1
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Kotschy J, Söldner B, Singh H, Vasa SK, Linser R. Microsecond Timescale Conformational Dynamics of a Small-Molecule Ligand within the Active Site of a Protein. Angew Chem Int Ed Engl 2024; 63:e202313947. [PMID: 37974542 DOI: 10.1002/anie.202313947] [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: 09/18/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The possible internal dynamics of non-isotope-labeled small-molecule ligands inside a target protein is inherently difficult to capture. Whereas high crystallographic temperature factors can denote either static disorder or motion, even moieties with very low B-factors can be subject to vivid motion between symmetry-related sites. Here we report the experimental identification of internal μs timescale dynamics of a high-affinity, natural-abundance ligand tightly bound to the enzyme human carbonic anhydrase II (hCAII) even within a crystalline lattice. The rotamer jumps of the ligand's benzene group manifest themselves both, in solution and fast magic-angle spinning solid-state NMR 1 H R1ρ relaxation dispersion, for which we obtain further mechanistic insights from molecular-dynamics (MD) simulations. The experimental confirmation of rotameric jumps in bound ligands within proteins in solution or the crystalline state may improve understanding of host-guest interactions in biology and supra-molecular chemistry and may facilitate medicinal chemistry for future drug campaigns.
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Affiliation(s)
- Julia Kotschy
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benedikt Söldner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Himanshu Singh
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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2
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Maltarollo VG, Shevchenko E, Lima IDDM, Cino EA, Ferreira GM, Poso A, Kronenberger T. Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels. J Chem Inf Model 2022; 62:5746-5761. [PMID: 36343333 DOI: 10.1021/acs.jcim.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The enzyme enoyl-ACP reductase (FabI) is the limiting step of the membrane's fatty acid biosynthesis in bacteria and a druggable target for novel antibacterial agents. The FabI active form is a homotetramer, which displays the highest affinity to inhibitors. Herein, molecular dynamics studies were carried out using the structure of FabI in complex with known inhibitors to investigate their effects on tetramerization. Our results suggest that multimerization is essential for the integrity of the catalytic site and that inhibitor binding enables the multimerization by stabilizing the substrate binding loop (SBL, L:195-200) coupled with changes in the H4/5 (QR interface). We also observed that AFN-1252 (naphtpyridinone derivative) promotes unique conformational changes affecting monomer-monomer interfaces. These changes are induced by AFN-1252 interaction with key residues in the binding sites (Ala95, Tyr146, and Tyr156). In addition, the analysis of water trajectories indicated that AFN-1252 complexes allow more water molecules to enter the binding site than triclosan and MUT056399 complexes. FabI-AFN-1252 simulations show accumulation of water molecules near the Tyr146/147 pocket, which can become a hotspot to the design of novel FabI inhibitors.
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Affiliation(s)
- Vinicius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Igor Daniel de Miranda Lima
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Elio A Cino
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000 São Paulo, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
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3
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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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4
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Karges J, Stokes RW, Cohen SM. Computational Prediction of the Binding Pose of Metal-Binding Pharmacophores. ACS Med Chem Lett 2022; 13:428-435. [PMID: 35300086 PMCID: PMC8919381 DOI: 10.1021/acsmedchemlett.1c00584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/14/2022] [Indexed: 01/22/2023] Open
Abstract
Computational modeling of inhibitors for metalloenzymes in virtual drug development campaigns has proven challenging. To overcome this limitation, a technique for predicting the binding pose of metal-binding pharmacophores (MBPs) is presented. Using a combination of density functional theory (DFT) calculations and docking using a genetic algorithm, inhibitor binding was evaluated in silico and compared with inhibitor-enzyme cocrystal structures. The predicted binding poses were found to be consistent with the cocrystal structures. The computational strategy presented represents a useful tool for predicting metalloenzyme-MBP interactions.
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Affiliation(s)
- Johannes Karges
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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5
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Pantsar T, Kaiser PD, Kudolo M, Forster M, Rothbauer U, Laufer SA. Decisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors. Nat Commun 2022; 13:569. [PMID: 35091547 PMCID: PMC8799644 DOI: 10.1038/s41467-022-28164-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/06/2022] [Indexed: 12/31/2022] Open
Abstract
Target residence time plays a crucial role in the pharmacological activity of small molecule inhibitors. Little is known, however, about the underlying causes of inhibitor residence time at the molecular level, which complicates drug optimization processes. Here, we employ all-atom molecular dynamics simulations (~400 μs in total) to gain insight into the binding modes of two structurally similar p38α MAPK inhibitors (type I and type I½) with short and long residence times that otherwise show nearly identical inhibitory activities in the low nanomolar IC50 range. Our results highlight the importance of protein conformational stability and solvent exposure, buried surface area of the ligand and binding site resolvation energy for residence time. These findings are further confirmed by simulations with a structurally diverse short residence time inhibitor SB203580. In summary, our data provide guidance in compound design when aiming for inhibitors with improved target residence time. The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.
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Affiliation(s)
- Tatu Pantsar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Mark Kudolo
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Michael Forster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany. .,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany. .,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany.
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6
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Berrino E, Michelet B, Martin‐Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emanuela Berrino
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Bastien Michelet
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Agnès Martin‐Mingot
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Fabrizio Carta
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Claudiu T. Supuran
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Sébastien Thibaudeau
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
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7
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Nocentini A, Angeli A, Carta F, Winum JY, Zalubovskis R, Carradori S, Capasso C, Donald WA, Supuran CT. Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase. J Enzyme Inhib Med Chem 2021; 36:561-580. [PMID: 33615947 PMCID: PMC7901698 DOI: 10.1080/14756366.2021.1882453] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.
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Affiliation(s)
- Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | | | - Raivis Zalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
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8
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Berrino E, Michelet B, Martin-Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021; 60:23068-23082. [PMID: 34028153 DOI: 10.1002/anie.202103211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/19/2021] [Indexed: 12/19/2022]
Abstract
The insertion of fluorine atoms and/or fluoroalkyl groups can lead to many beneficial effects in biologically active molecules, such as enhanced metabolic stability, bioavailability, lipophilicity, and membrane permeability, as well as a strengthening of protein-ligand binding interactions. However, this "magic effect" of fluorine atom(s) insertion can often be meaningless. Taking advantage of the wide range of data coming from the quest for carbonic anhydrase (CA) fluorinated inhibitors, this Minireview attempts to give "general guidelines" on how to wisely insert fluorine atom(s) within an inhibitor moiety to precisely enhance or disrupt ligand-protein interactions, depending on the target location of the fluorine substitution in the ligand. Multiple approaches such as ITC, kinetic and inhibition studies, X-ray crystallography, and NMR spectroscopy are useful in dissecting single binding contributions to the overall observed effect. The exploitation of innovative directions made in the field of protein and ligand-based fluorine NMR screening is also discussed to avoid misconduct and finely tune the exploitation of selective fluorine atom insertion in the future.
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Affiliation(s)
- Emanuela Berrino
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Bastien Michelet
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Agnès Martin-Mingot
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Sébastien Thibaudeau
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
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9
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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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10
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Effendi SSW, Tan SI, Ting WW, Ng IS. Genetic design of co-expressed Mesorhizobium loti carbonic anhydrase and chaperone GroELS to enhancing carbon dioxide sequestration. Int J Biol Macromol 2020; 167:326-334. [PMID: 33275972 DOI: 10.1016/j.ijbiomac.2020.11.189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022]
Abstract
Mesorhizobium loti carbonic anhydrase (MlCA), an intrinsically high catalytic enzyme, has been employed for carbon dioxide capture and sequestration. However, recombinant expression of MlCA in Escherichia coli often forms inclusion bodies. Hence, protein partners such as fusion-tags and molecular chaperones are involved in regarding reduce the harshness of protein folding. TrxA-tag and GroELS have been chosen to co-express with MlCA in E. coli under an inducible T7 promoter or a constitutive J23100 promoter to compare productivity and activity. The results possessed that coupling protein partners effectively increased soluble MlCA up to 2.9-folds under T7 promoter, thus enhancing the CA activity by 120% and achieving a 5.2-folds turnover rate. Besides, it has also shifted the optimum temperature from 40 °C to 50 °C, promoted stability in the broad pH range (4.5 to 9.5) and the presence of various metal ions. Based on the in vitro assay and isothermal titration calorimetry (ITC) analysis, GroELS enhancing CA activity was due to change the intrinsic thermodynamic properties of the enzyme from endothermic to exothermic reaction (i.e., ∆H = 89.8 to -121.8 kJ/mol). Therefore, the collaboration of TrxA-MlCA with GroELS successfully augmented CO2 biomineralization.
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Affiliation(s)
- Sefli Sri Wahyu Effendi
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC.
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11
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Glöckner S, Klebe G. Simultaneous determination of thermodynamic and kinetic data by isothermal titration calorimetry. Biochim Biophys Acta Gen Subj 2020; 1865:129772. [PMID: 33191201 DOI: 10.1016/j.bbagen.2020.129772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Thermodynamic and binding kinetic data increasingly support and guide the drug optimization process. METHODS Because ITC thermograms contain binding thermodynamic and kinetic information, an efficient protocol for the simultaneous extraction of thermodynamic and kinetic data for 1:1 protein ligand reactions from AFFINImeter kinITC in one single experiment are presented. RESULTS The effort to apply this protocol requires the same time as for the standard protocol but increases the precision of both thermodynamic and kinetic data. CONCLUSIONS The protocol enables reliable extraction of both thermodynamic and kinetic data for 1:1 protein-ligand binding reactions with improved precision compared to the 'standard protocol'. GENERAL SIGNIFICANCE Thermodynamic and kinetic data are recorded under exactly the same conditions in solution without any labeling or immobilization from a protein sample that is not 100% active and would otherwise render the extraction of kinetic parameters impossible.
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Affiliation(s)
- Steffen Glöckner
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
| | - Gerhard Klebe
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
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12
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Kaur J, Cao X, Abutaleb NS, Elkashif A, Graboski AL, Krabill AD, AbdelKhalek AH, An W, Bhardwaj A, Seleem MN, Flaherty DP. Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus. J Med Chem 2020; 63:9540-9562. [PMID: 32787141 DOI: 10.1021/acs.jmedchem.0c00734] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Vancomycin-resistant enterococci (VRE) are the second leading cause of hospital-acquired infections (HAIs) attributed to a drug-resistant bacterium in the United States, and resistance to the frontline treatments is well documented. To combat VRE, we have repurposed the FDA-approved carbonic anhydrase drug acetazolamide to design potent antienterococcal agents. Through structure-activity relationship optimization we have arrived at two leads possessing improved potency against clinical VRE strains from MIC = 2 μg/mL (acetazolamide) to MIC = 0.007 μg/mL (22) and 1 μg/mL (26). Physicochemical properties were modified to design leads that have either high oral bioavailability to treat systemic infections or low intestinal permeability to treat VRE infections in the gastrointestinal tract. Our data suggest the intracellular targets for the molecules are putative α-carbonic and γ-carbonic anhydrases, and homology modeling and molecular dynamics simulations were performed. Together, this study presents potential anti-VRE therapeutic options to provide alternatives for problematic VRE infections.
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Affiliation(s)
- Jatinder Kaur
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Nader S Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Ahmed Elkashif
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Amanda L Graboski
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Ahmed Hassan AbdelKhalek
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Weiwei An
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Atul Bhardwaj
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States.,Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute of Inflammation, Immunology and Infectious Disease, 207 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute of Inflammation, Immunology and Infectious Disease, 207 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
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Glöckner S, Heine A, Klebe G. A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II. Biomolecules 2020; 10:biom10040518. [PMID: 32235320 PMCID: PMC7226012 DOI: 10.3390/biom10040518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022] Open
Abstract
Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.
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Glöckner S, Ngo K, Wagner B, Heine A, Klebe G. The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II. Biomolecules 2020; 10:E509. [PMID: 32230853 PMCID: PMC7226267 DOI: 10.3390/biom10040509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022] Open
Abstract
The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.
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Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Björn Wagner
- F. Hoffmann-La Roche AG, Pharmaceutical Research & Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland;
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany; (S.G.); (K.N.); (A.H.)
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