1
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Tsikas D. Acetazolamide and human carbonic anhydrases: retrospect, review and discussion of an intimate relationship. J Enzyme Inhib Med Chem 2024; 39:2291336. [PMID: 38078375 DOI: 10.1080/14756366.2023.2291336] [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: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Acetazolamide (AZM) is a strong pharmacological sulphonamide-type (R-SO2-NH2, pKa 7.2) inhibitor of the activity of several carbonic anhydrase (CA) isoforms, notably of renal CA II (Ki, 12 nM) and CA IV (Ki, 74 nM). AZM is clinically used for about eighty years in various diseases including epilepsy and glaucoma. Pharmacological AZM increases temporarily the urinary excretion of bicarbonate (HCO3-) and sodium ions (Na+) and sustainably the urinary pH. AZM is excreted almost unchanged over several hours at high rates in the urine. Closely parallel concentrations of circulating and excretory AZM are observed upon administration of therapeutical doses of AZM. In a proof-of-principle study, we investigated the effects of the ingestion of a 250-mg AZM-containing tablet by a healthy volunteer on the urinary excretion of organic and inorganic substances over 5 h (range, 0, 0.5, 1, 1.5, 2, 3, 4, 5 h). Measured analytes included: AZM, amino acids and their metabolites such as guanidinoacetate, i.e. the precursor of creatine, of asymmetrically (ADMA) and symmetrically (SDMA) dimethylated arginine, nitrite (O = N-O-, pKa 3.4) and nitrate (O2N-O-, pKa -1.37), the major metabolites of nitric oxide (NO), the C-H acidic malondialdehyde (MDA; (CHO)2CH2, pKa 4.5), and creatinine for correction of analytes excretion. All analytes were measured by validated isotopologues using gas chromatography-mass spectrometry (GC-MS) methods. AZM excretion in the urine reached its maximum value after 2 h and was fairly stable for the next 3 h. Time series analysis by the ARIMA method was performed. AZM ingestion increased temporarily the urinary excretion of the amino acids Leu + Ile, nitrite and nitrate, decreased temporarily the urinary excretion of other amino acids. AZM decreased sustainably the urinary excretion of MDA, a biomarker of oxidative stress (i.e. lipid peroxidation). Whether this decrease is due to inhibition of the excretion of MDA or attenuation of oxidative stress by AZM is unknown. The acute and chronic effects of AZM on the urinary excretion of electrolytes and physiological substances reported in the literature are discussed in depth in the light of its extraordinary pharmacokinetics and pharmacodynamics. Tolerance development/drug resistance to AZM in chronic use and potential mechanisms are also addressed.
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Affiliation(s)
- Dimitrios Tsikas
- Core Unit Proteomics, Institute of Toxicology, Hannover Medical School, Hannover, Germany
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2
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Shams Ghamsary M, Ghiasi M, Naghavi SS. Insight into the activation mechanism of carbonic anhydrase(II) through 2-(2-aminoethyl)-pyridine: a promising pathway for enhanced enzymatic activity. Phys Chem Chem Phys 2024; 26:10382-10391. [PMID: 38502117 DOI: 10.1039/d3cp05687b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Activation of human carbonic anhydrase II (hCA II) holds great promise for treating memory loss symptoms associated with Alzheimer's disease. Despite its importance, the activation mechanism of hCA II has been largely overlooked in favor of the well-studied inhibition mechanism. To address this unexplored realm, we use first-principles calculations to tease out the activation mechanism of hCA II using 2-(2-aminoethyl)-pyridine (2-2AEPy), a promising in vitro activator. We explored both stepwise and concerted mechanisms via both available nitrogen sites of 2-2AEPy: (i) aminoethyl group (Nα) and (ii) pyridine ring (Nβ). Our results show that a concerted mechanism via Nα holds the key to hCA II activation. The activation process of the concerted mechanism exhibits the characteristics of an exergonic reaction, wherein the transition state resembles the reactant with a notably low imaginary frequency of 452.4i cm-1 and barrier height of 5.2 kcal mol-1. Such meager transition barriers propel the activation of hCA II at in vivo temperatures. These findings initiate future research into hCA II activation mechanisms and the development of efficient activators, which may lead to promising therapeutic interventions for Alzheimer's disease.
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Affiliation(s)
- Masoumeh Shams Ghamsary
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran.
| | - Mina Ghiasi
- Department of Physical Chemistry and Nano chemistry, Faculty of Chemistry, Alzahra University, 1993893973, Tehran, Iran.
| | - S Shahab Naghavi
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran.
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3
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Drago VN, Campos C, Hooper M, Collins A, Gerlits O, Weiss KL, Blakeley MP, Phillips RS, Kovalevsky A. Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography. Commun Chem 2023; 6:162. [PMID: 37532884 PMCID: PMC10397204 DOI: 10.1038/s42004-023-00964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin B6-derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.
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Affiliation(s)
- Victoria N Drago
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Claudia Campos
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Mattea Hooper
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Aliyah Collins
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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4
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Marcelo GA, Montpeyó D, Galhano J, Martínez-Máñez R, Capelo-Martínez JL, Lorenzo J, Lodeiro C, Oliveira E. Development of New Targeted Nanotherapy Combined with Magneto-Fluorescent Nanoparticles against Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24076612. [PMID: 37047582 PMCID: PMC10095016 DOI: 10.3390/ijms24076612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
The need for non-invasive therapies capable of conserving drug efficiency and stability while having specific targetability against colorectal cancer (CRC), has made nanoparticles preferable vehicles and principal building blocks for the development of complex and multi-action anti-tumoral approaches. For that purpose, we herein report the production of a combinatory anti-tumoral nanotherapy using the production of a new targeting towards CRC lines. To do so, Magneto-fluorescent NANO3 nanoparticles were used as nanocarriers for a combination of the drugs doxorubicin (DOX) and ofloxacin (OFLO). NANO3 nanoparticles’ surface was modified with two different targeting agents, a newly synthesized (anti-CA IX acetazolamide derivative (AZM-SH)) and a commercially available (anti-epidermal growth factor receptor (EGFR), Cetuximab). The cytotoxicity revealed that only DOX-containing nanosystems showed significant and even competitive cytotoxicity when compared to that of free DOX. Interestingly, surface modification with AZM-SH promoted an increased cellular uptake in the HCT116 cell line, surpassing even those functionalized with Cetuximab. The results show that the new target has high potential to be used as a nanotherapy agent for CRC cells, surpassing commercial targets. As a proof-of-concept, an oral administration form of NANO3 systems was successfully combined with Eudragit® enteric coating and studied under extreme conditions.
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Affiliation(s)
- Gonçalo A. Marcelo
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
| | - David Montpeyó
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Joana Galhano
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
| | - José Luis Capelo-Martínez
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
- PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2825-182 Caparica, Portugal
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina, Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Carlos Lodeiro
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
- PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2825-182 Caparica, Portugal
| | - Elisabete Oliveira
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
- PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2825-182 Caparica, Portugal
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5
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Fang M, Wu O, Cupp-Sutton KA, Smith K, Wu S. Elucidating Protein-Ligand Interactions in Cell Lysates Using High-Throughput Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Protein Thermal Depletion. Anal Chem 2023; 95:10.1021/acs.analchem.2c04266. [PMID: 36608260 PMCID: PMC10323047 DOI: 10.1021/acs.analchem.2c04266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is a powerful technique for the characterization of protein-ligand interactions. Currently, there is a growing need for breakthroughs in the application of HDX-MS analysis to protein-ligand interactions in highly complex biological samples such as cell lysates. However, HDX-MS analysis in such systems suffers from extreme spectral complexity as a result of high sample complexity and limited LC separation power due to the traditional use of short LC gradients. Here, we introduced protein thermal depletion (PTD) to reduce protein complexity in E. coli cell lysate for our subzero-temperature long gradient UPLC-HDX-MS platform (PTD-HDX-MS) to facilitate high-throughput analysis of protein-ligand interactions in cell lysates. We spiked bovine carbonic anhydrase II (CaII) and its inhibitor acetazolamide (AZM) into E. coli cell lysate as a model system in our study. We demonstrated that PTD at 60 °C greatly reduces protein complexity in cell lysates, while the AZM-targeted CaII complex remains in solution due to improved thermal stability upon binding. Using both PTD to reduce sample complexity and subzero-temperature long gradient UPLC to boost LC separation power, we successfully elucidated the interaction sites between AZM and CaII in E. coli cell lysate from the high-throughput HDX-MS analysis of thousands of deuterated peptides from hundreds of proteins. Our results highlight the great promise of the PTD-HDX-MS platform for the identification of ligand targets and characterization of protein-ligand interactions in highly complex biological samples such as cell lysates.
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Affiliation(s)
- Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Oliver Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | | | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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6
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Mandal M, Xiao L, Pan W, Scapin G, Li G, Tang H, Yang SW, Pan J, Root Y, de Jesus RK, Yang C, Prosise W, Dayananth P, Mirza A, Therien AG, Young K, Flattery A, Garlisi C, Zhang R, Chu D, Sheth P, Chu I, Wu J, Markgraf C, Kim HY, Painter R, Mayhood TW, DiNunzio E, Wyss DF, Buevich AV, Fischmann T, Pasternak A, Dong S, Hicks JD, Villafania A, Liang L, Murgolo N, Black T, Hagmann WK, Tata J, Parmee ER, Weber AE, Su J, Tang H. Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates. J Med Chem 2022; 65:16234-16251. [PMID: 36475645 DOI: 10.1021/acs.jmedchem.2c00766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the emergence and rapid spreading of NDM-1 and existence of clinically relevant VIM-1 and IMP-1, discovery of pan inhibitors targeting metallo-beta-lactamases (MBLs) became critical in our battle against bacterial infection. Concurrent with our fragment and high-throughput screenings, we performed a knowledge-based search of known metallo-beta-lactamase inhibitors (MBLIs) to identify starting points for early engagement of medicinal chemistry. A class of compounds exemplified by 11, discovered earlier as B. fragilis metallo-beta-lactamase inhibitors, was selected for in silico virtual screening. From these efforts, compound 12 was identified with activity against NDM-1 only. Initial exploration on metal binding design followed by structure-guided optimization led to the discovery of a series of compounds represented by 23 with a pan MBL inhibition profile. In in vivo studies, compound 23 in combination with imipenem (IPM) robustly lowered the bacterial burden in a murine infection model and became the lead for the invention of MBLI clinical candidates.
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Affiliation(s)
- Mihirbaran Mandal
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Weidong Pan
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Giovanna Scapin
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Guoqing Li
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Haiqun Tang
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Shu-Wei Yang
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Jianping Pan
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Yuriko Root
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | | | - Christine Yang
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Winnie Prosise
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Priya Dayananth
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Asra Mirza
- Antibacterial/antifungal, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Alex G Therien
- Antibacterial/antifungal, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Katherine Young
- Antibacterial/antifungal, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Amy Flattery
- In vivo biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Charles Garlisi
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Rumin Zhang
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Donald Chu
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Payal Sheth
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Inhou Chu
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Jin Wu
- Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Carrie Markgraf
- Nonclinical Drug Safety, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Hai-Young Kim
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Ronald Painter
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Todd W Mayhood
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Edward DiNunzio
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Daniel F Wyss
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Alexander Pasternak
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Shuzhi Dong
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Jacqueline D Hicks
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Artjohn Villafania
- In-vitro biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Lianzhu Liang
- In vivo biology, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Nicholas Murgolo
- Antibacterial/antifungal, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Todd Black
- Antibacterial/antifungal, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - William K Hagmann
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Jim Tata
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Emma R Parmee
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Ann E Weber
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Jing Su
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
| | - Haifeng Tang
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
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7
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Kim D, Kim S, Park G, Choi H, Ryu JH. Spatiotemporal Self-Assembly of Peptide Amphiphiles by Carbonic Anhydrase IX-Targeting Induces Cancer-Lysosomal Membrane Disruption. JACS AU 2022; 2:2539-2547. [PMID: 36465549 PMCID: PMC9709935 DOI: 10.1021/jacsau.2c00422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
To achieve spatiotemporal control, an enzyme-instructed self-assembly system is widely used, but this approach typically has a small effect on cellular fate. In this study, we show that the intralysosomal assembly by a carbonic anhydrase IX (CAIX)-targeting peptide amphiphile (Pep-AT) can control cellular fate with a low therapeutic dose by tuning the surface charge based on pH change. Pep-AT self-assembles into a fibrous aggregate with a negative surface charge in an extracellular environment near CAIX. During endocytosis, it changes into a nanofiber with a positive surface charge at the lysosome. Then, it can disrupt the lysosomal membrane and induce cellular apoptosis. This study demonstrates that a spatiotemporal assembly induced by a cancer enzyme and specific organelle can control the cellular fate of cancer.
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Küçükoğlu K, Acar Çevik U, Nadaroglu H, Celik I, Işık A, Bostancı HE, Özkay Y, Kaplancıklı ZA. Design, synthesis and molecular docking studies of novel benzimidazole-1,3,4-oxadiazole hybrids for their carbonic anhydrase inhibitory and antioxidant effects. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02943-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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9
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Beta and Gamma Amino Acid-Substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases. Pharmaceuticals (Basel) 2022; 15:ph15040477. [PMID: 35455474 PMCID: PMC9033141 DOI: 10.3390/ph15040477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
A series of novel benzenesulfonamide derivatives were synthesized bearing para-N β,γ-amino acid or para-N β-amino acid and thiazole moieties and their binding to the human carbonic anhydrase (CA) isozymes determined. These enzymes are involved in various illnesses, such as glaucoma, altitude sickness, epilepsy, obesity, and even cancer. There are numerous compounds that are inhibitors of CA and used as pharmaceuticals. However, most of them bind to most CA isozymes with little selectivity. The design of high affinity and selectivity towards one CA isozyme remains a significant challenge. The beta and gamma amino acid-substituted compound affinities were determined by the fluorescent thermal shift assay and isothermal titration calorimetry for all 12 catalytically active human carbonic anhydrase isozymes, showing the full affinity and selectivity profile. The structures of several compounds were determined by X-ray crystallography, and the binding mode in the active site of CA enzyme was shown.
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10
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Novel 1,3,5-Triazinyl Aminobenzenesulfonamides Incorporating Aminoalcohol, Aminochalcone and Aminostilbene Structural Motifs as Potent Anti-VRE Agents, and Carbonic Anhydrases I, II, VII, IX, and XII Inhibitors. Int J Mol Sci 2021; 23:ijms23010231. [PMID: 35008657 PMCID: PMC8745223 DOI: 10.3390/ijms23010231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/29/2022] Open
Abstract
A series of 1,3,5-triazinyl aminobenzenesulfonamides substituted by aminoalcohol, aminostilbene, and aminochalcone structural motifs was synthesized as potential human carbonic anhydrase (hCA) inhibitors. The compounds were evaluated on their inhibition of tumor-associated hCA IX and hCA XII, hCA VII isoenzyme present in the brain, and physiologically important hCA I and hCA II. While the test compounds had only a negligible effect on physiologically important isoenzymes, many of the studied compounds significantly affected the hCA IX isoenzyme. Several compounds showed activity against hCA XII; (E)-4-{2-[(4-[(2,3-dihydroxypropyl)amino]-6-[(4-styrylphenyl)amino]-1,3,5-triazin-2-yl)amino]ethyl}benzenesulfonamide (31) and (E)-4-{2-[(4-[(4-hydroxyphenyl)amino]-6-[(4-styrylphenyl)amino]-1,3,5-triazin-2-yl)amino]ethyl}benzenesulfonamide (32) were the most effective inhibitors with KIs = 4.4 and 5.9 nM, respectively. In addition, the compounds were tested against vancomycin-resistant Enterococcus faecalis (VRE) isolates. (E)-4-[2-({4-[(4-cinnamoylphenyl)amino]-6-[(4-hydroxyphenyl)amino]-1,3,5-triazin-2-yl}amino)ethyl]benzenesulfonamide (21) (MIC = 26.33 µM) and derivative 32 (MIC range 13.80-55.20 µM) demonstrated the highest activity against all tested strains. The most active compounds were evaluated for their cytotoxicity against the Human Colorectal Tumor Cell Line (HCT116 p53 +/+). Only 4,4'-[(6-chloro-1,3,5-triazin-2,4-diyl)bis(iminomethylene)]dibenzenesulfonamide (7) and compound 32 demonstrated an IC50 of ca. 6.5 μM; otherwise, the other selected derivatives did not show toxicity at concentrations up to 50 µM. The molecular modeling and docking of active compounds into various hCA isoenzymes, including bacterial carbonic anhydrase, specifically α-CA present in VRE, was performed to try to outline a possible mechanism of selective anti-VRE activity.
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11
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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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12
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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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13
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Potential anticancer activities of Rhus coriaria (sumac) extract against human cancer cell lines. Biosci Rep 2021; 41:228452. [PMID: 33891003 PMCID: PMC8112848 DOI: 10.1042/bsr20204384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 12/27/2022] Open
Abstract
Therapeutic strategies of plant origin are a better choice as both dietary plant products or its isolated active constituents against the development and progression of cancer. The present study aims to evaluate the anticancer activity of sumac (Rhus coriaria) against different human cancer MCF-7, PC-3, and SKOV3 cell lines. In addition, the study tries to explore a prospective mechanism of action, assessment of in vitro enzyme-inhibitory capacity of sumac extract against hCA I, II, IX, and XII. In the present study, the potential antitumor effects of sumac (Rhus coriaria) were explored in the human cancer cell lines; MCF-7, PC-3, and SKOV3 using in vitro assays. Apoptotic, cell survival, ELISA immunoassays were also conducted to reveal the inhibitory effects of sumac extract against hCA I, II, IX, and XII. In addition, both Clioquinol and Acetazolamide (AZM) were used as standards to explore the in vitro enzyme-inhibitory capacity of sumac extract against hCA I, II, IX, and XII. The hydro-alcoholic extract of R. coriaria (Sumac) was subjected to phytochemical analysis using GC/MS assays. Sumac at non-cytotoxic doses of 50 and 100 µM significantly modulates the growth of the MCF-7, PC-3, and SKOV3 cancer cells with a higher inhibitory effect and selectivity to carbonic anhydrase (CA) isoforms; hCA I, II, hCA IX, and XII. The data showed that sumac at doses of 50 and 100 µM significantly inhibited the growth, proliferation, and viability of cancer cells by activating the apoptotic process via caspase-3 overexpression and the regulation of Bcl-2 anti-apoptotic protein.
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14
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Xu Y, Zhang Z, Shi J, Liu X, Tang W. Recent developments of synthesis and biological activity of sultone scaffolds in medicinal chemistry. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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15
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Clabbers MTB, Xu H. Macromolecular crystallography using microcrystal electron diffraction. Acta Crystallogr D Struct Biol 2021; 77:313-324. [PMID: 33645535 PMCID: PMC7919406 DOI: 10.1107/s2059798320016368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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16
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Patel S, McKeon D, Sao K, Yang C, Naranjo NM, Svitkina TM, Petrie RJ. Myosin II and Arp2/3 cross-talk governs intracellular hydraulic pressure and lamellipodia formation. Mol Biol Cell 2021; 32:579-589. [PMID: 33502904 PMCID: PMC8101460 DOI: 10.1091/mbc.e20-04-0227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Human fibroblasts can switch between lamellipodia-dependent and -independent migration mechanisms on two-dimensional surfaces and in three-dimensional (3D) matrices. RhoA GTPase activity governs the switch from low-pressure lamellipodia to high-pressure lobopodia in response to the physical structure of the 3D matrix. Inhibiting actomyosin contractility in these cells reduces intracellular pressure and reverts lobopodia to lamellipodial protrusions via an unknown mechanism. To test the hypothesis that high pressure physically prevents lamellipodia formation, we manipulated pressure by activating RhoA or changing the osmolarity of the extracellular environment and imaged cell protrusions. We find RhoA activity inhibits Rac1-mediated lamellipodia formation through two distinct pathways. First, RhoA boosts intracellular pressure by increasing actomyosin contractility and water influx but acts upstream of Rac1 to inhibit lamellipodia formation. Increasing osmotic pressure revealed a second RhoA pathway, which acts through nonmuscle myosin II (NMII) to disrupt lamellipodia downstream from Rac1 and elevate pressure. Interestingly, Arp2/3 inhibition triggered a NMII-dependent increase in intracellular pressure, along with lamellipodia disruption. Together, these results suggest that actomyosin contractility and water influx are coordinated to increase intracellular pressure, and RhoA signaling can inhibit lamellipodia formation via two distinct pathways in high-pressure cells.
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Affiliation(s)
- Shivani Patel
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Donna McKeon
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Kimheak Sao
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Changsong Yang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Nicole M Naranjo
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Tatyana M Svitkina
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ryan J Petrie
- Department of Biology, Drexel University, Philadelphia, PA 19104
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17
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From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds. Methods Mol Biol 2021; 2266:263-277. [PMID: 33759132 DOI: 10.1007/978-1-0716-1209-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although science and technology have progressed rapidly, de novo drug development has been a costly and time-consuming process over the past decades. In this scenario, drug repurposing has appeared as an alternative tool to accelerate the drug development process. Herein, we applied such an approach to the highly popular human Carbonic Anhydrase (hCA) VA drug target, that is involved in ureagenesis, gluconeogenesis, lipogenesis, and in the metabolism regulation. Albeit several hCA inhibitors have been designed and are currently in clinical use, serious drug interactions have been reported due to their poor selectivity. In this perspective, the drug repurposing approach could be a useful tool for investigating the drug promiscuity/polypharmacology profile. In this chapter, we describe a combination of virtual screening techniques and in vitro assays aimed to identify novel selective hCA VA inhibitors and to repurpose drugs known for other clinical indications.
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18
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The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Singh H, Das CK, Vasa SK, Grohe K, Schäfer LV, Linser R. The Active Site of a Prototypical "Rigid" Drug Target is Marked by Extensive Conformational Dynamics. Angew Chem Int Ed Engl 2020; 59:22916-22921. [PMID: 32965765 PMCID: PMC7756556 DOI: 10.1002/anie.202009348] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/16/2020] [Indexed: 12/23/2022]
Abstract
Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off-target effects, information on protein motion is important. Herein, we demonstrate for the prototypical textbook example of an allegedly "rigid protein" that substantial active-site dynamics have generally remained unrecognized, despite thousands of medicinal-chemistry studies on this model over decades. Comparing cryogenic X-ray structures, solid-state NMR on micro-crystalline protein at room temperature, and solution NMR structure and dynamics, supported by MD simulations, we show that under physiologically relevant conditions the pocket is in fact shaped by pronounced open/close conformational-exchange dynamics. The study, which is of general significance for pharmacological research, evinces a generic pitfall in drug discovery routines.
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Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Suresh K Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Kristof Grohe
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
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20
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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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21
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Andring JT, Fouch M, Akocak S, Angeli A, Supuran CT, Ilies MA, McKenna R. Structural Basis of Nanomolar Inhibition of Tumor-Associated Carbonic Anhydrase IX: X-Ray Crystallographic and Inhibition Study of Lipophilic Inhibitors with Acetazolamide Backbone. J Med Chem 2020; 63:13064-13075. [PMID: 33085484 DOI: 10.1021/acs.jmedchem.0c01390] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This study provides a structure-activity relationship study of a series of lipophilic carbonic anhydrase (CA) inhibitors with an acetazolamide backbone. The inhibitors were tested against the tumor-expressed CA isozyme IX (CA IX), and the cytosolic CA I, CA II, and membrane-bound CA IV. The study identified several low nanomolar potent inhibitors against CA IX, with lipophilicities spanning two log units. Very potent pan-inhibitors with nanomolar potency against CA IX and sub-nanomolar potency against CA II and CA IV, and with potency against CA I one order of magnitude better than the parent acetazolamide 1 were also identified in this study, together with compounds that displayed selectivity against membrane-bound CA IV. A comprehensive X-ray crystallographic study (12 crystal structures), involving both CA II and a soluble CA IX mimetic (CA IX-mimic), revealed the structural basis of this particular inhibition profile and laid the foundation for further developments toward more potent and selective inhibitors for the tumor-expressed CA IX.
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Affiliation(s)
- Jacob T Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Mallorie Fouch
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Suleyman Akocak
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Andrea Angeli
- NEUROFARBA Department, Pharmaceutical Sciences Section, Universita degli Studi di Firenze, Polo Scientifico, Via Ugo Schiff no. 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical Sciences Section, Universita degli Studi di Firenze, Polo Scientifico, Via Ugo Schiff no. 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marc A Ilies
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
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22
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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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Clabbers MTB, Fisher SZ, Coinçon M, Zou X, Xu H. Visualizing drug binding interactions using microcrystal electron diffraction. Commun Biol 2020; 3:417. [PMID: 32737395 PMCID: PMC7395157 DOI: 10.1038/s42003-020-01155-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/15/2020] [Indexed: 01/30/2023] Open
Abstract
Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED). However, so far no drug binding interactions could unambiguously be resolved by electron diffraction alone. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected on a conventional transmission electron microscope from thin hydrated microcrystals soaked with the clinical drug acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the bound inhibitor. We anticipate MicroED can play an important role in facilitating in-house fragment screening for drug discovery, complementing existing methods in structural biology such as X-ray and neutron diffraction. Clabbers et al. utilize MicroED to present the structure of both apo and inhibitor-bound human carbonic anhydrase II at a high resolution to clearly identify the interaction of the inhibitor, acetazolamide. This method eases the difficulty of both crystallizing the protein and soaking the inhibitor in a smaller protein crystal.
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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Kerber T, Vrielink A. The role of hydrogen atoms in redox catalysis by the flavoenzyme cholesterol oxidase. Methods Enzymol 2020; 634:361-377. [PMID: 32093840 DOI: 10.1016/bs.mie.2019.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Flavoenzymes comprise a large class of proteins that carry out a diverse range of important redox chemistry. Although X-ray crystal structures of many flavoenzymes have been determined, there are still unresolved questions regarding the actual oxidation state of the flavin cofactors in these structures due to photoreduction by the ionizing radiation of the X-ray beam during the diffraction experiment. Additionally, the ability to visualize hydrogen atoms in X-ray structures is difficult due to the weak scattering capability of these atoms. Since hydrogen atoms affect the electrostatic nature of enzyme active sites and play important roles in the chemistry of key amino acid residues, visualizing the precise positions of these atoms provides a more detailed understanding of their role in enzyme catalysis. Single crystal neutron diffraction is an alternative method to structure determination, circumventing problems associated with photoreduction of the sample thus providing a clearer view of the structural features of a flavoenzyme in different redox states. Additionally, the larger neutron scattering factors for hydrogen and deuterium atoms enables one to visualize these atoms much more easily than from X-ray scattering measurements. In this chapter we give an overview of neutron and X-ray crystallography studies on the flavoenzyme, cholesterol oxidase and how the observations of unusual hydrogen atom positions provide insight into the redox chemistry of the flavin cofactor.
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Affiliation(s)
- Tatiana Kerber
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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Abstract
The use of neutron protein crystallography (NPX) is expanding rapidly, with most structures determined in the last decade. This growth is stimulated by a number of developments, spanning from the building of new NPX beamlines to the availability of improved software for structure refinement. The main bottleneck preventing structural biologists from adding NPX to the suite of methods commonly used is the large volume of the individual crystals required for a successful experiment. A survey of deposited NPX structures in the Protein Data Bank shows that about two-thirds came from crystals prepared using vapor diffusion, while batch and dialysis-based methods all-together contribute to most of the remaining one-third. This chapter explains the underlying principles of these protein crystallization methods and provides practical examples that may help others to successfully prepare large crystals for NPX.
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Zakšauskas A, Čapkauskaitė E, Jezepčikas L, Linkuvienė V, Paketurytė V, Smirnov A, Leitans J, Kazaks A, Dvinskis E, Manakova E, Gražulis S, Tars K, Matulis D. Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Eur J Med Chem 2020; 185:111825. [PMID: 31740053 DOI: 10.1016/j.ejmech.2019.111825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
By applying an approach of a "ring with two tails", a series of novel inhibitors possessing high-affinity and significant selectivity towards selected carbonic anhydrase (CA) isoforms has been designed. The "ring" consists of 2-chloro/bromo-benzenesulfonamide, where the sulfonamide group is as an anchor coordinating the Zn(II) in the active site of CAs, and halogen atom orients the ring affecting the affinity and selectivity. First "tail" is a substituent containing carbonyl, carboxyl, hydroxyl, ether groups or hydrophilic amide linkage. The second "tail" contains aryl- or alkyl-substituents attached through a sulfanyl or sulfonyl group. Both "tails" are connected to the benzene ring and play a crucial role in selectivity. Varying the substituents, we designed compounds selective for CA VII, CA IX, CA XII, or CA XIV. Since due to binding-linked protonation reactions the binding-ready fractions of the compound and protein are much lower than one, the "intrinsic" affinities were calculated that should be used to study correlations between crystal structures and the thermodynamics of binding for rational drug design. The "intrinsic" affinities together with the intrinsic enthalpies and entropies of binding together with co-crystal structures were used demonstrate structural factors determining major contributions for compound affinity and selectivity.
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Affiliation(s)
- Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Linas Jezepčikas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elviss Dvinskis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Saulius Gražulis
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV, 1067, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania.
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28
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Combs JE, Andring JT, McKenna R. Neutron crystallographic studies of carbonic anhydrase. Methods Enzymol 2020; 634:281-309. [DOI: 10.1016/bs.mie.2020.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Koruza K, Lafumat B, Nyblom M, Mahon BP, Knecht W, McKenna R, Fisher SZ. Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:895-903. [PMID: 31588921 PMCID: PMC6778848 DOI: 10.1107/s2059798319010027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022]
Abstract
In this work, the X-ray crystal structures of four different deuterium-labelled versions of a surface variant of human carbonic anhydrase IX are compared and discussed. The results show that the overall structure and active-site organization of each version are essentially the same, paving the way for future neutron protein crystallography studies. Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX–inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal contacts and packing reveals different arrangements of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography.
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Affiliation(s)
- K Koruza
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B Lafumat
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - M Nyblom
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B P Mahon
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - W Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - R McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - S Z Fisher
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
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Costa G, Carta F, Ambrosio FA, Artese A, Ortuso F, Moraca F, Rocca R, Romeo I, Lupia A, Maruca A, Bagetta D, Catalano R, Vullo D, Alcaro S, Supuran CT. A computer-assisted discovery of novel potential anti-obesity compounds as selective carbonic anhydrase VA inhibitors. Eur J Med Chem 2019; 181:111565. [PMID: 31387062 DOI: 10.1016/j.ejmech.2019.111565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/25/2022]
Abstract
The human Carbonic anhydrases (hCA) VA and VB play a key role in ureagenesis, gluconeogenesis, lipogenesis and in the metabolism regulation, thus representing highly popular drug targets. Albeit several hCA inhibitors have been designed and are currently in clinical use, serious drug interactions have been reported due to their poor selectivity. In this perspective, the drug repurposing approach could be a useful tool in order to investigate the drug promiscuity/polypharmacology profile. In this study, virtual screening techniques and in vitro assays were combined to identify novel selective hCA VA inhibitors from among around 94000 compounds. The docking analysis highlighted 12 promising best hits, biologically characterized in terms of their hCA VA inhibitory activity. Interestingly, among them, the anticancer agents fludarabine and lenvatinib and the antiepileptic rufinamide were able to selectively inhibit the enzyme activity in the micromolar range, while a pyrido-indole derivative, the homovanillic acid sulfate and the desacetyl metabolite of the antibacterial cephapirin in the nanomolar range.
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Affiliation(s)
- Giosuè Costa
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Fabrizio Carta
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy.
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Federica Moraca
- Department of Pharmacy, University "Federico II" of Naples, Via D. Montesano, 49 I-80131, Naples, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie chimiche, Università della Calabria, Via Pietro Bucci, 87036, Arcavacata di Rende, Cosenza, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Antonio Lupia
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Annalisa Maruca
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Donatella Bagetta
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Raffaella Catalano
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Daniela Vullo
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Net4Science Academic Spin-Off, "Magna Græcia" University of Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Claudiu T Supuran
- Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università; degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
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Caine BA, Bronzato M, Popelier PLA. Experiment stands corrected: accurate prediction of the aqueous p K a values of sulfonamide drugs using equilibrium bond lengths. Chem Sci 2019; 10:6368-6381. [PMID: 31341593 PMCID: PMC6601425 DOI: 10.1039/c9sc01818b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/19/2019] [Indexed: 12/14/2022] Open
Abstract
We show here for the first time that strongly correlated linear relationships exist between equilibrium bond lengths of the sulfonamide group and aqueous pKa values.
We show here for the first time that strongly correlated linear relationships exist between equilibrium bond lengths of the sulfonamide group and aqueous pKa values. Models are constructed for three variants of the SO2NHR group: primary benzene sulfonamide derivatives (e.g. diuretic drugs furosemide and hydrochlorothiazide), N-phenyl substituted 4-amino-N-phenylbenzenesulfonamide analogues (e.g. the sulfa antibiotic sulfadiazine) and phenylsulfonylureas (e.g. insulin secretagogue, glimepiride). In the context of these compounds, we present solutions to some of the more complex challenges in pKa prediction: (i) prediction for multiprotic compounds, (ii) predicting macroscopic values for compounds that tautomerize, and (iii) quantum chemical pKa prediction for compounds with more than 50 atoms. Using bond lengths as a powerful descriptor of ionization feasibility, we also identify that literature values for drug compounds celecoxib, glimepiride and glipizide are inaccurate. Our newly measured experimental values match our initial predictions to within 0.26 pKa units, whereas previous values were found to deviate by up to 1.68 pKa units. For glimepiride, our corrected value denotes a percentage of ionization at intracellular pH, which is only now in excellent agreement with its known therapeutic efficacy. We propose that linear relationships between bond lengths and pKa should emerge for any set of congeners, thus providing a powerful method of pKa prediction in instances where pKa data exist for close congeners, thereby obviating the need for thermodynamic cycles.
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Affiliation(s)
- Beth A Caine
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street , Manchester M1 7DN , UK . .,School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | | | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street , Manchester M1 7DN , UK . .,School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
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Vasa SK, Singh H, Grohe K, Linser R. Charakterisierung eines großen Enzym‐Wirkstoff‐Komplexes mittels protonendetektierter Festkörper‐NMR ohne Deuterierung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Suresh K. Vasa
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Himanshu Singh
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
- Fakultät für Chemie und Chemische BiologieTechnische Universität Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Kristof Grohe
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Rasmus Linser
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
- Fakultät für Chemie und Chemische BiologieTechnische Universität Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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Vasa SK, Singh H, Grohe K, Linser R. Assessment of a Large Enzyme–Drug Complex by Proton‐Detected Solid‐State NMR Spectroscopy without Deuteration. Angew Chem Int Ed Engl 2019; 58:5758-5762. [DOI: 10.1002/anie.201811714] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/07/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Suresh K. Vasa
- Faculty for Chemistry and PharmacyLudwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Himanshu Singh
- Faculty for Chemistry and PharmacyLudwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
- Faculty of Chemistry and Chemical BiologyTechnical University Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Germany
| | - Kristof Grohe
- Faculty for Chemistry and PharmacyLudwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Rasmus Linser
- Faculty for Chemistry and PharmacyLudwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
- Faculty of Chemistry and Chemical BiologyTechnical University Dortmund Otto-Hahn-Straße 4a 44227 Dortmund Germany
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35
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Koruza K, Mahon BP, Blakeley MP, Ostermann A, Schrader TE, McKenna R, Knecht W, Fisher SZ. Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative. J Struct Biol 2019; 205:147-154. [DOI: 10.1016/j.jsb.2018.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 11/25/2022]
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Hermann J, Nowotny P, Schrader TE, Biggel P, Hekmat D, Weuster-Botz D. Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways. Acta Crystallogr F Struct Biol Commun 2018; 74:754-764. [PMID: 30511668 PMCID: PMC6277964 DOI: 10.1107/s2053230x18015273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 01/13/2023] Open
Abstract
Lactobacillus brevis alcohol dehydrogenase (LbADH) is a well studied homotetrameric enzyme which catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. LbADH is stable and enzymatically active at elevated temperatures and accepts a broad range of substrates, making it a valuable tool in industrial biocatalysis. Here, the expression, purification and crystallization of LbADH to generate large, single crystals with a volume of up to 1 mm3 suitable for neutron diffraction studies are described. Neutron diffraction data were collected from an H/D-exchanged LbADH crystal using the BIODIFF instrument at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany to a resolution dmin of 2.15 Å in 16 days. This allowed the first neutron crystal structure of LbADH to be determined. The neutron structure revealed new details of the hydrogen-bonding network originating from the ion-binding site of LbADH and provided new insights into the reasons why divalent magnesium (Mg2+) or manganese (Mn2+) ions are necessary for its activity. X-ray diffraction data were obtained from the same crystal at the European Synchrotron Radiation Facility (ESRF), Grenoble, France to a resolution dmin of 1.48 Å. The high-resolution X-ray structure suggested partial occupancy of Mn2+ and Mg2+ at the ion-binding site. This is supported by the different binding affinity of Mn2+ and Mg2+ to the tetrameric structure calculated via free-energy molecular-dynamics simulations.
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Affiliation(s)
- Johannes Hermann
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Phillip Nowotny
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Centre (MLZ), Research Centre Jülich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Philipp Biggel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Dariusch Hekmat
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
- Research Centre for Industrial Biotechnology, Technical University of Munich, Ernst-Otto-Fischer-Strasse 3, 85748 Garching, Germany
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Mboge MY, Chen Z, Wolff A, Mathias JV, Tu C, Brown KD, Bozdag M, Carta F, Supuran CT, McKenna R, Frost SC. Selective inhibition of carbonic anhydrase IX over carbonic anhydrase XII in breast cancer cells using benzene sulfonamides: Disconnect between activity and growth inhibition. PLoS One 2018; 13:e0207417. [PMID: 30452451 PMCID: PMC6242694 DOI: 10.1371/journal.pone.0207417] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Carbonic anhydrases (CAs) have been linked to tumor progression, particularly membrane-bound CA isoform IX (CA IX). The role of CA IX in the context of breast cancer is to regulate the pH of the tumor microenvironment. In contrast to CA IX, expression of CA XII, specifically in breast cancer, is associated with better outcome despite performing the same catalytic function. In this study, we have structurally modeled the orientation of bound ureido-substituted benzene sulfonamides (USBs) within the active site of CA XII, in comparison to CA IX and cytosolic off-target CA II, to understand isoform specific inhibition. This has identified specific residues within the CA active site, which differ between isoforms that are important for inhibitor binding and isoform specificity. The ability of these sulfonamides to block CA IX activity in breast cancer cells is less effective than their ability to block activity of the recombinant protein (by one to two orders of magnitude depending on the inhibitor). The same is true for CA XII activity but now they are two to three orders of magnitude less effective. Thus, there is significantly greater specificity for CA IX activity over CA XII. While the inhibitors block cell growth, without inducing cell death, this again occurs at two orders of magnitude above the Ki values for inhibition of CA IX and CA XII activity in their respective cell types. Surprisingly, the USBs inhibited cell growth even in cells where CA IX and CA XII expression was ablated. Despite the potential for these sulfonamides as chemotherapeutic agents, these data suggest that we reconsider the role of CA activity on growth potentiation.
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Affiliation(s)
- Mam Y. Mboge
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Zhijuan Chen
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Alyssa Wolff
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - John V. Mathias
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Chingkuang Tu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Kevin D. Brown
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Murat Bozdag
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Claudiu T. Supuran
- University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Sesto Fiorentino (Florence), Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - Susan C. Frost
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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Yano N, Yamada T, Hosoya T, Ohhara T, Tanaka I, Niimura N, Kusaka K. Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer. Acta Crystallogr D Struct Biol 2018; 74:1041-1052. [PMID: 30387763 PMCID: PMC6213574 DOI: 10.1107/s2059798318012081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022] Open
Abstract
The STARGazer data-processing software is used for neutron time-of-flight (TOF) single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC). This software creates hkl intensity data from three-dimensional (x, y, TOF) diffraction data. STARGazer is composed of a data-processing component and a data-visualization component. The former is used to calculate the hkl intensity data. The latter displays the three-dimensional diffraction data with searched or predicted peak positions and is used to determine and confirm integration regions. STARGazer has been developed to make it easier to use and to obtain more accurate intensity data. For example, a profile-fitting method for peak integration was developed and the data statistics were improved. STARGazer and its manual, containing installation and data-processing components, have been prepared and provided to iBIX users. This article describes the status of the STARGazer data-processing software and its data-processing algorithms.
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Affiliation(s)
- Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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Lomelino CL, Andring JT, McKenna R. Crystallography and Its Impact on Carbonic Anhydrase Research. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:9419521. [PMID: 30302289 PMCID: PMC6158936 DOI: 10.1155/2018/9419521] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
X-ray and neutron crystallography are powerful techniques utilized to study the structures of biomolecules. Visualization of enzymes in complex with substrate/product and the capture of intermediate states can be related to activity to facilitate understanding of the catalytic mechanism. Subsequent analysis of small molecule binding within the enzyme active site provides insight into mechanisms of inhibition, supporting the design of novel inhibitors using a structure-guided approach. The first X-ray crystal structures were determined for small, ubiquitous enzymes such as carbonic anhydrase (CA). CAs are a family of zinc metalloenzymes that catalyze the hydration of CO2, producing HCO3 - and a proton. The CA structure and ping-pong mechanism have been extensively studied and are well understood. Though the function of CA plays an important role in a variety of physiological functions, CA has also been associated with diseases such as glaucoma, edema, epilepsy, obesity, and cancer and is therefore recognized as a drug target. In this review, a brief history of crystallography and its impact on CA research is discussed.
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Affiliation(s)
- Carrie L. Lomelino
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
| | - Jacob T. Andring
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
| | - Robert McKenna
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
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Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:2906519. [PMID: 30112206 PMCID: PMC6077552 DOI: 10.1155/2018/2906519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.
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Koruza K, Lafumat B, Végvári Á, Knecht W, Fisher S. Deuteration of human carbonic anhydrase for neutron crystallography: Cell culture media, protein thermostability, and crystallization behavior. Arch Biochem Biophys 2018. [DOI: 10.1016/j.abb.2018.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Linkuvienė V, Talibov VO, Danielson UH, Matulis D. Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design. J Med Chem 2018; 61:2292-2302. [DOI: 10.1021/acs.jmedchem.7b01408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
| | - Vladimir O. Talibov
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
| | - U. Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
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44
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R. "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Structure 2018; 26:383-390.e3. [PMID: 29429876 DOI: 10.1016/j.str.2018.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/15/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX.
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Affiliation(s)
- Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Mayank Aggarwal
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hector Velazquez
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew J Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - S Zoë Fisher
- Scientific Activities Division, Science Directorate, European Spallation Source ERIC, 22100 Lund, Sweden; Department of Biology, Lund University, 35 Sölvegatan, 22362 Lund, Sweden
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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Alkaya ZA, İlkimen H, Yenikaya C, Kaygısız Y, Bülbül M, Tunç T, Sarı M. A novel proton transfer salt of 2-amino-6-sulfamoylbenzothiazole and its metal complexes: the evaluation of their inhibition effects on human cytosolic carbonic anhydrases. J Enzyme Inhib Med Chem 2017; 32:231-239. [PMID: 28100079 PMCID: PMC6009966 DOI: 10.1080/14756366.2016.1247058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 10/26/2022] Open
Abstract
A novel proton transfer compound (SMHABT)+(HDPC)- (1) obtained from 2-amino-6-sulfamoylbenzothiazole (SMABT) and 2,6-pyridinedicarboxylic acid (H2DPC) and its Fe(III), Co(II), Ni(II) complexes (2-4), and Fe(II) complex of SMABT (5) have been prepared and characterized by spectroscopic techniques. Additionally, single crystal X-ray diffraction techniques were applied to complexes (2-4). All complexes (2-4) have distorted octahedral conformations and the structure of 5 might be proposed as octahedral according to spectral and analytical results. All compounds, including acetazolamide (AAZ) as the control compound, were also evaluated for their in vitro inhibition effects on human hCA I and hCA II for their hydratase and esterase activities. The synthesized compounds have remarkable inhibitory activities on hCA I and hCA II. Especially, the inhibition potentials of the salt and the metal complexes (1-5) are comparable with AAZ. Inhibition data have been analyzed by using a one-way analysis of variance for multiple comparisons (p < .0001).
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Affiliation(s)
- Zeynep Alkan Alkaya
- Department of Chemistry and Chemical Processing Technologies, Banaz Vocational School, Usak University, Uşak, Turkey
| | - Halil İlkimen
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupinar University, Kütahya, Turkey
| | - Cengiz Yenikaya
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupinar University, Kütahya, Turkey
| | - Yasemin Kaygısız
- Department of Biochemistry, Faculty of Arts and Sciences, Dumlupinar University, KütahyaTurkey
| | - Metin Bülbül
- Department of Biochemistry, Faculty of Arts and Sciences, Dumlupinar University, KütahyaTurkey
| | - Tuncay Tunç
- Department of Science Education, Faculty of Education, Aksaray University, Aksaray, Turkey
| | - Musa Sarı
- Department of Physics Education, Gazi University, Ankara, Turkey
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Improved molecular recognition of Carbonic Anhydrase IX by polypeptide conjugation to acetazolamide. Bioorg Med Chem 2017; 25:5838-5848. [DOI: 10.1016/j.bmc.2017.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 02/04/2023]
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48
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Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
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Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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49
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Chen JCH, Unkefer CJ. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. IUCRJ 2017; 4:72-86. [PMID: 28250943 PMCID: PMC5331467 DOI: 10.1107/s205225251601664x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
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Affiliation(s)
- Julian C.-H. Chen
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Clifford J. Unkefer
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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50
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Yano N, Yamada T, Hosoya T, Ohhara T, Tanaka I, Kusaka K. Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX. Sci Rep 2016; 6:36628. [PMID: 27905404 PMCID: PMC5131355 DOI: 10.1038/srep36628] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
We developed and employed a profile fitting method for the peak integration of neutron time-of-flight diffraction data collected by the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC) for protein ribonuclease A and α-thrombin single crystals. In order to determine proper fitting functions, four asymmetric functions were evaluated using strong intensity peaks. A Gaussian convolved with two back-to-back exponentials was selected as the most suitable fitting function, and a profile fitting algorithm for the integration method was developed. The intensity and structure refinement data statistics of the profile fitting method were compared to those of the summation integration method. It was clearly demonstrated that the profile fitting method provides more accurate integrated intensities and model structures than the summation integration method at higher resolution shells. The integration component with the profile fitting method has already been implemented in the iBIX data processing software STARGazer and its user manual has been prepared.
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Affiliation(s)
- Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.,College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki, 316-8511, Japan
| | - Takashi Ohhara
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.,College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki, 316-8511, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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