1
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Wang G, Moitessier N, Mittermaier AK. Computational and biophysical methods for the discovery and optimization of covalent drugs. Chem Commun (Camb) 2023; 59:10866-10882. [PMID: 37609777 DOI: 10.1039/d3cc03285j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Drugs that act by covalently attaching to their targets have been used to treat human diseases for over a hundred years. However, the deliberate design of covalent drugs was discouraged due to concerns of toxicity and off-target effects. Recent successes in covalent drug discovery have sparked fresh interest in this field. New screening and testing methods aimed at covalent inhibitors can play pivotal roles in facilitating the discovery process. This feature article focuses on computational and biophysical advances originating from our labs over the past decade and how these approaches have contributed to the design of prolyl oligopeptidase (POP) and SARS-CoV-2 3CLpro covalent inhibitors.
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Affiliation(s)
- Guanyu Wang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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2
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Barry CJ, Pillay CS, Rohwer JM. Modelling the Decamerisation Cycle of PRDX1 and the Inhibition-like Effect on Its Peroxidase Activity. Antioxidants (Basel) 2023; 12:1707. [PMID: 37760010 PMCID: PMC10525498 DOI: 10.3390/antiox12091707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Peroxiredoxins play central roles in the detoxification of reactive oxygen species and have been modelled across multiple organisms using a variety of kinetic methods. However, the peroxiredoxin dimer-to-decamer transition has been underappreciated in these studies despite the 100-fold difference in activity between these forms. This is due to the lack of available kinetics and a theoretical framework for modelling this process. Using published isothermal titration calorimetry data, we obtained association and dissociation rate constants of 0.050 µM-4·s-1 and 0.055 s-1, respectively, for the dimer-decamer transition of human PRDX1. We developed an approach that greatly reduces the number of reactions and species needed to model the peroxiredoxin decamer oxidation cycle. Using these data, we simulated horse radish peroxidase competition and NADPH-oxidation linked assays and found that the dimer-decamer transition had an inhibition-like effect on peroxidase activity. Further, we incorporated this dimer-decamer topology and kinetics into a published and validated in vivo model of PRDX2 in the erythrocyte and found that it almost perfectly reconciled experimental and simulated responses of PRDX2 oxidation state to hydrogen peroxide insult. By accounting for the dimer-decamer transition of peroxiredoxins, we were able to resolve several discrepancies between experimental data and available kinetic models.
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Affiliation(s)
- Christopher J. Barry
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
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3
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El-Araby AM, Feltzer R, Kim C, Mobashery S. Application of 2D-ITC to the Elucidation of the Enzymatic Mechanism of N-Acetylmuramic Acid/ N-Acetylglucosamine Kinase (AmgK) from Pseudomonas aeruginosa. Biochemistry 2023; 62:1337-1341. [PMID: 36971350 DOI: 10.1021/acs.biochem.3c00090] [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: 03/29/2023]
Abstract
Characterization of the turnover mechanism of bisubstrate enzymes is a tedious task. Molecular tools for studying the enzymatic mechanism are not readily available for all enzymes (e.g., radioactive substrates, substrate-competitive inhibitors, etc.). Wang and Mittermaier recently introduced two-dimensional isothermal titration calorimetry (2D-ITC) for determining the bisubstrate mechanism at high resolution while simultaneously quantifying the kinetic parameters for substrate turnover in a single reporter-free experiment. We demonstrate the utility of 2D-ITC in studying N-acetylmuramic acid/N-acetylglucosamine kinase (AmgK) from Pseudomonas aeruginosa. This enzyme is involved in cytoplasmic cell-wall-recycling events as a step in the peptidoglycan salvage pathway. Furthermore, AmgK phosphorylates N-acetylglucosamine and N-acetylmuramic acid, linking the recycling events to de novo cell-wall synthesis. We document in a 2D-ITC experiment that AmgK follows an ordered-sequential mechanism, where ATP binds first and ADP is released last. We also show that classical enzyme kinetic methods support the results of 2D-ITC and that 2D-ITC could overcome the shortcomings of these classical methodologies. We provide evidence for inhibition of AmgK by the catalytic product ADP, but not by the phosphorylated sugar product. These results provide a full kinetic characterization of the bacterial kinase AmgK. This work highlights 2D-ITC as a versatile tool for the mechanistic evaluation of bisubstrate enzymes, as an alternative for classical methods.
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Affiliation(s)
- Amr M El-Araby
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Borko V, Friganović T, Weitner T. Glycoproteomics meets thermodynamics: A calorimetric study of the effect of sialylation and synergistic anion on the binding of iron to human serum transferrin. J Inorg Biochem 2023; 244:112207. [PMID: 37054508 DOI: 10.1016/j.jinorgbio.2023.112207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/20/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
The thermodynamic parameters for the binding of ferric ions to human serum transferrin (hTf) as the major mediator of iron transport in blood plasma were determined by isothermal titration calorimetry in the presence of carbonate and oxalate as synergistic anions at pH 7.4. The results indicate that the binding of ferric ions to the two binding sites of hTf is driven both enthalpically and entropically in a lobe-dependent manner: binding to the C-site is mainly enthalpically driven, whereas binding to the N-site is mainly entropically driven. Lower sialic acid content of hTf leads to more exothermic apparent binding enthalpies for both lobes, while the increased apparent binding constants for both sites were found in the presence of carbonate. Sialylation also unequally affected the heat change rates for both sites only in the presence of carbonate, but not in the presence of oxalate. Overall, the results suggest that the desialylated hTf has a higher iron sequestering ability, which may have implications for iron metabolism.
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5
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Tso SC, Jowitt TA, Brautigam CA. The feasibility of determining kinetic constants from isothermal titration calorimetry data. Biophys J 2022; 121:2474-2484. [PMID: 35490299 DOI: 10.1016/j.bpj.2022.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/11/2022] [Accepted: 04/27/2022] [Indexed: 11/02/2022] Open
Abstract
Isothermal titration calorimetry (ITC) has long been established as an excellent means to determine the thermodynamic parameters of biomolecular interactions. More recently, efforts have focused on exploiting the power/time trace (the "thermogram") resulting from ITC experiments to glean kinetic association and dissociation rates for these interactions. The ability to do so rests on the ability of algorithms to simulate with high accuracy the output of the calorimeter. Thus, several critical factors must be taken into account: the injection protocol, the kinetics of the interaction, accurate discovery of the instrumental response to heat signals, and the addition of unrelated signals. All of these aspects of extracting kinetic constants from thermograms have been considered and addressed in the current work. To validate the resultant methods, we performed several ITC experiments, titrating small-molecule inhibitors into solutions of bovine carbonic anhydrase II or titrating lysozyme into solutions of anti-lysozyme nanobodies. We found that our methods could arrive at kinetic constants that were close to the known values for these interactions taken from other methods. Finally, the effort to improve ITC kinetic characterizations uncovered a set of best practices for both the calorimetric experiment and the subsequent analyses (termed "kinetically optimized ITC" or "KO-ITC") that is detailed in this work.
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Affiliation(s)
- Shih-Chia Tso
- Departments of Biophysics and UT Southwestern Medical Center, Dallas, TX 75390 USA
| | - Thomas A Jowitt
- Wellcome Trust Centre Cell Matrix Research, Faculty of Biology Medicine and Health, University of Manchester, Manchester, England
| | - Chad A Brautigam
- Departments of Biophysics and UT Southwestern Medical Center, Dallas, TX 75390 USA; Departments of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390 USA.
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6
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Gygli G. On the reproducibility of enzyme reactions and kinetic modelling. Biol Chem 2022; 403:717-730. [PMID: 35357794 DOI: 10.1515/hsz-2021-0393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/09/2022] [Indexed: 12/20/2022]
Abstract
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modeling meticulously executed. Furthermore, to enable quality control of enzyme reaction parameters, the experimental conditions, the modeling process as well as the raw data need to be reported comprehensively. By taking these steps, enzyme reaction parameters can be open and FAIR (findable, accessible, interoperable, re-usable) as well as repeatable, replicable and reproducible. This review discusses these requirements and provides a practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and gives an open, FAIR and re-editable example of the kinetic modeling of an enzyme reaction. Both the guide and example are scripted with Python in Jupyter Notebooks and are publicly available (https://fairdomhub.org/investigations/483/snapshots/1). Finally, the prerequisites of automated data analysis and machine learning algorithms are briefly discussed to provide further motivation for the comprehensive, open and FAIR reporting of enzyme reaction parameters.
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Affiliation(s)
- Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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7
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Tan X, Sawczyk M, Chang Y, Wang Y, Usman A, Fu C, Král P, Peng H, Zhang C, Whittaker AK. Revealing the Molecular-Level Interactions between Cationic Fluorinated Polymer Sorbents and the Major PFAS Pollutant PFOA. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiao Tan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michał Sawczyk
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yixin Chang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yiqing Wang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Adil Usman
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Changkui Fu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Hui Peng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cheng Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew K. Whittaker
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Brisbane, QLD 4072, Australia
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8
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Wang Y, Hanrahan G, Azar FA, Mittermaier A. Binding interactions in a kinase active site modulate background ATP hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140720. [PMID: 34597835 DOI: 10.1016/j.bbapap.2021.140720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Kinases play central roles in many cellular processes, transferring the terminal phosphate groups of nucleoside triphosphates (NTPs) onto substrates. In the absence of substrates, kinases can also hydrolyse NTPs producing NDPs and inorganic phosphate. Hydrolysis is usually much less efficient than the native phosphoryl transfer reaction. This may be related to the fact that NTP hydrolysis is metabolically unfavorable as it unproductively consumes the cell's energy stores. It has been suggested that substrate interactions could drive changes in NTP binding pocket, activating catalysis only when substrates are present. Structural data show substrate-induced conformational rearrangements, however there is a lack of corresponding functional information. To better understand this phenomenon, we developed a suite of isothermal titration calorimetry (ITC) kinetics methods to characterize ATP hydrolysis by the antibiotic resistance enzyme aminoglycoside-3'-phosphotransferase-IIIa (APH(3')-IIIa). We measured Km, kcat, and product inhibition constants and single-turnover kinetics in the presence and absence of non-substrate aminoglycosides (nsAmgs) that are structurally similar to the native substrates. We found that the presence of an nsAmg increased the chemical step of cleaving the ATP γ-phosphate by at least 10- to 20-fold under single-turnover conditions, supporting the existence of interactions that link substrate binding to substantially enhanced catalytic rates. Our detailed kinetic data on the association and dissociation rates of nsAmgs and ADP shed light on the biophysical processes underlying the enzyme's Theorell-Chance reaction mechanism. Furthermore, they provide clues on how to design small-molecule effectors that could trigger efficient ATP hydrolysis and generate selective pressure against bacteria harboring the APH(3')-IIIa.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Grace Hanrahan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Frederic Abou Azar
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada.
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9
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Wang Y, Mittermaier AK. Characterizing Bi-substrate Enzyme Kinetics at High Resolution by 2D-ITC. Anal Chem 2021; 93:12723-12732. [PMID: 34514786 DOI: 10.1021/acs.analchem.1c02705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There is growing interest in using isothermal titration calorimetry (ITC) to characterize enzyme kinetics by measuring the heat produced or absorbed by catalysis in real time. Since virtually all chemical reactions are associated with changes in enthalpy, ITC represents a robust and nearly universal experimental approach. Nevertheless, there are technical challenges that limit ITC's applicability. For instance, the full kinetic characterization of enzymes with two substrates (bi-substrate enzymes), which comprise the majority of known examples, requires a series of experiments to be performed as the concentrations of both substrates are varied. This is a time-consuming and expensive process using current ITC methods since many (>5) individual experiments must be performed independently to obtain a sufficient quantity of data. We have developed a new ITC method, which we term 2D-ITC, which maps the reaction velocity as a function of two substrate concentrations in a single, roughly 2 h long experiment. This method provides a level of detail that rivals or exceeds any existing enzyme assay, as a single experiment generates on the order of 7000 catalytic rate measurements. In a proof-of-principle application to rabbit muscle pyruvate kinase (rMPK), the method correctly identified the enzyme's random sequential mechanism and allosteric catalytic suppression by the amino acid phenylalanine (Phe). Unexpectedly, we found that while Phe reduces affinity for the substrate phosphoenolpyruvate, a known phenomenon, it also alleviates inhibition by the reaction product ATP, which had not been reported previously. Given the relative abundance of ATP in the cell, this opposing effect is expected to have a substantial impact on rMPK activity.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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12
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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14
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Plescia J, Dufresne C, Janmamode N, Wahba AS, Mittermaier AK, Moitessier N. Discovery of covalent prolyl oligopeptidase boronic ester inhibitors. Eur J Med Chem 2020; 185:111783. [DOI: 10.1016/j.ejmech.2019.111783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 01/22/2023]
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15
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Totea A, Dorin I, Gavrilov G, Laity P, Conway B, Waters L, Asare-Addo K. Real time calorimetric characterisation of clay – drug complex dispersions and particles. Int J Pharm X 2019; 1:100003. [PMID: 31545854 PMCID: PMC6733304 DOI: 10.1016/j.ijpx.2018.100003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/17/2022] Open
Abstract
Single loaded and double loaded MAS-PPN complexes successfully made. ATR-FTIR confirmed adsorption of PPN onto MAS via hydrogen bonding. SEM/EDX showed changes in MAS microstructure upon complexation. Drug recovery varied in three media types. SIM and MIM experiments showed overall change in enthalpy to be exothermic SIM and MIM showed small entropic contribution to the total change in Gibbs free energy.
Isothermal titration calorimetry (ITC) along with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX) and high-performance liquid chromatography (HPLC) were employed to investigate the process of adsorption of propranolol hydrochloride (PPN) onto magnesium aluminium silicate (MAS) and to characterise the MAS-PPN particles formed upon complexation. The composition of MAS was confirmed by infrared (IR) spectroscopy and a calcimeter. The calorimetric results confirmed the binding between PPN and MAS at various pHs and temperatures. The overall change in enthalpy was found to be exothermic with a comparatively small entropic contribution to the total change in Gibbs free energy. These findings suggest that the binding process was enthalpically driven and entropically unfavourable (lower affinity) suggesting hydrogen bonding and electrostatic interactions dominating the interaction. The variation of pH and temperature did not have a great impact on the thermodynamics of the binding process, as observed from the similarity in enthalpy (ΔH), entropy (ΔS) or Gibbs free energy (ΔG). A slight reduction in the binding affinity (Ka) with varing pH and temperature was however observed. SEM/EDX studies showed the occurrence of changes in the microstructural properties of MAS following complexation which may explain the potential of MAS-PPN complexes for controlled drug release promoting pharmaceutical innovation.
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Affiliation(s)
- A.M. Totea
- School of Applied Sciences, Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - I. Dorin
- Malvern Panalytical Ltd., Malvern, UK
| | - G. Gavrilov
- Wienerberger, Baneasa Business & Technology Park, Bucharest, Romania
| | - P.R. Laity
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK
| | - B.R. Conway
- School of Applied Sciences, Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - L. Waters
- School of Applied Sciences, Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - K. Asare-Addo
- School of Applied Sciences, Department of Pharmacy, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
- Corresponding author.
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16
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Abis G, Pacheco-Gómez R, Bui TTT, Conte MR. Isothermal Titration Calorimetry Enables Rapid Characterization of Enzyme Kinetics and Inhibition for the Human Soluble Epoxide Hydrolase. Anal Chem 2019; 91:14865-14872. [PMID: 31660733 PMCID: PMC7041903 DOI: 10.1021/acs.analchem.9b01847] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Isothermal titration
calorimetry (ITC) is conventionally used to
acquire thermodynamic data for biological interactions. In recent
years, ITC has emerged as a powerful tool to characterize enzyme kinetics.
In this study, we have adapted a single-injection method (SIM) to
study the kinetics of human soluble epoxide hydrolase (hsEH), an enzyme
involved in cardiovascular homeostasis, hypertension, nociception,
and insulin sensitivity through the metabolism of epoxy-fatty acids
(EpFAs). In the SIM method, the rate of reaction is determined by
monitoring the thermal power, while the substrate is being depleted,
overcoming the need for synthetic substrates and reducing postreaction
processing. Our results show that ITC enables the detailed, rapid,
and reproducible characterization of the hsEH-mediated hydrolysis
of several natural EpFA substrates. Furthermore, we have applied a
variant of the single-injection ITC method for the detailed description
of enzyme inhibition, proving the power of this approach in the rapid
screening and discovery of new hsEH inhibitors using the enzyme’s
physiological substrates. The methods described herein will enable
further studies on EpFAs’ metabolism and biology, as well as
drug discovery investigations to identify and characterize hsEH inhibitors.
This also promises to provide a general approach for the characterization
of lipid catalysis, given the challenges that lipid metabolism studies
pose to traditional spectroscopic techniques.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences , King's College London , London , SE1 1UL , United Kingdom
| | - Raúl Pacheco-Gómez
- Malvern Panalytical Ltd , Enigma Business Park, Grovewood Road , Malvern , WR14 1XZ , United Kingdom
| | - Tam T T Bui
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences , King's College London , London , SE1 1UL , United Kingdom.,Centre for Biomolecular Spectroscopy , King's College London , London , SE1 1UL , United Kingdom
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences , King's College London , London , SE1 1UL , United Kingdom.,Centre for Biomolecular Spectroscopy , King's College London , London , SE1 1UL , United Kingdom
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17
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Luo XA, Zhao P, Zhang H, Feng SY, Chen KX, Chen ZX. Improved hydrolysis of α-tocopherol acetate emulsion and its bioaccessibility in the presence of polysaccharides and PEG2000. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.123837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Wang Y, Guan J, Di Trani JM, Auclair K, Mittermaier AK. Inhibition and Activation of Kinases by Reaction Products: A Reporter-Free Assay. Anal Chem 2019; 91:11803-11811. [PMID: 31426630 DOI: 10.1021/acs.analchem.9b02456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Kinases are widely distributed in nature and are implicated in many human diseases. Thus, an understanding of their activity and regulation is of fundamental importance. Several kinases are known to be inhibited by ADP. However, thorough investigation of this phenomenon is hampered by the lack of a simple and effective assay for studying this inhibition. We now present a quick, general approach for measuring the effects of reaction products on kinase activity. The method, based on isothermal titration calorimetry, is the first universal, reporter-free, continuous assay for probing kinase inhibition or activation by ADP. In applications to an aminoglycoside phosphotransferase [APH(3')-IIIa] and pantothenate kinases from Escherichia coli (EcPanK) and Pseudomonas aeruginosa (PaPanK), we found ADP to be an efficient inhibitor of all three kinases, with inhibition constant (Ki) values similar to or lower than the Michaelis-Menten constant (Km) values of ATP. Interestingly, ADP was an activator at low concentrations and an inhibitor at high concentrations for EcPanK. This unusual effect was quantitatively modeled and attributed to cooperative interactions between the two subunits of the dimeric enzyme. Importantly, our results suggest that, at typical bacterial intracellular concentrations of ATP and ADP (approximately 1.5 mM and 180 μM, respectively), all three kinases are partially inhibited by ADP, allowing enzyme activity to rapidly respond to changes in the levels of both metabolites.
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Affiliation(s)
- Yun Wang
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Jinming Guan
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Justin M Di Trani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Anthony K Mittermaier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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19
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Probing the bilayer-monolayer switching of capping agents on Au nanorods and its interaction with guest molecules
$$^{\S }$$
§. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Kammer MN, Kussrow AK, Olmsted IR, Bornhop DJ. A Highly Compensated Interferometer for Biochemical Analysis. ACS Sens 2018; 3:1546-1552. [PMID: 29984991 DOI: 10.1021/acssensors.8b00361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here we report an improved interferometric sensing approach that facilitates high sensitivity nanovolume refractive index (RI) measurements and molecular interaction assays without a temperature controller. The compensated backscattering interferometer (CBSI) is based on a helium-neon (He-Ne) laser, a microfluidic chip, and a CCD array. The CBSI enables simultaneous differential RI measurements within nanoliter volumes, at a compensation level of ca. 5 × 10-8 RIU in the presence of large thermal perturbations (8 °C). This level of d n/d T compensation is enabled by elongating the laser beam along the central axis of the microfluidic channel and measuring the difference in positional shift of interference patterns from two adjacent regions of the channel. By separating two solutions by an air gap or oil droplet, CBSI can discriminate the difference in RI for the sample and reference at a detection limit of 7 × 10-7 RIU in the absence of electronic filtering. At this level of ΔRI sensitivity, it is possible to perform label-free, free-solution biochemical assays at the 10s of nM level without the typical high-resolution temperature control needed in conventional interferometers. Here we illustrate the effective use of CBSI by quantifying the binding affinities for mannose-concanavalin A and Ca2+-recoverin interactions.
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Affiliation(s)
- Michael N. Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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21
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Di Trani JM, Moitessier N, Mittermaier AK. Complete Kinetic Characterization of Enzyme Inhibition in a Single Isothermal Titration Calorimetric Experiment. Anal Chem 2018; 90:8430-8435. [DOI: 10.1021/acs.analchem.8b00993] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Di Trani JM, De Cesco S, O'Leary R, Plescia J, do Nascimento CJ, Moitessier N, Mittermaier AK. Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry. Nat Commun 2018; 9:893. [PMID: 29497037 PMCID: PMC5832847 DOI: 10.1038/s41467-018-03263-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/31/2018] [Indexed: 11/23/2022] Open
Abstract
Although drug development typically focuses on binding thermodynamics, recent studies suggest that kinetic properties can strongly impact a drug candidate’s efficacy. Robust techniques for measuring inhibitor association and dissociation rates are therefore essential. To address this need, we have developed a pair of complementary isothermal titration calorimetry (ITC) techniques for measuring the kinetics of enzyme inhibition. The advantages of ITC over standard techniques include speed, generality, and versatility; ITC also measures the rate of catalysis directly, making it ideal for quantifying rapid, inhibitor-dependent changes in enzyme activity. We used our methods to study the reversible covalent and non-covalent inhibitors of prolyl oligopeptidase (POP). We extracted kinetics spanning three orders of magnitude, including those too rapid for standard methods, and measured sub-nM binding affinities below the typical ITC limit. These results shed light on the inhibition of POP and demonstrate the general utility of ITC-based enzyme inhibition kinetic measurements. There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.
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Affiliation(s)
- Justin M Di Trani
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Stephane De Cesco
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Rebecca O'Leary
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Jessica Plescia
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Claudia Jorge do Nascimento
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada.,Institute of Biosciences, Federal University of the State of Rio de Janeiro, Urca, 22290-240, Rio de Janeiro, Brazil
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
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