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Khatun S, Dasgupta I, Sen S, Amin SA, Qureshi IA, Jha T, Gayen S. Histone deacetylase 8 in focus: Decoding structural prerequisites for innovative epigenetic intervention beyond hydroxamates. Int J Biol Macromol 2025; 284:138119. [PMID: 39608552 DOI: 10.1016/j.ijbiomac.2024.138119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 11/21/2024] [Accepted: 11/25/2024] [Indexed: 11/30/2024]
Abstract
Histone deacetylase 8 (HDAC8) inhibitors play a pivotal role in epigenetic regulation. Numerous HDAC8 inhibitors (HDAC8is), that are non-hydroxamates have been identified to date, and a few of them exhibit antiproliferative activity that is on par with hydroxamates. While many non-hydroxamate-based HDAC8is have demonstrated selectivity, hydroxamate-based HDAC8is, like Vorinostat and TSA, have a tendency of non-specificity among the different HDAC isoforms. Moreover, because of the unfavorable toxic side effects, there are significant concerns surrounding the use of hydroxamate derivatives as therapeutic agents in cancer as well as other chronic diseases. Consequently, the research on non-hydroxamate-based HDAC8is is of utmost priority. In the present study, a comprehensive study was presented to unravel the structural requirements of non-hydroxamate-based HDAC8is from a diverse set of 866 compounds. The study utilized Classification-based Quantitative Structure-Activity Relationship (QSAR) analysis, incorporating Bayesian classification, Recursive partitioning, and other machine learning methods to pinpoint the key structural features essential for HDAC8 inhibition. To underscore and gain deeper insights into the identified structural features, molecular docking, and molecular dynamic (MD) simulation studies were conducted. The integration of these computational approaches unveiled key structural motifs essential for potent HDAC8 inhibitory activity, shedding light on the molecular basis of HDAC8 inhibition using non-hydroxamates.
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Affiliation(s)
- Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Indrasis Dasgupta
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Sourish Sen
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India; Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Tarun Jha
- Natural Science Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India.
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Capdevila DA, Rondón JJ, Edmonds KA, Rocchio JS, Dujovne MV, Giedroc DP. Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking. Chem Rev 2024. [PMID: 39658019 DOI: 10.1021/acs.chemrev.4c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
Abstract
Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.
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Affiliation(s)
- Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - Johnma J Rondón
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Joseph S Rocchio
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Matias Villarruel Dujovne
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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Basit A, Choudhury D, Bandyopadhyay P. Prediction of Ca 2+ Binding Site in Proteins With a Fast and Accurate Method Based on Statistical Mechanics and Analysis of Crystal Structures. Proteins 2024. [PMID: 39258438 DOI: 10.1002/prot.26743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/12/2024]
Abstract
Predicting the precise locations of metal binding sites within metalloproteins is a crucial challenge in biophysics. A fast, accurate, and interpretable computational prediction method can complement the experimental studies. In the current work, we have developed a method to predict the location of Ca2+ ions in calcium-binding proteins using a physics-based method with an all-atom description of the proteins, which is substantially faster than the molecular dynamics simulation-based methods with accuracy as good as data-driven approaches. Our methodology uses the three-dimensional reference interaction site model (3D-RISM), a statistical mechanical theory, to calculate Ca2+ ion density around protein structures, and the locations of the Ca2+ ions are obtained from the density. We have taken previously used datasets to assess the efficacy of our method as compared to previous works. Our accuracy is 88%, comparable with the FEATURE program, one of the well-known data-driven methods. Moreover, our method is physical, and the reasons for failures can be ascertained in most cases. We have thoroughly examined the failed cases using different structural and crystallographic measures, such as B-factor, R-factor, electron density map, and geometry at the binding site. It has been found that x-ray structures have issues in many of the failed cases, such as geometric irregularities and dubious assignment of ion positions. Our algorithm, along with the checks for structural accuracy, is a major step in predicting calcium ion positions in metalloproteins.
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Affiliation(s)
- Abdul Basit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Dixit H, Upadhyay V, Kulharia M, Verma SK. The Study of Metalloproteome of DNA Viruses: Identification, Functional Annotation, and Diversity Analysis of Viral Metal-Binding Proteins. J Proteome Res 2024; 23:4014-4026. [PMID: 39134029 DOI: 10.1021/acs.jproteome.4c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Metalloproteins are fundamental to diverse biological processes but still lack extensive investigation in viral contexts. This study reveals the prevalence and functional diversity of metal-binding proteins in DNA viruses. Among a subset of 1432 metalloproteins, zinc and magnesium-binding proteins are notably abundant, indicating their importance in viral biology. Furthermore, significant numbers of proteins binding to iron, manganese, copper, nickel, mercury, and cadmium were also detected. Human-infecting viral proteins displayed a rich landscape of metalloproteins, with MeBiPred (964 proteins) and Pfam (666) yielding the highest numbers. Interestingly, many essential viral proteins exhibited metal-binding capabilities, including polymerases, DNA binding proteins, helicases, dUPTase, thymidine kinase, and various structural and accessory proteins. This study sheds light on the ubiquitous presence of metalloproteins, their functional signatures, subcellular placements, and metal-utilization patterns, providing valuable insights into viral biology. A similar metal utilization pattern was observed in similar functional proteins across the various DNA viruses. Furthermore, these findings provide a foundation for identifying potential drug targets for combating viral infections.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
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Kushwah AS, Dixit H, Upadhyay V, Verma SK, Prasad R. The study of iron- and copper-binding proteome of Fusarium oxysporum and its effector candidates. Proteins 2024; 92:1097-1112. [PMID: 38666709 DOI: 10.1002/prot.26696] [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: 07/05/2023] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Fusarium oxysporum f.sp. lycopersici is a phytopathogen which causes vascular wilt disease in tomato plants. The survival tactics of both pathogens and hosts depend on intricate interactions between host plants and pathogenic microbes. Iron-binding proteins (IBPs) and copper-binding proteins (CBPs) play a crucial role in these interactions by participating in enzyme reactions, virulence, metabolism, and transport processes. We employed high-throughput computational tools at the sequence and structural levels to investigate the IBPs and CBPs of F. oxysporum. A total of 124 IBPs and 37 CBPs were identified in the proteome of Fusarium. The ranking of amino acids based on their affinity for binding with iron is Glu > His> Asp > Asn > Cys, and for copper is His > Asp > Cys respectively. The functional annotation, determination of subcellular localization, and Gene Ontology analysis of these putative IBPs and CBPs have unveiled their potential involvement in a diverse array of cellular and biological processes. Three iron-binding glycosyl hydrolase family proteins, along with four CBPs with carbohydrate-binding domains, have been identified as potential effector candidates. These proteins are distinct from the host Solanum lycopersicum proteome. Moreover, they are known to be located extracellularly and function as enzymes that degrade the host cell wall during pathogen-host interactions. The insights gained from this report on the role of metal ions in plant-pathogen interactions can help develop a better understanding of their fundamental biology and control vascular wilt disease in tomato plants.
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Affiliation(s)
- Ankita Singh Kushwah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, North Campus, Delhi, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Mahboubi-Rabbani M, Abdolghaffari AH, Ghesmati M, Amini A, Zarghi A. Selective COX-2 inhibitors as anticancer agents: a patent review (2018-2023). Expert Opin Ther Pat 2024; 34:733-757. [PMID: 38958471 DOI: 10.1080/13543776.2024.2373771] [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: 12/11/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION COX-2 is a crucial enzyme in the manufacture of prostaglandins. The enzyme's metabolites might have an important function as regulators of the inflammatory response and other medical conditions such as cancer. Selective COX-2 inhibitors are believed to enhance or reverse the response of cancer chemotherapeutics. AREAS COVERED This study addresses the chemical structures as well as the antitumor activity of new COX-2 inhibitors produced in the recent five years, aiming to provide an insight into the mechanism of COX-2 induced PGE2 powerful signal in cancer development. EXPERT OPINION The significance of selective COX-2 inhibitors as an efficient superfamily of compounds with anti-inflammatory, anti-Alzheimer's, anti-Parkinson's disease, and anticancer properties has piqued the passion of academics in the field of drug development. Long-term usage of selective COX-2 inhibitors, such as celecoxib has been proven in clinical trials to lower the incidence of several human malignancies. Furthermore, celecoxib has the potential to greatly increase the effectiveness of chemotherapy. Our extensive understanding of selective COX-2 inhibitor SAR may aid in the development of safer and more effective selective COX-2 inhibitors as cancer chemopreventive agents. This review focuses on the different structural classes of selective COX-2 inhibitors, with a particular emphasis on their SAR.
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Affiliation(s)
- Mohammad Mahboubi-Rabbani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Amir Hossein Abdolghaffari
- Department of Toxicology & Pharmacology, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- GI Pharmacology Interest Group (GPIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahsa Ghesmati
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Amini
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [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: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Chin KJ, Ünal B, Sanderson M, Aboderin F, Nüsslein K. Selective trace elements significantly enhanced methane production in coal bed methane systems by stimulating microbial activity. Microbiol Spectr 2024; 12:e0350823. [PMID: 38236038 PMCID: PMC10846109 DOI: 10.1128/spectrum.03508-23] [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: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 01/19/2024] Open
Abstract
Trace elements are associated with the microbial degradation of organic matter and methanogenesis, as enzymes in metabolic pathways often employ trace elements as essential cofactors. However, only a few studies investigated the effects of trace elements on the metabolic activity of microbial communities associated with biogenic coalbed methane production. We aimed to determine the effects of strategically selected trace elements on structure and function of active bacterial and methanogenic communities to stimulate methane production in subsurface coalbeds. Microcosms were established with produced water and coal from coalbed methane wells located in the Powder River Basin, Wyoming, USA. In initial pilot experiments with eight different trace elements, individual amendments of Co, Cu, and Mo lead to significantly higher methane production. Transcript levels of mcrA, the key marker gene for methanogenesis, positively correlated with increased methane production. Phylogenetic analysis of the mcrA cDNA library demonstrated compositional shifts of the active methanogenic community and increase of their diversity, particularly of hydrogenotrophic methanogens. High-throughput sequencing of cDNA obtained from 16S rRNA demonstrated active and abundant bacterial groups in response to trace element amendments. Active Acetobacterium members increased in response to Co, Cu, and Mo additions. The findings of this study yield new insights into the importance of essential trace elements on the metabolic activity of microbial communities involved in subsurface coalbed methane and provide a better understanding of how microbial community composition is shaped by trace elements.IMPORTANCEMicrobial life in the deep subsurface of coal beds is limited by nutrient replenishment. While coal bed microbial communities are surrounded by carbon sources, we hypothesized that other nutrients such as trace elements needed as cofactors for enzymes are missing. Amendment of selected trace elements resulted in compositional shifts of the active methanogenic and bacterial communities and correlated with higher transcript levels of mcrA. The findings of this study yield new insights to not only identify possible limitations of microbes by replenishment of trace elements within their specific hydrological placement but also into the importance of essential trace elements for the metabolic activity of microbial communities involved in subsurface coalbed methane production and provides a better understanding of how microbial community composition is shaped by trace elements. Furthermore, this finding might help to revive already spent coal bed methane well systems with the ultimate goal to stimulate methane production.
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Affiliation(s)
- Kuk-Jeong Chin
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Burcu Ünal
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Environmental Engineering, RheinMain University of Applied Sciences, Wiesbaden, Germany
| | - Michael Sanderson
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Feranmi Aboderin
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Li W, Lv BM, Quan Y, Zhu Q, Zhang HY. Associations between Serum Mineral Nutrients, Gut Microbiota, and Risk of Neurological, Psychiatric, and Metabolic Diseases: A Comprehensive Mendelian Randomization Study. Nutrients 2024; 16:244. [PMID: 38257137 PMCID: PMC10818407 DOI: 10.3390/nu16020244] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Recent observational studies have reported associations between serum mineral nutrient levels, gut microbiota composition, and neurological, psychiatric, and metabolic diseases. However, the causal effects of mineral nutrients on gut microbiota and their causal associations with diseases remain unclear and require further investigation. This study aimed to identify the associations between serum mineral nutrients, gut microbiota, and risk of neurological, psychiatric, and metabolic diseases using Mendelian randomization (MR). We conducted an MR study using the large-scale genome-wide association study (GWAS) summary statistics of 5 serum mineral nutrients, 196 gut microbes at the phylum, order, family, and genus levels, and a variety of common neurological, psychiatric, and metabolic diseases. Initially, the independent causal associations of mineral nutrients and gut microbiota with diseases were examined by MR. Subsequently, the causal effect of mineral nutrients on gut microbiota was estimated to investigate whether specific gut microbes mediated the association between mineral nutrients and diseases. Finally, we performed sensitivity analyses to assess the robustness of the study results. After correcting for multiple testing, we identified a total of 33 causal relationships among mineral nutrients, gut microbiota, and diseases. Specifically, we found 4 causal relationships between 3 mineral nutrition traits and 3 disease traits, 15 causal associations between 14 gut microbiota traits and 6 disease traits, and 14 causal associations involving 4 mineral nutrition traits and 15 gut microbiota traits. Meanwhile, 118 suggestive associations were identified. The current study reveals multiple causal associations between serum mineral nutrients, gut microbiota, risk of neurological, psychiatric, and metabolic diseases, and potentially provides valuable insights for subsequent nutritional therapies.
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Affiliation(s)
- Wang Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (W.L.); (B.-M.L.); (Y.Q.); (H.-Y.Z.)
| | - Bo-Min Lv
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (W.L.); (B.-M.L.); (Y.Q.); (H.-Y.Z.)
- Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (W.L.); (B.-M.L.); (Y.Q.); (H.-Y.Z.)
| | - Qiang Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (W.L.); (B.-M.L.); (Y.Q.); (H.-Y.Z.)
- Key Laboratory of Smart Farming for Agricultural Animals, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (W.L.); (B.-M.L.); (Y.Q.); (H.-Y.Z.)
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Dixit H, Kulharia M, Verma SK. Metal-binding proteins and proteases in RNA viruses: unravelling functional diversity and expanding therapeutic horizons. J Virol 2023; 97:e0139923. [PMID: 37982624 PMCID: PMC10734521 DOI: 10.1128/jvi.01399-23] [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: 09/09/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Metal-binding proteins are pivotal components with diverse functions in organisms, including viruses. Despite their significance, many metalloproteins in viruses remain uncharacterized, posing challenges to understanding viral systems. This study addresses this knowledge gap by identifying and analyzing metal-binding proteins and proteases in RNA viruses. The findings emphasize the prevalence of these proteins as essential functional classes within viruses and shed light on the role of metal ions and metalloproteins in viral replication and pathogenesis. Moreover, this research serves as a crucial foundation for further investigations in this field, offering the potential for developing innovative antiviral strategies. Additionally, the study enhances our understanding of the distribution and evolutionary patterns of metal-binding proteases in major human viruses. Continually exploring metal-binding proteomes across diverse viruses will deepen our knowledge of metal-dependent biological processes and provide valuable insights for combating viral infections, including respiratory viruses and other life-threatening diseases.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
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12
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Liu H, Wu X, Wang D, Li Q, Zhang X, Xu L. Unveiling the role of miR-137-3p/miR-296-5p/SERPINA3 signaling in colorectal cancer progression: integrative analysis of gene expression profiles and in vitro studies. BMC Med Genomics 2023; 16:327. [PMID: 38087342 PMCID: PMC10714458 DOI: 10.1186/s12920-023-01763-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a prevalent malignancy worldwide, with increasing incidence and mortality rates. Although treatment options have improved, CRC remains a leading cause of death due to metastasis. Early intervention can significantly improve patient outcomes, making it crucial to understand the molecular mechanisms underlying CRC metastasis. In this study, we performed bioinformatics analysis to identify potential genes associated with CRC metastasis. METHODS We downloaded and integrated gene expression datasets (GSE89393, GSE100243, and GSE144259) from GEO database. Differential expression analysis was conducted, followed by Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The hub gene SERPINA3 was selected for further in vitro functional studies. Additionally, the role of miR-137-3p/miR-296-5p/ Serpin family A member 3 (SERPINA3) in CRC cell function was investigated using in vitro assays. RESULTS Analysis of the gene expression datasets revealed differentially expressed genes (DEGs) associated with CRC metastasis. GO analysis showed enrichment in biological processes such as blood coagulation regulation and wound healing. Cellular component analysis highlighted extracellular matrix components and secretory granules. Molecular function analysis identified activities such as serine-type endopeptidase inhibition and lipoprotein receptor binding. KEGG analysis revealed involvement in pathways related to complement and coagulation cascades, cholesterol metabolism, and immune responses. The common DEGs among the datasets were further investigated. We identified SERPINA3 as a hub gene associated with CRC metastasis. SERPINA3 exerted enhanced effects on migration, proliferation and epithelial-mesenchymal transition (EMT) and inhibitory effects on caspase-3/-9 activities in HT29 and SW620 cells. MiR-137-3p overexpression increased activities of caspase-3/-9, decreased migration and proliferation, and also repressed EMT in HT29 cells, which were obviously attenuated by SERPINA3 enforced overexpression. Consistently, SERPINA3 enforced overexpression also largely reversed miR-296-5p mimics-induced increased in activities of caspase-3/-9, decrease in migration, proliferation and EMT in HT29 cells. CONCLUSION Through bioinformatics analysis, we identified potential genes associated with CRC metastasis. The functional studies focusing on SERPINA3/miR-137-3p/miR-296-5p further consolidated its role in regulating CRC progression. Our findings provide insights into novel mechanisms underlying CRC metastasis and might contribute to the development of effective treatment strategies. However, the role of SERPINA3/miR-137-3p/miR-296-5p signaling in CRC still requires further investigation.
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Affiliation(s)
- Huimin Liu
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Xingxing Wu
- Department of Pediatric Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Dandan Wang
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Quanxi Li
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Xin Zhang
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Liang Xu
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, China.
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13
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Laveglia V, Bazayeva M, Andreini C, Rosato A. Hunting down zinc(II)-binding sites in proteins with distance matrices. Bioinformatics 2023; 39:btad653. [PMID: 37878807 PMCID: PMC10630175 DOI: 10.1093/bioinformatics/btad653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
MOTIVATION In recent years, high-throughput sequencing technologies have made available the genome sequences of a huge variety of organisms. However, the functional annotation of the encoded proteins often still relies on low-throughput and costly experimental studies. Bioinformatics approaches offer a promising alternative to accelerate this process. In this work, we focus on the binding of zinc(II) ions, which is needed for 5%-10% of any organism's proteins to achieve their physiologically relevant form. RESULTS To implement a predictor of zinc(II)-binding sites in the 3D structures of proteins, we used a neural network, followed by a filter of the network output against the local structure of all known sites. The latter was implemented as a function comparing the distance matrices of the Cα and Cβ atoms of the sites. We called the resulting tool Master of Metals (MOM). The structural models for the entire proteome of an organism generated by AlphaFold can be used as input to our tool in order to achieve annotation at the whole organism level within a few hours. To demonstrate this, we applied MOM to the yeast proteome, obtaining a precision of about 76%, based on data for homologous proteins. AVAILABILITY AND IMPLEMENTATION Master of Metals has been implemented in Python and is available at https://github.com/cerm-cirmmp/Master-of-metals.
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Affiliation(s)
- Vincenzo Laveglia
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
| | - Milana Bazayeva
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
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14
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Baj J, Kowalska B, Flieger W, Radzikowska-Büchner E, Forma A, Czeczelewski M, Kędzierawski P, Karakuła K, Flieger M, Majerek D, Teresiński G, Maciejewski R, Flieger J. Assessment of the Concentration of 51 Elements in the Liver and in Various Parts of the Human Brain-Profiling of the Mineral Status. Nutrients 2023; 15:2799. [PMID: 37375704 DOI: 10.3390/nu15122799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The anthropogenic environment and diet introduce many metals into the human body, both essential and toxic. Absorption leads to systemic exposure and accumulation in body fluids and tissues. Both excess and deficiency of trace elements are health hazards. The primary aim of the present study was to evaluate the concentration of 51 elements in liver samples and 11 selected brain regions obtained at post-mortem examination from a population of adults living in south-eastern Poland (n = 15). A total of 180 analyses were performed by inductively coupled plasma mass spectrometry in two independent replicates. The collected data show very high individual variability in the content of the investigated elements. Macroelements such as sodium, magnesium, phosphorus, potassium, calcium, iron, and zinc occurred in the highest concentrations and with the greatest statistically significant variations. Although the elemental content of the brain and liver differed significantly, the strongest positive correlation between liver and polus frontalis was observed for the essential element selenium (0.9338) and the strongest negative one for manganese (-0.4316) and lanthanum (-0.5110). The brain areas studied have different requirements for phosphorus, manganese, iron, and molybdenum. In addition, males had a significantly (p < 0.05) higher brain content of lanthanides and actinides than females. The results of this study show that the inhabitants of south-eastern Poland are exposed to a fairly uniform accumulation of aluminum and vanadium in the brain, which have the highest affinity to the thalamus dorsalis. This result proves that there is environmental exposure to these elements.
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Affiliation(s)
- Jacek Baj
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Beata Kowalska
- Department of Water Supply and Wastewater Disposal, Lublin University of Technology, 20-618 Lublin, Poland
| | - Wojciech Flieger
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | | | - Alicja Forma
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Marcin Czeczelewski
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Paweł Kędzierawski
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Kaja Karakuła
- I Department of Psychiatry, Psychotherapy, and Early Intervention, Medical University of Lublin, 20-439 Lublin, Poland
| | - Michał Flieger
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dariusz Majerek
- Department of Applied Mathematics, University of Technology, 20-618 Lublin, Poland
| | - Grzegorz Teresiński
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | | | - Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland
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15
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Khan N, Ullah J, Hashmi S, Ali A, Siddiqui AJ, Sami SA, Bokhari SS, Sharif H, Uddin J, El-Seedi HR, Musharraf SG. Dysregulation of metalloproteins in ischemic heart disease patients with systolic dysfunction. Int J Biol Macromol 2023; 232:123435. [PMID: 36716834 DOI: 10.1016/j.ijbiomac.2023.123435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 01/29/2023]
Abstract
Ischemic heart disease (IHD) is the leading cause of mortality worldwide. Metalloproteins have been linked to human health and diseases. The molecular functions of metalloproteins in IHD is not well understood and require further exploration. The objective of this study was to find out the role of metalloproteins in the pericardial fluid of IHD patients having normal (EF > 45) and impaired (EF < 45) left ventricular ejection fraction (LVEF). IHD patients were grouped into two categories: LVEF<45 (n = 12) and LVEF >45 (n = 33). Pooled samples of pericardial fluid were fractionated by using ZOOM-isoelectric focusing (IEF) followed by further processing using one-dimensional gel electrophoresis (1D SDS-PAGE) and filter-aided sample preparation (FASP). Tryptic peptides of each fraction and differential bands were then analyzed by nano-LC-ESI-MS/MS. Protein identification was performed through a Mascot search engine using NCBI-Prot and SwissProt databases. A total of 1082 proteins including 154 metalloproteins were identified. In the differential bands, 60 metalloproteins were identified, while 115 metalloproteins were identified in all ZOOM-IEF fractions. Twelve differentially expressed metalloproteins were selected in the intense bands according to their molecular weight (MW) and isoelectric point (pI). The 12 differentially expressed metalloprotein includes ceruloplasmin, Prothrombin, Vitamin K-dependent protein, Fibulin-1, Ribosomal protein S6 kinase alpha-6, nidogen, partial, Serum albumin, Hemopexin, C-reactive protein, Serum amyloid P-component, and Intelectin-1 protein which were all up-regulated while serotransferrin is the only metalloprotein that was down-regulated in impaired (LVEF<45) group. Among the metalloproteins, Zn-binding proteins are 36.5 % followed by Ca-binging 32.2 %, and Fe-binging 12.2 %. KEGG, pathway analysis revealed the association of ceruloplasmin and serotransferrin with the ferroptosis pathway. In conclusion, 154 metalloproteins were identified of them the Zn-binding protein followed by Ca-binding and Fe-binding proteins were the most abundant metalloproteins. The two metalloproteins, the Cu-binding protein ceruloplasmin, and Fe-binding protein serotransferrin are involved in the ferroptosis pathway, an iron-dependent form of regulated cell death that has been linked to cardiac pathology, especially in IHD patients having impaired systolic (LVEF<45) dysfunction. However, further research is required to validate these findings.
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Affiliation(s)
- Noman Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Junaid Ullah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Satwat Hashmi
- Department of Biological and Biomedical Sciences, Agha Khan University, Karachi 74800, Pakistan
| | - Arslan Ali
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Amna Jabbar Siddiqui
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Shahid Ahmed Sami
- Department of Surgery, The Aga Khan University Hospital, Karachi 74800, Pakistan
| | - Syeda Saira Bokhari
- Department of Medicine, The Aga Khan University Hospital, Karachi 74800, Pakistan
| | - Hasanat Sharif
- Department of Surgery, The Aga Khan University Hospital, Karachi 74800, Pakistan
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Asir 61421, Saudi Arabia
| | - Hesham R El-Seedi
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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16
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Wang J, Xiu L, Qiao Y, Zhang Y. Virulence regulation of Zn2+ uptake system znuABC on mesophilic Aeromonas salmonicida SRW-OG1. Front Vet Sci 2023; 10:1172123. [PMID: 37065252 PMCID: PMC10090552 DOI: 10.3389/fvets.2023.1172123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Psychrophilic Aeromonas salmonicida could not grow above 25°C and therefore thought unable to infect mammals and humans. In our previous study, a mesophilic A. salmonicida SRW-OG1 was isolated from Epinephelus coioides with furunculosis. Through the analysis of preliminary RNA-seq, it was found that the Zn2+ uptake related genes znuA, znuB and znuC might be involved in the virulence regulation of A. salmonicida SRW-OG1. Therefore, the purpose of this study was to explore the effect of znuABC silencing on the virulence regulation of A. salmonicida SRW-OG1. The results showed that the growth of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains was severely restricted under the Fe2+ starvation, but surprisingly there was no significant difference under the Zn2+ restriction. In the absence of Zn2+ and Fe2+, the expression level of znuABC was significantly increased. The motility, biofilm formation, adhesion and hemolysis of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains were significantly reduced. We also detected the expression of znuABC under different growth periods, temperatures, pH, as well as Cu2+ and Pb2+ stresses. The results showed that znuABC was significantly up-regulated in the logarithmic phase and the decline phase of A. salmonicida. Interestingly, the trend of expression levels of the znuABC at 18, 28, and 37°C was reversed to another Zn2+ uptake related gene zupT. Taken together, these indicated that the znuABC was necessary for A. salmonicida SRW-OG1 pathogenicity and environmental adaptability, and was cross regulated by iron starvation, but it was not irreplaceable for A. salmonicida SRW-OG1 Zn2+ uptake in the host.
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Affiliation(s)
- Jiajia Wang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Lijun Xiu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Ying Qiao
- Fourth Institute of Oceanography, Key Laboratory of Tropical Marine Ecosystem and Bioresource, Ministry of Natural Resources, Beihai, China
| | - Youyu Zhang
- Institute of Electromagnetics and Acoustics, School of Electronic Science and Engineering, Xiamen University, Xiamen, China
- *Correspondence: Youyu Zhang
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17
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Mansour RES, Abdulwahab HG, El-Sehrawi HM. Novel benzimidazole-linked (thio)barbiturates as non-hydroxamate HDAC6 inhibitors targeting leukemia: Design, synthesis, and structure-activity relationship. Arch Pharm (Weinheim) 2023:e2200433. [PMID: 36942938 DOI: 10.1002/ardp.202200433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/10/2023] [Accepted: 02/25/2023] [Indexed: 03/23/2023]
Abstract
Based on the well-established pharmacophoric features required for histone deacetylase (HDAC) inhibition, novel easy-to-prepare benzimidazole-linked (thio)barbiturate derivatives were designed and synthesized as HDAC6 inhibitors. The proposed structures of the title compounds were confirmed based on their spectral data and elemental analyses. The newly synthesized compounds were screened in vitro against HDAC6. All tested compounds showed potent HDAC6 inhibition at the nanomolar level. Several compounds displayed a remarkable HDAC6 inhibitory activity (IC50 = 48.85-75.62 nM), superior to that of the reference drug suberoylanilide hydroxamic acid (SAHA; IC50 = 91.73 nM). The most potent derivatives were further assessed for their in vitro anticancer activity against two human leukemia cell lines. Thiobarbiturate 3e was two times more potent than SAHA against the tested cells. The detailed structure-activity relationship was also described. Furthermore, molecular docking simulation revealed the ability of the title compounds to chelate the catalytic Zn+2 ion located within the binding pocket of HDAC6. In silico evaluation of physicochemical properties indicated that the target compounds are promising candidates in terms of pharmacokinetic aspects.
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Affiliation(s)
- Reda El-Sayed Mansour
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Hanan Gaber Abdulwahab
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Hend M El-Sehrawi
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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18
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Pham VN, Chang CJ. Metalloallostery and Transition Metal Signaling: Bioinorganic Copper Chemistry Beyond Active Sites. Angew Chem Int Ed Engl 2023; 62:e202213644. [PMID: 36653724 PMCID: PMC10754205 DOI: 10.1002/anie.202213644] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Indexed: 01/20/2023]
Abstract
Transition metal chemistry is essential to life, where metal binding to DNA, RNA, and proteins underpins all facets of the central dogma of biology. In this context, metals in proteins are typically studied as static active site cofactors. However, the emergence of transition metal signaling, where mobile metal pools can transiently bind to biological targets beyond active sites, is expanding this conventional view of bioinorganic chemistry. This Minireview focuses on the concept of metalloallostery, using copper as a canonical example of how metals can regulate protein function by binding to remote allosteric sites (e.g., exosites). We summarize advances in and prospects for the field, including imaging dynamic transition metal signaling pools, allosteric inhibition or activation of protein targets by metal binding, and metal-dependent signaling pathways that underlie nutrient vulnerabilities in diseases spanning obesity, fatty liver disease, cancer, and neurodegeneration.
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Affiliation(s)
- Vanha N Pham
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
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19
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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20
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Pham VN, Chang CJ. Metalloallostery and Transition Metal Signaling: Bioinorganic Copper Chemistry Beyond Active Sites. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202213644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Vanha N. Pham
- Department of Chemistry University of California Berkeley CA 94720 USA
| | - Christopher J. Chang
- Department of Chemistry University of California Berkeley CA 94720 USA
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
- Helen Wills Neuroscience Institute University of California Berkeley CA 94720 USA
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21
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Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. J Biol Chem 2023; 299:102899. [PMID: 36639030 PMCID: PMC9930159 DOI: 10.1016/j.jbc.2023.102899] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Metallothioneins (MTs) are essential mammalian metal chaperones. MT isoform 1 (MT1) is expressed in the kidneys and isoform 3 (MT3) is expressed in nervous tissue. For MTs, the solution-based NMR structure was determined for metal-bound MT1 and MT2, and only one X-ray diffraction structure on a crystallized mixed metal-bound MT2 has been reported. The structure of solution-based metalated MT3 is partially known using NMR methods; however, little is known about the fluxional de novo apo-MT3 because the structure cannot be determined by traditional methods. Here, we used cysteine modification coupled with electrospray ionization mass spectrometry, denaturing reactions with guanidinium chloride, stopped-flow methods measuring cysteine modification and metalation, and ion mobility mass spectrometry to reveal that apo-MT3 adopts a compact structure under physiological conditions and an extended structure under denaturing conditions, with no intermediates. Compared with apo-MT1, we found that this compact apo-MT3 binds to a cysteine modifier more cooperatively at equilibrium and 0.5 times the rate, providing quantitative evidence that many of the 20 cysteines of apo-MT3 are less accessible than those of apo-MT1. In addition, this compact apo-MT3 can be identified as a distinct population using ion mobility mass spectrometry. Furthermore, proposed structural models can be calculated using molecular dynamics methods. Collectively, these findings provide support for MT3 acting as a noninducible regulator of the nervous system compared with MT1 as an inducible scavenger of trace metals and toxic metals in the kidneys.
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22
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Dixit H, Upadhyay V, Kulharia M, Verma SK. The putative metal-binding proteome of the Coronaviridae family. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2023; 15:6969429. [PMID: 36610727 DOI: 10.1093/mtomcs/mfad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023]
Abstract
Metalloproteins are well-known for playing various physicochemical processes in all life forms, including viruses. Some life-threatening viruses (such as some members of the Coronaviridae family of viruses) are emerged and remerged frequently and are rapidly transmitted throughout the globe. This study aims to identify and characterize the metal-binding proteins (MBPs) of the Coronaviridae family of viruses and further provides insight into the MBP's role in sustaining and propagating viruses inside a host cell and in the outer environment. In this study, the available proteome of the Coronaviridae family was exploited. Identified potential MBPs were analyzed for their functional domains, structural aspects, and subcellular localization. We also demonstrate phylogenetic aspects of all predicted MBPs among other Coronaviridae family members to understand the evolutionary trend among their respective hosts. A total of 256 proteins from 51 different species of coronaviruses are predicted as MBPs. These MBPs perform various key roles in the replication and survival of viruses within the host cell. Cysteine, aspartic acid, threonine, and glutamine are key amino acid residues interacting with respective metal ions. Our observations also indicate that the metalloproteins of this family of viruses circulated and evolved in different hosts, which supports the zoonotic nature of coronaviruses. The comprehensive information on MBPs of the Coronaviridae family may be further helpful in designing novel therapeutic metalloprotein targets. Moreover, the study of viral MBPs can also help to understand the roles of MBPs in virus pathogenesis and virus-host interactions.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India.,Department of Environmental Studies, University of Delhi, Delhi110007, India
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23
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Camponeschi F, Banci L. Metal trafficking in the cell: Combining atomic resolution with cellular dimension. FEBS Lett 2023; 597:122-133. [PMID: 36285633 DOI: 10.1002/1873-3468.14524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/14/2023]
Abstract
Metals are widely present in biological systems as simple ions or complex cofactors, and are involved in a variety of processes essential for life. Their transport inside cells and insertion into the binding sites of the proteins that need metals to function occur through complex and selective pathways involving dedicated multiprotein machineries specifically and transiently interacting with each other, often sharing the coordination of metal ions and/or cofactors. The understanding of these machineries requires integrated approaches, ranging from bioinformatics to experimental investigations, possibly in the cellular context. In this review, we report two case studies where the use of integrated in vitro and in cellulo approaches is necessary to clarify at atomic resolution essential aspects of metal trafficking in cells.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.,Department of Chemistry, University of Florence, Italy
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24
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Chen ZF, Wu LZ, Chen ZT, Su LJ, Fu CJ. The potential mechanisms of neuroblastoma in children based on bioinformatics big data. Transl Pediatr 2022; 11:1908-1919. [PMID: 36643678 PMCID: PMC9834953 DOI: 10.21037/tp-22-504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In recent years, miRNAs have become a research hotspot, which is related to the occurrence and development of a variety of malignant tumors, but there are few studies in neuroblastoma. In this study, the differentially expressed microRNAs (miRNAs) in neuroblastoma were identified and analyzed using bioinformatics, and their biological functions and related signaling pathways were examined. METHODS The neuroblastoma miRNA chip GSE121513 was obtained from the Gene Expression Omnibus (GEO) database and the data of 95 neuroblastoma samples and normal fetal adrenal neuroblastoma samples were analyzed to screen the differential miRNAs. The target genes of the differentially expressed miRNAs were predicted using |log fold change (FC)| ≥4. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed to construct a protein-protein interaction network and identify the core target genes. RESULTS A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs. The target genes of the differential miRNAs (P<0.05, |logFC| ≥4) were pretested, and 602 target genes were obtained. Functional analysis showed that these genes were mainly located in the extracellular matrix region of proteins, and were involved in the negative regulation of cytoplasmic translation, mRNA 3'-untranslated region (UTR) binding, and binding to nucleic acid to inhibit the activity of translation factors. They were also involved in RNA degradation, adhesion pathways, and the phosphatidylinositol-3-kinase (PI3K)-Akt signaling pathway. Ten key target genes were identified via protein interaction network screening. CONCLUSIONS The differential miRNAs may be related to the occurrence of neuroblastoma were screened.
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Affiliation(s)
- Ze-Fu Chen
- Department of Pediatrics, Hainan General Hospital, Haikou, China
| | - Li-Zhen Wu
- Department of Operating Theater, Hainan General Hospital, Haikou, China
| | - Ze-Ting Chen
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
| | - Liang-Ju Su
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
| | - Ce-Jun Fu
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
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25
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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26
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Katheria S. Ruthenium Complexes as Potential Cancer Cell Growth Inhibitors for Targeted Chemotherapy. ChemistrySelect 2022. [DOI: 10.1002/slct.202201645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022; 23:7684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.
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Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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28
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Killilea DW, Killilea AN. Mineral requirements for mitochondrial function: A connection to redox balance and cellular differentiation. Free Radic Biol Med 2022; 182:182-191. [PMID: 35218912 DOI: 10.1016/j.freeradbiomed.2022.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/20/2022]
Abstract
Professor Bruce Ames demonstrated that nutritional recommendations should be adjusted in order to 'tune-up' metabolism and reduce mitochondria decay, a hallmark of aging and many disease processes. A major subset of tunable nutrients are the minerals, which despite being integral to every aspect of metabolism are often deficient in the typical Western diet. Mitochondria are particularly rich in minerals, where they function as essential cofactors for mitochondrial physiology and overall cellular health. Yet substantial knowledge gaps remain in our understanding of the form and function of these minerals needed for metabolic harmony. Some of the minerals have known activities in the mitochondria but with incomplete regulatory detail, whereas other minerals have no established mitochondrial function at all. A comprehensive metallome of the mitochondria is needed to fully understand the patterns and relationships of minerals within metabolic processes and cellular development. This brief overview serves to highlight the current progress towards understanding mineral homeostasis in the mitochondria and to encourage more research activity in key areas. Future work may likely reveal that adjusting the amounts of specific nutritional minerals has longevity benefits for human health.
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Affiliation(s)
- David W Killilea
- Office of Research, University of California, San Francisco, CA, USA.
| | - Alison N Killilea
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
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29
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Yu Y, Wang R, Teo RD. Machine Learning Approaches for Metalloproteins. Molecules 2022; 27:1277. [PMID: 35209064 PMCID: PMC8878495 DOI: 10.3390/molecules27041277] [Citation(s) in RCA: 2] [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: 02/02/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 01/10/2023] Open
Abstract
Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.
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Affiliation(s)
- Yue Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu 215316, China;
- Department of Physics, Duke University, Durham, NC 27708, USA
| | - Ruobing Wang
- Department of Chemistry, Duke University, Durham, NC 27708, USA;
| | - Ruijie D. Teo
- Department of Chemistry, Duke University, Durham, NC 27708, USA;
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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30
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Kirin V, Demkin A, Sukhikh T, Ilyicheva T, Maksakov V. Cobalt complexes with biguanide derivatives – Synthesis, structure and antiviral activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Leite CM, Honorato J, Martin ACBM, Silveira RG, Colombari FM, Amaral JC, Costa AR, Cominetti MR, Plutín AM, de Aguiar D, Vaz BG, Batista AA. Experimental and Theoretical DFT Study of Cu(I)/ N, N-Disubstituted- N'-acylthioureato Anticancer Complexes: Actin Cytoskeleton and Induction of Death by Apoptosis in Triple-Negative Breast Tumor Cells. Inorg Chem 2022; 61:664-677. [PMID: 34928593 DOI: 10.1021/acs.inorgchem.1c03389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Six complexes with the general formula [Cu(acylthioureato)(PPh3)2] were synthesized and characterized using spectroscopic techniques (IR, UV/visible, and 1D and 2D NMR), mass spectrometry, elemental analysis, and X-ray diffraction. Interpretation of the in vitro cytotoxicity data of Cu(I) complexes took into account their stability in cell culture medium. DFT calculations showed that NMR properties, such as the shielding of carbon atoms, are affected by relativistic effects, supported by the ZORA Hamiltonian in the theoretical calculations. Additionally, the calculation of the energies of the frontier molecular orbitals predicted that the structural changes of the acylthiourea ligands did not cause marked changes in the reactivity descriptors. All complexes were cytotoxic to the evaluated tumor cell lines [MDA-MB-231 (triple-negative breast cancer, TNBC), MCF-7 (breast cancer), and A549 (lung cancer)]. In the MDA-MB-231 cell line, complex 1 significantly altered the cytoskeleton of the cells, reducing the density and promoting the condensation of F-actin filaments. In addition, the compound caused an increase in the percentage of cells in the fragmented DNA region (sub-G0) and induced cell death via the apoptotic pathway starting at the IC50 concentration. Taken together, the results show that complex 1 has cytotoxic and apoptotic effects on TNBC cells, which is a cell line originating from an aggressive, difficult-to-treat breast cancer.
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Affiliation(s)
- Celisnolia M Leite
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - João Honorato
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | | | - Rafael G Silveira
- Instituto Federal Goiano, Campus Ceres, Ceres, Goiás 76300000, Brazil
| | - Felippe M Colombari
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biorrenováveis, Campinas, São Paulo 13083-970, Brazil
| | - Jéssica C Amaral
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - Analu R Costa
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - Márcia R Cominetti
- Departamento de Gerontologia, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - Ana M Plutín
- Laboratório de Síntesis Orgánica, Facultad de Química, Universidad de La Habana - UH, Habana 10400, Cuba
| | - Debora de Aguiar
- Instituto de Química, Universidade Federal de Goiás, Goiania, Goiás 74690900, Brazil
| | - Boniek G Vaz
- Instituto de Química, Universidade Federal de Goiás, Goiania, Goiás 74690900, Brazil
| | - Alzir A Batista
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
- Instituto de Química, Universidade Federal de Goiás, Goiania, Goiás 74690900, Brazil
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32
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Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
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33
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Wu D, Saleem M, He T, He G. The Mechanism of Metal Homeostasis in Plants: A New View on the Synergistic Regulation Pathway of Membrane Proteins, Lipids and Metal Ions. MEMBRANES 2021; 11:membranes11120984. [PMID: 34940485 PMCID: PMC8706360 DOI: 10.3390/membranes11120984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/04/2021] [Accepted: 12/11/2021] [Indexed: 12/15/2022]
Abstract
Heavy metal stress (HMS) is one of the most destructive abiotic stresses which seriously affects the growth and development of plants. Recent studies have shown significant progress in understanding the molecular mechanisms underlying plant tolerance to HMS. In general, three core signals are involved in plants' responses to HMS; these are mitogen-activated protein kinase (MAPK), calcium, and hormonal (abscisic acid) signals. In addition to these signal components, other regulatory factors, such as microRNAs and membrane proteins, also play an important role in regulating HMS responses in plants. Membrane proteins interact with the highly complex and heterogeneous lipids in the plant cell environment. The function of membrane proteins is affected by the interactions between lipids and lipid-membrane proteins. Our review findings also indicate the possibility of membrane protein-lipid-metal ion interactions in regulating metal homeostasis in plant cells. In this review, we investigated the role of membrane proteins with specific substrate recognition in regulating cell metal homeostasis. The understanding of the possible interaction networks and upstream and downstream pathways is developed. In addition, possible interactions between membrane proteins, metal ions, and lipids are discussed to provide new ideas for studying metal homeostasis in plant cells.
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Affiliation(s)
- Danxia Wu
- College of Agricultural, Guizhou University, Guiyang 550025, China;
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | - Tengbing He
- College of Agricultural, Guizhou University, Guiyang 550025, China;
- Institute of New Rural Development, West Campus, Guizhou University, Guiyang 550025, China
- Correspondence: (T.H.); (G.H.)
| | - Guandi He
- College of Agricultural, Guizhou University, Guiyang 550025, China;
- Correspondence: (T.H.); (G.H.)
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34
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Riedel F, Aparicio-Soto M, Curato C, Thierse HJ, Siewert K, Luch A. Immunological Mechanisms of Metal Allergies and the Nickel-Specific TCR-pMHC Interface. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10867. [PMID: 34682608 PMCID: PMC8535423 DOI: 10.3390/ijerph182010867] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
Besides having physiological functions and general toxic effects, many metal ions can cause allergic reactions in humans. We here review the immune events involved in the mediation of metal allergies. We focus on nickel (Ni), cobalt (Co) and palladium (Pd), because these allergens are among the most prevalent sensitizers (Ni, Co) and immediate neighbors in the periodic table of the chemical elements. Co-sensitization between Ni and the other two metals is frequent while the knowledge on a possible immunological cross-reactivity using in vivo and in vitro approaches remains limited. At the center of an allergic reaction lies the capability of a metal allergen to form T cell epitopes that are recognized by specific T cell receptors (TCR). Technological advances such as activation-induced marker assays and TCR high-throughput sequencing recently provided new insights into the interaction of Ni2+ with the αβ TCR-peptide-major histocompatibility complex (pMHC) interface. Ni2+ functionally binds to the TCR gene segment TRAV9-2 or a histidine in the complementarity determining region 3 (CDR3), the main antigen binding region. Thus, we overview known, newly identified and hypothesized mechanisms of metal-specific T cell activation and discuss current knowledge on cross-reactivity.
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Affiliation(s)
- Franziska Riedel
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
| | - Marina Aparicio-Soto
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Caterina Curato
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Hermann-Josef Thierse
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Katherina Siewert
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Andreas Luch
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
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35
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Witkowska D, Słowik J, Chilicka K. Heavy Metals and Human Health: Possible Exposure Pathways and the Competition for Protein Binding Sites. Molecules 2021; 26:molecules26196060. [PMID: 34641604 PMCID: PMC8511997 DOI: 10.3390/molecules26196060] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Heavy metals enter the human body through the gastrointestinal tract, skin, or via inhalation. Toxic metals have proven to be a major threat to human health, mostly because of their ability to cause membrane and DNA damage, and to perturb protein function and enzyme activity. These metals disturb native proteins’ functions by binding to free thiols or other functional groups, catalyzing the oxidation of amino acid side chains, perturbing protein folding, and/or displacing essential metal ions in enzymes. The review shows the physiological and biochemical effects of selected toxic metals interactions with proteins and enzymes. As environmental contamination by heavy metals is one of the most significant global problems, some detoxification strategies are also mentioned.
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Lamarche J, Ronga L, Szpunar J, Lobinski R. Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry. Int J Mol Sci 2021; 22:ijms22126283. [PMID: 34208081 PMCID: PMC8230778 DOI: 10.3390/ijms22126283] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Selenoprotein P (SELENOP) is an emerging marker of the nutritional status of selenium and of various diseases, however, its chemical characteristics still need to be investigated and methods for its accurate quantitation improved. SELENOP is unique among selenoproteins, as it contains multiple genetically encoded SeCys residues, whereas all the other characterized selenoproteins contain just one. SELENOP occurs in the form of multiple isoforms, truncated species and post-translationally modified variants which are relatively poorly characterized. The accurate quantification of SELENOP is contingent on the availability of specific primary standards and reference methods. Before recombinant SELENOP becomes available to be used as a primary standard, careful investigation of the characteristics of the SELENOP measured by electrospray MS and strict control of the recoveries at the various steps of the analytical procedures are strongly recommended. This review critically discusses the state-of-the-art of analytical approaches to the characterization and quantification of SELENOP. While immunoassays remain the standard for the determination of human and animal health status, because of their speed and simplicity, mass spectrometry techniques offer many attractive and complementary features that are highlighted and critically evaluated.
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Affiliation(s)
- Jérémy Lamarche
- IPREM UMR5254, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux, CNRS, Université de Pau et des Pays de l’Adour, Hélioparc, 64053 Pau, France; (L.R.); (J.S.); (R.L.)
- Correspondence:
| | - Luisa Ronga
- IPREM UMR5254, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux, CNRS, Université de Pau et des Pays de l’Adour, Hélioparc, 64053 Pau, France; (L.R.); (J.S.); (R.L.)
| | - Joanna Szpunar
- IPREM UMR5254, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux, CNRS, Université de Pau et des Pays de l’Adour, Hélioparc, 64053 Pau, France; (L.R.); (J.S.); (R.L.)
| | - Ryszard Lobinski
- IPREM UMR5254, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux, CNRS, Université de Pau et des Pays de l’Adour, Hélioparc, 64053 Pau, France; (L.R.); (J.S.); (R.L.)
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, IM Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
- Chair of Analytical Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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Lin J, Zangi M, Kumar TVH, Shakar Reddy M, Reddy LVR, Sadhukhan SK, Bradley DP, Moreira-Walsh B, Edwards TC, O’Dea AT, Tavis JE, Meyers MJ, Donlin MJ. Synthetic Derivatives of Ciclopirox are Effective Inhibitors of Cryptococcus neoformans. ACS OMEGA 2021; 6:8477-8487. [PMID: 33817509 PMCID: PMC8015083 DOI: 10.1021/acsomega.1c00273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/09/2021] [Indexed: 05/04/2023]
Abstract
Opportunistic fungal infections caused by Cryptococcus neoformans are a significant source of mortality in immunocompromised patients. They are challenging to treat because of a limited number of antifungal drugs, and novel and more effective anticryptococcal therapies are needed. Ciclopirox olamine, a N-hydroxypyridone, has been in use as an approved therapeutic agent for the treatment of topical fungal infections for more than two decades. It is a fungicide, with broad activity across multiple fungal species. We synthesized 10 N-hydroxypyridone derivatives to develop an initial structure-activity understanding relative to efficacy as a starting point for the development of systemic antifungals. We screened the derivatives for antifungal activity against C. neoformans and Cryptococcus gattii and counter-screened for specificity in Candida albicans and two Malassezia species. Eight of the ten show inhibition at 1-3 μM concentration (0.17-0.42 μg per mL) in both Cryptococcus species and in C. albicans, but poor activity in the Malassezia species. In C. neoformans, the N-hydroxypyridones are fungicides, are not antagonistic with either fluconazole or amphotericin B, and are synergistic with multiple inhibitors of the mitochondrial electron transport chain. They appear to function primarily by chelating iron within the active site of iron-dependent enzymes. This preliminary structure-activity relationship points to the need for a lipophilic functional group at position six of the N-hydroxypyridone ring and identifies positions four and six as sites where further substitution may be tolerated. These molecules provide a clear starting point for future optimization for efficacy and target identification.
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Affiliation(s)
- Jeffrey Lin
- Department
of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Maryam Zangi
- Department
of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | | | - Makala Shakar Reddy
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Lingala Vijaya Raghava Reddy
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Subir Kumar Sadhukhan
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Daniel P. Bradley
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Brenda Moreira-Walsh
- Edward
A. Doisy Department of Biochemistry, Saint
Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United
States
| | - Tiffany C. Edwards
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Austin T. O’Dea
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - John E. Tavis
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Marvin J. Meyers
- Department
of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Maureen J. Donlin
- Edward
A. Doisy Department of Biochemistry, Saint
Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United
States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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