1
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Miura K, Nakamura H. Development of carbonic anhydrase IX-targeting molecular-targeted photodynamic therapy. Bioorg Med Chem Lett 2024; 109:129821. [PMID: 38810709 DOI: 10.1016/j.bmcl.2024.129821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
The efficacy of molecular-targeted photodynamic therapy (MT-PDT) targeting carbonic anhydrase (CA) IX, a cancer-specific molecule, was demonstrated. CA ligand-directed photosensitizers 1-3 were evaluated for their ability to deactivate CAIX protein in cells. Compounds 2 and 3 selectively deactivated CAIX protein under 540 nm light without affecting internal standard proteins. Mechanistic studies revealed that compound 3 not only induced CAIX-selective light inactivation via singlet oxygen but also induced cell membrane damage, resulting in an anti-tumor effect. In vivo studies of CAIX-targeting MT-PDT revealed that treatment with compound 3 followed by light irradiation exhibited remarkable anti-tumor activity, leading to tumor degeneration and necrosis.
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Affiliation(s)
- Kazuki Miura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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2
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Gao Y, Guo Y, Wang Q, Zhang B, Wu X. Efficient Biodegradation of Multiple Aryloxyphenoxypropionate Herbicides by Corynebacterium sp. Z-1 and the Proposed Degradation Mechanism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39038232 DOI: 10.1021/acs.jafc.4c02786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Esterases are crucial for aryloxyphenoxypropionate herbicide (AOPP) biodegradation. However, the underlying molecular mechanisms of AOPP biodegradation by esterases are poorly understood. In the current work, Corynebacterium sp. Z-1 was isolated and found to degrade multiple AOPPs, including quizalofop-p-ethyl (QPE), haloxyfop-p-methyl (HPM), fenoxaprop-p-ethyl (FPE), cyhalofop-butyl (CYB), and clodinafop-propargyl (CFP). A novel esterase, QfeH, which catalyzes the cleavage of ester bonds in AOPPs to form AOPP acids, was identified from strain Z-1. The catalytic activities of QfeH toward AOPPs decreased in the following order: CFP > FPE > CYB > QPE > HPM. Molecular docking, computational analyses, and site-directed mutagenesis indicated the catalytic mechanisms of QfeH-mediated degradation of different AOPPs. Notably, the key residue S159 is essential for the activity of QfeH. Moreover, V222Y, T227M, T227A, A271R, and M275K mutants, exhibiting 2.9-5.0 times greater activity than QfeH, were constructed. This study facilitates the mechanistic understanding of AOPPs bioremediation by esterases.
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Affiliation(s)
- Yongsheng Gao
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yurui Guo
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Qingyuan Wang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Baoyu Zhang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
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3
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Paketurytė-Latvė V, Smirnov A, Manakova E, Baranauskiene L, Petrauskas V, Zubrienė A, Matulienė J, Dudutienė V, Čapkauskaitė E, Zakšauskas A, Leitans J, Gražulis S, Tars K, Matulis D. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system. IUCRJ 2024; 11:556-569. [PMID: 38856178 PMCID: PMC11220870 DOI: 10.1107/s2052252524004627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.
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Affiliation(s)
- Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, 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
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- 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
| | - Jurgita Matulienė
- 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
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Saulius Gražulis
- Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - 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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4
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Baronas D, Knašienė B, Mickevičiūtė A, Jachno J, Naujalis E, Zubrienė A, Matulis D. Inhibitor binding to metal-substituted metalloenzyme: Sulfonamide affinity for carbonic anhydrase IX. J Inorg Biochem 2024; 256:112547. [PMID: 38581802 DOI: 10.1016/j.jinorgbio.2024.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Transition metal ions are structural and catalytic cofactors of many proteins including human carbonic anhydrase (CA), a Zn-dependent hydrolase. Sulfonamide inhibitors of CA recognize and form a coordination bond with the Zn ion located in the active site of the enzyme. The Zn ion may be removed or substituted with other metal ions. Such CA protein retains the structure and could serve as a tool to study metal ion role in the recognition and binding affinity of inhibitor molecules. We measured the affinities of selected divalent transition metal ions, including Mn, Fe, Co, Ni, Cu, Cd, Hg, and Zn to metal-free CA isozymes CA I, CA II, and CAIX by fluorescence-based thermal shift assay, prepared metal-substituted CAs, and determined binding of diverse sulfonamide compounds. Sulfonamide inhibitor binding to metal substituted CA followed a U-shape pH dependence. The binding was dissected to contributing binding-linked reactions and the intrinsic binding reaction affinity was calculated. This value is independent of pH and protonation reactions that occur simultaneously upon binding native CA and as demonstrated here, to metal substituted CA. Sulfonamide inhibitor binding to cancer-associated isozyme CAIX diminished in the order: Zn > Co > Hg > Cu > Cd > Mn > Ni. Energetic contribution of the inhibitor-metal coordination bond was determined for all above metals. The understanding of the principles of metal influence on ligand affinity and selectivity should help design new drugs targeting metalloenzymes.
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Affiliation(s)
- Denis Baronas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Birutė Knašienė
- Center for Physical Sciences and Technology, Saulėtekio 3, 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
| | - Jelena Jachno
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Evaldas Naujalis
- Center for Physical Sciences and Technology, Saulėtekio 3, 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
| | - 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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5
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Žvinys G, Petrosiute A, Zakšauskas A, Zubrienė A, Ščerbavičienė A, Kalnina Z, Čapkauskaitė E, Juozapaitienė V, Mickevičiu̅tė A, Shubin K, Grincevičienė Š, Raišys S, Tars K, Matulienė J, Matulis D. High-Affinity NIR-Fluorescent Inhibitors for Tumor Imaging via Carbonic Anhydrase IX. Bioconjug Chem 2024; 35:790-803. [PMID: 38750635 PMCID: PMC11191402 DOI: 10.1021/acs.bioconjchem.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 06/21/2024]
Abstract
Tumor imaging and delivery of therapeutic agents may be achieved by designing high-affinity and high-selectivity compounds recognizing a tumor cell-expressing biomarker, such as carbonic anhydrase IX (CA IX). The CAIX, overexpressed in many hypoxic solid tumors, helps adjust to the energy requirements of the hypoxic environment, reduces intracellular acidification, and participates in the metastatic invasion of adjacent tissues. Here, we designed a series of sulfonamide compounds bearing CAIX-recognizing, high-affinity, and high-selectivity groups conjugated via a PEG linker to near-infrared (NIR) fluorescent probes used in the clinic for optically guided cancer surgery. We determined compound affinities for CAIX and other 11 catalytically active CA isozymes by the thermal shift assay and showed that the affinity Kd value of CAIX was in the subnanomolar range, hundred to thousand-fold higher than those of other CA isozymes. Similar affinities were also observed for CAIX expressed on the cancer cell surface in live HeLa cell cultures, as determined by the competition assay. The NIR-fluorescent compounds showed excellent properties in visualizing CAIX-positive tumors but not CAIX-negative knockout tumors in a nude mice xenograft model. These compounds would therefore be helpful in optically guided cancer surgery and could potentially be developed for anticancer treatment by radiotherapy.
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Affiliation(s)
- Gediminas Žvinys
- Department
of Biothermodynamics and Drug Design, Institute of Biotechnology,
Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Agne Petrosiute
- 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
| | - Asta Zubrienė
- Department
of Biothermodynamics and Drug Design, Institute of Biotechnology,
Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Alvilė Ščerbavičienė
- Department
of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Zane Kalnina
- Latvian
Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Edita Čapkauskaitė
- Department
of Biothermodynamics and Drug Design, Institute of Biotechnology,
Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Vaida Juozapaitienė
- Department
of Biothermodynamics and Drug Design, Institute of Biotechnology,
Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Aurelija Mickevičiu̅tė
- 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 21, Riga LV-1006, Latvia
| | - Švitrigailė Grincevičienė
- Department
of Biothermodynamics and Drug Design, Institute of Biotechnology,
Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Steponas Raišys
- Institute
of Photonics and Nanotechnology, National Center for Physical Sciences
and Technology, Vilnius University, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Kaspars Tars
- Latvian
Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Jurgita Matulienė
- Department
of Biothermodynamics and Drug Design, 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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6
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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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7
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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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8
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Hadi Ali Janvand S, Ladefoged LK, Zubrienė A, Sakalauskas A, Christiansen G, Dudutienė V, Schiøtt B, Matulis D, Smirnovas V, Otzen DE. Inhibitory effects of fluorinated benzenesulfonamides on insulin fibrillation. Int J Biol Macromol 2023; 227:590-600. [PMID: 36529223 DOI: 10.1016/j.ijbiomac.2022.12.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/15/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Amyloid fibrils are protein aggregates formed by protein assembly through cross β structures. Inhibition of amyloid fibril formation may contribute to therapy against amyloid-related disorders like Parkinson's, Alzheimer's, and type 2 diabetes. Here we report that several fluorinated sulfonamide compounds, previously shown to inhibit human carbonic anhydrase, also inhibit the fibrillation of different proteins. Using a range of spectroscopic, microscopic and chromatographic techniques, we found that the two fluorinated sulfonamide compounds completely inhibit insulin fibrillation over a period of 16 h and moderately suppress α-synuclein and Aβ fibrillation. In addition, these compounds decreased cell toxicity of insulin incubated under fibrillation-inducing conditions. We ascribe these effects to their ability to maintain insulin in the native monomeric state. Molecular dynamic simulations suggest that these compounds inhibit insulin self-association by interacting with residues at the dimer interface. This highlights the general anti-aggregative properties of aromatic sulfonamides and suggests that sulfonamide compounds which inhibit carbonic anhydrase activity may have potential as therapeutic agents against amyloid-related disorders.
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Affiliation(s)
- Saeid Hadi Ali Janvand
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Lucy Kate Ladefoged
- iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gunna Christiansen
- Department of Health Science and Technology, Medical Microbiology and Immunology, Aalborg University, Fredrik Bajers Vej 3b, DK-9220 Aalborg Ø, Denmark
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Birgit Schiøtt
- iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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9
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Minetti CA, Remeta DP. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:1438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [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: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Affiliation(s)
- Conceição A. Minetti
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David P. Remeta
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
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10
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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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11
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Katheria S. Ruthenium Complexes as Potential Cancer Cell Growth Inhibitors for Targeted Chemotherapy. ChemistrySelect 2022. [DOI: 10.1002/slct.202201645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Gedgaudas M, Baronas D, Kazlauskas E, Petrauskas V, Matulis D. Thermott: a comprehensive online tool for protein–ligand binding constant determination. Drug Discov Today 2022; 27:2076-2079. [DOI: 10.1016/j.drudis.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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13
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Khatua S, Taraphder S. In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II. J Biomol Struct Dyn 2022; 41:3187-3204. [PMID: 35257634 DOI: 10.1080/07391102.2022.2048075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The crystal structure of human carbonic anhydrase (HCA) II bound to an inhibitor molecule, 6-hydroxy-2-thioxocoumarin (FC5), shows FC5 to be located in a hydrophobic pocket at the active site. The present work employs classical molecular dynamics (MD) simulation to follow the FC5 molecule for 1 μs as it unbinds from its binding location, adopts the path of substrate/product diffusion (path 1) to leave the active site at around 75 ns. It is then found to undergo repeated binding and unbinding at different locations on the surface of the enzyme in water. Several transient excursions through different regions of the enzyme are also observed prior to its exit from the active site. These transient paths are combined with functionally relevant cavities/channels to enlist five additional pathways (path 2-6). Pathways 1-6 are subsequently explored using steered MD and umbrella sampling simulations. A free energy barrier of 0.969 kcal mol-1 is encountered along path 1, while barriers in the range of 0.57-2.84 kcal mol-1 are obtained along paths 2, 4 and 5. We also analyze in detail the interaction between FC5 and the enzyme along each path as the former leaves the active site of HCA II. Our results indicate path 1 to be the major exit pathway for FC5, although competing contributions may also come from the paths 2, 4 and 5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Satyajit Khatua
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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14
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Skvarnavičius G, Toleikis Z, Matulis D, Petrauskas V. Denaturant- or ligand-induced change in protein volume by pressure shift assay. Phys Chem Chem Phys 2022; 24:17279-17288. [DOI: 10.1039/d2cp01046a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in protein volume and compressibility upon binding a ligand are pressure-related parameters that are...
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15
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Zakšauskas A, Čapkauskaitė E, Paketurytė-Latvė V, Smirnov A, Leitans J, Kazaks A, Dvinskis E, Stančaitis L, Mickevičiūtė A, Jachno J, Jezepčikas L, Linkuvienė V, Sakalauskas A, Manakova E, Gražulis S, Matulienė J, Tars K, Matulis D. Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX. Int J Mol Sci 2021; 23:130. [PMID: 35008553 PMCID: PMC8745178 DOI: 10.3390/ijms23010130] [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: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 01/01/2023] Open
Abstract
Among the twelve catalytically active carbonic anhydrase isozymes present in the human body, the CAIX is highly overexpressed in various solid tumors. The enzyme acidifies the tumor microenvironment enabling invasion and metastatic processes. Therefore, many attempts have been made to design chemical compounds that would exhibit high affinity and selective binding to CAIX over the remaining eleven catalytically active CA isozymes to limit undesired side effects. It has been postulated that such drugs may have anticancer properties and could be used in tumor treatment. Here we have designed a series of compounds, methyl 5-sulfamoyl-benzoates, which bear a primary sulfonamide group, a well-known marker of CA inhibitors, and determined their affinities for all twelve CA isozymes. Variations of substituents on the benzenesulfonamide ring led to compound 4b, which exhibited an extremely high observed binding affinity to CAIX; the Kd was 0.12 nM. The intrinsic dissociation constant, where the binding-linked protonation reactions have been subtracted, reached 0.08 pM. The compound also exhibited more than 100-fold selectivity over the remaining CA isozymes. The X-ray crystallographic structure of compound 3b bound to CAIX showed the structural position, while several structures of compounds bound to other CA isozymes showed structural reasons for compound selectivity towards CAIX. Since this series of compounds possess physicochemical properties suitable for drugs, they may be developed for anticancer therapeutic purposes.
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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, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia; (J.L.); (A.K.); (E.D.); (K.T.)
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia; (J.L.); (A.K.); (E.D.); (K.T.)
| | - Elviss Dvinskis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia; (J.L.); (A.K.); (E.D.); (K.T.)
| | - Laimonas Stančaitis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Jelena Jachno
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Linas Jezepčikas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Andrius Sakalauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Elena Manakova
- Department of Protein—DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.M.); (S.G.)
| | - Saulius Gražulis
- Department of Protein—DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.M.); (S.G.)
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia; (J.L.); (A.K.); (E.D.); (K.T.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (A.Z.); (E.Č.); (V.P.-L.); (A.S.); (L.S.); (A.M.); (J.J.); (L.J.); (V.L.); (A.S.); (J.M.)
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16
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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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Luchinat E, Barbieri L, Cremonini M, Pennestri M, Nocentini A, Supuran CT, Banci L. Determination of intracellular protein-ligand binding affinity by competition binding in-cell NMR. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1270-1281. [PMID: 34605430 PMCID: PMC8489230 DOI: 10.1107/s2059798321009037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Structure-based drug development suffers from high attrition rates due to the poor activity of lead compounds in cellular and animal models caused by low cell penetrance, off-target binding or changes in the conformation of the target protein in the cellular environment. The latter two effects cause a change in the apparent binding affinity of the compound, which is indirectly assessed by cellular activity assays. To date, direct measurement of the intracellular binding affinity remains a challenging task. In this work, in-cell NMR spectroscopy was applied to measure intracellular dissociation constants in the nanomolar range by means of protein-observed competition binding experiments. Competition binding curves relative to a reference compound could be retrieved either from a series of independent cell samples or from a single real-time NMR bioreactor run. The method was validated using a set of sulfonamide-based inhibitors of human carbonic anhydrase II with known activity in the subnanomolar to submicromolar range. The intracellular affinities were similar to those obtained in vitro, indicating that these compounds selectively bind to the intracellular target. In principle, the approach can be applied to any soluble intracellular target that gives rise to measurable chemical shift changes upon ligand binding.
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Affiliation(s)
- Enrico Luchinat
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Pennestri
- Pharmaceutical Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, United Kingdom
| | - Alessio Nocentini
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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Tomašič T, Zubrienė A, Skok Ž, Martini R, Pajk S, Sosič I, Ilaš J, Matulis D, Bryant SD. Selective DNA Gyrase Inhibitors: Multi-Target in Silico Profiling with 3D-Pharmacophores. Pharmaceuticals (Basel) 2021; 14:ph14080789. [PMID: 34451886 PMCID: PMC8400042 DOI: 10.3390/ph14080789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of antibacterial agents, there is currently no representative used in therapy, largely due to unwanted off-target activities. Selectivity of GyrB inhibitors against closely related human ATP-binding enzymes should be evaluated early in development to avoid off-target binding to homologous binding domains. To address this challenge, we developed selective 3D-pharmacophore models for GyrB, human topoisomerase IIα (TopoII), and the Hsp90 N-terminal domain (NTD) to be used in in silico activity profiling paradigms to identify molecules selective for GyrB over TopoII and Hsp90, as starting points for hit expansion and lead optimization. The models were used to profile highly active GyrB, TopoII, and Hsp90 inhibitors. Selected compounds were tested in in vitro assays. GyrB inhibitors 1 and 2 were inactive against TopoII and Hsp90, while 3 and 4, potent Hsp90 inhibitors, displayed no inhibition of GyrB and TopoII, and TopoII inhibitors 5 and 6 were inactive at GyrB and Hsp90. The results provide a proof of concept for the use of target activity profiling methods to identify selective starting points for hit and lead identification.
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Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
- Correspondence: ; Tel.: +386-1-4769-556
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Žiga Skok
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Riccardo Martini
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
- Discngine S.A.S., 79 Avenue Ledru Rollin, 75012 Paris, France
| | - Stane Pajk
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (Ž.S.); (S.P.); (I.S.); (J.I.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (A.Z.); (D.M.)
| | - Sharon D. Bryant
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria; (R.M.); (S.D.B.)
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Sharma S, Bhatia V. Nanoscale Drug Delivery Systems for Glaucoma: Experimental and In Silico Advances. Curr Top Med Chem 2021; 21:115-125. [PMID: 32962618 DOI: 10.2174/1568026620666200922114210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022]
Abstract
In this review, nanoscale-based drug delivery systems, particularly in relevance to the antiglaucoma drugs, have been discussed. In addition to that, the latest computational/in silico advances in this field are examined in brief. Using nanoscale materials for drug delivery is an ideal option to target tumours, and the drug can be released in areas of the body where traditional drugs may fail to act. Nanoparticles, polymeric nanomaterials, single-wall carbon nanotubes (SWCNTs), quantum dots (QDs), liposomes and graphene are the most important nanomaterials used for drug delivery. Ocular drug delivery is one of the most common and difficult tasks faced by pharmaceutical scientists because of many challenges like circumventing the blood-retinal barrier, corneal epithelium and the blood-aqueous barrier. Authors found compelling empirical evidence of scientists relying on in-silico approaches to develop novel drugs and drug delivery systems for treating glaucoma. This review in nanoscale drug delivery systems will help us understand the existing queries and evidence gaps and will pave the way for the effective design of novel ocular drug delivery systems.
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Affiliation(s)
- Smriti Sharma
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Vinayak Bhatia
- ICARE Eye Hospital and Postgraduate Institute, Noida, UP, India
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20
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Baranauskiene L, Škiudaitė L, Michailovienė V, Petrauskas V, Matulis D. Thiazide and other Cl-benzenesulfonamide-bearing clinical drug affinities for human carbonic anhydrases. PLoS One 2021; 16:e0253608. [PMID: 34166457 PMCID: PMC8224972 DOI: 10.1371/journal.pone.0253608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022] Open
Abstract
Twelve carbonic anhydrase (CA) isoforms catalyze carbon dioxide hydration to bicarbonate and acid protons and are responsible for many biological functions in human body. Despite their vital functions, they are also responsible for, or implicated in, numerous ailments and diseases such as glaucoma, high altitude sickness, and cancer. Because CA isoforms are highly homologous, clinical drugs designed to inhibit enzymatic activity of a particular isoform, can also bind to others with similar affinity causing toxic side effects. In this study, the affinities of twelve CA isoforms have been determined for nineteen clinically used drugs used to treat hypertension related diseases, i.e. thiazides, indapamide, and metolazone. Their affinities were determined using a fluorescent thermal shift assay. Stopped flow assay and isothermal titration calorimetry were also employed on a subset of compounds and proteins to confirm inhibition of CA enzymatic activity and verify the quantitative agreement between different assays. The findings of this study showed that pharmaceuticals could bind to human CA isoforms with variable affinities and inhibit their catalytic activity, even though the drug was intended to interact with a different (non-CA) protein target. Relatively minor structural changes of the compounds may cause significant changes in affinity and selectivity for a particular CA isoform.
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Affiliation(s)
- Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Škiudaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Pharmacy Center, Institute of Biomedical Science, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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21
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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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22
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Skvarnavičius G, Toleikis Z, Michailovienė V, Roumestand C, Matulis D, Petrauskas V. Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure. J Phys Chem B 2021; 125:5823-5831. [PMID: 34032445 PMCID: PMC8279561 DOI: 10.1021/acs.jpcb.1c02917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Proteins
undergo changes in their partial volumes in numerous biological
processes such as enzymatic catalysis, unfolding–refolding,
and ligand binding. The change in the protein volume upon ligand binding—a
parameter termed the protein–ligand binding volume—can
be extensively studied by high-pressure NMR spectroscopy. In this
study, we developed a method to determine the protein–ligand
binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum
at different pressures, if the exchange between ligand-free and ligand-bound
states of a protein is slow in the NMR time-scale. This approach required
a significantly lower amount of protein and NMR time to determine
the protein–ligand binding volume of two carbonic anhydrase
isozymes upon binding their ligands. The proposed method can be used
in other protein–ligand systems and expand the knowledge about
protein volume changes upon small-molecule binding.
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Affiliation(s)
- Gediminas Skvarnavičius
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Zigmantas Toleikis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania.,Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Vilma Michailovienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université s de Montpellier, 34000 Montpellier, France
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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23
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Abstract
Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments. Here, we evaluate binding affinity quantification based on thermal shifts. We present four protein systems with different binding affinity ligands, ranging from nM to high μM. Our study suggests that binding affinities determined by isothermal analysis are in better agreement with those from established biophysical techniques (ITC and MST) compared to apparent Kds obtained from melting temperatures. In addition, we describe a method to optionally fit the heat capacity change upon unfolding (\documentclass[12pt]{minimal}
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\begin{document}$$\Delta {C}_{p}$$\end{document}ΔCp) during the isothermal analysis. This publication includes the release of a web server for easy and accessible application of isothermal analysis to nDSF data.
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24
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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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25
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Kazlauskas E, Petrauskas V, Paketurytė V, Matulis D. Standard operating procedure for fluorescent thermal shift assay (FTSA) for determination of protein-ligand binding and protein stability. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:373-379. [PMID: 33914114 DOI: 10.1007/s00249-021-01537-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 01/29/2023]
Abstract
A standard operating procedure for a fluorescence-based thermal shift assay (FTSA) is provided describing its typical applications, advantages and limitations. FTSA is a simple, robust, universal and quick assay to determine protein-ligand binding affinities and protein stabilities in the presence of various excipients and solution conditions. Therefore, the assay is very useful for the straightforward characterization of new recombinantly produced proteins. The assay has a wide dynamic range enabling simultaneous determination of affinities in the milimolar to picomolar range. The assay could be used for essentially any protein that is sufficiently soluble and stable in the studied aqueous solution. Here we provide examples and typical experimental protocols for both affinity and stability determinations.
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Affiliation(s)
- Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
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26
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Ge X, Chen L, Li D, Liu R, Ge G. Estimation of non-constant variance in isothermal titration calorimetry using an ITC measurement model. PLoS One 2020; 15:e0244739. [PMID: 33378411 PMCID: PMC7773272 DOI: 10.1371/journal.pone.0244739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the gold standard for accurate measurement of thermodynamic parameters in solution reactions. In the data processing of ITC, the non-constant variance of the heat requires special consideration. The variance function approach has been successfully applied in previous studies, but is found to fail under certain conditions in this work. Here, an explicit ITC measurement model consisting of main thermal effects and error components has been proposed to quantitatively evaluate and predict the non-constant variance of the heat data under various conditions. Monte Carlo simulation shows that the ITC measurement model provides higher accuracy and flexibility than variance function in high c-value reactions or with additional error components, for example, originated from the fluctuation of the concentrations or other properties of the solutions. The experimental design of basic error evaluation is optimized accordingly and verified by both Monte Carlo simulation and experiments. An easy-to-run Python source code is provided to illustrate the establishment of the ITC measurement model and the estimation of heat variances. The accurate and reliable non-constant variance of heat is helpful to the application of weighted least squares regression, the proper evaluation or selection of the reaction model.
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Affiliation(s)
- Xiujie Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lan Chen
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Dexing Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
| | - Renxiao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Guanglu Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
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27
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Matulis D. Structural details of the enzymatic catalysis of carbonic anhydrase II via a mutation of valine to isoleucine. IUCRJ 2020; 7:953-954. [PMID: 33209309 PMCID: PMC7642797 DOI: 10.1107/s2052252520014244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Kim and co-workers [IUCrJ (2020). 7, 985-994] advance our understanding of the catalytic mechanism of carbonic anhydrase II by studying a mutant V143I where the change (of one hydrophobic amino acid to another that differs by a single CH2 group) is probably the smallest alteration that can be introduced into a protein. The study was performed at high pressure in a CO2 atmosphere to visualize the bound substrate; it showed the behavior of the entrance conduit waters and the substrate alteration due to the mutation.
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Affiliation(s)
- Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
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28
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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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29
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Hoxie RS, Street TO. Hsp90 chaperones have an energetic hot-spot for binding inhibitors. Protein Sci 2020; 29:2101-2111. [PMID: 32812680 PMCID: PMC7513732 DOI: 10.1002/pro.3933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022]
Abstract
Although Hsp90-family chaperones have been extensively targeted with ATP-competitive inhibitors, it is unknown whether high affinity is achieved from a few highly stabilizing contacts or from many weaker contacts within the ATP-binding pocket. A large-scale analysis of Hsp90α:inhibitor structures shows that inhibitor hydrogen-bonding to a conserved aspartate (D93 in Hsp90α) stands out as most universal among Hsp90 inhibitors. Here we show that the D93 region makes a dominant energetic contribution to inhibitor binding for both cytosolic and organelle-specific Hsp90 paralogs. For inhibitors in the resorcinol family, the D93:inhibitor hydrogen-bond is pH-dependent because the associated inhibitor hydroxyl group is titratable, rationalizing a linked-protonation event previously observed by the Matulis group. The inhibitor hydroxyl group pKa associated with the D93 hydrogen-bond is therefore critical for optimizing the affinity of resorcinol derivatives, and we demonstrate that spectrophotometric measurements can determine this pKa value. Quantifying the energetic contribution of the D93 hotspot is best achieved with the mitochondrial Hsp90 paralog, yielding 3-6 kcal/mol of stabilization (35-60% of the total binding energy) for a diverse set of inhibitors. The Hsp90 Asp93➔Asn substitution has long been known to abolish nucleotide binding, yet puzzlingly, native sequences of structurally similar ATPases, such as Topoisomerasese II, have an asparagine at this same crucial site. While aspartate and asparagine sidechains can both act as hydrogen bond acceptors, we show that a steric clash prevents the Hsp90 Asp93➔Asn sidechain from adopting the necessary rotamer, whereas this steric restriction is absent in Topoisomerasese II.
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Affiliation(s)
- Reyal S. Hoxie
- Department of BiochemistryBrandeis UniversityWalthamMassachusettsUSA
| | - Timothy O. Street
- Department of BiochemistryBrandeis UniversityWalthamMassachusettsUSA
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30
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Jonsson BH, Liljas A. Perspectives on the Classical Enzyme Carbonic Anhydrase and the Search for Inhibitors. Biophys J 2020; 119:1275-1280. [PMID: 32910900 DOI: 10.1016/j.bpj.2020.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 01/19/2023] Open
Abstract
Carbonic anhydrase (CA) is a thoroughly studied enzyme. Its primary role is the rapid interconversion of carbon dioxide and bicarbonate in the cells, where carbon dioxide is produced, and in the lungs, where it is released from the blood. At the same time, it regulates pH homeostasis. The inhibitory function of sulfonamides on CA was discovered some 80 years ago. There are numerous physiological-therapeutic conditions in which inhibitors of carbonic anhydrase have a positive effect, such as glaucoma, or act as diuretics. With the realization that several isoenzymes of carbonic anhydrase are associated with the development of several types of cancer, such as brain and breast cancer, the development of inhibitor drugs specific to those enzyme forms has exploded. We would like to highlight the breadth of research on the enzyme as well as draw the attention to some problems in recent published work on inhibitor discovery.
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Affiliation(s)
- Bengt-Harald Jonsson
- Department of Physics, Chemistry, and Biology, Division of Chemistry, Linköping University, Linköping, Sweden
| | - Anders Liljas
- Departments of Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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31
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Tykvart J, Navrátil V, Kugler M, Šácha P, Schimer J, Hlaváčková A, Tenora L, Zemanová J, Dejmek M, Král V, Potáček M, Majer P, Jahn U, Brynda J, Řezáčová P, Konvalinka J. Identification of Novel Carbonic Anhydrase IX Inhibitors Using High-Throughput Screening of Pooled Compound Libraries by DNA-Linked Inhibitor Antibody Assay (DIANA). SLAS DISCOVERY 2020; 25:1026-1037. [PMID: 32452709 DOI: 10.1177/2472555220918836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The DNA-linked inhibitor antibody assay (DIANA) has been recently validated for ultrasensitive enzyme detection and for quantitative evaluation of enzyme inhibitor potency. Here we present its adaptation for high-throughput screening of human carbonic anhydrase IX (CAIX), a promising drug and diagnostic target. We tested DIANA's performance by screening a unique compound collection of 2816 compounds consisting of lead-like small molecules synthesized at the Institute of Organic Chemistry and Biochemistry (IOCB) Prague ("IOCB library"). Additionally, to test the robustness of the assay and its potential for upscaling, we screened a pooled version of the IOCB library. The results from the pooled screening were in agreement with the initial nonpooled screen with no lost hits and no false positives, which shows DIANA's potential to screen more than 100,000 compounds per day.All DIANA screens showed a high signal-to-noise ratio with a Z' factor of >0.89. The DIANA screen identified 13 compounds with Ki values equal to or better than 10 µM. All retested hits were active also in an orthogonal enzymatic assay showing zero false positives. However, further biophysical validation of identified hits revealed that the inhibition activity of several hits was caused by a single highly potent CAIX inhibitor, being present as a minor impurity. This finding eventually led us to the identification of three novel CAIX inhibitors from the screen. We confirmed the validity of these compounds by elucidating their mode of binding into the CAIX active site by x-ray crystallography.
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Affiliation(s)
- Jan Tykvart
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,DIANA Biotechnologies, Prague, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,DIANA Biotechnologies, Prague, Czech Republic
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Šácha
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Schimer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,DIANA Biotechnologies, Prague, Czech Republic
| | - Anna Hlaváčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Tenora
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jitka Zemanová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,DIANA Biotechnologies, Prague, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Potáček
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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32
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Balandis B, Ivanauskaitė G, Smirnovienė J, Kantminienė K, Matulis D, Mickevičius V, Zubrienė A. Synthesis and structure-affinity relationship of chlorinated pyrrolidinone-bearing benzenesulfonamides as human carbonic anhydrase inhibitors. Bioorg Chem 2020; 97:103658. [PMID: 32088419 DOI: 10.1016/j.bioorg.2020.103658] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
A novel set of pyrrolidinone-based chlorinated benzenesulfonamide derivatives were synthesized and investigated for their binding affinity and selectivity against recombinant human carbonic anhydrases I-XIV using fluorescent thermal shift, p-nitrophenyl acetate hydrolysis and stopped-flow enzymatic inhibition assays. The hydrazones 10-22 prepared from 1-(2-chloro-4-sulfamoylphenyl)-5-oxopyrrolidine-3-carboxylic acid exhibited low nanomolar affinity against cancer-related CA IX (Kd in the range of 5.0-37 nM). Compounds with triazole or oxadiazole groups attached directly to pyrrolidinone moiety bound all CAs weaker than compounds with more flexible tail groups. Chloro group at the meta position of benzenesulfonamide derivatives increased affinity to all CAs as compared with binding data for nonchlorinated compounds. The compounds have a potential for further development of CA inhibitors with higher selectivity for a particular CA isozyme.
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Affiliation(s)
- Benas Balandis
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Guostė Ivanauskaitė
- 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
| | - Kristina Kantminienė
- Department of Physical and Inorganic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
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33
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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: 13] [Impact Index Per Article: 3.3] [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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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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35
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Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov 2019; 14:755-768. [DOI: 10.1080/17460441.2019.1623202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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