R224 sites on CL binding. Overall, this novel native MS approach provides unique insights into the binding of lipids to specific sites on membrane proteins.
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Affiliation(s)
- Hiruni S. Jayasekera
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Farhana Afrin Mohona
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Megan Ewbank
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721
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3
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Harvey SR, Gadkari VV, Ruotolo BT, Russell DH, Wysocki VH, Zhou M. Expanding Native Mass Spectrometry to the Masses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:646-652. [PMID: 38303101 DOI: 10.1021/jasms.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
At the 33rd ASMS Sanibel Meeting, on Membrane Proteins and Their Complexes, a morning roundtable discussion was held discussing the current challenges facing the field of native mass spectrometry and approaches to expanding the field to nonexperts. This Commentary summarizes the discussion and current initiatives to address these challenges.
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Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77844, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Mowei Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310058, China
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4
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Gu Y, Liu M, Ma L, Quinn RJ. Identification of Ligands for Ion Channels: TRPM2. Chembiochem 2024; 25:e202300790. [PMID: 38242853 DOI: 10.1002/cbic.202300790] [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: 11/23/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable, nonselective cation channel with a widespread distribution throughout the body. It is involved in many pathological and physiological processes, making it a potential therapeutic target for various diseases, including Alzheimer's disease, Parkinson's disease, and cancers. New analytical techniques are beneficial for gaining a deeper understanding of its involvement in disease pathogenesis and for advancing the drug discovery for TRPM2-related diseases. In this work, we present the application of collision-induced affinity selection mass spectrometry (CIAS-MS) for the direct identification of ligands binding to TRPM2. CIAS-MS circumvents the need for high mass detection typically associated with mass spectrometry of large membrane proteins. Instead, it focuses on the detection of small molecules dissociated from the ligand-protein-detergent complexes. This affinity selection approach consolidates all affinity selection steps within the mass spectrometer, resulting in a streamlined process. We showed the direct identification of a known TRPM2 ligand dissociated from the protein-ligand complex. We demonstrated that CIAS-MS can identify binding ligands from complex mixtures of compounds and screened a compound library against TRPM2. We investigated the impact of voltage increments and ligand concentrations on the dissociation behavior of the binding ligand, revealing a dose-dependent relationship.
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Affiliation(s)
- Yushu Gu
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
- School of Environment and Science, Griffith University, N34 1.29, Nathan Campus, Brisbane, Queensland, 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Rd, Brisbane, Queensland, 4111, Australia
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5
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Li X, Sawada K, Shioji H. Determination and gas-phase stability evaluation of metal complexes by nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9649. [PMID: 37953546 DOI: 10.1002/rcm.9649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 11/14/2023]
Abstract
RATIONALE The structures of metal complexes determine their stable functioning in product performance. Electrospray ionization mass spectrometry (ESI-MS) is used in studying metal complexes despite exhibiting limitations in analyzing labile complexes. Therefore, identifying a method for detecting unstable complexes and evaluating their stabilities is necessary, providing a theoretical basis for material selection and performance evaluation. METHODS The standard complexes Zn(BTZ)2 , Fe(acac)3 , and Sn(Oct)2 were analyzed using nanoESI quadrupole orbitrap MS (nanoESI-MS) and compared with ESI-MS for two temperature modes. The three complexes and alkylamine-Ag+ complexes were analyzed using nanoESI and collision-induced dissociation MS/MS (CID-MS/MS). Breakdown plots of the survival yield against collision energies expressed in terms of the center-of-mass were constructed according to the obtained product ion spectra. Quantum chemical calculations based on density functional theory were performed to calculate the binding energies between the alkylamines and Ag+ . RESULTS The three standard complexes were detected in the native structures using nanoESI-MS, confirming the advantage of nanoESI over ESI for detecting unstable complexes. The gas-phase stabilities of the amine-Ag+ complexes, estimated using the breakdown plots constructed by plotting the data obtained via nanoESI and CID-MS/MS, were consistent with the established theories, previous studies, and binding energies calculated using computational methods. CONCLUSIONS NanoESI-MS is suitable for detecting labile complexes and enables the structural analyses of unknown complex additives. A novel approach based on nanoESI and CID-MS/MS was developed to determine the gas-phase stabilities of complexes, enabling their quantification and comparison and providing a technical basis for product improvement, which is essential in developing industrial materials.
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Affiliation(s)
- Xi Li
- Organic Analysis Laboratory, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Keisuke Sawada
- Research and Development Planning Department, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Hirotaka Shioji
- Organic Analysis Laboratory, Toray Research Center, Inc., Otsu, Shiga, Japan
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6
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Liu S, Abboud M, Mikhailov V, Liu X, Reinbold R, Schofield CJ. Differentiating Inhibition Selectivity and Binding Affinity of Isocitrate Dehydrogenase 1 Variant Inhibitors. J Med Chem 2023; 66:5279-5288. [PMID: 36952395 PMCID: PMC10108345 DOI: 10.1021/acs.jmedchem.3c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 03/25/2023]
Abstract
Isocitrate dehydrogenase (IDH) 1/2 gain-of-function variants catalyze the production of the oncometabolite 2-hydroxyglutarate and are validated targets for leukemia treatment. We report binding and inhibition studies on 13 IDH1/2 variant inhibitors, including clinical candidates and drugs, with wild-type (wt) IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors bind wt IDH1 despite not, or only weakly, inhibiting it. Selective inhibition of the IDH1 R132H variant over wt IDH1 does not principally relate to the affinities of the inhibitors for the resting forms of the enzymes. Rather, the independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes the variant more susceptible to allosteric inhibition, compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wt IDH1. The results highlight that binding affinity need not correlate with inhibition selectivity and have implications for interpretation of inhibitor screening results with IDH and related enzymes using turnover versus binding assays.
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Affiliation(s)
| | | | - Victor Mikhailov
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Xiao Liu
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Raphael Reinbold
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department
of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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7
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [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: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
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Affiliation(s)
- Deseree J. Reid
- Chemical and Biological Signature SciencesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Stephanie Thibert
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Mowei Zhou
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
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8
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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9
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Saikusa K, Kinumi T, Kato M. Development of native mass spectrometry with nanoelectrospray ionization coupled to size exclusion chromatography for proteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9395. [PMID: 36068720 DOI: 10.1002/rcm.9395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/07/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Native mass spectrometry (MS) is an analytical technique used to determine the molecular mass of protein complexes without cross-linking. Size exclusion chromatography (SEC) coupled with native MS using conventional electrospray ionization (ESI) has been reported to allow online buffer exchange. To detect a wide variety of protein complexes without a collapse in the ionization process, it is important to build an online system that enables robust analysis with a low flow rate. METHODS We created an online native MS system equipped with nanoESI connected to the SEC component (online SEC/nanoESI system) and optimized several parameters for SEC separation and ionization. The constructed system was used to measure a solution consisting of a protein mixture of various molecular masses (10-300 kDa) to verify characteristics such as the measurable molecular mass range, reproducibility, and online buffer exchange. RESULTS The optimal flow rates for SEC separation and nanoESI analysis using this system were 200 and 1 μL/min, respectively. This system was able to analyze proteins in the ranges of 10-300 and 20-300 kDa for protein samples in ammonium acetate and nonvolatile buffer, respectively. Furthermore, the results of consecutive measurements showed that the relative standard deviations of the retention times and observed masses for each protein were sufficiently small. CONCLUSIONS We created an online SEC/nanoESI system and evaluated its utility for the analysis of various proteins in conventional measurement solvent and nonvolatile buffer. As a result, the structural stability and resolution of the proteins were found to be sufficient when using online buffer exchange. Therefore, this online SEC/nanoESI system would be a useful technique for obtaining mass spectra of various proteins automatically with good resolution, simply by loading samples into an autosampler.
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Affiliation(s)
- Kazumi Saikusa
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Tomoya Kinumi
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Megumi Kato
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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10
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Illes-Toth E, Stubbs CJ, Sisley EK, Bellamy-Carter J, Simmonds AL, Mize TH, Styles IB, Goodwin RJA, Cooper HJ. Quantitative Characterization of Three Carbonic Anhydrase Inhibitors by LESA Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1168-1175. [PMID: 35675480 PMCID: PMC9264382 DOI: 10.1021/jasms.2c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liquid extraction surface analysis (LESA) coupled to native mass spectrometry (MS) presents unique analytical opportunities due to its sensitivity, speed, and automation. Here, we examine whether this tool can be used to quantitatively probe protein-ligand interactions through calculation of equilibrium dissociation constants (Kd values). We performed native LESA MS analyses for a well-characterized system comprising bovine carbonic anhydrase II and the ligands chlorothiazide, dansylamide, and sulfanilamide, and compared the results with those obtained from direct infusion mass spectrometry and surface plasmon resonance measurements. Two LESA approaches were considered: In one approach, the protein and ligand were premixed in solution before being deposited and dried onto a solid substrate for LESA sampling, and in the second, the protein alone was dried onto the substrate and the ligand was included in the LESA sampling solvent. Good agreement was found between the Kd values derived from direct infusion MS and LESA MS when the protein and ligand were premixed; however, Kd values determined from LESA MS measurements where the ligand was in the sampling solvent were inconsistent. Our results suggest that LESA MS is a suitable tool for quantitative analysis of protein-ligand interactions when the dried sample comprises both protein and ligand.
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Affiliation(s)
- Eva Illes-Toth
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Christopher J. Stubbs
- Mechanistic
and Structural Biology, Discovery Sciences,
R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Emma K. Sisley
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | | | - Anna L. Simmonds
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Todd H. Mize
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Iain B. Styles
- School
of Computer Science and Centre of Membrane Proteins and Receptors
(COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
- University of Nottingham, Midlands NG7 2RD, United Kingdom
| | - Richard J. A. Goodwin
- Imaging and
Data Analytics, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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11
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Wang L, Zhang W, Shao Y, Zhang D, Guo G, Wang X. Analytical methods for obtaining binding parameters of drug–protein interactions: A review. Anal Chim Acta 2022; 1219:340012. [DOI: 10.1016/j.aca.2022.340012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
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12
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Opening opportunities for K d determination and screening of MHC peptide complexes. Commun Biol 2022; 5:488. [PMID: 35606511 PMCID: PMC9127112 DOI: 10.1038/s42003-022-03366-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/13/2022] [Indexed: 01/15/2023] Open
Abstract
An essential element of adaptive immunity is selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes. Using native mass spectrometry, we analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule and, due to its unique stability, we determine binding affinities of complexes loaded with truncated or charge-reduced peptides. We find that the two anchor positions can be stabilized independently, and we further analyze the contribution of additional amino acid positions to the binding strength. As a complement to computational prediction tools, our method estimates binding strength of even low-affinity peptides to MHC class I complexes quickly and efficiently. It has huge potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy. The authors present a sensitive and rapid method to determine the binding strength of MHC class 1 peptide complexes using native mass spectrometry.
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13
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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14
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Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field's recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
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15
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Płonka D, Kotuniak R, Dąbrowska K, Bal W. Electrospray-Induced Mass Spectrometry Is Not Suitable for Determination of Peptidic Cu(II) Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2766-2776. [PMID: 34738801 PMCID: PMC8640992 DOI: 10.1021/jasms.1c00206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The toolset of mass spectrometry (MS) is still expanding, and the number of metal ion complexes researched this way is growing. The Cu(II) ion forms particularly strong peptide complexes of biological interest which are frequent objects of MS studies, but quantitative aspects of some reported results are at odds with those of experiments performed in solution. Cu(II) complexes are usually characterized by fast ligand exchange rates, despite their high affinity, and we speculated that such kinetic lability could be responsible for the observed discrepancies. In order to resolve this issue, we selected peptides belonging to the ATCUN family characterized with high and thoroughly determined Cu(II) binding constants and re-estimated them using two ESI-MS techniques: standard conditions in combination with serial dilution experiments and very mild conditions for competition experiments. The sample acidification, which accompanies the electrospray formation, was simulated with the pH-jump stopped-flow technique. Our results indicate that ESI-MS should not be used for quantitative studies of Cu(II)-peptide complexes because the electrospray formation process compromises the entropic contribution to the complex stability, yielding underestimations of complex stability constants.
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16
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Liu S, Abboud MI, John T, Mikhailov V, Hvinden I, Walsby-Tickle J, Liu X, Pettinati I, Cadoux-Hudson T, McCullagh JSO, Schofield CJ. Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1. Commun Biol 2021; 4:1243. [PMID: 34725432 PMCID: PMC8560763 DOI: 10.1038/s42003-021-02743-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a 'gain-of-function' to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+ KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.
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Affiliation(s)
- Shuang Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Xiao Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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17
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Kaeslin J, Brunner C, Ghiasikhou S, Schneider G, Zenobi R. Bioaffinity Screening with a Rapid and Sample-Efficient Autosampler for Native Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:13342-13350. [PMID: 34546705 DOI: 10.1021/acs.analchem.1c03130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fast and efficient handling of ligands and biological targets are required in bioaffinity screening based on native electrospray ionization mass spectrometry (ESI-MS). We use a prototype microfluidic autosampler, called the "gap sampler", to sequentially mix and electrospray individual small molecule ligands together with a target protein and compare the screening results with data from thermal shift assay and surface plasmon resonance. In a first round, all three techniques were used for a screening of 110 ligands against bovine carbonic anhydrase II, which resulted in five mutual hits and some false positives with ESI-MS presumably due to the high ligand concentration or interferences from dimethyl sulfoxide. In a second round, 33 compounds were screened in lower concentrations and in a less complex matrix, resulting in only true positives with ESI-MS. Within a cycle time of 30 s, dissociation constants were determined within an order of magnitude accuracy consuming only 5 pmol of ligand and less than 15 pmol of protein per screened compound. In a third round, dissociation constants of five compounds were accurately determined in a titration experiment. Thus, the gap sampler can rapidly and efficiently be used for high-throughput screening.
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Affiliation(s)
- Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sahar Ghiasikhou
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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18
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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19
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Chagovets VV, Starodubtseva NL, Frankevich VE. Complexes of fluconazole with alanine, lysine and threonine: mass spectrometry and theoretical modeling. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Investigation of the triazole-derived drugs action mechanisms and understanding of their affinity and specificity molecular basis may contribute to the new drugs development. The study was aimed to investigate the triazoles class representative (fluconazole) complexes with amino acids using mass spectrometry, molecular dynamics and ab initio quantum chemistry calculations. During the experimental study, the fluconazole, alanine, lysine and threonine solutions were analyzed by electrospray ionization mass spectrometry and tandem mass spectrometry. The molecular dynamics modeling of the fluconazole–amino acid complexes was performed using the CHARMM force field. The quantum chemistry calculations of the complexes structure and energy parameters were carried out using the density-functional theory by B3LYP calculations (3-21G and 6-311++G** basis sets). Mass spectra indicated that fluconazole formed stable complexes with amino acids in the 1 : 1 stoichiometric ratio. In accordance with the tandem mass spectrometry with varying fluconazole–amino acid associates ion fragmentation energy, the following sequence was obtained: [Fluc + Ala + H]+ < [Fluc + Lys + H]+ < [Fluc + Thr + H]+. The fluconazole–amino acid interaction energy values resulting from the quantum chemistry calculations formed the sequence similar to that obtained by experiment. Thus, as seen in the case of fluconazole–amino acid complexes, it is possible to combine the experimental mass spectrometry studies with quantum chemical modeling for the complexes properties assessment.
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Affiliation(s)
- VV Chagovets
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
| | - NL Starodubtseva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
| | - VE Frankevich
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
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20
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Elnaas AR, Grice D, Han J, Feng Y, Capua AD, Mak T, Laureanti JA, Buchko GW, Myler PJ, Cook G, Quinn RJ, Liu M. Discovery of a Natural Product That Binds to the Mycobacterium tuberculosis Protein Rv1466 Using Native Mass Spectrometry. Molecules 2020; 25:molecules25102384. [PMID: 32455540 PMCID: PMC7288112 DOI: 10.3390/molecules25102384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
Elucidation of the mechanism of action of compounds with cellular bioactivity is important for progressing compounds into future drug development. In recent years, phenotype-based drug discovery has become the dominant approach to drug discovery over target-based drug discovery, which relies on the knowledge of a specific drug target of a disease. Still, when targeting an infectious disease via a high throughput phenotypic assay it is highly advantageous to identifying the compound’s cellular activity. A fraction derived from the plant Polyalthia sp. showed activity against Mycobacterium tuberculosis at 62.5 μge/μL. A known compound, altholactone, was identified from this fraction that showed activity towards M. tuberculosis at an minimum inhibitory concentration (MIC) of 64 μM. Retrospective analysis of a target-based screen against a TB proteome panel using native mass spectrometry established that the active fraction was bound to the mycobacterial protein Rv1466 with an estimated pseudo-Kd of 42.0 ± 6.1 µM. Our findings established Rv1466 as the potential molecular target of altholactone, which is responsible for the observed in vivo toxicity towards M. tuberculosis.
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Affiliation(s)
- Ali R. Elnaas
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia;
| | - Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Angela Di Capua
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Peter J. Myler
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA;
| | - Gregory Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; (A.R.E.); (J.H.); (Y.F.); (A.D.C.); (T.M.); (R.J.Q.)
- Correspondence: ; Tel.: +61-7-3735-6077
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21
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A Phenotarget Approach for Identifying an Alkaloid Interacting with the Tuberculosis Protein Rv1466. Mar Drugs 2020; 18:md18030149. [PMID: 32150903 PMCID: PMC7143284 DOI: 10.3390/md18030149] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/11/2020] [Accepted: 02/20/2020] [Indexed: 01/10/2023] Open
Abstract
In recent years, there has been a revival of interest in phenotypic-based drug discovery (PDD) due to target-based drug discovery (TDD) falling below expectations. Both PDD and TDD have their unique advantages and should be used as complementary methods in drug discovery. The PhenoTarget approach combines the strengths of the PDD and TDD approaches. Phenotypic screening is conducted initially to detect cellular active components and the hits are then screened against a panel of putative targets. This PhenoTarget protocol can be equally applied to pure compound libraries as well as natural product fractions. Here we described the use of the PhenoTarget approach to identify an anti-tuberculosis lead compound. Fractions from Polycarpa aurata were identified with activity against Mycobacterium tuberculosis H37Rv. Native magnetic resonance mass spectrometry (MRMS) against a panel of 37 proteins from Mycobacterium proteomes showed that a fraction from a 95% ethanol re-extraction specifically formed a protein-ligand complex with Rv1466, a putative uncharacterized Mycobacterium tuberculosis protein. The natural product responsible was isolated and characterized to be polycarpine. The molecular weight of the ligand bound to Rv1466, 233 Da, was half the molecular weight of polycarpine less one proton, indicating that polycarpine formed a covalent bond with Rv1466.
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22
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Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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23
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Characterization of the binding of per- and poly-fluorinated substances to proteins: A methodological review. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Steyer DJ, Kennedy RT. High-Throughput Nanoelectrospray Ionization-Mass Spectrometry Analysis of Microfluidic Droplet Samples. Anal Chem 2019; 91:6645-6651. [PMID: 31033282 PMCID: PMC7848793 DOI: 10.1021/acs.analchem.9b00571] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Droplet microfluidics enables high-throughput manipulation of fL-μL volume samples. Methods implemented for the chemical analysis of microfluidic droplets have been limited in scope, leaving some applications of droplet microfluidics difficult to perform or out of reach entirely. Nanoelectrospray ionization-mass spectrometry (nESI-MS) is an attractive approach for droplet analysis, because it allows rapid, label-free, information-rich analysis with high mass sensitivity and resistance to matrix effects. Previous proof-of-concept systems for the nESI-MS analysis of droplets have been limited by the microfluidics used so that stable, long-term operation needed for high-throughput applications has not been demonstrated. We describe a platform for the stable analysis of microfluidic droplet samples by nESI-MS. Continuous infusion of droplets to an nESI emitter was demonstrated for as long as 2.5 h, corresponding to analysis of over 20 000 samples. Stable signal was observed for droplets as small as 65 pL and for throughputs as high as 10 droplets/s. A linear-concentration-based response and sample-to-sample carryover of <3% were also shown. The system is demonstrated for measuring products of in-droplet enzymatic reactions.
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Affiliation(s)
- Daniel J Steyer
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Robert T Kennedy
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
- Department of Pharmacology , University of Michigan , 1150 W. Medical Center Drive , Ann Arbor , Michigan 48109 , United States
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25
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Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
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Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
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26
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Shirzadeh M, Boone CD, Laganowsky A, Russell DH. Topological Analysis of Transthyretin Disassembly Mechanism: Surface-Induced Dissociation Reveals Hidden Reaction Pathways. Anal Chem 2019; 91:2345-2351. [PMID: 30642177 PMCID: PMC6464633 DOI: 10.1021/acs.analchem.8b05066] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The proposed mechanism of fibril formation of transthyretin (TTR) involves self-assembly of partially unfolded monomers. However, the mechanism(s) of disassembly to monomer and potential intermediates involved in this process are not fully understood. In this study, native mass spectrometry and surface-induced dissociation (SID) are used to investigate the TTR disassembly mechanism(s) and the effects of temperature and ionic strength on the kinetics of TTR complex formation. Results from the SID of hybrid tetramers formed during subunit exchange provide strong evidence for a two-step mechanism whereby the tetramer dissociates to dimers that then dissociate to monomers. Also, the SID results uncovered a hidden pathway in which a specific topology of the hybrid tetramer is directly produced by assembly of dimers in the early steps of TTR disassembly. Implementation of SID to dissect protein topology during subunit exchange provides unique opportunities to gain unparalleled insight into disassembly pathways.
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Affiliation(s)
- Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher D. Boone
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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27
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Wang Y, Park H, Lin H, Kitova EN, Klassen JS. Multipronged ESI–MS Approach for Studying Glycan-Binding Protein Interactions with Glycoproteins. Anal Chem 2019; 91:2140-2147. [DOI: 10.1021/acs.analchem.8b04673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yilin Wang
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Heajin Park
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Hong Lin
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Ren C, Bailey AO, VanderPorten E, Oh A, Phung W, Mulvihill MM, Harris SF, Liu Y, Han G, Sandoval W. Quantitative Determination of Protein–Ligand Affinity by Size Exclusion Chromatography Directly Coupled to High-Resolution Native Mass Spectrometry. Anal Chem 2018; 91:903-911. [DOI: 10.1021/acs.analchem.8b03829] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Aaron O. Bailey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
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29
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Gavriilidou AFM, Holding FP, Coyle JE, Zenobi R. Application of Native ESI-MS to Characterize Interactions between Compounds Derived from Fragment-Based Discovery Campaigns and Two Pharmaceutically Relevant Proteins. SLAS DISCOVERY 2018; 23:951-959. [PMID: 29852073 DOI: 10.1177/2472555218775921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Native electrospray ionization mass spectrometry (ESI-MS) was applied to analyze the binding of compounds generated during fragment-based drug discovery (FBDD) campaigns against two functionally distinct proteins, the X-linked inhibitor of apoptosis protein (XIAP) and cyclin-dependent kinase 2 (CDK2). Compounds of different molecular weights and a wide range of binding affinities obtained from the hits to leads and lead optimization stages of FBDD campaigns were studied, and their dissociation constants (Kd) were measured by native ESI-MS. We demonstrate that native ESI-MS has the potential to be applied to the stages of an FBDD campaign downstream of primary screening for the detection and quantification of protein-ligand binding. Native ESI-MS was used to derive Kd values for compounds binding to XIAP, and the dissociation of the complex between XIAP and a peptide derived from the second mitochondria-derived activator of caspases (SMAC) protein induced by one of the test compounds was also investigated. Affinities of compounds binding to CDK2 gave Kd values in the low nanomolar to low millimolar range, and Kd values generated by MS and isothermal titration calorimetry (ITC) followed the same trend for both proteins. Practical considerations for the application of native ESI-MS are discussed in detail.
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Affiliation(s)
- Agni F M Gavriilidou
- 1 Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Renato Zenobi
- 1 Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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30
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Clark DD. Preliminary investigation of deoxyoligonucleotide binding to ribonuclease A using mass spectrometry: An attempt to develop a lab experience for undergraduates. F1000Res 2018; 7:340. [PMID: 29721314 PMCID: PMC5897785 DOI: 10.12688/f1000research.14268.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2018] [Indexed: 11/28/2022] Open
Abstract
Deoxyoligonucleotide binding to bovine pancreatic ribonuclease A (RNase A) was investigated using electrospray ionization ion-trap mass spectrometry (ESI-IT-MS). Deoxyoligonucleotides included CCCCC (dC
5) and CCACC (dC
2AC
2). This work was an attempt to develop a biochemistry lab experience that would introduce undergraduates to the use of mass spectrometry for the analysis of protein-ligand interactions. Titration experiments were performed using a fixed RNase A concentration and variable deoxyoligonucleotide concentrations. Samples at equilibrium were infused directly into the mass spectrometer under native conditions. For each deoxyoligonucleotide, mass spectra showed one-to-one binding stoichiometry, with marked increases in the total ion abundance of ligand-bound RNase A complexes as a function of concentration, but the accurate determination of dC
5 and dC
2AC
2 dissociation constants was problematic.
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Affiliation(s)
- Daniel D Clark
- Department of Chemistry and Biochemistry, California State University, Chico, Chico, CA, 95929-0210, USA
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31
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Chi Q, Li Z, Huang J, Ma J, Wang X. Interactions of perfluorooctanoic acid and perfluorooctanesulfonic acid with serum albumins by native mass spectrometry, fluorescence and molecular docking. CHEMOSPHERE 2018; 198:442-449. [PMID: 29425944 DOI: 10.1016/j.chemosphere.2018.01.152] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 05/22/2023]
Abstract
The binding information of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) with bovine and human serum albumins was investigated and characterized in details by using a combination method of electrospray ionization mass spectrometry (ESI-MS), fluorescence, circular dichroism (CD) and molecular docking (MD). The ESI-MS analysis revealed that maximally eight PFOA or PFOS molecules could bind to serum albumins at high mole ratios of PFOA/PFOS. Association constants were measured by ESI-MS and suggested that PFOS had a better binding affinity than PFOA. PFOA and PFOS were likely to bind with serum albumins in more than one pocket. The CD data demonstrated that binding of PFOA and PFOS could change the conformation of serum albumins with decreasing α-helix content, which may affect the protein physiological function. The phenomenon of protein fluorescence quenching by the binding of PFOA and PFOS indicated that the hydrophobic pocket proximate to Trp 214 in human serum albumin might be one of the dominated binding sites. This assumption was further confirmed by MD simulation. Consistent to ESI-MS observation, MD results also displayed a stronger binding affinity of PFOS than PFOA according to the calculated binding free energy, which is probably ascribed to one more hydrogen bond formed in the PFOS-bound protein complexes.
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Affiliation(s)
- Quan Chi
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Zhixiong Li
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Juan Huang
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Jieyao Ma
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074, PR China.
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32
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How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions? Methods 2018; 144:3-13. [PMID: 29704661 DOI: 10.1016/j.ymeth.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/21/2018] [Indexed: 01/16/2023] Open
Abstract
Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques. Despite the maturation of native MS and greatly expanded range of applications in recent decades, further dissemination is needed to make the community aware of such a technique. In this review, we attempt to provide an overview of the current body of knowledge regarding major aspects of native MS and explain how such technique contributes to the characterization of biomacromolecular higher-order structure and interactions.
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Chi Q, Liu YZ, Wang X. Study on the Structural Effect of Maltoligosaccharides on Cytochrome c Complexes Stabilities by Native Mass Spectrometry. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:57-61. [PMID: 29380206 PMCID: PMC5803145 DOI: 10.1007/s13659-017-0150-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/13/2017] [Indexed: 05/05/2023]
Abstract
Noncovalent interactions between ligands and targeting proteins are essential for understanding molecular mechanisms of proteins. In this work, we investigated the interaction of Cytochrome c (Cyt c) with maltoligosaccharides, namely maltose (Mal II), maltotriose (Mal III), maltotetraose (Mal IV), maltopentaose (Mal V), maltohexaose (Mal VI) and maltoheptaose (Mal VII). Using electrospray ionization mass spetrometry (ESI-MS) assay, the 1:1 and 1:2 complexes formed by Cyt c with maltoligosaccharide ligand were observed. The corresponding association constants were calculated according to the deconvoluted spectra. The order of the relative binding affinities of the selected oligosaccharides with Cyt c were as Mal III > Mal IV > Mal II > Mal V > Mal VI > Mal VII. The results indicated that the stability of noncovalent protein complexes was intimately correlated to the molecular structure of bound ligand. The relevant functional groups that could form H-bonds, electrostatic or hydrophobic forces with protein's amino residues played an important role for the stability of protein complexes. In addition, the steric structure of ligand was also critical for an appropriate interaction with the binding pocket of proteins.
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Affiliation(s)
- Quan Chi
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China
| | - Ying-Zhi Liu
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei, 430074, People's Republic of China.
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34
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Mass spectrometry for fragment screening. Essays Biochem 2017; 61:465-473. [PMID: 28986384 DOI: 10.1042/ebc20170071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening.
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35
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Quantifying Na(I)-insulin and K(I)-insulin non-covalent complexes by ESI–MS method and calculation of their equilibrium constants. Int J Biol Macromol 2017; 103:910-918. [DOI: 10.1016/j.ijbiomac.2017.05.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/05/2017] [Accepted: 05/25/2017] [Indexed: 01/10/2023]
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36
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Guo H, Peng H, Emili A. Mass spectrometry methods to study protein-metabolite interactions. Expert Opin Drug Discov 2017; 12:1271-1280. [DOI: 10.1080/17460441.2017.1378178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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37
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Chrysanthopoulos PK, Mujumdar P, Woods LA, Dolezal O, Ren B, Peat TS, Poulsen SA. Identification of a New Zinc Binding Chemotype by Fragment Screening. J Med Chem 2017; 60:7333-7349. [PMID: 28817930 DOI: 10.1021/acs.jmedchem.7b00606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.
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Affiliation(s)
| | - Prashant Mujumdar
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Lucy A Woods
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Olan Dolezal
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Bin Ren
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Sally-Ann Poulsen
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
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38
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Li W, Yu J, Kane MA. Quantitation of the Noncovalent Cellular Retinol-Binding Protein, Type 1 Complex Through Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:29-37. [PMID: 27709511 PMCID: PMC5728378 DOI: 10.1007/s13361-016-1499-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 05/22/2023]
Abstract
Native mass spectrometry (MS) has become a valuable tool in probing noncovalent protein-ligand interactions in a sample-efficient way, yet the quantitative application potential of native MS has not been fully explored. Cellular retinol binding protein, type I (CrbpI) chaperones retinol and retinal in the cell, protecting them from nonspecific oxidation and delivering them to biosynthesis enzymes where the bound (holo-) and unbound (apo-) forms of CrbpI exert distinct biological functions. Using nanoelectrospray, we developed a native MS assay for probing apo- and holo-CrbpI abundance to facilitate exploring their biological functions in retinoid metabolism and signaling. The methods were developed on two platforms, an Orbitrap-based Thermo Exactive and a Q-IMS-TOF-based Waters Synapt G2S, where similar ion behaviors under optimized conditions were observed. Overall, our results suggested that within the working range (~1-10 μM), gas-phase ions in the native state linearly correspond to solution concentration and relative ion intensities of the apo- and holo-protein ions can linearly respond to the solution ratios, suggesting native MS is a viable tool for relative quantitation in this system. Graphical Abstract ᅟ.
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Affiliation(s)
- Wenjing Li
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N. Pine Street, Room 723, Baltimore, MD, 21201, USA
| | - Jianshi Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N. Pine Street, Room 723, Baltimore, MD, 21201, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N. Pine Street, Room 723, Baltimore, MD, 21201, USA.
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Ključarić V, Kobetić R, Rinkovec J, Kazazić S, Gembarovski D, Saftić D, Matić J, Ban Ž, Žinić B. ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:998-1005. [PMID: 27405069 DOI: 10.1002/jms.3810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/16/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)2 Cl2 , 3 and Cu(1-MsC-N3)2 Cl2 and 4 with biologically important cations: Na+ , K+ , Ca2+ , Mg2+ and Zn2+ . The formation of various complex metal ions was observed. The alkali metals Na+ and K+ formed clusters because of electrostatic interactions. Ca2+ and Mg2+ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn2+ with 1-4 produced monometal and dimetal Zn2+ complexes as a result of the affinity of Zn2+ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Valentina Ključarić
- Ministry of Defense of the Republic of Croatia, "Dr. Franjo Tuđman" Croatian Defense Academy, Ilica 256 b, Zagreb, Croatia
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia.
| | - Jasmina Rinkovec
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10 000, Zagreb, Croatia
| | - Snježana Kazazić
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | | | - Dijana Saftić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Željka Ban
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Biserka Žinić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia.
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40
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Gülfen M, Özdemir A, Lin JL, Chen CH. Investigation of non-covalent complexations of Ca(II) and Mg(II) ions with insulin by using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2171-2182. [PMID: 27469404 DOI: 10.1002/rcm.7683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/20/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Insulin is a peptide hormone secreted by pancreatic β-cells. Ca(II) and Mg(II) ions play an important role in the secretion of insulin. There is no study about a direct complexation of Ca(II) or Mg(II) with insulin and their equilibrium constants. Electrospray ionization mass spectrometry (ESI-MS) is a practical method for the monitoring of non-covalent complexes such as Ca(II)-insulin and Mg(II)-insulin. Here, the equilibrium constants of Ca(II)-insulin and Mg(II)-insulin non-covalent complexes have been calculated after ESI-MS measurements in aqueous solutions. METHODS The effects of pH, competitive binding, ion exchange, and Na(I) and K(I) ions on Ca(II)-insulin and Mg(II)-insulin complexation have been examined by measuring by ESI-MS. The dissociation equilibrium constants (K1 and K2 ) of Ca(II)-insulin and Mg(II)-insulin complexes were calculated from the binomial graph derived from the ESI-MS normalized peak intensities. The MS/MS spectra of the complexes have been examined. RESULTS The dissociation equilibrium constants were found to K1 : 1.29 × 10(-4) M and K2 : 9.69 × 10(-4) M for the Ca(II)-insulin complexes, and K1 : 1.37 × 10(-4) M and K2 : 9.12 × 10(-4) M for Mg(II)-insulin complexes. Ca(II) ions have higher complexation capability with insulin than Mg(II) ions. CONCLUSIONS The binding equilibrium constants of Ca(II)- and Mg(II)-insulin non-covalent complexes have been determined successfully by ESI-MS. Ca(II) and Mg(II) ions are involved in the insulin secretion by forming non-covalent complexes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mustafa Gülfen
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187, Sakarya, Turkey
| | - Abdil Özdemir
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187, Sakarya, Turkey
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Abstract
A fully automated chip-based nanoelectrospray (nanoESI) system, NanoMate® 100 (Advion Bio-Sciences, Inc., Ithaca, NY), was evaluated for its application on quantitative bioanalysis of small molecules in support of exploratory pharmacokinetic (PK) studies. The NanoMate® 100 was compared with the conventional autosampler coupled with liquid chromatography-electrospray (LC-ESI) interface. An API® 3000 triple quadrupole mass spectrometer (Applied Biosystems, Inc., Foster City, CA) was used for the evaluation. The results show that the NanoMate® 100 performs comparably to LC-ESI in terms of standard curve fitting, low limit of quantitation (LLOQ), dynamic range, accuracy, and precision. Parallel analyses of exploratory PK study samples show high correlation ( R2 = 0.971) between the NanoMate® 100 and the LC-ESI. The NanoMate® 100 exhibits advantages in carryover, sample consumption, sample cycle time, and the ability to be full automated. Despite these advantages, the necessarily rigorous sample preparation process limits the application of the NanoMate® 100 for quantitative analysis in areas such as exploratory PK studies, which often involve multiple compounds in one study and require rapid turnaround. However, the NanoMate® 100 has great potential in qualitative work (e.g., metabolite identification) as well as in high-throughput quantitative analysis of compound in the development stage (i.e., a single analyte with a well-established sample extraction method). (JALA 2004;9:109-16)
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42
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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Ishii K, Noda M, Uchiyama S. Mass spectrometric analysis of protein-ligand interactions. Biophys Physicobiol 2016; 13:87-95. [PMID: 27924262 PMCID: PMC5042164 DOI: 10.2142/biophysico.13.0_87] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 12/01/2022] Open
Abstract
The interactions of small molecules with proteins (protein–ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein–ligand interactions. These interactions typically accompany association–dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development. Mass spectrometry (MS) has been used to determine the precise molecular masses of molecules. Recent advancements in MS enable us to determine the molecular masses of protein–ligand complexes without disrupting the non-covalent interactions through the gentle desolvation of the complexes by increasing the vacuum pressure of a chamber in a mass spectrometer. This method is called MS under non-denaturing conditions or native MS and allows the unambiguous determination of protein–ligand interactions. Under a few assumptions, MS has also been applied to determine the dissociation constants for protein–ligand interactions. The structural information of a protein–ligand interaction, such as the location of the interaction and conformational change in a protein, can also be analyzed using hydrogen/deuterium exchange MS. In this paper, we briefly describe the history, principle, and recent applications of MS for the study of protein–ligand interactions.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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44
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Woods LA, Dolezal O, Ren B, Ryan JH, Peat TS, Poulsen SA. Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination. J Med Chem 2016; 59:2192-204. [PMID: 26882437 DOI: 10.1021/acs.jmedchem.5b01940] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
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Affiliation(s)
- Lucy A Woods
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
| | - Olan Dolezal
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Bin Ren
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - John H Ryan
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Sally-Ann Poulsen
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
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45
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Yang Y, Han F, Ouyang J, Zhao Y, Han J, Na N. In-situ nanoelectrospray for high-throughput screening of enzymes and real-time monitoring of reactions. Anal Chim Acta 2016; 902:135-141. [DOI: 10.1016/j.aca.2015.10.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/26/2015] [Indexed: 12/24/2022]
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46
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Quintyn RS, Zhou M, Yan J, Wysocki VH. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes. Anal Chem 2015; 87:11879-86. [PMID: 26499904 DOI: 10.1021/acs.analchem.5b03441] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Royston S. Quintyn
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Mowei Zhou
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Jing Yan
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Vicki H. Wysocki
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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47
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Gavriilidou AFM, Gülbakan B, Zenobi R. Influence of Ammonium Acetate Concentration on Receptor–Ligand Binding Affinities Measured by Native Nano ESI-MS: A Systematic Study. Anal Chem 2015; 87:10378-84. [DOI: 10.1021/acs.analchem.5b02478] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Agni F. M. Gavriilidou
- ETH Zurich, Department of Chemistry and Applied
Biosciences, CH-8093 Zurich, Switzerland
| | - Basri Gülbakan
- Institute
of Child Health, Division of Pediatric Basic Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Renato Zenobi
- ETH Zurich, Department of Chemistry and Applied
Biosciences, CH-8093 Zurich, Switzerland
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48
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Feng X, Liu BF, Li J, Liu X. Advances in coupling microfluidic chips to mass spectrometry. MASS SPECTROMETRY REVIEWS 2015; 34:535-57. [PMID: 24399782 DOI: 10.1002/mas.21417] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 05/26/2023]
Abstract
Microfluidic technology has shown advantages of low sample consumption, reduced analysis time, high throughput, and potential for integration and automation. Coupling microfluidic chips to mass spectrometry (Chip-MS) can greatly improve the overall analytical performance of MS-based approaches and expand their potential applications. In this article, we review the advances of Chip-MS in the past decade, covering innovations in microchip fabrication, microchips coupled to electrospray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-MS. Development of integrated microfluidic systems for automated MS analysis will be further documented, as well as recent applications of Chip-MS in proteomics, metabolomics, cell analysis, and clinical diagnosis.
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MESH Headings
- Animals
- Chromatography, Liquid/instrumentation
- Chromatography, Liquid/methods
- Electrophoresis, Microchip/instrumentation
- Electrophoresis, Microchip/methods
- Equipment Design
- Humans
- Lab-On-A-Chip Devices
- Lipids/analysis
- Metabolomics/instrumentation
- Metabolomics/methods
- Polysaccharides/analysis
- Proteins/analysis
- Proteomics/instrumentation
- Proteomics/methods
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Xiaojun Feng
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjun Li
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6
| | - Xin Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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49
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Garcia AF, Dyszy F, Munte CE, DeMarco R, Beltramini LM, Oliva G, Costa-Filho AJ, Araujo AP. THI1, a protein involved in the biosynthesis of thiamin in Arabidopsis thaliana: Structural analysis of THI1(A140V) mutant. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1094-103. [DOI: 10.1016/j.bbapap.2014.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/28/2014] [Accepted: 03/07/2014] [Indexed: 01/21/2023]
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50
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Martí I, Bolte M, Burguete MI, Vicent C, Alfonso I, Luis SV. Tight and Selective Caging of Chloride Ions by a Pseudopeptidic Host. Chemistry 2014; 20:7458-64. [DOI: 10.1002/chem.201303604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 03/24/2014] [Indexed: 11/12/2022]
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