1
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Lingė D, Gedgaudas M, Merkys A, Petrauskas V, Vaitkus A, Grybauskas A, Paketurytė V, Zubrienė A, Zakšauskas A, Mickevičiūtė A, Smirnovienė J, Baranauskienė L, Čapkauskaitė E, Dudutienė V, Urniežius E, Konovalovas A, Kazlauskas E, Shubin K, Schiöth HB, Chen WY, Ladbury JE, Gražulis S, Matulis D. PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters. Database (Oxford) 2023; 2023:baad040. [PMID: 37290059 PMCID: PMC10250011 DOI: 10.1093/database/baad040] [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: 01/31/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
We introduce a protein-ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein-ligand crystal structures, enabling structure-thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein-ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein-ligand recognition and could be integrated into small molecule drug design. Database URL https://plbd.org/.
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Affiliation(s)
- Darius Lingė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Andrius Merkys
- Sector of Crystallography and Cheminformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Antanas Vaitkus
- Sector of Crystallography and Cheminformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Algirdas Grybauskas
- Sector of Crystallography and Cheminformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Joana Smirnovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Lina Baranauskienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Ernestas Urniežius
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Aleksandras Konovalovas
- Department of Biochemistry and Molecular Biology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Kirill Shubin
- Latvian Institute of Organic Synthesis, Aizkraukles Street 21, Riga LV-1006, Latvia
| | - Helgi B Schiöth
- Functional Pharmacology and Neuroscience, Department of Surgical Sciences, Uppsala University, Kirurgiska Vetenskaper, Box 593, Uppsala 751 24, Sweden
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, Jhong-Li 320, Taiwan
| | - John E Ladbury
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Saulius Gražulis
- Sector of Crystallography and Cheminformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
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2
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Matulienė J, Žvinys G, Petrauskas V, Kvietkauskaitė A, Zakšauskas A, Shubin K, Zubrienė A, Baranauskienė L, Kačenauskaitė L, Kopanchuk S, Veiksina S, Paketurytė-Latvė V, Smirnovienė J, Juozapaitienė V, Mickevičiūtė A, Michailovienė V, Jachno J, Stravinskienė D, Sližienė A, Petrošiūtė A, Becker HM, Kazokaitė-Adomaitienė J, Yaromina A, Čapkauskaitė E, Rinken A, Dudutienė V, Dubois LJ, Matulis D. Picomolar fluorescent probes for compound affinity determination to carbonic anhydrase IX expressed in live cancer cells. Sci Rep 2022; 12:17644. [PMID: 36271018 PMCID: PMC9586938 DOI: 10.1038/s41598-022-22436-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/14/2022] [Indexed: 01/18/2023] Open
Abstract
Numerous human cancers, especially hypoxic solid tumors, express carbonic anhydrase IX (CAIX), a transmembrane protein with its catalytic domain located in the extracellular space. CAIX acidifies the tumor microenvironment, promotes metastases and invasiveness, and is therefore considered a promising anticancer target. We have designed a series of high affinity and high selectivity fluorescein-labeled compounds targeting CAIX to visualize and quantify CAIX expression in cancer cells. The competitive binding model enabled the determination of common CA inhibitors' dissociation constants for CAIX expressed in exponentially growing cancer cells. All tested sulfonamide compounds bound the proliferating cells with similar affinity as to recombinantly purified CAIX. The probes are applicable for the design of selective drug-like compounds for CAIX and the competition strategy could be applied to other drug targets.
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Affiliation(s)
- Jurgita Matulienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Gediminas Žvinys
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Agnė Kvietkauskaitė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Kirill Shubin
- grid.419212.d0000 0004 0395 6526Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006 Latvia
| | - Asta Zubrienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Lina Baranauskienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Lina Kačenauskaitė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Sergei Kopanchuk
- grid.10939.320000 0001 0943 7661Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Santa Veiksina
- grid.10939.320000 0001 0943 7661Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Vaida Paketurytė-Latvė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Joana Smirnovienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vaida Juozapaitienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Aurelija Mickevičiūtė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vilma Michailovienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Jelena Jachno
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Dovilė Stravinskienė
- grid.6441.70000 0001 2243 2806Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Aistė Sližienė
- grid.6441.70000 0001 2243 2806Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Agnė Petrošiūtė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Holger M. Becker
- Zoology and Animal Physiology, Institute of Zoology, TU Dresden, 01217 Dresden, Germany
| | - Justina Kazokaitė-Adomaitienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania ,grid.430814.a0000 0001 0674 1393Present Address: Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ala Yaromina
- grid.5012.60000 0001 0481 6099The M-Lab, Department of Precision Medicine, GROW – School for Oncology and Reproduction, Maastricht University, Universiteitssingel 50/23, 6200 MD Maastricht, The Netherlands
| | - Edita Čapkauskaitė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Ago Rinken
- grid.10939.320000 0001 0943 7661Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Virginija Dudutienė
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Ludwig J Dubois
- grid.5012.60000 0001 0481 6099The M-Lab, Department of Precision Medicine, GROW – School for Oncology and Reproduction, Maastricht University, Universiteitssingel 50/23, 6200 MD Maastricht, The Netherlands
| | - Daumantas Matulis
- grid.6441.70000 0001 2243 2806Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
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3
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Linkuvienė V, Zubrienė A, Matulis D. Intrinsic affinity of protein - ligand binding by differential scanning calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140830. [PMID: 35934299 DOI: 10.1016/j.bbapap.2022.140830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Differential scanning calorimetry (DSC) determines the enthalpy change upon protein unfolding and the melting temperature of the protein. Performing DSC of a protein in the presence of increasing concentrations of specifically-binding ligand yields a series of curves that can be fit to obtain the protein-ligand dissociation constant as done in the fluorescence-based thermal shift assay (FTSA, ThermoFluor, DSF). The enthalpy of unfolding, as directly determined by DSC, helps improving the precision of the fit. If the ligand binding is linked to protonation reactions, the intrinsic binding constant can be determined by performing the affinity determination at a series of pH values. Here, the intrinsic, pH-independent, affinity of acetazolamide binding to carbonic anhydrase (CA) II was determined. A series of high-affinity ligands binding to CAIX, an anticancer drug target, and CAII showed recognition and selectivity for the anticancer isozyme. Performing the DSC experiment in buffers of highly different enthalpies of protonation enabled to observe the ligand unbinding-linked protonation reactions and estimate the intrinsic enthalpy of binding. The heat capacity of combined unfolding and unbinding was determined by varying the ligand concentrations. Taken together, these parameters provided a detailed thermodynamic picture of the linked ligand binding and protein unfolding process.
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Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania.
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4
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Baronas D, Dudutienė V, Paketurytė V, Kairys V, Smirnov A, Juozapaitienė V, Vaškevičius A, Manakova E, Gražulis S, Zubrienė A, Matulis D. Structure and mechanism of secondary sulfonamide binding to carbonic anhydrases. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:993-1011. [PMID: 34328515 DOI: 10.1007/s00249-021-01561-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Zinc-containing metalloenzyme carbonic anhydrase (CA) binds primary sulfonamides with extremely high, up to picomolar, affinity by forming a coordination bond between the negatively charged amino group and the zinc ion and making hydrogen bonds and hydrophobic contacts with other parts of the inhibitor molecule. However, N-methyl-substituted, secondary or tertiary sulfonamides bind CA with much lower affinity. In search for an explanation for this diminished affinity, a series of secondary sulfonamides were synthesized and, together with analogous primary sulfonamides, the affinities for 12 recombinant catalytically active human CA isoforms were determined by the fluorescent thermal shift assay, stopped-flow assay of the inhibition of enzymatic activity and isothermal titration calorimetry. The binding profile of secondary sulfonamides as a function of pH showed the same U-shape dependence seen for primary sulfonamides. This dependence demonstrated that there were protein binding-linked protonation reactions that should be dissected for the estimation of the intrinsic binding constants to perform structure-thermodynamics analysis. X-ray crystallographic structures of secondary sulfonamides and computational modeling dissected the atomic contributions to the binding energetics. Secondary sulfonamides bind to carbonic anhydrases via coordination bond between the negatively charged nitrogen of alkylated amino group and Zn(II) in the active site of CA. The binding reaction is linked to deprotonation of the amino group and protonation of the Zn(II)-bound hydroxide. To perform the structure-thermodynamics analysis, contributions of these linked reactions must be subtracted to determine the intrinsic energetics. In this aspect, the secondary sulfonamides are similar to primary sulfonamides as CA inhibitors.
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Affiliation(s)
- Denis Baronas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Vaida Juozapaitienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Aivaras Vaškevičius
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania.
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5
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Kazokaitė-Adomaitienė J, Becker HM, Smirnovienė J, Dubois LJ, Matulis D. Experimental Approaches to Identify Selective Picomolar Inhibitors for Carbonic Anhydrase IX. Curr Med Chem 2021; 28:3361-3384. [PMID: 33138744 DOI: 10.2174/0929867327666201102112841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Carbonic anhydrases (CAs) regulate pH homeostasis via the reversible hydration of CO2, thereby emerging as essential enzymes for many vital functions. Among 12 catalytically active CA isoforms in humans, CA IX has become a relevant therapeutic target because of its role in cancer progression. Only two CA IX inhibitors have entered clinical trials, mostly due to low affinity and selectivity properties. OBJECTIVE The current review presents the design, development, and identification of the selective nano- to picomolar CA IX inhibitors VD11-4-2, VR16-09, and VD12-09. METHODS AND RESULTS Compounds were selected from our database, composed of over 400 benzensulfonamides, synthesized at our laboratory, and tested for their binding to 12 human CAs. Here we discuss the CA CO2 hydratase activity/inhibition assay and several biophysical techniques, such as fluorescent thermal shift assay and isothermal titration calorimetry, highlighting their contribution to the analysis of compound affinity and structure- activity relationships. To obtain sufficient amounts of recombinant CAs for inhibitor screening, several gene cloning and protein purification strategies are presented, including site-directed CA mutants, heterologous CAs from Xenopus oocytes, and native endogenous CAs. The cancer cell-based methods, such as clonogenicity, extracellular acidification, and mass spectrometric gas-analysis are reviewed, confirming nanomolar activities of lead inhibitors in intact cancer cells. CONCLUSIONS Novel CA IX inhibitors are promising derivatives for in vivo explorations. Furthermore, the simultaneous targeting of several proteins involved in proton flux upon tumor acidosis and the disruption of transport metabolons might improve cancer management.
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Affiliation(s)
- Justina Kazokaitė-Adomaitienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Holger M Becker
- Institute of Physiological Chemistry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Joana Smirnovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, Netherlands
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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6
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Smirnovienė J, Smirnov A, Zakšauskas A, Zubrienė A, Petrauskas V, Mickevičiūtė A, Michailovienė V, Čapkauskaitė E, Manakova E, Gražulis S, Baranauskienė L, Chen W, Ladbury JE, Matulis D. Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII. ChemistryOpen 2021; 10:567-580. [PMID: 33945229 PMCID: PMC8095314 DOI: 10.1002/open.202100042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Indexed: 01/02/2023] Open
Abstract
A key part of the optimization of small molecules in pharmaceutical inhibitor development is to vary the molecular design to enhance complementarity of chemical features of the compound with the positioning of amino acids in the active site of a target enzyme. Typically this involves iterations of synthesis, to modify the compound, and biophysical assay, to assess the outcomes. Selective targeting of the anti-cancer carbonic anhydrase isoform XII (CA XII), this process is challenging because the overall fold is very similar across the twelve CA isoforms. To enhance drug development for CA XII we used a reverse engineering approach where mutation of the key six amino acids in the active site of human CA XII into the CA II isoform was performed to provide a protein chimera (chCA XII) which is amenable to structure-based compound optimization. Through determination of structural detail and affinity measurement of the interaction with over 60 compounds we observed that the compounds that bound CA XII more strongly than CA II, switched their preference and bound more strongly to the engineered chimera, chCA XII, based on CA II, but containing the 6 key amino acids from CA XII, behaved as CA XII in its compound recognition profile. The structures of the compounds in the chimeric active site also resembled those determined for complexes with CA XII, hence validating this protein engineering approach in the development of new inhibitors.
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Affiliation(s)
- Joana Smirnovienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Elena Manakova
- Department of Protein-DNA InteractionsInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA InteractionsInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Lina Baranauskienė
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
| | - Wen‐Yih Chen
- Department of Chemical and Materials EngineeringInstitute of Systems Biology and BioinformaticsNational Central UniversityTaiwan
| | - John E. Ladbury
- School of Molecular and Cellular BiologyUniversity of LeedsLC Miall BuildingLeedsLS2 9JTUK
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug DesignInstitute of BiotechnologyLife Sciences CenterVilnius UniversitySaulėtekio 7Vilnius10257Lithuania
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7
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Smirnovienė J, Baranauskienė L, Zubrienė A, Matulis D. A standard operating procedure for an enzymatic activity inhibition assay. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:345-352. [PMID: 33864100 DOI: 10.1007/s00249-021-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/12/2021] [Accepted: 03/26/2021] [Indexed: 01/08/2023]
Abstract
This Standard Operating Protocol (SOP) describes the key steps of experimental setup for an inhibition assay of enzymatic activity. The protocol begins with the design of an experiment, including the choice of a catalytic reaction, optimal conditions, fraction and concentration of the active enzyme, substrate and inhibitor concentrations and the positive and negative controls. The protocol ends with the data analysis followed by a typical example of an experiment. Despite an apparently standard procedure, the assay has a number of possible pitfalls such as low fraction of the active enzyme or errors in the analysis such as application of an improper model or incorrect determination of the inhibition constant while not recognizing the dependence on enzyme concentration. The protocol provides examples of necessary steps and controls to avoid these problems and obtain highly reliable results.
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Affiliation(s)
- Joana Smirnovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Lina Baranauskienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania.
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8
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Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:661-670. [PMID: 33837826 DOI: 10.1007/s00249-021-01518-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/05/2021] [Accepted: 03/13/2021] [Indexed: 01/18/2023]
Abstract
Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change ΔGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and ΔGb are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and ΔGb values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.
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9
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Camadan Y, Çiçek B, Adem Ş, Çalişir Ü, Akkemik E. Investigation of in vitro and in silico effects of some novel carbazole Schiff bases on human carbonic anhydrase isoforms I and II. J Biomol Struct Dyn 2021; 40:6965-6973. [PMID: 33645441 DOI: 10.1080/07391102.2021.1892527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Carbonic anhydrases (CAs, EC4.2.1.1) are metalloenzymes that catalyse reversible hydration reaction of carbon dioxide to bicarbonate and protons. In recent years, there has been a great interest in inhibitors/activators of carbonic anhydrase isoenzymes. Therefore, we investigated the effects of four different carbazole Schiff base derivatives, which are believed to have a potential to be used as a drug, on human carbonic anhydrase (hCA) isoenzymes I and II under in vitro conditions. The IC50 values of carbazole Schiff base derivatives were found to be in the range of 32.09-151.2 μM for hCA isoenzyme I and 21.82-40.54 μM for hCA isoenzyme II. Among all compounds, (E)-3-(((9-Octyl-9H-carbazole-3-yl)imino)methyl)benzene-1,2-diol (C3) had the strongest inhibitory effect on hCA isoenzyme II. It was determined that 2,3,4-trimethoxy and 4-hydroxy phenyl containing carbazole compounds have selective inhibition against hCA II isoenzyme. Docking studies were performed against hCA I and II receptors using induced-fit docking method. The compounds had affinity scores varying from -7.74 ± 0.27 to -6.27 ± 0.07 kcal/mol for hCA I and from -8.04 ± 0.17 to -7.27 ± 0.18 kcal/mol for hCA II.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasemin Camadan
- Vocational School of Health Services, Artvin Coruh University, Artvin, Turkey
| | - Baki Çiçek
- Faculty Arts and Sciences, Chemistry Department, Balıkesir University, Balıkesir, Turkey
| | - Şevki Adem
- Faculty Arts and Sciences, Chemistry Department, Cankiri Karatekin University, Cankiri, Turkey
| | - Ümit Çalişir
- Science and Technology Research and Application Center, Siirt University, Siirt, Turkey
| | - Ebru Akkemik
- Science and Technology Research and Application Center, Siirt University, Siirt, Turkey.,Faculty of Engineering, Food Engineering, Siirt University, Siirt, Turkey
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Dudutienė V, Zubrienė A, Kairys V, Smirnov A, Smirnovienė J, Leitans J, Kazaks A, Tars K, Manakova L, Gražulis S, Matulis D. Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle. Biophys J 2020; 119:1513-1524. [PMID: 32971003 PMCID: PMC7642266 DOI: 10.1016/j.bpj.2020.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 10/23/2022] Open
Abstract
In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an approach of augmenting the substituents attached to the benzenesulfonamide scaffold in three ways, namely, substitutions at the 3,5- or 2,4,6-positions or expansion of the condensed ring system. The increased size of the substituents determined the spatial limitations of the active sites of the 12 catalytically active human carbonic anhydrase (CA) isoforms until no binding was observed because of the inability of the compounds to fit in the active site. This approach led to the discovery of high-affinity and high-selectivity compounds for the anticancer target CA IX and antiobesity target CA VB. The x-ray crystallographic structures of compounds bound to CA IX showed the positions of the bound compounds, whereas computational modeling confirmed that steric clashes prevent the binding of these compounds to other isoforms and thus avoid undesired side effects. Such an approach, based on the Lock-and-Key principle, could be used for the development of enzyme-specific drug candidate compounds.
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Affiliation(s)
- Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania
| | - Joana Smirnovienė
- Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Lena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Vilnius University, Vilnius, Lithuania.
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11
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Zakšauskas A, Čapkauskaitė E, Jezepčikas L, Linkuvienė V, Paketurytė V, Smirnov A, Leitans J, Kazaks A, Dvinskis E, Manakova E, Gražulis S, Tars K, Matulis D. Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Eur J Med Chem 2020; 185:111825. [PMID: 31740053 DOI: 10.1016/j.ejmech.2019.111825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
By applying an approach of a "ring with two tails", a series of novel inhibitors possessing high-affinity and significant selectivity towards selected carbonic anhydrase (CA) isoforms has been designed. The "ring" consists of 2-chloro/bromo-benzenesulfonamide, where the sulfonamide group is as an anchor coordinating the Zn(II) in the active site of CAs, and halogen atom orients the ring affecting the affinity and selectivity. First "tail" is a substituent containing carbonyl, carboxyl, hydroxyl, ether groups or hydrophilic amide linkage. The second "tail" contains aryl- or alkyl-substituents attached through a sulfanyl or sulfonyl group. Both "tails" are connected to the benzene ring and play a crucial role in selectivity. Varying the substituents, we designed compounds selective for CA VII, CA IX, CA XII, or CA XIV. Since due to binding-linked protonation reactions the binding-ready fractions of the compound and protein are much lower than one, the "intrinsic" affinities were calculated that should be used to study correlations between crystal structures and the thermodynamics of binding for rational drug design. The "intrinsic" affinities together with the intrinsic enthalpies and entropies of binding together with co-crystal structures were used demonstrate structural factors determining major contributions for compound affinity and selectivity.
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Affiliation(s)
- Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Linas Jezepčikas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elviss Dvinskis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Saulius Gražulis
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania.
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12
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Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors. Sci Rep 2019; 9:12710. [PMID: 31481705 PMCID: PMC6722136 DOI: 10.1038/s41598-019-49094-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 08/15/2019] [Indexed: 01/25/2023] Open
Abstract
Secretory human carbonic anhydrase VI (CA VI) has emerged as a potential drug target due to its role in pathological states, such as excess acidity-caused dental caries and injuries of gastric epithelium. Currently, there are no available CA VI-selective inhibitors or crystallographic structures of inhibitors bound to CA VI. The present study focuses on the site-directed CA II mutant mimicking the active site of CA VI for inhibitor screening. The interactions between CA VI-mimic and a series of benzenesulfonamides were evaluated by fluorescent thermal shift assay, stopped-flow CO2 hydration assay, isothermal titration calorimetry, and X-ray crystallography. Kinetic parameters showed that A65T, N67Q, F130Y, V134Q, L203T mutations did not influence catalytic properties of CA II, but inhibitor affinities resembled CA VI, exhibiting up to 0.16 nM intrinsic affinity for CA VI-mimic. Structurally, binding site of CA VI-mimic was found to be similar to CA VI. The ligand interactions with mutated side chains observed in three crystallographic structures allowed to rationalize observed variation of binding modes and experimental binding affinities to CA VI. This integrative set of kinetic, thermodynamic, and structural data revealed CA VI-mimic as a useful model to design CA VI-specific inhibitors which could be beneficial for novel therapeutic applications.
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13
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Kocyigit UM, Budak Y, Gürdere MB, Dürü N, Taslimi P, Gülçin İ, Ceylan M. Synthesis and investigation of anticancer, antibacterial activities and carbonic anhydrase, acetylcholinesterase inhibition profiles of novel (3aR,4S,7R,7aS)-2-[4-[1-acetyl-5-(aryl/heteroaryl)-4,5-dihydro-1H-pyrazol-3-yl]phenyl]-3a,4,7,7a-tetrahydro-1H-4,7-methanoisoindole-1,3(2H)-diones. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-2350-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Baranauskiene L, Kuo TC, Chen WY, Matulis D. Isothermal titration calorimetry for characterization of recombinant proteins. Curr Opin Biotechnol 2018; 55:9-15. [PMID: 30031160 DOI: 10.1016/j.copbio.2018.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 12/11/2022]
Abstract
Isothermal titration calorimetry is widely used to measure the affinities and enthalpies of interaction between proteins and/or small molecules. The quantitative nature of the technique is especially useful in the characterization of recombinant proteins while determining the fraction of protein capable of binding a specific ligand and thus the protein purity. The revealed thermodynamic information sheds light on the binding mechanism, important for the targeted drug design of the biologics. Here we show examples how, together with the thermal shift assay, combination of both techniques enables characterization of protein stability and ligand binding. Furthermore, the binding-linked reactions that strongly affect the observed thermodynamic parameters and must be dissected to obtain the intrinsic parameters that are necessary for the structure-based rational drug design are being demonstrated using inhibitors of Hsp90, an anticancer target protein.
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Affiliation(s)
- Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Tai-Chih Kuo
- Department of Biochemistry, Taipei Medical University, Taipei, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, Taoyuan City, Taiwan.
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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16
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Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:2906519. [PMID: 30112206 PMCID: PMC6077552 DOI: 10.1155/2018/2906519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.
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17
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Channar PA, Saeed A, Shahzad D, Larik FA, Hassan M, Raza H, Abbas Q, Seo SY. Extending the scope of amantadine drug by incorporation of phenolic azo Schiff bases as potent selective inhibitors of carbonic anhydrase II, drug-likeness and binding analysis. Chem Biol Drug Des 2018; 92:1692-1698. [DOI: 10.1111/cbdd.13335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 03/14/2018] [Accepted: 04/16/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Aamer Saeed
- Department of Chemistry; Quaid-I-Azam University; Islamabad Pakistan
| | - Danish Shahzad
- Department of Chemistry; Quaid-I-Azam University; Islamabad Pakistan
| | - Fayaz Ali Larik
- Department of Chemistry; Quaid-I-Azam University; Islamabad Pakistan
| | - Mubashir Hassan
- Department of Biological Sciences; College of Natural Sciences; Kongju National University; Gongju, Chungnam Korea
| | - Hussain Raza
- Department of Biological Sciences; College of Natural Sciences; Kongju National University; Gongju, Chungnam Korea
| | - Qamar Abbas
- Department of Physiology; University of Sindh; Jamshoro Pakistan
| | - Sung-Yum Seo
- Department of Biological Sciences; College of Natural Sciences; Kongju National University; Gongju, Chungnam Korea
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18
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Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells. Oncotarget 2018; 9:26800-26816. [PMID: 29928486 PMCID: PMC6003569 DOI: 10.18632/oncotarget.25508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/14/2018] [Indexed: 12/11/2022] Open
Abstract
Human carbonic anhydrase (CA) IX has emerged as a promising anticancer target and a diagnostic biomarker for solid hypoxic tumors. Novel fluorinated CA IX inhibitors exhibited up to 50 pM affinity towards the recombinant human CA IX, selectivity over other CAs, and direct binding to Zn(II) in the active site of CA IX inducing novel conformational changes as determined by X-ray crystallography. Mass spectrometric gas-analysis confirmed the CA IX-based mechanism of the inhibitors in a CRISPR/Cas9-mediated CA IX knockout in HeLa cells. Hypoxia-induced extracellular acidification was significantly reduced in HeLa, H460, MDA-MB-231, and A549 cells exposed to the compounds, with the IC50 values up to 1.29 nM. A decreased clonogenic survival was observed when hypoxic H460 3D spheroids were incubated with our lead compound. These novel compounds are therefore promising agents for CA IX-specific therapy.
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Čapkauskaitė E, Zubrienė A, Paketurytė V, Timm DD, Tumkevičius S, Matulis D. Thiazole-substituted benzenesulfonamides as inhibitors of 12 human carbonic anhydrases. Bioorg Chem 2018; 77:534-541. [PMID: 29459130 DOI: 10.1016/j.bioorg.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 12/26/2022]
Abstract
Four series of para or meta - substituted thiazolylbenzenesulfonamides bearing Cl substituents were designed, synthesized, and evaluated as inhibitors of all 12 catalytically active recombinant human carbonic anhydrase (CA) isoforms. Observed affinities were determined by the fluorescent thermal shift assay and the intrinsic affinities were calculated based on the fractions of binding-ready deprotonated sulfonamide and CA bearing protonated hydroxide bound to the catalytic Zn(II) in the active site. Several compounds exhibited selectivity towards CA IX, an anticancer target. Intrinsic affinities reached 30 pM, while the observed affinities - 70 nM. The structure-intrinsic affinity relationship map of the compounds showed the energetic contributions of the thiazole ring and its substituents.
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Affiliation(s)
- Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - David D Timm
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Sigitas Tumkevičius
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.
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20
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Smirnov A, Zubrienė A, Manakova E, Gražulis S, Matulis D. Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding. PeerJ 2018; 6:e4412. [PMID: 29503769 PMCID: PMC5831161 DOI: 10.7717/peerj.4412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/04/2018] [Indexed: 11/28/2022] Open
Abstract
The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.
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Affiliation(s)
- Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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21
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Linkuvienė V, Talibov VO, Danielson UH, Matulis D. Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design. J Med Chem 2018; 61:2292-2302. [DOI: 10.1021/acs.jmedchem.7b01408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
| | - Vladimir O. Talibov
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
| | - U. Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
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22
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Kazokaitė J, Aspatwar A, Parkkila S, Matulis D. An update on anticancer drug development and delivery targeting carbonic anhydrase IX. PeerJ 2017; 5:e4068. [PMID: 29181278 PMCID: PMC5702504 DOI: 10.7717/peerj.4068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022] Open
Abstract
The expression of carbonic anhydrase (CA) IX is up-regulated in many types of solid tumors in humans under hypoxic and acidic microenvironment. Inhibition of CA IX enzymatic activity with selective inhibitors, antibodies or labeled probes has been shown to reverse the acidic environment of solid tumors and reduce the tumor growth establishing the significant role of CA IX in tumorigenesis. Thus, the development of potent antitumor drugs targeting CA IX with minimal toxic effects is important for the target-specific tumor therapy. Recently, several promising antitumor agents against CA IX have been developed to treat certain types of cancers in combination with radiation and chemotherapy. Here we review the inhibition of CA IX by small molecule compounds and monoclonal antibodies. The methods of enzymatic assays, biophysical methods, animal models including zebrafish and Xenopus oocytes, and techniques of diagnostic imaging to detect hypoxic tumors using CA IX-targeted conjugates are discussed with the aim to overview the recent progress related to novel therapeutic agents that target CA IX in hypoxic tumors.
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Affiliation(s)
- Justina Kazokaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Ashok Aspatwar
- Faculty of Medicine and Life sciences, University of Tampere, Tampere, Finland.,Fimlab Ltd, Tampere, Finland
| | - Seppo Parkkila
- Faculty of Medicine and Life sciences, University of Tampere, Tampere, Finland.,Fimlab Ltd, Tampere, Finland
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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23
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Sarı Y, Aktaş A, Taslimi P, Gök Y, Gulçin İ. NovelN-propylphthalimide- and 4-vinylbenzyl-substituted benzimidazole salts: Synthesis, characterization, and determination of their metal chelating effects and inhibition profiles against acetylcholinesterase and carbonic anhydrase enzymes. J Biochem Mol Toxicol 2017; 32. [DOI: 10.1002/jbt.22009] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yakup Sarı
- Department of Chemistry, Faculty of Arts and Sciences; Inönü University; Malatya 44280 Turkey
| | - Aydın Aktaş
- Department of Chemistry, Faculty of Arts and Sciences; Inönü University; Malatya 44280 Turkey
| | - Parham Taslimi
- Department of Chemistry, Faculty of Sciences; Atatürk University; Erzurum 25240 Turkey
| | - Yetkin Gök
- Department of Chemistry, Faculty of Arts and Sciences; Inönü University; Malatya 44280 Turkey
| | - İlhami Gulçin
- Department of Chemistry, Faculty of Sciences; Atatürk University; Erzurum 25240 Turkey
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