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Koper K, Han SW, Kothadia R, Salamon H, Yoshikuni Y, Maeda HA. Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proc Natl Acad Sci U S A 2024; 121:e2405524121. [PMID: 38885378 PMCID: PMC11214133 DOI: 10.1073/pnas.2405524121] [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: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism, essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here, we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread nonorthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterization of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multisubstrate specificity by employing different nonconserved active site residues. These findings illustrate that AT family enzymes had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multifunctional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Sang-Woo Han
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Biotechnology, Konkuk University, Chungju27478, South Korea
| | - Ramani Kothadia
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Hugh Salamon
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan 060-8589
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo183-8538, Japan
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
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Tripathi A, Dubey KD. The mechanistic insights into different aspects of promiscuity in metalloenzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:23-66. [PMID: 38960476 DOI: 10.1016/bs.apcsb.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.
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Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India.
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Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM. Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. SCIENCE ADVANCES 2024; 10:eadk7283. [PMID: 38728392 PMCID: PMC11086599 DOI: 10.1126/sciadv.adk7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]
Abstract
Cyanobacterial CO2 concentrating mechanisms (CCMs) sequester a globally consequential proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in α-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present a structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium sp. PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial α-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.
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Affiliation(s)
- Sacha B. Pulsford
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan A. Outram
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Timothy Rhodes
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simon J. Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Murray R. Badger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - G. Dean Price
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Colin J. Jackson
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Benedict M. Long
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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4
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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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Supuran CT. Drug interactions of carbonic anhydrase inhibitors and activators. Expert Opin Drug Metab Toxicol 2024; 20:143-155. [PMID: 38450431 DOI: 10.1080/17425255.2024.2328152] [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: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
INTRODUCTION Carbonic anhydrases (CAs, EC 4.2.1.1) have been established drug targets for decades, with their inhibitors and activators possessing relevant pharmacological activity and applications in various fields. At least 11 sulfonamides/sulfamates are clinically used as diuretics, antiglaucoma, antiepileptic, or antiobesity agents and one derivative, SLC-0111, is in clinical trials as antitumor/antimetastatic agent. The activators were less investigated with no clinically used agent. AREAS COVERED Drug interactions between CA inhibitors/activators and various other agents are reviewed in publications from the period March 2020 - January 2024. EXPERT OPINION Drug interactions involving these agents revealed several interesting findings. Acetazolamide plus loop diuretics is highy effective in acute decompensated heart failure, whereas ocular diseases such as X-linked retinoschisis and macular edema were treated by acetazolamide plus bevacizumab or topical NSAIDs. Potent anti-infective effects of acetazolamide and other CAIs, alone or in combination with other agents were demonstrated for the management of Neisseria gonorrhoea, vancomycin resistant enterococci, Acanthamoeba castellanii, Trichinella spiralis, and Cryptococcus neoformans infections. Topiramate, in combination with phentermine is incresingly used for the management of obesity, whereas zonisamide plus levodopa is highly effective for Parkinson's disease. Acetazolamide, methazolamide, ethoxzolamide, and SLC-0111 showed synergistic antitumor/antimetastatic action in combination with many other antitumor drugs.
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Affiliation(s)
- Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, FI, Italy
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Scott KM, Payne RR, Gahramanova A. Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways. Appl Environ Microbiol 2024; 90:e0155723. [PMID: 38299815 PMCID: PMC10880623 DOI: 10.1128/aem.01557-23] [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] [Indexed: 02/02/2024] Open
Abstract
Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
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Affiliation(s)
- Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Ren R. Payne
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Arin Gahramanova
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
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Iizuka R, Hattori S, Kosaka Y, Masaki Y, Kawano Y, Ohtsu I, Hibbett D, Katayama Y, Yoshida M. Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum. Appl Environ Microbiol 2024; 90:e0201523. [PMID: 38299812 PMCID: PMC10880591 DOI: 10.1128/aem.02015-23] [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: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is clade D of the β-class carbonic anhydrase subfamily enzyme with high specificity for COS but low activity for CO2 hydration, showed that the COSase is involved in COS assimilation. Comparison of sulfur metabolites of strain THIF08 revealed a higher relative abundance of reduced sulfur compounds under the COS-supplemented condition than the sulfate-supplemented condition, suggesting that sulfur assimilation is more energetically efficient with COS than with sulfate because there is no redox change of sulfur. Phylogenetic analysis of the genes encoding COSase, which are distributed in a wide range of fungal taxa, suggests that the common ancestor of Ascomycota, Basidiomycota, and Mucoromycota acquired COSase at about 790-670 Ma.IMPORTANCEThe biological assimilation of gaseous CO2 and N2 involves essential processes known as carbon fixation and nitrogen fixation, respectively. In this study, we found that the fungus Trichoderma harzianum strain THIF08 can grow with gaseous carbonyl sulfide (COS), the most abundant and ubiquitous gaseous sulfur compound, as a sulfur source. When the fungus grew in these conditions, COS was assimilated into sulfur metabolites, and the key enzyme of this assimilation process is COS hydrolase (COSase), which specifically degrades COS. Moreover, the pathway was more energy efficient than the typical sulfate assimilation pathway. COSase genes are widely distributed in Ascomycota, Basidiomycota, and Mucoromycota and also occur in some Chytridiomycota, indicating that COS assimilation is widespread in fungi. Phylogenetic analysis of these genes revealed that the acquisition of COSase in filamentous fungi was estimated to have occurred at about 790-670 Ma, around the time that filamentous fungi transitioned to a terrestrial environment.
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Affiliation(s)
- Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shohei Hattori
- International Center for Isotope Effects Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu, China
| | - Yusuke Kosaka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yusuke Kawano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - Iwao Ohtsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Euglena Co., Ltd., Minato‑ku, Tokyo, Japan
| | - David Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties, Taito-ku, Tokyo, Japan
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Shalileh F, Gheibzadeh MS, Lloyd JR, Fietz S, Shahbani Zahiri H, Zolfaghari Emameh R. Evolutionary analysis and quality assessment of ζ-carbonic anhydrase sequences from environmental microbiome. J Basic Microbiol 2023; 63:1412-1425. [PMID: 37670218 DOI: 10.1002/jobm.202300323] [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: 06/10/2023] [Revised: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023]
Abstract
Carbonic anhydrase (CA) is one of the most vital enzymes in living cells. This study has been performed due to the significance of this metalloenzyme for life and the novelty of some CA families like ζ-CA to evaluate evolutionary processes and quality check their sequences. In this study, bioinformatics methods revealed the presence of ζ-CA in some eukaryotic and prokaryotic microorganisms. Notably, it has not been previously reported in prokaryotes. The coexistence of β- and ζ-CAs in some microorganisms is also a novel finding as well. Also, our analysis identified several CA proteins with 6-14 amino acid intervals between histidine and cysteine in the second highly conserved motif, which can be classified as the novel ζ-CA subfamily members that emerged under the Zn deficiency of aquatic ecosystems and selection pressure in these environments. There is also a possibility that the achieved results are rooted in the contamination of samples from the environmental microbiome genome with genomes of diatom species and the occurrence of errors was observed in the DNA sequencing outcomes. Combining of all results from evolutionary analysis to quality control of ζ-CA DNA sequences is the incentive motivation to explore more the hidden aspects of ζ-CAs.
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Affiliation(s)
- Farzaneh Shalileh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mohammad S Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - James R Lloyd
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Susanne Fietz
- Department of Earth Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Plotniece A, Sobolev A, Supuran CT, Carta F, Björkling F, Franzyk H, Yli-Kauhaluoma J, Augustyns K, Cos P, De Vooght L, Govaerts M, Aizawa J, Tammela P, Žalubovskis R. Selected strategies to fight pathogenic bacteria. J Enzyme Inhib Med Chem 2023; 38:2155816. [PMID: 36629427 PMCID: PMC9848314 DOI: 10.1080/14756366.2022.2155816] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised in vitro and in vivo models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems.
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Affiliation(s)
- Aiva Plotniece
- Latvian Institute of Organic Synthesis, Riga, Latvia,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Riga Stradiņš University, Riga, Latvia,CONTACT Aiva Plotniece Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Carta
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Koen Augustyns
- Infla-Med, Centre of Excellence, University of Antwerp, Antwerp, Belgium,Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Juliana Aizawa
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia,Faculty of Materials Science and Applied Chemistry, Institute of Technology of Organic Chemistry, Riga Technical University, Riga, Latvia
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10
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Supuran CT. Carbonic anhydrase versatility: from pH regulation to CO 2 sensing and metabolism. Front Mol Biosci 2023; 10:1326633. [PMID: 38028557 PMCID: PMC10676200 DOI: 10.3389/fmolb.2023.1326633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
While the carbonic anhydrase (CA, EC 4.2.1.1) superfamily of enzymes has been described primarily as involved only in pH regulation for decades, it also has many other important functions. CO2, bicarbonate, and protons, the physiological substrates of CA, are indeed the main buffering system in organisms belonging to all life kingdoms; however, in the last period, relevant progress has been made in the direction of elucidating the involvement of the eight genetically distinct CA families in chemical sensing, metabolism, and several other crucial physiological processes. Interference with CA activity, both by inhibiting and activating these enzymes, has thus led to novel applications for CA inhibitors and activators in the field of innovative biomedicine and environment and health. In this perspective article, I will discuss the recent advances which have allowed for a deeper understanding of the biochemistry of these versatile enzymes and various applications of their modulators of activity.
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Affiliation(s)
- Claudiu T. Supuran
- Neurofarba Department, Section of Pharmaceutical Sciences, University of Florence, Florence, Italy
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11
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Supuran CT. Targeting carbonic anhydrases for the management of hypoxic metastatic tumors. Expert Opin Ther Pat 2023; 33:701-720. [PMID: 37545058 DOI: 10.1080/13543776.2023.2245971] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
INTRODUCTION Several isoforms of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) are connected with tumorigenesis. Hypoxic tumors overexpress CA IX and XII as a consequence of HIF activation cascade, being involved in pH regulation, metabolism, and metastases formation. Other isoforms (CA I, II, III, IV) were also reported to be present in some tumors. AREAS COVERED Some CA isoforms are biomarkers for disease progression or response to therapy. Inhibitors, antibodies, and other procedures for targeting these enzymes for the treatment of tumors/metastases are discussed. Sulfonamides and coumarins represent the most investigated classes of inhibitors, but carboxylates, selenium, and tellurium-containing inhibitors were also investigated. Hybrid drugs of CA inhibitors with other antitumor agents for multitargeted therapy were reported. EXPERT OPINION Targeting CAs present in solid or hematological tumors with selective, targeted inhibitors is a validated approach, which has been consolidated in the last years. A host of new preclinical data and several clinical trials of antibodies and small-molecule inhibitors are ongoing, which connected with the large number of new chemotypes/procedures discovered to be effective, may lead to a breakthrough in this therapeutic area. The scientific/patent literature has been searched for on PubMed, ScienceDirect, Espacenet, and PatentGuru, from 2018 to 2023.
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Affiliation(s)
- Claudiu T Supuran
- Department of NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Firenze, Italy
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12
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Zhang F, Chen F, Zhong M, Shen R, Zhao Z, Wei H, Zhang B, Fang J. Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe. Anal Chem 2023; 95:14833-14841. [PMID: 37747928 DOI: 10.1021/acs.analchem.3c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Fan Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Ruipeng Shen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Zhengjia Zhao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Haopai Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu 210094, China
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13
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Supuran CT. A simple yet multifaceted 90 years old, evergreen enzyme: Carbonic anhydrase, its inhibition and activation. Bioorg Med Chem Lett 2023; 93:129411. [PMID: 37507055 DOI: 10.1016/j.bmcl.2023.129411] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Advances in the carbonic anhydrase (CA, EC 4.2.1.1) research over the last three decades are presented, with an emphasis on the deciphering of the activation mechanism, the development of isoform-selective inhibitors/ activators by the tail approach and their applications in the management of obesity, hypoxic tumors, neurological conditions, and as antiinfectives.
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Affiliation(s)
- Claudiu T Supuran
- Neurofarba Department, University of Florence, Section of Pharmaceutical Sciences, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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14
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Jiao M, He W, Ouyang Z, Qin Q, Guo Y, Zhang J, Bai Y, Guo X, Yu Q, She J, Hwang PM, Zheng F, Wen Y. Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii. Structure 2023; 31:935-947.e4. [PMID: 37329879 DOI: 10.1016/j.str.2023.05.015] [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: 12/01/2022] [Revised: 03/28/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
PaaY is a thioesterase that enables toxic metabolites to be degraded through the bacterial phenylacetic acid (PA) pathway. The Acinetobacter baumannii gene FQU82_01591 encodes PaaY, which we demonstrate to possess γ-carbonic anhydrase activity in addition to thioesterase activity. The crystal structure of AbPaaY in complex with bicarbonate reveals a homotrimer with a canonical γ-carbonic anhydrase active site. Thioesterase activity assays demonstrate a preference for lauroyl-CoA as a substrate. The AbPaaY trimer structure shows a unique domain-swapped C-termini, which increases the stability of the enzyme in vitro and decreases its susceptibility to proteolysis in vivo. The domain-swapped C-termini impact thioesterase substrate specificity and enzyme efficacy without affecting carbonic anhydrase activity. AbPaaY knockout reduced the growth of Acinetobacter in media containing PA, decreased biofilm formation, and impaired hydrogen peroxide resistance. Collectively, AbPaaY is a bifunctional enzyme that plays a key role in the metabolism, growth, and stress response mechanisms of A. baumannii.
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Affiliation(s)
- Min Jiao
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Wenbo He
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhenlin Ouyang
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qian Qin
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yucheng Guo
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jiaxin Zhang
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yixin Bai
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaolong Guo
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qinyue Yu
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Junjun She
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Peter M Hwang
- Departments of Medicine and Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Fang Zheng
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yurong Wen
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China; The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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15
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Degiacomi G, Gianibbi B, Recchia D, Stelitano G, Truglio GI, Marra P, Stamilla A, Makarov V, Chiarelli LR, Manetti F, Pasca MR. CanB, a Druggable Cellular Target in Mycobacterium tuberculosis. ACS OMEGA 2023; 8:25209-25220. [PMID: 37483251 PMCID: PMC10357428 DOI: 10.1021/acsomega.3c02311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023]
Abstract
Treatment against tuberculosis can lead to the selection of drug-resistant Mycobacterium tuberculosis strains. To tackle this serious threat, new targets from M. tuberculosis are needed to develop novel effective drugs. In this work, we aimed to provide a possible workflow to validate new targets and inhibitors by combining genetic, in silico, and enzymological approaches. CanB is one of the three M. tuberculosis β-carbonic anhydrases that catalyze the reversible reaction of CO2 hydration to form HCO3- and H+. To this end, we precisely demonstrated that CanB is essential for the survival of the pathogen in vitro by constructing conditional mutants. In addition, to search for CanB inhibitors, conditional canB mutants were also constructed using the Pip-ON system. By molecular docking and minimum inhibitory concentration assays, we selected three molecules that inhibit the growth in vitro of M. tuberculosis wild-type strain and canB conditional mutants, thus implementing a target-to-drug approach. The lead compound also showed a bactericidal activity by the time-killing assay. We further studied the interactions of these molecules with CanB using enzymatic assays and differential scanning fluorimetry thermal shift analysis. In conclusion, the compounds identified by the in silico screening proved to have a high affinity as CanB ligands endowed with antitubercular activity.
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Affiliation(s)
- Giulia Degiacomi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Beatrice Gianibbi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Deborah Recchia
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Giovanni Stelitano
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | | | - Paola Marra
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Alessandro Stamilla
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Vadim Makarov
- Bakh
Institute of Biochemistry, Russian Academy
of Science, Moscow 119071, Russia
| | - Laurent Robert Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Fabrizio Manetti
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
- Fondazione
IRCCS Policlinico San Matteo, Pavia 27100, Italy
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16
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Supuran CT. An overview of novel antimicrobial carbonic anhydrase inhibitors. Expert Opin Ther Targets 2023; 27:897-910. [PMID: 37747071 DOI: 10.1080/14728222.2023.2263914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/24/2023] [Indexed: 09/26/2023]
Abstract
INTRODUCTION Four different genetic families of the enzyme carbonic anhydrase (CA, EC 4.2.1.1) are present in bacteria, α-, β-, γ- and ι-CAs. They play relevant functions related to CO2, HCO3-/H+ ions homeostasis, being involved in metabolic biosynthetic pathways, pH regulation, and represent virulence and survival factors for bacteria in various niches. Bacterial CAs started to be considered druggable targets in the last decade, as their inhibition impairs survival, growth, and virulence of these pathogens. AREAS COVERED Significant advances were registered in the last years for designing effective inhibitors of sulfonamide type for Helicobacter pylori α-CA, Neisseria gonorrhoeae α-CA, vacomycin-resistant enterococci (VRE) α- and γ-CAs, for which the in vivo validation has also been achieved. MIC-s in the range of 0.25-4.0 µg/mL for wild type and drug resistant N. gonorrhoeae strains, and of 0.007-2.0 µg/mL for VRE were observed for some 1,3,4-thiadiazole-2-sulfonamides, and acetazolamide was effective in gut decolonization from VRE. EXPERT OPINION Targeting bacterial CAs from other pathogens, among which Vibrio cholerae, Mycobacterium tuberculosis, Brucella suis, Salmonella enterica serovar Typhimurium, Legionella pneumophila, Porphyromonas gingivalis, Clostridium perfringens, Streptococcus mutans, Burkholderia pseudomallei, Francisella tularensis, Escherichia coli, Mammaliicoccus (Staphylococcus) sciuri, Pseudomonas aeruginosa, may lead to novel antibacterials devoid of drug resistance problems.
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Affiliation(s)
- Claudiu T Supuran
- Department of NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Firenze, Italy
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17
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Ujiié Y, Ishitani Y, Nagai Y, Takaki Y, Toyofuku T, Ishii S. Unique evolution of foraminiferal calcification to survive global changes. SCIENCE ADVANCES 2023; 9:eadd3584. [PMID: 37343099 DOI: 10.1126/sciadv.add3584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Foraminifera, the most ancient known calcium carbonate-producing eukaryotes, are crucial players in global biogeochemical cycles and well-used environmental indicators in biogeosciences. However, little is known about their calcification mechanisms. This impedes understanding the organismal responses to ocean acidification, which alters marine calcium carbonate production, potentially leading to biogeochemical cycle changes. We conducted comparative single-cell transcriptomics and fluorescent microscopy and identified calcium ion (Ca2+) transport/secretion genes and α-carbonic anhydrases that control calcification in a foraminifer. They actively take up Ca2+ to boost mitochondrial adenosine triphosphate synthesis during calcification but need to pump excess intracellular Ca2+ to the calcification site to prevent cell death. Unique α-carbonic anhydrase genes induce the generation of bicarbonate and proton from multiple CO2 sources. These control mechanisms have evolved independently since the Precambrian to enable the development of large cells and calcification despite decreasing Ca2+ concentrations and pH in seawater. The present findings provide previously unknown insights into the calcification mechanisms and their subsequent function in enduring ocean acidification.
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Affiliation(s)
- Yurika Ujiié
- Marine Core Research Institute, Kochi University, Kōchi, Japan
| | - Yoshiyuki Ishitani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukiko Nagai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- National Museum of Nature and Science, Tokyo, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Toyofuku
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Tokyo University of Marine Science and Technology (TUMSAT), Tokyo, Japan
| | - Shun'ichi Ishii
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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18
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Tyne RL, Barry PH, Lawson M, Lloyd KG, Giovannelli D, Summers ZM, Ballentine CJ. Identifying and Understanding Microbial Methanogenesis in CO 2 Storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37327355 DOI: 10.1021/acs.est.2c08652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.
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Affiliation(s)
- R L Tyne
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - P H Barry
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | | | - K G Lloyd
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - D Giovannelli
- University of Naples Federico II, Naples 80138 Italy
| | - Z M Summers
- LanzaTech, Skokie, Illinois 60077, United States
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19
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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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20
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Chen G, Gao X, Zhang Y, Ma C, Ma W, Zhou Z. The carboxypeptidase B and carbonic anhydrase genes play a reproductive regulatory role during multiple matings in Ophraella communa. Front Mol Biosci 2023; 10:1095645. [PMID: 37266330 PMCID: PMC10229896 DOI: 10.3389/fmolb.2023.1095645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Seminal fluid proteins (SFPs) are key factors in sexual reproduction and are transferred to females during mating with sperm. SFPs have a nutritional value because they protect and activate sperm storage and release to optimize fecundity. Multiple matings promote ovipositioning in several insect species. Therefore, insects may obtain more SFP through multiple matings to maximize reproduction, but this process has not yet been clearly confirmed. Here, the relationship between multiple matings and the SFPs in Ophraella communa (Coleoptera: Chrysomelidae), a biological control agent of the common ragweed Ambrosia artemisiifolia (Asterales: Asteraceae), was studied. Multiple matings significantly increased female fecundity and ovary egg deposition. Carboxypeptidase B (OcCpb) and carbonic anhydrase (OcCa) genes were identified as putative SFP genes in O. communa and they showed strong male-biased expression. Additionally, OcCpb and OcCa expression was upregulated in the bursa copulatrix of mating females compared to that in virgin females, but their expression gradually declined after copulation. Furthermore, OcCpb and OcCa knockdown in males led to a decrease in insect fecundity compared to that in the control. The reproductive tract of females mated with dsRNA-treated males was dissected and observed and, notably, the ovaries produced significantly fewer eggs. These data suggest that OcCpb and OcCa play regulatory roles during multiple matings in O. communa.
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Affiliation(s)
- Guangmei Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Xuyuan Gao
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Chao Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Weihua Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhongshi Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
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21
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Karahan ZC, Altinsoy İ, Çalişkan BN, Dede S, Kayiş G, Türkoğlu HC, Evren E, Doğanay Erdoğan B, Kiliç SG, Dolapçi İ, Tekeli A. Investigation of the presence of Capnophilic bacteria in routine urine cultures. Eur J Clin Microbiol Infect Dis 2023; 42:519-524. [PMID: 36811709 DOI: 10.1007/s10096-023-04570-4] [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: 06/19/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
Capnophilic Escherichia coli (CEC) strains are rarely isolated from urinary tract infections (UTIs). The purpose of this research was to look into the incidence and traits of the CEC strains that cause UTIs. Nine (0.11%) epidemiologically unrelated CEC isolates with varying antibiotic susceptibility patterns were identified from patients with various co-morbidities after the evaluation of 8500 urine samples. Three of these strains belonged to the O25b-ST131 clone, and none of them possessed the yadF gene. Due to adverse incubation conditions, CEC isolation is difficult. Although rare, capnophilic incubation of urine cultures may be considered particularly for patients with underlying predisposing conditions.
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Affiliation(s)
- Zeynep Ceren Karahan
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey.
- Central Microbiology Laboratory, Ibn-I Sina Hospital, Ankara University School of Medicine, Ankara, Turkey.
| | - İrem Altinsoy
- Ankara University School of Medicine, Ankara, Turkey
| | | | - Sıla Dede
- Ankara University School of Medicine, Ankara, Turkey
| | - Görkem Kayiş
- Ankara University School of Medicine, Ankara, Turkey
| | | | - Ebru Evren
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
- Central Microbiology Laboratory, Ibn-I Sina Hospital, Ankara University School of Medicine, Ankara, Turkey
| | | | - Selin Gamze Kiliç
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - İştar Dolapçi
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - Alper Tekeli
- Department of Medical Microbiology, Ankara University School of Medicine, Ankara, Turkey
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22
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Pyrrolyl and Indolyl α-γ-Diketo Acid Derivatives Acting as Selective Inhibitors of Human Carbonic Anhydrases IX and XII. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Solid tumors are active tissues containing hypoxic regions and producing metabolic acids. By decreasing pH, cancer cells create a hostile environment for surrounding host cells and foster tumor growth and progression. By governing acid/base regulation, carbonic anhydrases (CAs) are involved in several physiological/pathological processes, including tumors. Indeed, CAs are clinically relevant in cancer therapy as among the fifteen human isoforms, two of them, namely CA IX (overexpressed in solid tumors and associated with increased metastasis and poor prognosis) and CA XII (overexpressed in some tumors) are involved in tumorigenesis. Targeting these two isoforms is considered as a pertinent approach to develop new cancer therapeutics. Several CA inhibitors (CAIs) have been described, even though they are unselective inhibitors of different isoforms. Thus, efforts are needed to find new selective CAIs. In this work, we described new diketo acid derivatives as CAIs, with the best acting compounds 1c and 5 as nanomolar inhibitors of CA IX and XII, being also two orders of magnitude selective over CAs I and II. Molecular modeling studies showed the different binding poses of the best acting CAIs within CA II and IX, highlighting the key structural features that could confer the ability to establish specific interactions within the enzymes. In different tumor cell lines overexpressing CA IX and XII, the tested compounds showed antiproliferative activity already at 24 h treatment, with no effects on somatic not transformed cells.
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23
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Krueger LA, Koester LR, Jones DF, Spangler DA. Carbon dioxide equivalent emissions from corn silage fermentation. Front Microbiol 2023; 13:1092315. [PMID: 36699579 PMCID: PMC9869070 DOI: 10.3389/fmicb.2022.1092315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
The European Climate Law recently codified the goal for European climate neutrality by 2050, highlighting the need for sustainable farming practices within a robust and transparent carbon dioxide equivalent (CO2e) accounting system. In the present study, a series of equations were proposed for the estimation of CO2e emissions from corn silage fermentation. Systematic review of previous meta-analyses of corn silage fermentation identified the mean and standard deviation statistics for key model inputs of acetic acid, ethanol, lactic acid, ammonia, and volatile-corrected dry matter loss. Estimates of CO2e emissions were determined for a mock dataset comprising 1,000 iterations of randomly-generated values for each metric in accordance with mean and variance statistics of the source data. Estimates for CO2e emissions of corn silage based on meta-analysis review of laboratory experiments were 1.9 ± 5.6% (GWP20) and 0.2 ± 5.5% (GWP100) of silage dry matter. Furthermore, model results demonstrated a precedent for CO2 recycling by silage microorganisms, which was supported by genome annotation of strains belonging to common silage species. Linear model equations for GWP20 and GWP100 with inputs and outputs in mg kg-1 silage dry matter were developed, where inputs are acetic acid (A), ethanol (E), lactic acid (L), and volatile corrected dry matter loss (DV). Linear equations are (for GWP20; Eq. 11): GWP 20 = - 3626.1 - 0.04343 A + 0.8011 E - 0.03173 L + 1.46573 D V and for GWP100; Eq. 12: GWP 100 = - 8526.10 - 0.22403 A - 0.11963 E - 0.03173 L + 1.46573 D V . .
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Affiliation(s)
- Lucas A Krueger
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - Lucas R Koester
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - David F Jones
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
| | - David A Spangler
- Department of Research, Development, and Biotechnology, Agri-King, Inc., Fulton, IL, United States
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Abstract
Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form-i.e., lacking a single gene-cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3-, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.
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Naranjo D. A scenario for the origin of life: Volume regulation by bacteriorhodopsin required extremely voltage sensitive Na‐channels and very selective K‐channels. Bioessays 2022; 44:e2100210. [DOI: 10.1002/bies.202100210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/25/2022]
Affiliation(s)
- David Naranjo
- Instituto de Neurociencia, Facultad de Ciencias Universidad de Valparaíso Playa Ancha Valparaíso Chile
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26
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de Oliveira Maciel A, Christakopoulos P, Rova U, Antonopoulou I. Carbonic anhydrase to boost CO 2 sequestration: Improving carbon capture utilization and storage (CCUS). CHEMOSPHERE 2022; 299:134419. [PMID: 35364080 DOI: 10.1016/j.chemosphere.2022.134419] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
CO2 Capture Utilization and Storage (CCUS) is a fundamental strategy to mitigate climate change, and carbon sequestration, through absorption, can be one of the solutions to achieving this goal. In nature, carbonic anhydrase (CA) catalyzes the CO2 hydration to bicarbonates. Targeting the development of novel biotechnological routes which can compete with traditional CO2 absorption methods, CA utilization has presented a potential to expand as a promising catalyst for CCUS applications. Driven by this feature, the search for novel CAs as biocatalysts and the utilization of enzyme improvement techniques, such as protein engineering and immobilization methods, has resulted in suitable variants able to catalyze CO2 absorption at relevant industrial conditions. Limitations related to enzyme recovery and recyclability are still a concern in the field, affecting cost efficiency. Under different absorption approaches, CA enhances both kinetics and CO2 absorption yields, besides reduced energy consumption. However, efforts directed to process optimization and demonstrative plants are still limited. A recent topic with great potential for development is the CA utilization in accelerated weathering, where industrial residues could be re-purposed towards becoming carbon sequestrating agents. Furthermore, research of new solvents has identified potential candidates for integration with CA in CO2 capture, and through techno-economic assessments, CA can be a path to increase the competitiveness of alternative CO2 absorption systems, offering lower environmental costs. This review provides a favorable scenario combining the enzyme and CO2 capture, with possibilities in reaching an industrial-like stage in the future.
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Affiliation(s)
- Ayanne de Oliveira Maciel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Io Antonopoulou
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden.
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27
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Steger F, Reich J, Fuchs W, Rittmann SKMR, Gübitz GM, Ribitsch D, Bochmann G. Comparison of Carbonic Anhydrases for CO 2 Sequestration. Int J Mol Sci 2022; 23:957. [PMID: 35055147 PMCID: PMC8777876 DOI: 10.3390/ijms23020957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Strategies for depleting carbon dioxide (CO2) from flue gases are urgently needed and carbonic anhydrases (CAs) can contribute to solving this problem. They catalyze the hydration of CO2 in aqueous solutions and therefore capture the CO2. However, the harsh conditions due to varying process temperatures are limiting factors for the application of enzymes. The current study aims to examine four recombinantly produced CAs from different organisms, namely CAs from Acetobacterium woodii (AwCA or CynT), Persephonella marina (PmCA), Methanobacterium thermoautotrophicum (MtaCA or Cab) and Sulphurihydrogenibium yellowstonense (SspCA). The highest expression yields and activities were found for AwCA (1814 WAU mg-1 AwCA) and PmCA (1748 WAU mg-1 PmCA). AwCA was highly stable in a mesophilic temperature range, whereas PmCA proved to be exceptionally thermostable. Our results indicate the potential to utilize CAs from anaerobic microorganisms to develop CO2 sequestration applications.
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Affiliation(s)
- Franziska Steger
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Johanna Reich
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Werner Fuchs
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Georg M Gübitz
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Günther Bochmann
- Institute of Environmental Biotechnology, Department for Agrobiotechnology, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, A-3430 Tulln, Austria
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Giovannuzzi S, Hewitt CS, Nocentini A, Capasso C, Flaherty DP, Supuran CT. Coumarins effectively inhibit bacterial α-carbonic anhydrases. J Enzyme Inhib Med Chem 2022; 37:333-338. [PMID: 34979838 PMCID: PMC8741243 DOI: 10.1080/14756366.2021.2012174] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Coumarins are known to act as prodrug inhibitors of mammalian α-carbonic anhydrases (CAs, EC 4.2.1.1) but they were not yet investigated for the inhibition of bacterial α-CAs. Here we demonstrate that such enzymes from the bacterial pathogens Neisseria gonorrhoeae (NgCAα) and Vibrio cholerae (VchCAα) are inhibited by a panel of simple coumarins incorporating hydroxyl, amino, ketone or carboxylic acid ester moieties in various positions of the ring system. The nature and the position of the substituents in the coumarin ring were the factors which strongly influenced inhibitory efficacy. NgCAα was inhibited with KIs in the range of 28.6-469.5 µM, whereas VchCAα with KIs in the range of 39.8-438.7 µM. The two human (h)CA isoforms included for comparison reason in the study, hCA I and II, were less prone to inhibition by these compounds, with KIs of 137-948.9 µM for hCA I and of 296.5-961.2 µM for hCA II, respectively. These findings are relevant for discovering coumarin bacterial CA inhibitors with selectivity for the bacterial over human isoform, with potential applications as novel antibacterial agents.
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Affiliation(s)
- Simone Giovannuzzi
- Pharmaceutical and Nutraceutical Section, Neurofarba Department, University of Florence, Florence, Italy
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Alessio Nocentini
- Pharmaceutical and Nutraceutical Section, Neurofarba Department, University of Florence, Florence, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| | - Claudiu T Supuran
- Pharmaceutical and Nutraceutical Section, Neurofarba Department, University of Florence, Florence, Italy
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29
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Vincent J, Colin B, Lanneluc I, Sabot R, Sopéna V, Turcry P, Mahieux PY, Refait P, Jeannin M, Sablé S. New Biocalcifying Marine Bacterial Strains Isolated from Calcareous Deposits and Immediate Surroundings. Microorganisms 2021; 10:76. [PMID: 35056526 PMCID: PMC8778039 DOI: 10.3390/microorganisms10010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 12/28/2021] [Indexed: 12/04/2022] Open
Abstract
Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.
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Affiliation(s)
- Julia Vincent
- Laboratoire Littoral Environnement et Sociétés, La Rochelle Université, UMR 7266 CNRS, 17000 La Rochelle, France; (J.V.); (B.C.); (I.L.); (V.S.)
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Béatrice Colin
- Laboratoire Littoral Environnement et Sociétés, La Rochelle Université, UMR 7266 CNRS, 17000 La Rochelle, France; (J.V.); (B.C.); (I.L.); (V.S.)
| | - Isabelle Lanneluc
- Laboratoire Littoral Environnement et Sociétés, La Rochelle Université, UMR 7266 CNRS, 17000 La Rochelle, France; (J.V.); (B.C.); (I.L.); (V.S.)
| | - René Sabot
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Valérie Sopéna
- Laboratoire Littoral Environnement et Sociétés, La Rochelle Université, UMR 7266 CNRS, 17000 La Rochelle, France; (J.V.); (B.C.); (I.L.); (V.S.)
| | - Philippe Turcry
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Pierre-Yves Mahieux
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Philippe Refait
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Marc Jeannin
- Laboratoire des Sciences de l’Ingénieur pour l’Environnement, La Rochelle Université, UMR 7356 CNRS, 17000 La Rochelle, France; (R.S.); (P.T.); (P.-Y.M.); (P.R.)
| | - Sophie Sablé
- Laboratoire Littoral Environnement et Sociétés, La Rochelle Université, UMR 7266 CNRS, 17000 La Rochelle, France; (J.V.); (B.C.); (I.L.); (V.S.)
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30
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Giovannuzzi S, Abutaleb NS, Hewitt CS, Carta F, Nocentini A, Seleem MN, Flaherty DP, Supuran CT. Dithiocarbamates effectively inhibit the α-carbonic anhydrase from Neisseria gonorrhoeae. J Enzyme Inhib Med Chem 2021; 37:1-8. [PMID: 34894954 PMCID: PMC8667944 DOI: 10.1080/14756366.2021.1988945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recently, inorganic anions and sulphonamides, two of the main classes of zinc-binding carbonic anhydrase inhibitors (CAIs), were investigated for inhibition of the α-class carbonic anhydrase (CA, EC 4.2.1.1) from Neisseria gonorrhoeae, NgCA. As an extension to our previous studies, we report that dithiocarbamates (DTCs) derived from primary or secondary amines constitute a class of efficient inhibitors of NgCA. KIs ranging between 83.7 and 827 nM were measured for a series of 31 DTCs that incorporated various aliphatic, aromatic, and heterocyclic scaffolds. A subset of DTCs were selected for antimicrobial testing against N. gonorrhoeae, and three molecules displayed minimum inhibitory concentration (MIC) values less than or equal to 8 µg/mL. As NgCA was recently validated as an antibacterial drug target, the DTCs may lead to development of novel antigonococcal agents.
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Affiliation(s)
- Simone Giovannuzzi
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Center for Emerging Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
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Staphylococcus aureus Genomes Harbor Only MpsAB-Like Bicarbonate Transporter but Not Carbonic Anhydrase as Dissolved Inorganic Carbon Supply System. Microbiol Spectr 2021; 9:e0097021. [PMID: 34730408 PMCID: PMC8567241 DOI: 10.1128/spectrum.00970-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In recent years, it became apparent that not only autotrophic but also most other bacteria require CO2 or bicarbonate for growth. Two systems are available for the acquisition of dissolved inorganic carbon supply (DICS): the cytoplasmic localized carbonic anhydrase (CA) and the more recently described bicarbonate transporter MpsAB (membrane potential generating system). In the pathogenic species Staphylococcus aureus, there are contradictions in the literature regarding the presence of a CA or MpsAB. Here, we address these contradictions in detail. We could demonstrate by careful BLASTp analyses with 259 finished and 4,590 unfinished S. aureus genomes that S. aureus does not contain CA and that the bicarbonate transporter MpsAB is the only DICS system in this species. This finding is further supported by two further pieces of evidence: (i) mpsAB deletion mutants in four different S. aureus strains failed to grow under atmospheric air, which should not be the case if they possess CAs, since we have previously shown that both CA and MpsAB can substitute for each other, and (ii) S. aureus is completely resistant to CA inhibitors, whereas Staphylococcus carnosus, which has been shown to have only CA, was inhibited by ethoxyzolamide (EZA). Taken together, we demonstrate beyond doubt that the species S. aureus possesses only the bicarbonate transporter MpsAB as its sole DICS system. IMPORTANCE The discrepancies in the current literature and even in NCBI database, which listed some protein sequences annotated as Staphylococcus aureus carbonic anhydrase (CA), are misleading. One of the existing problems in publicly available sequence databases is the presence of incorrectly annotated genes, especially if they originated from unfinished genomes. Here, we demonstrate that some of these unfinished genomes are of poor quality and should be interpreted with caution. In the present study, we aimed to address these discrepancies and correct the current literature about S. aureus CA, considering the medical relevance of S. aureus. If left unchecked, these misleading studies and wrongly annotated genes might lead to a continual propagation of wrong annotation and, consequently, wrong interpretations and wasted time. In addition, we also show that bicarbonate transporter MpsAB-harboring bacteria are resistant to CA inhibitor, suggesting that pathogens possessing both MpsAB and CA are not treatable with CA inhibitors.
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32
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Berrino E, Michelet B, Martin‐Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emanuela Berrino
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Bastien Michelet
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Agnès Martin‐Mingot
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Fabrizio Carta
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Claudiu T. Supuran
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Sébastien Thibaudeau
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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34
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Manzoor S, Petreni A, Raza MK, Supuran CT, Hoda N. Novel triazole-sulfonamide bearing pyrimidine moieties with carbonic anhydrase inhibitory action: Design, synthesis, computational and enzyme inhibition studies. Bioorg Med Chem Lett 2021; 48:128249. [PMID: 34237441 DOI: 10.1016/j.bmcl.2021.128249] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/26/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
A series of new triazole-sulfonamide bearing pyrimidine derivatives were designed and synthesized via click chemistry. All new compounds (SH-1 to SH-28) were validated by 1HNMR, 13CNMR, HRMS, and SH-3 was further structurally validated by X-Ray single diffraction study. These compounds (SH-1 to SH-28) were tested as inhibitors of human carbonic anhydrase (hCA) isoforms, such as hCA I, II, IX and XII, using a stopped flow CO2 hydrase assay. Most of the compounds exhibited significant inhibitory activity against hCA II and weak inhibitory activity against hCA I. The target compounds also displayed moderate to excellent inhibitory activity against tumor-related hCAs IX and XII. Some compounds, e.g., SH-20 (Ki = 9.4 nM), SH-26 (Ki = 1.8 nM) and SH-28 (Ki = 0.82 nM) exhibited excellent inhibitory activity and selectivity profile against hCAs XII over IX. SH-23 displayed promising inhibitory activity and selectivity profile against both tumor-related hCAs IX (Ki = 2.9 nM) as well as XII (Ki = 0.82 nM) over hCA I and II. To understand the molecular interactions, molecular docking study of compounds SH-20, SH-23, SH-26 and SH-28 with hCA XII and SH-23 also with hCA IX were performed. The computational study evidenced favorable interaction between the inhibitors and active residues of both proteins. Some of these derivatives are promising leads for the development of selective, anticancer agents based on CA inhibitors.
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Affiliation(s)
- Shoaib Manzoor
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
| | - Andrea Petreni
- University of Florence, Department of Neuroscience Psychology, Drug Research and Child's Health, Section of Pharmaceutical and Nutraceutical Sciences, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Md Kausar Raza
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Claudiu T Supuran
- University of Florence, Department of Neuroscience Psychology, Drug Research and Child's Health, Section of Pharmaceutical and Nutraceutical Sciences, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
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35
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Masaki Y, Iizuka R, Kato H, Kojima Y, Ogawa T, Yoshida M, Matsushita Y, Katayama Y. Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases. Microbes Environ 2021; 36. [PMID: 34024869 PMCID: PMC8209446 DOI: 10.1264/jsme2.me20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbonyl sulfide (COS) is the most abundant and long-lived sulfur-containing gas in the atmosphere. Soil is the main sink of COS in the atmosphere and uptake is dominated by soil microorganisms; however, biochemical research has not yet been conducted on fungal COS degradation. COS hydrolase (COSase) was purified from Trichoderma harzianum strain THIF08, which degrades COS at concentrations higher than 10,000 parts per million by volume from atmospheric concentrations, and its gene cos (492 bp) was cloned. The recombinant protein purified from Escherichia coli expressing the cos gene converted COS to H2S. The deduced amino acid sequence of COSase (163 amino acids) was assigned to clade D in the phylogenetic tree of the β-carbonic anhydrase (β-CA) family, to which prokaryotic COSase and its structurally related enzymes belong. However, the COSase of strain THIF08 differed from the previously known prokaryotic COSase and its related enzymes due to its low reactivity to CO2 and inability to hydrolyze CS2. Sequence comparisons of the active site amino acids of clade D β-CA family enzymes suggested that various Ascomycota, particularly Sordariomycetes and Eurotiomycetes, possess similar enzymes to the COSase of strain THIF08 with >80% identity. These fungal COSase were phylogenetically distant to prokaryotic clade D β-CA family enzymes. These results suggest that various ascomycetes containing COSase contribute to the uptake of COS by soil.
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Affiliation(s)
- Yoshihito Masaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Ryuka Iizuka
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University
| | - Yuka Kojima
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Makoto Yoshida
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | | | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties
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36
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Urbanski LJ, Vullo D, Parkkila S, Supuran CT. An anion and small molecule inhibition study of the β-carbonic anhydrase from Staphylococcus aureus. J Enzyme Inhib Med Chem 2021; 36:1088-1092. [PMID: 34056990 PMCID: PMC8168783 DOI: 10.1080/14756366.2021.1931863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pathogenic bacteria resistant to most antibiotics, including the methicillin-resistant Staphylococcus aureus (MRSA) represent a serious medical problem. The search for new antiinfectives, possessing a diverse mechanism of action compared to the clinically used antibiotics, has become an attractive research field. S. aureus DNA encodes a β-class carbonic anhydrase, SauBCA. It is a druggable target that can be inhibited by certain aromatic and heterocyclic sulphonamides. Here we investigated inorganic anions and some other small molecules for their inhibition of SauBCA. The halides, nitrite, nitrate, bicarbonate, carbonate, bisulphite, sulphate, stannate, and N,N-diethyldithiocarbamate were submillimolar SauBCA inhibitors with KIs in the range of 0.26 − 0.91 mM. The most effective inhibitors were sulfamide, sulfamate, phenylboronic acid, and phenylarsonic acid with KIs of 7 − 43 µM. Several interesting inhibitors detected here may be considered lead compounds for the development of even more effective derivatives, which should be investigated for their bacteriostatic effects.
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Affiliation(s)
- Linda J Urbanski
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Daniela Vullo
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| | - Claudiu T Supuran
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy
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37
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Nocentini A, Hewitt CS, Mastrolorenzo MD, Flaherty DP, Supuran CT. Anion inhibition studies of the α-carbonic anhydrases from Neisseria gonorrhoeae. J Enzyme Inhib Med Chem 2021; 36:1061-1066. [PMID: 34030562 PMCID: PMC8158254 DOI: 10.1080/14756366.2021.1929202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The bacterial pathogen Neisseria gonorrhoeae encodes for an α-class carbonic anhydrase (CA, EC 4.2.1.1), NgCA, which was investigated for its inhibition with a series of inorganic and organic anions. Perchlorate and hexafluorophosphate did not significantly inhibit NgCA CO2 hydrase activity, whereas the halides, azide, bicarbonate, carbonate, stannate, perosmate, diphosphate, divanadate, perruthenate, and trifluoromethanesulfonate showed inhibition constants in the range of 1.3–9.6 mM. Anions/small molecules such as cyanate, thiocyanate, nitrite, nitrate, bisulphite, sulphate, hydrogensulfide, phenylboronic acid, phenylarsonic acid, selenate, tellurate, tetraborate, perrhenate, peroxydisulfate, selenocyanate, iminodisulfonate, and fluorosulfonate showed KIs in the range of 0.15–1.0 mM. The most effective inhibitors detected in this study were sulfamide, sulfamate, trithiocarbonate and N,N-diethyldithiocarbamate, which had KIs in the range of 5.1–88 µM. These last compounds incorporating the CS2- zinc-binding group may be used as leads for developing even more effective NgCA inhibitors in addition to the aromatic/heterocyclic sulphonamides, as this enzyme was recently validated as an antibacterial drug target for obtaining novel antigonococcal agents
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Affiliation(s)
- Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Margaret D Mastrolorenzo
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,University of California, San Diego (UCSD), San Diego, CA, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
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38
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Berrino E, Michelet B, Martin-Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021; 60:23068-23082. [PMID: 34028153 DOI: 10.1002/anie.202103211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/19/2021] [Indexed: 12/19/2022]
Abstract
The insertion of fluorine atoms and/or fluoroalkyl groups can lead to many beneficial effects in biologically active molecules, such as enhanced metabolic stability, bioavailability, lipophilicity, and membrane permeability, as well as a strengthening of protein-ligand binding interactions. However, this "magic effect" of fluorine atom(s) insertion can often be meaningless. Taking advantage of the wide range of data coming from the quest for carbonic anhydrase (CA) fluorinated inhibitors, this Minireview attempts to give "general guidelines" on how to wisely insert fluorine atom(s) within an inhibitor moiety to precisely enhance or disrupt ligand-protein interactions, depending on the target location of the fluorine substitution in the ligand. Multiple approaches such as ITC, kinetic and inhibition studies, X-ray crystallography, and NMR spectroscopy are useful in dissecting single binding contributions to the overall observed effect. The exploitation of innovative directions made in the field of protein and ligand-based fluorine NMR screening is also discussed to avoid misconduct and finely tune the exploitation of selective fluorine atom insertion in the future.
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Affiliation(s)
- Emanuela Berrino
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Bastien Michelet
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Agnès Martin-Mingot
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Sébastien Thibaudeau
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
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39
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Immobilization of carbonic anhydrase for CO2 capture and its industrial implementation: A review. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101475] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Kumar S, Deshpande PA. Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA. PLoS One 2021; 16:e0249866. [PMID: 33857217 PMCID: PMC8049272 DOI: 10.1371/journal.pone.0249866] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 01/23/2023] Open
Abstract
Molecular basis of protein stability at different temperatures is a fundamental problem in protein science that is substantially far from being accurately and quantitatively solved as it requires an explicit knowledge of the temperature dependence of folding free energy of amino acid residues. In the present study, we attempted to gain insights into the thermodynamic stability of SazCA and its implications on protein folding/unfolding. We report molecular dynamics simulations of water solvated SazCA in a temperature range of 293-393 K to study the relationship between the thermostability and flexibility. Our structural analysis shows that the protein maintains the highest structural stability at 353 K and the protein conformations are highly flexible at temperatures above 353 K. Larger exposure of hydrophobic surface residues to the solvent medium for conformations beyond 353 K were identified from H-bond analysis. Higher number of secondary structure contents exhibited by SazCA at 353 K corroborated the conformations at 353 K to exhibit the highest thermal stability. The analysis of thermodynamics of protein stability revealed that the conformations that denature at higher melting temperatures tend to have greater maximum thermal stability. Our analysis shows that 353 K conformations have the highest melting temperature, which was found to be close to the experimental optimum temperature. The enhanced protein stability at 353 K due the least value of heat capacity at unfolding suggested an increase in folding. Comparative Gibbs free energy analysis and funnel shaped energy landscape confirmed a transition in folding/unfolding pathway of SazCA at 353 K.
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Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
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41
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Abutaleb NS, Elhassanny AEM, Flaherty DP, Seleem MN. In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci. PeerJ 2021; 9:e11059. [PMID: 33850651 PMCID: PMC8018244 DOI: 10.7717/peerj.11059] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log10 (99.9%) and 3.86-log10 (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log10 (98.2%) reduction) and ileal contents (1.5-log10 (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.
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Affiliation(s)
- Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States of America
| | - Ahmed E M Elhassanny
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, United States of America.,Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States of America
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42
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Kim S, Yeon J, Sung J, Kim NJ, Hong S, Jin MS. Structural insights into novel mechanisms of inhibition of the major β-carbonic anhydrase CafB from the pathogenic fungus Aspergillus fumigatus. J Struct Biol 2021; 213:107700. [PMID: 33545350 DOI: 10.1016/j.jsb.2021.107700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 01/04/2023]
Abstract
In fungi the β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes that are essential for growth, survival, differentiation, and virulence. Aspergillus fumigatus is the most important pathogen responsible for invasive aspergillosis and possesses two major β-CAs, CafA and CafB. Recently we reported the biochemical characterization and 1.8 Å crystal structure of CafA. Here, we report a crystallographic analysis of CafB revealing the mechanism of enzyme catalysis and establish the relationship of this enzyme to other β-CAs. While CafA has a typical open conformation, CafB, when exposed to acidic pH and/or an oxidative environment, has a novel type of active site in which a disulfide bond is formed between two zinc-ligating cysteines, expelling the zinc ion and stabilizing the inactive form of the enzyme. Based on the structural data, we generated an oxidation-resistant mutant (Y159A) of CafB. The crystal structure of the mutant under reducing conditions retains a catalytic zinc at the expected position, tetrahedrally coordinated by three residues (C57, H113 and C116) and an aspartic acid (D59), and replacing the zinc-bound water molecule in the closed form. Furthermore, the active site of CafB crystals grown under zinc-limiting conditions has a novel conformation in which the solvent-exposed catalytic cysteine (C116) is flipped out of the metal coordination sphere, facilitating release of the zinc ion. Taken together, our results suggest that A. fumigatus use sophisticated activity-inhibiting strategies to enhance its survival during infection.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jungyoon Yeon
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jongmin Sung
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Na Jin Kim
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Semi Hong
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.
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43
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Ghorab MM, Soliman AM, Bua S, Supuran CT. Biological evaluation, radiosensitizing activity and structural insights of novel halogenated quinazoline-sulfonamide conjugates as selective human carbonic anhydrases IX/XII inhibitors. Bioorg Chem 2021; 107:104618. [PMID: 33485104 DOI: 10.1016/j.bioorg.2020.104618] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/23/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022]
Abstract
A library of iodoquinazolinones endowed with benzenesulfonamide moiety was designed and synthesized as human carbonic anhydrase (hCA) inhibitors. Compounds 4-17 showed generally poor activity against the cytosolic hCA I and hCA II isoforms. Contrarily they were more potent and showed a variable spectrum of selectivity against the tumor-specific isoforms hCA IX and hCA XII. The 4-iodophenyl derivative 12 and the 4-pyridinyl derivative 15 were the most active and selective in this series against hCA IX and hCA XII isoforms with KI of 18 and 9 nM, respectively. Compounds 12 and 15 were further screened for their cytotoxicity against MCF-7, HepG-2 and HCT-116 cancer cell lines besides WI38 and MCF-10A normal cell lines to determine their selectivity towards cancer cells. Compound 12 was selective towards HepG-2 and HCT-116 cell lines but less selective towards MCF-7. While compound 15 showed higher selectivity towards HepG-2 than HCT-116 and MCF-7 cell lines. The ability of compounds 12 and 15 to sensitize the cells against gamma irradiation's effect proved their potential radiosensitizing activity. Molecular docking analysis was carried out to discover the possible binding mode of the compounds within the active site of isoform hCA IX and XII. Compounds 12 and 15 revealed the probable fundamental interactions explaining the good activity and selectivity towards the tumor-specific isoforms.
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Affiliation(s)
- Mostafa M Ghorab
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), P.O Box 29, Nasr City, Cairo 11765, Egypt.
| | - Aiten M Soliman
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), P.O Box 29, Nasr City, Cairo 11765, Egypt
| | - Silvia Bua
- University of Florence, NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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44
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Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman. Appl Environ Microbiol 2021; 87:AEM.02068-20. [PMID: 33127818 DOI: 10.1128/aem.02068-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization.IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4 Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth's history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4 These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.
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45
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Kato H, Ogawa T, Ohta H, Katayama Y. Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method. Microbes Environ 2020; 35. [PMID: 32350165 PMCID: PMC7308577 DOI: 10.1264/jsme2.me19139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent approaches, such as the most probable number (MPN) method, because of the chemical hydrolysis of COS by water. We herein developed a two-step MPN method for COS-degrading microorganisms: the first step for chemoorganotrophic growth that supported a sufficient number of cells for COS degradation in the second step. Our new MPN analysis of various environmental samples revealed that the cell density of COS-degrading microorganisms in forest soils ranged between 106 and 108 MPN (g dry soil)–1, which was markedly higher than those in volcanic deposit and water samples, and strongly correlated with the rate of COS degradation in environmental samples. Numerically dominant COS degraders that were isolated from the MPN-positive culture were related to bacteria in the orders Bacillales and Actinomycetales. The present results provide numerical evidence for the ubiquity of COS-degrading microbes in natural environments.
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Affiliation(s)
- Hiromi Kato
- Graduate School of Life Sciences, Tohoku University
| | - Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Present address: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology.,Independent Administrative Institution, Tokyo National Research Institute for Cultural Properties
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46
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Angeli A, Prete SD, Ghobril C, Hitce J, Clavaud C, Marrat X, Donald WA, Capasso C, Supuran CT. Activation studies of the β-carbonic anhydrases from Malassezia restricta with amines and amino acids. J Enzyme Inhib Med Chem 2020; 35:824-830. [PMID: 32216477 PMCID: PMC7170391 DOI: 10.1080/14756366.2020.1743284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023] Open
Abstract
The β-carbonic anhydrase (CA, EC 4.2.1.1) from the genome of the opportunistic pathogen Malassezia restricta (MreCA), which was recently cloned and characterised, herein has been investigated for enzymatic activation by a panel of amines and amino acids. Of the 24 compounds tested in this study, the most effective MreCA activators were L-adrenaline (KA of 15 nM), 2-aminoethyl-piperazine/morpholine (KAs of 0.25-0.33 µM), histamine, L-4-amino-phenylalanine, D-Phe, L-/D-DOPA, and L-/D-Trp (KAs of 0.32 - 0.90 µM). The least effective activators were L-/D-Tyr, L-Asp, L-/D-Glu, and L-His, with activation constants ranging between 4.04 and 12.8 µM. As MreCA is involved in dandruff and seborrhoeic dermatitis, these results are of interest to identify modulators of the activity of enzymes involved in the metabolic processes of such fungi.
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Affiliation(s)
- Andrea Angeli
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Sonia Del Prete
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | | | - Julien Hitce
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Cécile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Xavier Marrat
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
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47
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Kim S, Yeon J, Sung J, Jin MS. Crystal Structure of β-Carbonic Anhydrase CafA from the Fungal Pathogen Aspergillus fumigatus. Mol Cells 2020; 43:831-840. [PMID: 32975213 PMCID: PMC7528686 DOI: 10.14348/molcells.2020.0168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 01/07/2023] Open
Abstract
The β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes widely distributed in the fungal kingdom that play essential roles in growth, survival, differentiation, and virulence by catalyzing the reversible interconversion of carbon dioxide (CO2) and bicarbonate (HCO3-). Herein, we report the biochemical and crystallographic characterization of the β-CA CafA from the fungal pathogen Aspergillus fumigatus, the main causative agent of invasive aspergillosis. CafA exhibited apparent in vitro CO2 hydration activity in neutral to weak alkaline conditions, but little activity at acidic pH. The high-resolution crystal structure of CafA revealed a tetramer comprising a dimer of dimers, in which the catalytic zinc ion is tetrahedrally coordinated by three conserved residues (C119, H175, C178) and an acetate anion presumably acquired from the crystallization solution, indicating a freely accessible ″open″ conformation. Furthermore, knowledge of the structure of CafA in complex with the potent inhibitor acetazolamide, together with its functional intolerance of nitrate (NO3-) ions, could be exploited to develop new antifungal agents for the treatment of invasive aspergillosis.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jungyoon Yeon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jongmin Sung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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Kaur J, Cao X, Abutaleb NS, Elkashif A, Graboski AL, Krabill AD, AbdelKhalek AH, An W, Bhardwaj A, Seleem MN, Flaherty DP. Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus. J Med Chem 2020; 63:9540-9562. [PMID: 32787141 DOI: 10.1021/acs.jmedchem.0c00734] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Vancomycin-resistant enterococci (VRE) are the second leading cause of hospital-acquired infections (HAIs) attributed to a drug-resistant bacterium in the United States, and resistance to the frontline treatments is well documented. To combat VRE, we have repurposed the FDA-approved carbonic anhydrase drug acetazolamide to design potent antienterococcal agents. Through structure-activity relationship optimization we have arrived at two leads possessing improved potency against clinical VRE strains from MIC = 2 μg/mL (acetazolamide) to MIC = 0.007 μg/mL (22) and 1 μg/mL (26). Physicochemical properties were modified to design leads that have either high oral bioavailability to treat systemic infections or low intestinal permeability to treat VRE infections in the gastrointestinal tract. Our data suggest the intracellular targets for the molecules are putative α-carbonic and γ-carbonic anhydrases, and homology modeling and molecular dynamics simulations were performed. Together, this study presents potential anti-VRE therapeutic options to provide alternatives for problematic VRE infections.
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Affiliation(s)
- Jatinder Kaur
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Nader S Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Ahmed Elkashif
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Amanda L Graboski
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Ahmed Hassan AbdelKhalek
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States
| | - Weiwei An
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Atul Bhardwaj
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, United States.,Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute of Inflammation, Immunology and Infectious Disease, 207 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, Indiana 47907, United States.,Purdue Institute of Inflammation, Immunology and Infectious Disease, 207 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
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49
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Moi D, Nocentini A, Deplano A, Osman SM, AlOthman ZA, Piras V, Balboni G, Supuran CT, Onnis V. Appliance of the piperidinyl-hydrazidoureido linker to benzenesulfonamide compounds: Synthesis, in vitro and in silico evaluation of potent carbonic anhydrase II, IX and XII inhibitors. Bioorg Chem 2020; 98:103728. [PMID: 32182519 DOI: 10.1016/j.bioorg.2020.103728] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/10/2023]
Abstract
Herein we report on a new series of hydrazidoureidobenzensulfonamides investigated as inhibitors of the cytosolic human (h) hCA I and II isoforms, as well as the transmembrane, tumor-associated enzymes hCA IX and XII. The reported derivatives contain a 4-substituted piperidine fragment in which the hydrazidoureido linker has been involved as spacer between the benzenesulfonamide fragment which binds the zinc ion from the active site, and the tail of the inhibitor. Depending on the substitution pattern at the piperidine ring, low nanomolar inhibitors were detected against hCA II, hCA IX and hCA XII, making the new class of sulfonamides of interest for various pharmacologic applications.
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Affiliation(s)
- Davide Moi
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato (CA), Italy
| | - Alessio Nocentini
- Department NEUROFARBA - Pharmaceutical and Nutraceutical Section, University of Firenze, via Ugo Schiff 6, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Alessandro Deplano
- Pharmacelera, Placa Pau Vila, 1, Sector 1, Edificio Palau de Mar, Barcelona 08039, Spain
| | - Sameh M Osman
- Chemistry Department, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Zeid A AlOthman
- Chemistry Department, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Valentina Piras
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato (CA), Italy
| | - Gianfranco Balboni
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato (CA), Italy
| | - Claudiu T Supuran
- Department NEUROFARBA - Pharmaceutical and Nutraceutical Section, University of Firenze, via Ugo Schiff 6, I-50019 Sesto Fiorentino, Firenze, Italy.
| | - Valentina Onnis
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato (CA), Italy.
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50
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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