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Cui Y, Du X, Li Y, Wang D, Lv Z, Yuan H, Chen Y, Liu J, Sun Y, Wang W. Imbalanced and Unchecked: The Role of Metal Dyshomeostasis in Driving COPD Progression. COPD 2024; 21:2322605. [PMID: 38591165 DOI: 10.1080/15412555.2024.2322605] [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: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/10/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic respiratory condition characterized by persistent inflammation and oxidative stress, which ultimately leads to progressive restriction of airflow. Extensive research findings have cogently suggested that the dysregulation of essential transition metal ions, notably iron, copper, and zinc, stands as a critical nexus in the perpetuation of inflammatory processes and oxidative damage within the lungs of COPD patients. Unraveling the intricate interplay between metal homeostasis, oxidative stress, and inflammatory signaling is of paramount importance in unraveling the intricacies of COPD pathogenesis. This comprehensive review aims to examine the current literature on the sources, regulation, and mechanisms by which metal dyshomeostasis contributes to COPD progression. We specifically focus on iron, copper, and zinc, given their well-characterized roles in orchestrating cytokine production, immune cell function, antioxidant depletion, and matrix remodeling. Despite the limited number of clinical trials investigating metal modulation in COPD, the advent of emerging methodologies tailored to monitor metal fluxes and gauge responses to chelation and supplementation hold great promise in unlocking the potential of metal-based interventions. We conclude that targeted restoration of metal homeostasis represents a promising frontier for ameliorating pathological processes driving COPD progression.
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Affiliation(s)
- Ye Cui
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Xinqian Du
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Yunqi Li
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Dan Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Zhe Lv
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Huihui Yuan
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Yan Chen
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Jie Liu
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Ying Sun
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
| | - Wei Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, People's Republic of China
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Baronas D, Knašienė B, Mickevičiūtė A, Jachno J, Naujalis E, Zubrienė A, Matulis D. Inhibitor binding to metal-substituted metalloenzyme: Sulfonamide affinity for carbonic anhydrase IX. J Inorg Biochem 2024; 256:112547. [PMID: 38581802 DOI: 10.1016/j.jinorgbio.2024.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Transition metal ions are structural and catalytic cofactors of many proteins including human carbonic anhydrase (CA), a Zn-dependent hydrolase. Sulfonamide inhibitors of CA recognize and form a coordination bond with the Zn ion located in the active site of the enzyme. The Zn ion may be removed or substituted with other metal ions. Such CA protein retains the structure and could serve as a tool to study metal ion role in the recognition and binding affinity of inhibitor molecules. We measured the affinities of selected divalent transition metal ions, including Mn, Fe, Co, Ni, Cu, Cd, Hg, and Zn to metal-free CA isozymes CA I, CA II, and CAIX by fluorescence-based thermal shift assay, prepared metal-substituted CAs, and determined binding of diverse sulfonamide compounds. Sulfonamide inhibitor binding to metal substituted CA followed a U-shape pH dependence. The binding was dissected to contributing binding-linked reactions and the intrinsic binding reaction affinity was calculated. This value is independent of pH and protonation reactions that occur simultaneously upon binding native CA and as demonstrated here, to metal substituted CA. Sulfonamide inhibitor binding to cancer-associated isozyme CAIX diminished in the order: Zn > Co > Hg > Cu > Cd > Mn > Ni. Energetic contribution of the inhibitor-metal coordination bond was determined for all above metals. The understanding of the principles of metal influence on ligand affinity and selectivity should help design new drugs targeting metalloenzymes.
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Affiliation(s)
- Denis Baronas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Birutė Knašienė
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Jelena Jachno
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Evaldas Naujalis
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
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Wang Y, Huang Y, Wang X, Jiang J. Exploring Enzyme-Mimicking Metal-Organic Frameworks for CO 2 Conversion through Vibrational Spectra-Based Machine Learning. J Phys Chem Lett 2024; 15:6654-6661. [PMID: 38889050 DOI: 10.1021/acs.jpclett.4c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
In pursuing the benefits of natural enzyme catalysts while overcoming their limitations, we find metal-organic frameworks (MOFs), renowned for their highly tunable functionalities, stand out in biomimetic applications. We used unsupervised machine learning on density functional theory-computed vibrational infrared and Raman spectral features to screen 300 Zn-MOFs for CO2 conversion, similar to carbonic anhydrase (CA). Our findings confirmed that MOFs with spectroscopic attributes closely resembling those of CA hold the potential for replicating CA's electronic and catalytic properties. Unlike previous studies that relied on heuristic or trial-and-error methods and focused on geometric configurations, our research uses vibrational spectral features to explore structure-property relationships, making them more accessible through spectroscopy. Moreover, we highlight vibrational spectral features as efficient carriers for highly dimensional chemical information, enabling the simultaneous optimization of multiple performance parameters. These findings pave the way for pioneering designs of enzyme-mimetic MOFs and concurrently expand the application scope of spectroscopic tools in biomimetic catalysis.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yan Huang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - X Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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Sun X, Zhou X, Shi X, Abed OA, An X, Lei YL, Moon JJ. Strategies for the development of metalloimmunotherapies. Nat Biomed Eng 2024:10.1038/s41551-024-01221-7. [PMID: 38914800 DOI: 10.1038/s41551-024-01221-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/30/2024] [Indexed: 06/26/2024]
Abstract
Metal ions play crucial roles in the regulation of immune pathways. In fact, metallodrugs have a long record of accomplishment as effective treatments for a wide range of diseases. Here we argue that the modulation of interactions of metal ions with molecules and cells involved in the immune system forms the basis of a new class of immunotherapies. By examining how metal ions modulate the innate and adaptive immune systems, as well as host-microbiota interactions, we discuss strategies for the development of such metalloimmunotherapies for the treatment of cancer and other immune-related diseases.
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Affiliation(s)
- Xiaoqi Sun
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Editas Medicine, Cambridge, MA, USA.
| | - Xingwu Zhou
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoyue Shi
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Omar A Abed
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xinran An
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Yu Leo Lei
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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Gu J, Guo C, Ruan J, Li K, Zhou Y, Gong X, Shi H. From ferroptosis to cuproptosis, and calcicoptosis, to find more novel metals-mediated distinct form of regulated cell death. Apoptosis 2024; 29:586-604. [PMID: 38324163 DOI: 10.1007/s10495-023-01927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 02/08/2024]
Abstract
Regulated cell death (RCD), also known as programmed cell death (PCD), plays a critical role in various biological processes, such as tissue injury/repair, development, and homeostasis. Dysregulation of RCD pathways can lead to the development of many human diseases, such as cancer, neurodegenerative disorders, and cardiovascular diseases. Maintaining proper metal ion homeostasis is critical for human health. However, imbalances in metal levels within cells can result in cytotoxicity and cell death, leading to a variety of diseases and health problems. In recent years, new types of metal overload-induced cell death have been identified, including ferroptosis, cuproptosis, and calcicoptosis. This has prompted us to examine the three defined metal-dependent cell death types, and discuss other metals-induced ferroptosis, cuproptosis, and disrupted Ca2+ homeostasis, as well as the roles of Zn2+ in metals' homeostasis and related RCD. We have reviewed the connection between metals-induced RCD and various diseases, as well as the underlying mechanisms. We believe that further research in this area will lead to the discovery of novel types of metal-dependent RCD, a better understanding of the underlying mechanisms, and the development of new therapeutic strategies for human diseases.
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Affiliation(s)
- Jie Gu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Chuanzhi Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Jiacheng Ruan
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Kongdong Li
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Yang Zhou
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212013, China.
| | - Haifeng Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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Capasso C, Supuran CT. Biomedical applications of prokaryotic carbonic anhydrases: an update. Expert Opin Ther Pat 2024; 34:351-363. [PMID: 38840307 DOI: 10.1080/13543776.2024.2365407] [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: 03/07/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
INTRODUCTION This review offers an updated perspective on the biomedical applications of prokaryotic carbonic anhydrases (CAs), emphasizing their potential as targets for drug development against antibiotic-resistant bacterial infections. A systematic review of literature from PubMed, Web of Science, and Google Scholar has been conducted to provide a comprehensive analysis. AREA COVERED It delves into the pivotal roles of prokaryotic CAs in bacterial metabolism and their distinctions from mammalian CAs. The review explores the diversity of CA classes in bacteria, discusses selective inhibitors targeting bacterial CAs, and explores their potential applications in biomedical research. Furthermore, it analyzes clinical trials investigating the efficacy of carbonic anhydrase inhibitors (CAIs) and patented approaches for developing antibacterial CAIs, highlighting their translational potential in creating innovative antibacterial agents. EXPERT OPINION Recent years have witnessed increased recognition of CA inhibition as a promising strategy against bacterial infections. Challenges persist in achieving selectivity over human isoforms and optimizing therapeutic efficacy. Structural biology techniques provide insights into unique active site architectures, guiding selective inhibitor design. The review underscores the importance of interdisciplinary collaborations, innovative drug delivery systems, and advanced drug discovery approaches in unlocking the full therapeutic potential of prokaryotic CA inhibitors. It emphasizes the significance of these efforts in addressing antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Florence, Italy
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Wang J, Lu X, Zhuge B, Zong H. Enhancing the catalytic efficiency of M32 carboxypeptidase by semi-rational design and its applications in food taste improvement. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38666395 DOI: 10.1002/jsfa.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Carboxypeptidase is an exopeptidase that hydrolyzes amino acids at the C-terminal end of the peptide chain and has a wide range of applications in food. However, in industrial applications, the relatively low catalytic efficiency of carboxypeptidases is one of the main limiting factors for industrialization. RESULTS The study has enhanced the catalytic efficiency of Bacillus megaterium M32 carboxypeptidase (BmeCPM32) through semi-rational design. Firstly, the specific activity of the optimal mutant, BmeCPM32-M2, obtained through single-site mutagenesis and combinatorial mutagenesis, was 2.2-fold higher than that of the wild type (187.9 versus 417.8 U mg-1), and the catalytic efficiency was 2.9-fold higher (110.14 versus 325.75 s-1 mmol-1). Secondly, compared to the wild type, BmeCPM32-M2 exhibited a 1.8-fold increase in half-life at 60 °C, with no significant changes in its enzymatic properties (optimal pH, optimal temperature). Finally, BmeCPM32-M2 significantly increased the umami intensity of soy protein isolate hydrolysate by 55% and reduced bitterness by 83%, indicating its potential in developing tasty protein components. CONCLUSION Our research has revealed that the strategy based on protein sequence evolution and computational residue mutation energy led to an improved catalytic efficiency of BmeCPM32. Molecular dynamics simulations have revealed that a smaller substrate binding pocket and increased enzyme-substrate affinity are the reasons for the enhanced catalytic efficiency. Furthermore the number of hydrogen bonds and solvent and surface area may contribute to the improvement of thermostability. Finally, the de-bittering effect of BmeCPM32-M2 in soy protein isolate hydrolysate suggests its potential in developing palatable protein components. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jinjiang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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8
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Borghesani V, Zastrow ML, Tolbert AE, Deb A, Penner-Hahn JE, Pecoraro VL. Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase. Chemistry 2024; 30:e202304367. [PMID: 38377169 PMCID: PMC11045307 DOI: 10.1002/chem.202304367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.
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Affiliation(s)
- Valentina Borghesani
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle, Scienze 11A, 43124, Parma, Italy
| | - Melissa L Zastrow
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX-77204, United States
| | - Audrey E Tolbert
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - Aniruddha Deb
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - James E Penner-Hahn
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - Vincent L Pecoraro
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
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Li L, Xu W, Wu Z, Geng W, Li S, Sun S, Wang M, Cheng C, Zhao C. Engineering Zinc-Organic Frameworks-Based Artificial Carbonic Anhydrase with Ultrafast Biomimetic Centers for Efficient Hydration Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307537. [PMID: 37939303 DOI: 10.1002/smll.202307537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Constructing effective and robust biocatalysts with carbonic anhydrase (CA)-mimetic activities offers an alternative and promising pathway for diverse CO2-related catalytic applications. However, there is very limited success has been achieved in controllably synthesizing CA-mimetic biocatalysts. Here, inspired by the 3D coordination environments of CAs, this study reports on the design of an ultrafast ZnN3-OH2 center via tuning the 3D coordination structures and mesoporous defects in a zinc-dipyrazolate framework to serve as new, efficient, and robust CA-mimetic biocatalysts (CABs) to catalyze the hydration reactions. Owing to the structural advantages and high similarity with the active center of natural CAs, the double-walled CAB with mesoporous defects displays superior CA-like reaction kinetics in p-NPA hydrolysis (V0 = 445.16 nM s-1, Vmax = 3.83 µM s-1, turnover number: 5.97 × 10-3 s-1), which surpasses the by-far-reported metal-organic frameworks-based biocatalysts. This work offers essential guidance in tuning 3D coordination environments in artificial enzymes and proposes a new strategy to create high-performance CA-mimetic biocatalysts for broad applications, such as CO2 hydration/capture, CO2 sensing, and abundant hydrolytic reactions.
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Affiliation(s)
- Lin Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Wenjie Xu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Zihe Wu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Wei Geng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Shuang Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Shudong Sun
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Mao Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Chong Cheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Changsheng Zhao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
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10
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Hull JA, Lee C, Kim JK, Lim SW, Park J, Park S, Lee SJ, Park G, Eom I, Kim M, Hyun H, Combs JE, Andring JT, Lomelino C, Kim CU, McKenna R. XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures. Acta Crystallogr D Struct Biol 2024; 80:194-202. [PMID: 38411550 PMCID: PMC10910541 DOI: 10.1107/s2059798324000482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/12/2024] [Indexed: 02/28/2024] Open
Abstract
The combination of X-ray free-electron lasers (XFELs) with serial femtosecond crystallography represents cutting-edge technology in structural biology, allowing the study of enzyme reactions and dynamics in real time through the generation of `molecular movies'. This technology combines short and precise high-energy X-ray exposure to a stream of protein microcrystals. Here, the XFEL structure of carbonic anhydrase II, a ubiquitous enzyme responsible for the interconversion of CO2 and bicarbonate, is reported, and is compared with previously reported NMR and synchrotron X-ray and neutron single-crystal structures.
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Affiliation(s)
- Joshua A. Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Cheol Lee
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seon Woo Lim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
- Department of Chemical Engineering, POSTECH, Pohang 37673, Republic of Korea
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - HyoJung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Republic of Korea
| | - Jacob E. Combs
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jacob T. Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Carrie Lomelino
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Katti SS, Igumenova TI. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565546. [PMID: 38405767 PMCID: PMC10888879 DOI: 10.1101/2023.11.03.565546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca 2+ and Zn 2+ . The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd 2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn 2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd 2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α 3 DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
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12
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Giovannuzzi S, Nikitjuka A, Pereira Resende BR, Smietana M, Nocentini A, Supuran CT, Winum JY. Boron-containing carbonic anhydrases inhibitors. Bioorg Chem 2024; 143:106976. [PMID: 38000350 DOI: 10.1016/j.bioorg.2023.106976] [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: 09/17/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023]
Abstract
Over the last decades, the medicinal chemistry of boron-based compounds has been extensively explored, designing valuable small molecule drugs to tackle diseases and conditions, such as cancer, infections, inflammatory and neurological disorders. Notably, boron has proven to also be a valuable element for the development of inhibitors of the metalloenzymes carbonic anhydrases (CAs), a class of drug targets with significant potential in medicinal chemistry. Incorporating boron into carbonic anhydrase inhibitors (CAIs) can modulate the ligand ability to recognize the target and/or influence selectivity towards different CA isoforms, using the tail approach and boron-based tails. The electron-deficient nature of boron and its associated properties have also led to the discovery of novel zinc-binding CAIs, such as boronic acids and the benzoxaboroles, capable of inhibiting the CAs upon a Lewis acid-base mechanism of action. The present manuscript reviews the state-of-the-art of boron-based CAIs. As research in the applications of boron compounds in medicinal chemistry continues, it is anticipated that new boron-based CAIs will soon expand the current array of such compounds. However, further research is imperative to fully unlock the potential of boron-based CAIs and to advance them towards clinical applications.
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Affiliation(s)
- Simone Giovannuzzi
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France; Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Anna Nikitjuka
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France; Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Bruna Rafaela Pereira Resende
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France; Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | | | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy.
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
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13
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Jafari M, Li Z, Song LF, Sagresti L, Brancato G, Merz KM. Thermodynamics of Metal-Acetate Interactions. J Phys Chem B 2024; 128:684-697. [PMID: 38226860 DOI: 10.1021/acs.jpcb.3c06567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C4 parameters for the 12-6-4 LJ nonbonded model to be used with three widely employed water models (Transferable Intermolecular Potential with 3 Points (TIP3P), Simple Point Charge Extended (SPC/E), and Optimal Point Charge (OPC) water models). These parameters can accurately match the experimental binding free energy between 11 metal ions and acetate. These parameters can be applied to the study of metalloproteins and transition metal ion channels and transporters, as acetate serves as a representative of the negatively charged amino acid side chains from aspartate and glutamate.
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Affiliation(s)
- Majid Jafari
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Luca Sagresti
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Kenneth M Merz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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14
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Nett RS, Dho Y, Tsai C, Passow D, Martinez Grundman J, Low YY, Sattely ES. Plant carbonic anhydrase-like enzymes in neuroactive alkaloid biosynthesis. Nature 2023; 624:182-191. [PMID: 37938780 PMCID: PMC10700139 DOI: 10.1038/s41586-023-06716-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
Plants synthesize numerous alkaloids that mimic animal neurotransmitters1. The diversity of alkaloid structures is achieved through the generation and tailoring of unique carbon scaffolds2,3, yet many neuroactive alkaloids belong to a scaffold class for which no biosynthetic route or enzyme catalyst is known. By studying highly coordinated, tissue-specific gene expression in plants that produce neuroactive Lycopodium alkaloids4, we identified an unexpected enzyme class for alkaloid biosynthesis: neofunctionalized α-carbonic anhydrases (CAHs). We show that three CAH-like (CAL) proteins are required in the biosynthetic route to a key precursor of the Lycopodium alkaloids by catalysing a stereospecific Mannich-like condensation and subsequent bicyclic scaffold generation. Also, we describe a series of scaffold tailoring steps that generate the optimized acetylcholinesterase inhibition activity of huperzine A5. Our findings suggest a broader involvement of CAH-like enzymes in specialized metabolism and demonstrate how successive scaffold tailoring can drive potency against a neurological protein target.
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Affiliation(s)
- Ryan S Nett
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- HHMI, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Yaereen Dho
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chun Tsai
- HHMI, Stanford University, Stanford, CA, USA
| | - Daria Passow
- Biophysics Program, Stanford University, Stanford, CA, USA
| | | | - Yun-Yee Low
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- HHMI, Stanford University, Stanford, CA, USA.
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15
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Li J, Liu S, Yang C, Keyhani NO, Pu H, Lin L, Li X, Jia P, Wu D, Pan J, Stevenson PC, Fernández-Grandon GM, Zhang L, Chen Y, Guan X, Qiu J. Characterization of an α-Amylase from the Honeybee Chalk Brood Pathogen Ascosphaera apis. J Fungi (Basel) 2023; 9:1082. [PMID: 37998887 PMCID: PMC10672707 DOI: 10.3390/jof9111082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
The insect pathogenic fungus, Ascosphaera apis, is the causative agent of honeybee chalk brood disease. Amylases are secreted by many plant pathogenic fungi to access host nutrients through the metabolism of starch, and the identification of new amylases can have important biotechnological applications. Production of amylase by A. apis in submerged culture was optimized using the response surface method (RSM). Media composition was modeled using Box-Behnken design (BBD) at three levels of three variables, and the model was experimentally validated to predict amylase activity (R2 = 0.9528). Amylase activity was highest (45.28 ± 1.16 U/mL, mean ± SE) in media composed of 46 g/L maltose and1.51 g/L CaCl2 at a pH of 6.6, where total activity was ~11-fold greater as compared to standard basal media. The enzyme was purified to homogeneity with a 2.5% yield and 14-fold purification. The purified enzyme had a molecular weight of 75 kDa and was thermostable and active in a broad pH range (> 80% activity at a pH range of 7-10), with optimal activity at 55 °C and pH = 7.5. Kinetic analyses revealed a Km of 6.22 mmol/L and a Vmax of 4.21 μmol/mL·min using soluble starch as the substrate. Activity was significantly stimulated by Fe2+ and completely inhibited by Cu2+, Mn2+, and Ba2+ (10 mM). Ethanol and chloroform (10% v/v) also caused significant levels of inhibition. The purified amylase essentially exhibited activity only on hydrolyzed soluble starch, producing mainly glucose and maltose, indicating that it is an endo-amylase (α-amylase). Amylase activity peaked at 99.38 U/mL fermented in a 3.7 L-bioreactor (2.15-fold greater than what was observed in flask cultures). These data provide a strategy for optimizing the production of enzymes from fungi and provide insight into the α-amylase of A. apis.
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Affiliation(s)
- Jincheng Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Sen Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Chenjie Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL 60607, USA;
| | - Huili Pu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Longbin Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Xiaoxia Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Peisong Jia
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Dongmei Wu
- Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China;
| | - Jieming Pan
- College of Biology & Pharmacy, Yulin Normal University, Yulin 537000, China;
| | - Philip C. Stevenson
- Natural Resources Institute, University of Greenwich, Chatham Maritime ME4 4TB, UK; (P.C.S.); (G.M.F.-G.)
| | | | - Liaoyuan Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Yuxi Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
| | - Xiayu Guan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junzhi Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (S.L.); (C.Y.); (H.P.); (L.L.); (X.L.); (L.Z.); (Y.C.)
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Fernandez-Lopez L, Cea-Rama I, Alvarez-Malmagro J, Ressmann AK, Gonzalez-Alfonso JL, Coscolín C, Shahgaldian P, Plou FJ, Modregger J, Pita M, Sanz-Aparicio J, Ferrer M. Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor. Chem Commun (Camb) 2023. [PMID: 37376994 DOI: 10.1039/d3cc01946b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Metal complexes introduced into protein scaffolds can generate versatile biomimetic catalysts endowed with a variety of catalytic properties. Here, we synthesized and covalently bound a bipyridinyl derivative to the active centre of an esterase to generate a biomimetic catalyst that shows catecholase activity and enantioselective catalytic oxidation of (+)-catechin.
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Affiliation(s)
| | - Isabel Cea-Rama
- Instituto de Quimica Fisica Rocasolano (IQFR), CSIC, Madrid 28006, Spain
| | | | | | | | - Cristina Coscolín
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | - Patrick Shahgaldian
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Francisco J Plou
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Marcos Pita
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
| | | | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid 28049, Spain.
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17
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Peerzada M, Vullo D, Paoletti N, Bonardi A, Gratteri P, Supuran CT, Azam A. Discovery of Novel Hydroxyimine-Tethered Benzenesulfonamides as Potential Human Carbonic Anhydrase IX/XII Inhibitors. ACS Med Chem Lett 2023; 14:810-819. [PMID: 37312840 PMCID: PMC10258898 DOI: 10.1021/acsmedchemlett.3c00094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/04/2023] [Indexed: 06/15/2023] Open
Abstract
To discover novel carbonic anhydrase (CA, EC 4.2.1.1) inhibitors for cancer treatment, a series of 4-{4-[(hydroxyimino)methyl]piperazin-1-yl}benzenesulfonamides were designed and synthesized using SLC-0111 as the lead molecule. The developed novel compounds 27-34 were investigated for the inhibition of human (h) isoforms hCA I, hCA II, hCA IX, and hCA XII. The hCA I was inhibited by compound 29 with a Ki value of 3.0 nM, whereas hCA II was inhibited by compound 32 with a Ki value of 4.4 nM. The tumor-associated hCA IX isoform was inhibited by compound 30 effectively with an Ki value of 43 nM, whereas the activity of another cancer-related isoform, hCA XII, was significantly inhibited by 29 and 31 with a Ki value of 5 nM. Molecular modeling showed that drug molecule 30 participates in significant hydrophobic and hydrogen bond interactions with the active site of the investigated hCAs and binds to zinc through the deprotonated sulfonamide group.
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Affiliation(s)
- Mudasir
Nabi Peerzada
- Medicinal
Chemistry and Drug Discovery Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
| | - Daniela Vullo
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Niccolò Paoletti
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessandro Bonardi
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Gratteri
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Amir Azam
- Medicinal
Chemistry and Drug Discovery Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
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18
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Martínez-Montiel M, Romero-Hernández LL, Giovannuzzi S, Begines P, Puerta A, Ahuja-Casarín AI, Fernandes MX, Merino-Montiel P, Montiel-Smith S, Nocentini A, Padrón JM, Supuran CT, Fernández-Bolaños JG, López Ó. Conformationally Restricted Glycoconjugates Derived from Arylsulfonamides and Coumarins: New Families of Tumour-Associated Carbonic Anhydrase Inhibitors. Int J Mol Sci 2023; 24:ijms24119401. [PMID: 37298353 DOI: 10.3390/ijms24119401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The involvement of carbonic anhydrases (CAs) in a myriad of biological events makes the development of new inhibitors of these metalloenzymes a hot topic in current Medicinal Chemistry. In particular, CA IX and XII are membrane-bound enzymes, responsible for tumour survival and chemoresistance. Herein, a bicyclic carbohydrate-based hydrophilic tail (imidazolidine-2-thione) has been appended to a CA-targeting pharmacophore (arylsulfonamide, coumarin) with the aim of studying the influence of the conformational restriction of the tail on the CA inhibition. For this purpose, the coupling of sulfonamido- or coumarin-based isothiocyanates with reducing 2-aminosugars, followed by the sequential acid-promoted intramolecular cyclization of the corresponding thiourea and dehydration reactions, afforded the corresponding bicyclic imidazoline-2-thiones in good overall yield. The effects of the carbohydrate configuration, the position of the sulfonamido motif on the aryl fragment, and the tether length and substitution pattern on the coumarin were analysed in the in vitro inhibition of human CAs. Regarding sulfonamido-based inhibitors, the best template turned out to be a d-galacto-configured carbohydrate residue, meta-substitution on the aryl moiety (9b), with Ki against CA XII within the low nM range (5.1 nM), and remarkable selectivity indexes (1531 for CA I and 181.9 for CA II); this provided an enhanced profile in terms of potency and selectivity compared to more flexible linear thioureas 1-4 and the drug acetazolamide (AAZ), used herein as a reference compound. For coumarins, the strongest activities were found for substituents devoid of steric hindrance (Me, Cl), and short linkages; derivatives 24h and 24a were found to be the most potent inhibitors against CA IX and XII, respectively (Ki = 6.8, 10.1 nM), and also endowed with outstanding selectivity (Ki > 100 µM against CA I, II, as off-target enzymes). Docking simulations were conducted on 9b and 24h to gain more insight into the key inhibitor-enzyme interactions.
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Affiliation(s)
- Mónica Martínez-Montiel
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla 72570, PUE, Mexico
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, E-41071 Seville, Spain
| | - Laura L Romero-Hernández
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla 72570, PUE, Mexico
| | - Simone Giovannuzzi
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019 Florence, Italy
| | - Paloma Begines
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019 Florence, Italy
| | - Adrián Puerta
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, c/Astrofísico Francisco Sánchez 2, E-38206 La Laguna, Spain
| | - Ana I Ahuja-Casarín
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla 72570, PUE, Mexico
| | - Miguel X Fernandes
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, c/Astrofísico Francisco Sánchez 2, E-38206 La Laguna, Spain
| | - Penélope Merino-Montiel
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla 72570, PUE, Mexico
| | - Sara Montiel-Smith
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla 72570, PUE, Mexico
| | - Alessio Nocentini
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019 Florence, Italy
| | - José M Padrón
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, c/Astrofísico Francisco Sánchez 2, E-38206 La Laguna, Spain
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019 Florence, Italy
| | - José G Fernández-Bolaños
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, E-41071 Seville, Spain
| | - Óscar López
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, E-41071 Seville, Spain
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Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
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Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
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20
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Singh D, Tomar S, Singh S, Chaudhary G, Singh AP, Gupta R. A fluorescent pH switch probe for the ‘turn-on’ dual-channel discriminative detection of magnesium and zinc ions. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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21
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Zeng J, Tang Y, Yang J, Yang Y, Li G, Wang X, Feng J, Chen K, Li H, Ouyang P. Inert enzyme nanoaggregates for simultaneous biodecarboxylation and CO2 conversion. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Human telomeric G-quadruplex DNA enabled preferential recognition of copper (II) and Iron (III) ions sensed by a red emissive probe. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Wu C, Guo D. Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants. Int J Mol Sci 2022; 23:ijms232012688. [PMID: 36293547 PMCID: PMC9604239 DOI: 10.3390/ijms232012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are modular functionalities regulating multiple cellular activities in prokaryotes and eukaryotes. As a consequence of higher plants adapting to arid and thermal conditions, C4 photosynthesis is the carbon fixation process involving multi-enzymes working in a coordinated fashion. However, how these enzymes interact with each other and whether they co-evolve in parallel to maintain interactions in different plants remain elusive to date. Here, we report our findings on the global protein co-evolution relationship and local dynamics of co-varying site shifts in key C4 photosynthetic enzymes. We found that in most of the selected key C4 photosynthetic enzymes, global pairwise co-evolution events exist to form functional couplings. Besides, protein-protein interactions between these enzymes may suggest their unknown functionalities in the carbon delivery process. For PEPC and PPCK regulation pairs, pocket formation at the interactive interface are not necessary for their function. This feature is distinct from another well-known regulation pair in C4 photosynthesis, namely, PPDK and PPDK-RP, where the pockets are necessary. Our findings facilitate the discovery of novel protein regulation types and contribute to expanding our knowledge about C4 photosynthesis.
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Sharma T, Sharma A, Xia CL, Lam SS, Khan AA, Tripathi S, Kumar R, Gupta VK, Nadda AK. Enzyme mediated transformation of CO 2 into calcium carbonate using purified microbial carbonic anhydrase. ENVIRONMENTAL RESEARCH 2022; 212:113538. [PMID: 35640707 DOI: 10.1016/j.envres.2022.113538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
In this study, a bacterial carbonic anhydrase (CA) was purified from Corynebacterium flavescens for the CO2 conversion into CaCO3. The synthesized CaCO3 can be utilized in the papermaking industry as filler material, construction material and in steel industry. Herein, the CA was purified by using a Sephadex G-100 column chromatography having 29.00 kDa molecular mass in SDS-PAGE analysis. The purified CA showed an optimal temperature of 35 °C and pH 7.5. In addition, a kinetic study of CA using p-NPA as substrate showed Vmax (166.66 μmoL/mL/min), Km (5.12 mM), and Kcat (80.56 sec-1) using Lineweaver Burk plot. The major inhibitors of CA activity were Na2+, K+, Mn2+, and Al3+, whereas Zn2+ and Fe2+ slightly enhanced it. The purified CA showed a good efficacy to convert the CO2 into CaCO3 with a total conversion rate of 65.05 mg CaCO3/mg of protein. In silico analysis suggested that the purified CA has conserved Zn2+ coordinating residues such as His 111, His 113, and His 130 in the active site center. Further analysis of the CO2 binding site showed conserved residues such as Val 132, Val 142, Leu 196, Thr 197, and Val 205. However, a substitution has been observed where Trp 208 of its closest structural homolog T. ammonificans CA is replaced with Arg 207 of C. flavescens. The presence of a hydrophilic mutation in the CO2 binding hydrophobic region is a further subject of investigation.
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Affiliation(s)
- Tanvi Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India
| | - Abhishek Sharma
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171 005, India
| | - Chang Lei Xia
- Co-Innovation Center of Efficient Processing and Utilization of Forestry Resources, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Azmat Ali Khan
- Pharmaceutical Biotechnological Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar Central University, Lucknow, Uttar Pradesh, 226025, India
| | - Raj Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173 234, India.
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Sink A, Banerjee S, Wolny JA, Imberti C, Lant EC, Walker M, Schünemann V, Sadler PJ. Kinetics and mechanism of sequential ring methyl C-H activation in cyclopentadienyl rhodium(III) complexes. Dalton Trans 2022; 51:16070-16081. [PMID: 36043856 DOI: 10.1039/d2dt02079c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied activation of the methyl C-H bonds in the cyclopentadienyl ligands of half-sandwich Rh(III) complexes [η5-CpXRh(N,N')Cl]+ by observing the dependence of sequential H/D exchange on variations in CpX = Cp* (complexes 1 and 2), Me4PhCp (CpXPh, 3) or Me4PhPhCp (CpXPhPh, 4), and chelated ligand N,N' (bpy, 1; phen, 2-4). H/D exchange was fastest in d4-MeOD (t1/2 = 10 min, 37 °C, complex 1), no H/D exchange was observed in DMSO/D2O, and d4-MeOD enhanced the rate in CD3CN. The proposed Rh(I)-fulvene intermediate was trapped by [4 + 2] Diels-Alder reactions with conjugated dienes and characterized. The Rh(I) oxidation state was confirmed by X-ray photoelectron spectroscopy (XPS). Influence of solvent on the mechanisms of activation and Diels-Alder adduct formation was modelled using DFT calculations with the CAM-B3LYP functional and CEP-31 g basis set, and influence on the reaction profile of the dimiine ligand and phenyl substituent using the larger qzvp basis set. The Rh(III)-OH intemediate is stabilised by H-bonding with methanol and a Cp* CH3 hydrogen. The Rh(I)(Me4fulvene) species, stabilised by interaction of methanol with a coordinated water, again by two H-bonds H2O-HOMe (1.49 Å) and fulvene CH2 (1.94 Å), arises from synchronous transfer of the methanol OH proton to a Rh(III)-OH ligand and Cp* methyl hydrogen to the methanol oxygen. Additionally, the observed trend in catalytic activity for complexes 1-4 was reproduced by DFT calculations. These complexes form a novel class of catalytic molecular motors with a tunable rate of operation that can be stalled in a given state. They provide a basis for elucidation of the effects of ligand design on the contributions of electronic, rotational and vibrational energies to each step in the reaction pathway at the atomic level, consideration of which will enhance the design principles for the next generation of molecular machines.
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Affiliation(s)
- Alexandra Sink
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Samya Banerjee
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. .,Department of Chemistry, Indian Institute of Technology (BHU), Varanasi, UP-221005, India.
| | - Juliusz A Wolny
- Department of Physics, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany.
| | - Cinzia Imberti
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Edward C Lant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Marc Walker
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Volker Schünemann
- Department of Physics, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663 Kaiserslautern, Germany.
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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Singh D, Ibrahim A, Kumar P, Gupta R. Methylene Spacer Mediated Detection Switch Between Copper and Zinc Ions by Two Coumarin‐Pyrene Based Chemosensors. ChemistrySelect 2022. [DOI: 10.1002/slct.202202574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Devender Singh
- Department of Chemistry University of Delhi New Delhi 110007 India
| | - Annan Ibrahim
- Department of Chemistry University of Delhi New Delhi 110007 India
| | - Pramod Kumar
- Department of Chemistry Mahamana Malviya College Khekra (Baghpat) C.C.S. University Meerut India
| | - Rajeev Gupta
- Department of Chemistry University of Delhi New Delhi 110007 India
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27
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Turn-on fluorescent detection of nickel and zinc ions by two related chemosensors containing naphthalimide ring(s). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Vikas, Sahu HK, Mehata AK, Viswanadh MK, Priya V, Muthu MS. Dual-receptor-targeted nanomedicines: emerging trends and advances in lung cancer therapeutics. Nanomedicine (Lond) 2022; 17:1375-1395. [PMID: 36317852 DOI: 10.2217/nnm-2021-0470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Cancer is the leading cause of mortality worldwide. Among all cancer types, lung cancer is recognized as the most lethal and highly metastatic. The application of targeted nanomedicine loaded with anticancer drugs is highly desirable for successful lung cancer treatment. However, due to the heterogenicity and complexity of lung cancer, the therapeutic effectiveness of a single receptor targeting nanomedicine is unfortunately limited. Therefore, the concept of dual-receptor-targeted nanomedicine is an emerging trend for the advancement in lung cancer therapeutics. In this review, the authors discuss various single- and dual-receptor-targeted nanomedicines that have been developed for lung cancer treatment. Furthermore, the authors also discussed all the types of receptors that can be utilized in combination for the development of dual-receptor-targeted nanomedicines.
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Affiliation(s)
- Vikas
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Hemendra Kumar Sahu
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Abhishesh Kumar Mehata
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Matte Kasi Viswanadh
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Vishnu Priya
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Madaswamy S Muthu
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, 221005, India
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Squaramide-Tethered Sulfonamides and Coumarins: Synthesis, Inhibition of Tumor-Associated CAs IX and XII and Docking Simulations. Int J Mol Sci 2022; 23:ijms23147685. [PMID: 35887037 PMCID: PMC9318203 DOI: 10.3390/ijms23147685] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: carbonic anhydrases (CAs) are attractive targets for the development of new anticancer therapies; in particular, CAs IX and XII isoforms are overexpressed in numerous tumors. (2) Methods: following the tail approach, we have appended a hydrophobic aromatic tail to a pharmacophore responsible for the CA inhibition (aryl sulfonamide, coumarin). As a linker, we have used squaramides, featured with strong hydrogen bond acceptor and donor capacities. (3) Results: Starting from easily accessible dimethyl squarate, the title compounds were successfully obtained as crystalline solids, avoiding the use of chromatographic purifications. Interesting and valuable SARs could be obtained upon modification of the length of the hydrocarbon chain, position of the sulfonamido moiety, distance of the aryl sulfonamide scaffold to the squaramide, stereoelectronic effects on the aromatic ring, as well as the number and type of substituents on C-3 and C-4 positions of the coumarin. (4) Conclusions: For sulfonamides, the best profile was achieved for the m-substituted derivative 11 (Ki = 29.4, 9.15 nM, CA IX and XII, respectively), with improved selectivity compared to acetazolamide, a standard drug. Coumarin derivatives afforded an outstanding selectivity (Ki > 10,000 nM for CA I, II); the lead compound (16c) was a strong CA IX and XII inhibitor (Ki = 19.2, 7.23 nM, respectively). Docking simulations revealed the key ligand-enzyme interactions.
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The production and biochemical characterization of α-carbonic anhydrase from Lactobacillus rhamnosus GG. Appl Microbiol Biotechnol 2022; 106:4065-4074. [PMID: 35612631 PMCID: PMC9200688 DOI: 10.1007/s00253-022-11990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022]
Abstract
Abstract
We report the production and biochemical characterization of an α-carbonic anhydrase (LrhCA) from gram-positive probiotic bacteria Lactobacillus rhamnosus GG. CAs form a family of metalloenzymes that catalyze hydration of CO2/interconversion between CO2 and water to bicarbonate ions and protons. They are divided into eight independent gene families (α, β, γ, δ, ζ, η, θ, and ι). Interestingly, many pathogens have been identified with only β- and/or γ-CAs, which can be targeted with CA-specific inhibitors (CAIs) acting as anti-pathogen drugs. Since it is important to study the potential off-target effects of CAIs for both the human body and its commensal bacteria, we took L. rhamnosus GG as our study subject. To date, only a single α-CA has been identified in L. rhamnosus GG, which was successfully produced and biochemically characterized. LrhCA showed moderate catalytic activity with the following kinetic parameters: kcat of 9.86 × 105 s−1 and kcat/KM of 1.41 × 107 s−1 M−1. Moderate inhibition was established with 11 of the 39 studied sulfonamides. The best inhibitors were 5-((4-aminophenyl)sulfonamido)-1,3,4-thiadiazole-2-sulfonamide, 4-(2-hydroxymethyl-4-nitrophenyl-sulfonamidoethyl)-benzenesulfonamide, and benzolamide with Ki values of 319 nM, 378 nM, and 387 nM, respectively. The other compounds showed weaker inhibitory effects. The Ki of acetazolamide, a classical CAI, was 733 nM. In vitro experiments with acetazolamide showed that it had no significant effect on cell growth in L. rhamnosus GG culture. Several sulfonamides, including acetazolamide, are in use as clinical drugs, making their inhibition data highly relevant to avoid any adverse off-target effects towards the human body and its probiotic organisms. Key points • The α-carbonic anhydrase from Lactobacillus rhamnosus GG (LrhCA) is 24.3 kDa. • LrhCA has significant catalytic activity with a kcat of 9.9 × 105 s-1. • Acetazolamide resulted in a marginal inhibitory effect on cell growth.
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Effect of Culture pH on Properties of Exopolymeric Substances from Synechococcus PCC7942: Implications for Carbonate Precipitation. GEOSCIENCES 2022. [DOI: 10.3390/geosciences12050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The role of culture conditions on the production of exopolymeric substances (EPS) by Synechococcus strain PCC7942 was investigated. Carbonate mineral precipitation in these EPS was assessed in forced precipitation experiments. Cultures were grown in HEPES-buffered medium and non-buffered medium. The pH of buffered medium remained constant at 7.5, but in non-buffered medium it increased to 9.5 within a day and leveled off at 10.5. The cell yield at harvest was twice as high in non-buffered medium than in buffered medium. High molecular weight (>10 kDa) and low molecular weight (3–10 kDa) fractions of EPS were obtained from both cultures. The cell-specific EPS production in buffered medium was twice as high as in non-buffered medium. EPS from non-buffered cultures contained more negatively charged macromolecules and more proteins than EPS from buffered cultures. The higher protein content at elevated pH may be due to the induction of carbon-concentrating mechanisms, necessary to perform photosynthetic carbon fixation in these conditions. Forced precipitation showed smaller calcite carbonate crystals in EPS from non-buffered medium and larger minerals in polymers from buffered medium. Vaterite formed only at low EPS concentrations. Experimental results are used to conceptually model the impact of pH on the potential of cyanobacterial blooms to produce minerals. We hypothesize that in freshwater systems, small crystal production may benefit the picoplankton by minimizing the mineral ballast, and thus prolonging the residence time in the photic zone, which might result in slow sinking rates.
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Kochoni E, Aharchaou I, Ohlund L, Rosabal M, Sleno L, Fortin C. New insights in copper handling strategies in the green alga Chlamydomonas reinhardtii under low-iron condition. Metallomics 2022; 14:6582230. [PMID: 35524697 DOI: 10.1093/mtomcs/mfac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/14/2022] [Indexed: 11/13/2022]
Abstract
Copper (Cu) is a redox-active transition element critical to various metabolic processes. These functions are accomplished in tandem with Cu binding ligands, mainly proteins. The main goal of this work was to understand the mechanisms that govern the intracellular fate of Cu in the freshwater green alga, Chlamydomonas reinhardtii, and more specifically to understand the mechanisms underlying Cu detoxification by algal cells in low-Fe conditions. We show that Cu accumulation was up to 51-fold greater for algae exposed to Cu in low-Fe medium as compared to the replete-Fe growth medium. Using the stable isotope 65Cu as a tracer, we studied the subcellular distribution of Cu within the various cell compartments of C. reinhardtii. These data were coupled with metallomic and proteomic approaches to identify potential Cu-binding ligands in the heat-stable protein and peptide fractions of the cytosol. Cu was mostly found in the organelles (78%), and in the heat-stable proteins and peptides (21%) fractions. The organelle fraction appeared to also be the main target compartment of Cu accumulation in Fe-depleted cells. As Fe levels in the medium were shown to influence Cu homeostasis, we found that C. reinhardtii can cope with this additional stress by utilizing different Cu-binding ligands. Indeed, in addition to expected Cu-binding ligands such as glutathione and phytochelatins, 25 proteins were detected that may also play a role in the Cu detoxification processes in C. reinhardtii. Our results shed new light on the coping mechanisms of C. reinhardtii when exposed to environmental conditions that induce high rates of Cu accumulation.
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Affiliation(s)
- Emeric Kochoni
- Institut national de la recherche scientifique, Centre Eau Terre Environnement, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada.,EcotoQ, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Imad Aharchaou
- Institut national de la recherche scientifique, Centre Eau Terre Environnement, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada.,EcotoQ, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Leanne Ohlund
- Département de Chimie, Université du Québec à Montréal (UQAM), 2101, rue Jeanne-Mance, Montréal, QC, H2×2J6, Canada
| | - Maikel Rosabal
- EcotoQ, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada.,Département des Sciences biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montréal, QC, H2×1Y4, Canada
| | - Lekha Sleno
- EcotoQ, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada.,Département de Chimie, Université du Québec à Montréal (UQAM), 2101, rue Jeanne-Mance, Montréal, QC, H2×2J6, Canada
| | - Claude Fortin
- Institut national de la recherche scientifique, Centre Eau Terre Environnement, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada.,EcotoQ, 490, rue de la Couronne, Québec, QC, G1K 9A9, Canada
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Genome-wide association and Mendelian randomization study of blood copper levels and 213 deep phenotypes in humans. Commun Biol 2022; 5:405. [PMID: 35501403 PMCID: PMC9061855 DOI: 10.1038/s42003-022-03351-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/10/2022] [Indexed: 11/29/2022] Open
Abstract
Metal elements are present in the human body, and their levels in the blood have important impacts on health. In this study, 2488 Chinese individuals were included in a genome-wide association study of 21 serum metal levels, with approximately 179,000 East Asian individuals in a bidirectional two-sample Mendelian randomization (MR) analysis, and 628,000 Europeans in a two-sample MR analysis. We identified two single nucleotide polymorphisms (SNPs) rs35691438 and rs671 that were significantly associated with serum copper levels (SCLs). The bidirectional two-sample MR analysis in the East Asian population showed that gamma-glutamyl transpeptidase levels have a causal effect on SCLs. SCLs have causal effects on six outcomes, namely risks of esophageal varix, glaucoma, sleep apnea syndrome, and systemic lupus erythematosus, white blood cell count, and usage of drugs affecting bone structure and mineralization. The two-sample MR analyses in the European population showed causal effects of erythrocyte copper levels on risks of carpal tunnel syndrome and compression fracture. Our results provide original insights into the causal relationship between blood metal levels and multiple human phenotypes. A genome-wide association study in a Chinese population identifies SNPs associated with serum copper levels. Mendelian randomization analysis reveals causal effects on multiple human phenotypes in East Asian and European populations.
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Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity. J Assist Reprod Genet 2022; 39:1261-1276. [PMID: 35501415 DOI: 10.1007/s10815-022-02495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/11/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The requirement of zinc for the development and maturation of germ lines and reproductive systems is deeply conserved across evolution. The nematode Caenorhabditis elegans offers a tractable platform to study the complex system of distributing zinc to the germ line. We investigated several zinc importers to investigate how zinc transporters play a role in the reproductive system in nematodes, as well as establish a platform to study zinc transporter biology in germline and reproductive development. METHODS Previous high throughput transcriptional datasets as well as phylogenetic analysis identified several putative zinc transporters that have a function in reproduction in worms. Phenotypic analysis of CRISPR-generated knockouts and tags included characterization of offspring output, gonad development, and protein localization. Light and immunofluorescence microscopy allowed for visualization of physiological and molecular effects of zinc transporter mutations. RESULTS Disruption of two zinc transporters, ZIPT-2.4 and ZIPT-15, was shown to lead to defects in reproductive output. A mutation in zipt-2.4 has subtle effects on reproduction, while a mutation in zipt-15 has a clear impact on gonad and germline development that translates into a more pronounced defect in fecundity. Both transporters have germline expression, as well as additional expression in other cell types. CONCLUSIONS Two ZIP-family zinc transporter orthologs of human ZIP6/10 and ZIP1/2/3 proteins are important for full reproductive fecundity and participate in development of the gonad. Notably, these zinc transporters are present in gut and reproductive tissues in addition to the germ line, consistent with a complex zinc trafficking network important for reproductive success.
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Wu S, Zhou Z, Zhu L, Zhong L, Dong Y, Wang G, Shi K. Cd immobilization mechanisms in a Pseudomonas strain and its application in soil Cd remediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127919. [PMID: 34894511 DOI: 10.1016/j.jhazmat.2021.127919] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/11/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
In this study, we isolated a highly cadmium (Cd)-resistant bacterium, Pseudomonas sp. B7, which immobilized 100% Cd(II) from medium. Culturing strain B7 with Cd(II) led to the change of functional groups, mediating extracellular Cd(II) adsorption. Proteomics showed that a carbonic anhydrase, CadW, was upregulated with Cd(II). CadW expression in Escherichia coli conferred resistance to Cd(II) and increased intracellular Cd(II) accumulation. Fluorescence assays demonstrated that CadW binds Cd(II) and the His123 residue affected Cd(II) binding activity, indicating that CadW participates in intracellular Cd(II) sequestration. Chinese cabbage pot experiments were performed using strain B7 and silicate [Si(IV)]. Compared with the control, Cd content in aboveground parts significantly decreased by 21.3%, 29.4% and 32.9%, and nonbioavailable Cd in soil significantly increased by 129.4%, 45.0% and 148.7% in B7, Si(IV) and B7 +Si(IV) treatments, respectively. The application of Si(IV) alone reduced chlorophyll content by 20.8% and arylsulfatase activity in soil by 33.9%, and increased malonaldehyde activity by 15.0%. The application of strain B7 alleviated the negative effect of Si(IV) on plant and soil enzymes. Overall, application of Si(IV) is most conducive to the decreased Cd accumulation in plant, and strain B7 is beneficial to maintaining soil and plant health.
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Affiliation(s)
- Shijuan Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zijie Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lin Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Limin Zhong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yixuan Dong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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Zheng Y, Yan W, Dou C, Zhou D, Chen Y, Jin Y, Yang L, Zeng X, Cheng W. Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes. MedComm (Beijing) 2022; 3:e99. [PMID: 35281791 PMCID: PMC8906456 DOI: 10.1002/mco2.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/05/2021] [Accepted: 10/20/2021] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes, a food-borne Gram-positive pathogen, often causes diseases such as gastroenteritis, bacterial sepsis, and meningitis. Newly discovered extracellular electron transfer (EET) from L. monocytogenes plays critical roles in the generation of redox molecules as electron carriers in bacteria. A Mg2+-dependent protein flavin mononucleotide (FMN) transferase (FmnB; UniProt: LMRG_02181) in EET is responsible for the transfer of electrons from intracellular to extracellular by hydrolyzing cofactor flavin adenine dinucleotide (FAD) and transferring FMN. FmnB homologs have been investigated in Gram-negative bacteria but have been less well studied in Gram-positive bacteria. In particular, the catalytic and inhibitory mechanisms of FmnB homologs remain elusive. Here, we report a series of crystal structures of apo-FmnB and FmnB complexed with substrate FAD, three inhibitors AMP, ADP, and ATP, revealing the unusual catalytic triad center (Asp301-Ser257-His273) of FmnB. The three inhibitors indeed inhibited the activity of FmnB in varying degrees by occupying the binding site of the FAD substrate. The key residue Arg262 of FmnB was profoundly affected by ADP but not AMP or ATP. Overall, our studies not only provide insights into the promiscuous ligand recognition behavior of FmnB but also shed light on its catalytic and inhibitory mechanisms.
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Affiliation(s)
- Yanhui Zheng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Weizhu Yan
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Chao Dou
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Dan Zhou
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Yunying Chen
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Ying Jin
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Lulu Yang
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Wei Cheng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
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Abstract
Zn2+ ions are essential in many physiological processes, including enzyme catalysis, protein structural stabilization, and the regulation of many proteins. The affinities of proteins for Zn2+ ions span several orders of magnitude, with catalytic Zn2+ ions generally held more tightly than structural or regulatory ones. Metal carrier proteins, most of which are not specific for Zn2+, bind these ions with a broad range of affinities that overlap those of catalytic, structural, and regulatory Zn2+ ions and are thought to be responsible for distributing the metal through most cells, tissues, and fluid compartments. While little is known about how many proteins obtain or release these ions, there is now considerable experimental evidence suggesting that metal carrier proteins may be responsible for transferring metals to and from some Zn2+-dependent proteins, thus serving as a major regulatory factor for them. In this review, the biological roles of Zn2+ and structures of Zn2+ binding sites are examined, and experimental evidence demonstrating the direct participation of metal carrier proteins in enzyme regulation is discussed. Mechanisms of metal ion transfer are also offered, and the potential physiological significance of this phenomenon is explored.
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38
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McConnell KD, Fitzkee NC, Emerson JP. Metal Ion Binding Induces Local Protein Unfolding and Destabilizes Human Carbonic Anhydrase II. Inorg Chem 2022; 61:1249-1253. [PMID: 34989562 PMCID: PMC8919859 DOI: 10.1021/acs.inorgchem.1c03271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human carbonic anhydrase II (HCA) is a robust metalloprotein and an excellent biological model system to study the thermodynamics of metal ion coordination. Apo-HCA binds one zinc ion or two copper ions. We studied these binding processes at five temperatures (15-35 °C) using isothermal titration calorimetry, yielding thermodynamic parameters corrected for pH and buffer effects. We then sought to identify binding-induced structural changes. Our data suggest that binding at the active site organizes 6-8 residues; however, copper binding near the N-terminus results in a net unfolding of 6-7 residues. This surprising destabilization was confirmed using circular dichroism and protein stability measurements. Metal binding induced unfolding may represent an important regulatory mechanism, but it may be easily missed by NMR and X-ray crystallography. Thus, in addition to highlighting a highly novel binding-induced unfolding event, we demonstrate the value of calorimetry for studying the structural implications of metal binding.
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Affiliation(s)
- Kayla D. McConnell
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Joseph P. Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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Fuentes-Aguilar A, Merino-Montiel P, Montiel-Smith S, Meza-Reyes S, Vega-Báez JL, Puerta A, Fernandes MX, Padrón JM, Petreni A, Nocentini A, Supuran CT, López Ó, Fernández-Bolaños JG. 2-Aminobenzoxazole-appended coumarins as potent and selective inhibitors of tumour-associated carbonic anhydrases. J Enzyme Inhib Med Chem 2021; 37:168-177. [PMID: 34894971 PMCID: PMC8667885 DOI: 10.1080/14756366.2021.1998026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have carried out the design, synthesis, and evaluation of a small library of 2-aminobenzoxazole-appended coumarins as novel inhibitors of tumour-related CAs IX and XII. Substituents on C-3 and/or C-4 positions of the coumarin scaffold, and on the benzoxazole moiety, together with the length of the linker connecting both units were modified to obtain useful structure-activity relationships. CA inhibition studies revealed a good selectivity towards tumour-associated CAs IX and XII (Ki within the mid-nanomolar range in most of the cases) in comparison with CAs I, II, IV, and VII (Ki > 10 µM); CA IX was found to be slightly more sensitive towards structural changes. Docking calculations suggested that the coumarin scaffold might act as a prodrug, binding to the CAs in its hydrolysed form, which is in turn obtained due to the esterase activity of CAs. An increase of the tether length and of the substituents steric hindrance was found to be detrimental to in vitro antiproliferative activities. Incorporation of a chlorine atom on C-3 of the coumarin moiety achieved the strongest antiproliferative agent, with activities within the low micromolar range for the panel of tumour cell lines tested.
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Affiliation(s)
- Alma Fuentes-Aguilar
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Penélope Merino-Montiel
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Sara Montiel-Smith
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Socorro Meza-Reyes
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - José Luis Vega-Báez
- Facultad de Ciencias Químicas, Ciudad Universitaria, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Adrián Puerta
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, La Laguna, Spain
| | - Miguel X Fernandes
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, La Laguna, Spain
| | - José M Padrón
- BioLab, Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Universidad de La Laguna, La Laguna, Spain
| | - Andrea Petreni
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence, Italy
| | - Óscar López
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Seville, Spain
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Duran-Meza E, Diaz-Espinoza R. Catalytic Amyloids as Novel Synthetic Hydrolases. Int J Mol Sci 2021; 22:ijms22179166. [PMID: 34502074 PMCID: PMC8431744 DOI: 10.3390/ijms22179166] [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: 06/29/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022] Open
Abstract
Amyloids are supramolecular assemblies composed of polypeptides stabilized by an intermolecular beta-sheet core. These misfolded conformations have been traditionally associated with pathological conditions such as Alzheimer’s and Parkinson´s diseases. However, this classical paradigm has changed in the last decade since the discovery that the amyloid state represents a universal alternative fold accessible to virtually any polypeptide chain. Moreover, recent findings have demonstrated that the amyloid fold can serve as catalytic scaffolds, creating new opportunities for the design of novel active bionanomaterials. Here, we review the latest advances in this area, with particular emphasis on the design and development of catalytic amyloids that exhibit hydrolytic activities. To date, three different types of activities have been demonstrated: esterase, phosphoesterase and di-phosphohydrolase. These artificial hydrolases emerge upon the self-assembly of small peptides into amyloids, giving rise to catalytically active surfaces. The highly stable nature of the amyloid fold can provide an attractive alternative for the design of future synthetic hydrolases with diverse applications in the industry, such as the in situ decontamination of xenobiotics.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile
- Correspondence:
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Shamna I, Kwan Jeong S, Margandan B. Covalent immobilization of carbonic anhydrase on amine functionalized alumino-Siloxane aerogel beads for biomimetic sequestration of CO2. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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42
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Tsikas D, Gambaryan S. Nitrous anhydrase activity of carbonic anhydrase II: cysteine is required for nitric oxide (NO) dependent phosphorylation of VASP in human platelets. J Enzyme Inhib Med Chem 2021; 36:525-534. [PMID: 33508993 PMCID: PMC7875556 DOI: 10.1080/14756366.2021.1874946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The carbonic anhydrase (CA) family does not only catalyse the reversible hydration of CO2 to bicarbonate, but it also possesses esterase and phosphatase activity. Recently, bovine CA II and human CA II have been reported to convert inorganic nitrite (O=N-O−) to nitric oxide (NO) and nitrous anhydride (N2O3). Given the ability of NO to mediate vasodilation and inhibit platelet aggregation, this CA II activity would represent a bioactivation of nitrite. There are contradictory reports in the literature and the physiological role of CA II nitrite bioactivation is still disputed. Here, we provide new experimental data in support of the nitrous anhydrase activity of CA II and the key role L-cysteine in the bioactivation of nitrite by CA II. Using washed human platelets and by measuring VASP phosphorylation we provide evidence that exogenous nitrite (10 µM) is bioactivated to NO in a manner strongly depending on L-cysteine (100 and 200 µM). The process is not inhibitable by acetazolamide, a potent CA inhibitor. The contradictory results of recently published studies in this area are thoroughly discussed.
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Affiliation(s)
- Dimitrios Tsikas
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Stepan Gambaryan
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Petersburg, Russia
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43
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Voigt O, Fradusco B, Gut C, Kevrekidis C, Vargas S, Wörheide G. Carbonic Anhydrases: An Ancient Tool in Calcareous Sponge Biomineralization. Front Genet 2021; 12:624533. [PMID: 33897759 PMCID: PMC8058475 DOI: 10.3389/fgene.2021.624533] [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: 10/31/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Enzymes of the α-carbonic anhydrase gene family (CAs) are essential for the deposition of calcium carbonate biominerals. In calcareous sponges (phylum Porifera, class Calcarea), specific CAs are involved in the formation of calcite spicules, a unique trait and synapomorphy of this class. However, detailed studies on the CA repertoire of calcareous sponges exist for only two species of one of the two Calcarea subclasses, the Calcaronea. The CA repertoire of the second subclass, the Calcinea, has not been investigated so far, leaving a considerable gap in our knowledge about this gene family in Calcarea. Here, using transcriptomic analysis, phylogenetics, and in situ hybridization, we study the CA repertoire of four additional species of calcareous sponges, including three from the previously unsampled subclass Calcinea. Our data indicate that the last common ancestor of Calcarea had four ancestral CAs with defined subcellular localizations and functions (mitochondrial/cytosolic, membrane-bound, and secreted non-catalytic). The evolution of membrane-bound and secreted CAs involved gene duplications and losses, whereas mitochondrial/cytosolic and non-catalytic CAs are evidently orthologous genes. Mitochondrial/cytosolic CAs are biomineralization-specific genes recruited for biomineralization in the last common ancestor of calcareous sponges. The spatial-temporal expression of these CAs differs between species, which may reflect differences between subclasses or be related to the secondary thickening of spicules during biomineralization that does not occur in all species. With this study, we extend the understanding of the role and the evolution of a key biomineralization gene in calcareous sponges.
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Affiliation(s)
- Oliver Voigt
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Benedetta Fradusco
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carolin Gut
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Charalampos Kevrekidis
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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44
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Tsikas D. Comment on the article Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase. IUCRJ 2021; 8:327-328. [PMID: 33708408 PMCID: PMC7924222 DOI: 10.1107/s2052252520016644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/23/2020] [Indexed: 05/15/2023]
Abstract
The paper discusses a recent paper [Andring et al. (2020). IUCrJ, 7, 287-293] on the nitrite reductase and nitrous anhydrase activity of carbonic anhydrase.
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Affiliation(s)
- Dimitrios Tsikas
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany
- Correspondence e-mail:
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45
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Nagao S, Idomoto A, Shibata N, Higuchi Y, Hirota S. Rational design of metal-binding sites in domain-swapped myoglobin dimers. J Inorg Biochem 2021; 217:111374. [PMID: 33578251 DOI: 10.1016/j.jinorgbio.2021.111374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The metal active site is precisely designed in metalloproteins. Here we applied 3D domain swapping, a phenomenon in which a partial protein structure is exchanged between molecules, to introduce metal sites in proteins. We designed multiple metal-binding sites specific to domain-swapped myoglobin (Mb) with His mutation. Stable dimeric Mbs with metal-binding sites were obtained by shifting the His position and introducing two Ala residues in the hinge region (K78H/G80A/H82A and K79H/G80A/H81A Mbs). The absorption and circular dichroism spectra of the monomer and dimer of K78H/G80A/H82A and K79H/G80A/H81A Mbs were similar to the corresponding spectra, respectively, of wild-type Mb. No negative peak due to dimer-to-monomer dissociation was observed below the denaturation temperature in the differential scanning calorimetry thermograms of K78H/G80A/H82A and K79H/G80A/H81A Mbs, whereas the dimer dissociates into monomers at 68 °C for wild-type Mb. These results show that the two mutants were stable in the dimer state. Metal ions bound to the metal-binding sites containing the introduced His in the domain-swapped Mb dimers. Co2+-bound and Ni2+-bound K78H/G80A/H82A Mb exhibited octahedral metal-coordination structures, where His78, His81, Glu85, and three H2O/OH- molecules coordinated to the metal ion. On the other hand, Co2+-bound and Zn2+-bound K79H/G80A/H81A Mb exhibited tetrahedral metal-coordination structures, where His79, His82, Asp141, and a H2O/OH- molecule coordinated to the metal ion. The Co2+-bound site exists deep inside the protein in the K79H/G80A/H81A Mb dimer, which may allow the unique tetrahedral coordination for the Co2+ ion. These results show that we can utilize domain swapping to construct artificial metalloproteins.
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Affiliation(s)
- Satoshi Nagao
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Ayaka Idomoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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46
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Adhikari A, Park WW, Kwon OH. Hydrogen-Bond Dynamics and Energetics of Biological Water. Chempluschem 2020; 85:2657-2665. [PMID: 33305536 DOI: 10.1002/cplu.202000744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/26/2020] [Indexed: 11/11/2022]
Abstract
Water molecules in the immediate vicinity of biomacromolecules and biomimetic organized assemblies often exhibit a markedly distinct behavior from that of their bulk counterparts. The overall sluggish behavior of biological water substantially affects the stability and integrity of biomolecules, as well as the successful execution of various crucial water-mediated biochemical phenomena. In this Minireview, insights are provided into the features of truncated hydrogen-bond networks that grant biological water its unique characteristics. In particular, experimental results and theoretical investigations, based on chemical kinetics, are presented that have shed light on the dynamics and energetics governing such characteristics. It is emphasized how such details help us to understand the energetics of biological water, an aspect relatively less explored than its dynamics. For instance, when biological water at hydrophilic or charged protein surfaces was explored, the free energy of H-bond breakage was found to be of the order of 0.4 kcal mol-1 higher than that of bulk water.
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Affiliation(s)
- Aniruddha Adhikari
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.,Department of Physics, UNIST, 44919, Ulsan, Republic of Korea
| | - Won-Woo Park
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
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