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Gautheron G, Péraldi-Roux S, Vaillé J, Belhadj S, Patyra A, Bayle M, Youl E, Omhmmed S, Guyot M, Cros G, Guichou JF, Uzan B, Movassat J, Quignard JF, Neasta J, Oiry C. The flavonoid resokaempferol improves insulin secretion from healthy and dysfunctional pancreatic β-cells. Br J Pharmacol 2024. [PMID: 39327688 DOI: 10.1111/bph.17304] [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: 06/19/2023] [Revised: 06/20/2024] [Accepted: 07/09/2024] [Indexed: 09/28/2024] Open
Abstract
BACKGROUND AND PURPOSE The pharmacology of flavonoids on β-cell function is largely undefined especially in the context of defective secretion of insulin. We sought to identify flavonoids that increased the insulin-secreting function of β-cells and to explore the underlying mechanisms. EXPERIMENTAL APPROACH INS-1 β-cells in culture and islets of Langerhans isolated from control and diabetic male rats were used for insulin secretion experiments. Pharmacological and electrophysiological approaches were used for mechanistic studies. KEY RESULTS Among a set of flavonoids, exposure of INS-1 β-cells to resokaempferol (ResoK) enhanced glucose-stimulated insulin secretion and therefore we further characterised its activity and its pharmacological mechanism. ResoK glucose-dependently enhanced insulin secretion in INS-1 β-cells and pancreatic islets isolated from rats. Mechanistically, whole cell patch clamp recordings in INS-1 cells showed that ResoK rapidly and dose-dependently enhanced the L-type Ca2+ current whereas it was inactive towards T-type Ca2+ current. Accordingly, pharmacological inhibition of L-type Ca2+ current but not T-type Ca2+ current blocked the effects of ResoK on glucose-stimulated insulin secretion. ResoK was still active on dysfunctional β-cells as it ameliorated glucose-stimulated insulin secretion in glucotoxicity-induced dysfunctional INS-1 cells and in pancreatic islets isolated from diabetic rats. CONCLUSION AND IMPLICATIONS ResoK is a glucose-dependent activator of insulin secretion. Our results indicated that the effects of ResoK on insulin secretion involved its capacity to stimulate L-type Ca2+ currents in cultured β-cells. As ResoK was also effective on dysfunctional β-cells, our work provides a new approach to stimulating insulin secretion, using compounds based on the structure of ResoK.
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Affiliation(s)
| | | | - Justine Vaillé
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sahla Belhadj
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Andrzej Patyra
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
- Department of Pharmaceutical Biology, Medical University of Warsaw, Warsaw, Poland
| | - Morgane Bayle
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Estelle Youl
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Mélanie Guyot
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Gérard Cros
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Benjamin Uzan
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Jamileh Movassat
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Jean-François Quignard
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, Pessac, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, Pessac, France
| | - Jérémie Neasta
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Catherine Oiry
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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2
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Melo TS, Andrade BS. Advancing rational pesticide development against Drosophila suzukii: bioinformatics tools and applications-a systematic review. J Mol Model 2024; 30:319. [PMID: 39222282 DOI: 10.1007/s00894-024-06113-w] [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: 02/26/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
CONTEXT Drosophila suzukii (Matsumura, 1931) is a widespread agricultural pest responsible for significant damage to various soft-skinned fruit hosts. The revolutionary potential of bioinformatics in agriculture emerges from its ability to provide extensive information on pests, fungi, chemical resistance, implications of non-target species, and other critical aspects. This wealth of information allows researchers to engage in projects and applied research in diverse agricultural domains that face these challenges. In this context, bioinformatics tools play a fundamental role. The negative impact of pests on crops, resulting in substantial economic losses, has highlighted the importance of in silico methods. METHODS To achieve this, we conducted a systematic search in scientific databases using as keywords "Drosophila suzukii," "biopesticides," "simulations computational," and "in-silico." After applying the filters of relevance and publication date, we organized the articles and prioritized those that directly addressed that matched the keywords and the use of bioinformatics tools. Additionally, we included studies focusing on in silico assays of biopesticides, such as molecular docking. Our review aimed to present a collection of recent literature on biopesticides against Drosophila suzukii, emphasizing bioinformatics methods. Through this work, we strive to contribute to the literature of new perspectives on the development and efficiency of biopesticides, along with to advance research that may improve pest control strategies. RESULTS In the results of the systematic review, we found 2734 articles related to the selected keywords. Six of these articles directly address Drosophila suzukii and the use of bioinformatics tools in the search for alternatives in pest control. In the selected studies, we observed that two articles tend to focus on phylogenetic approaches, searching for gene sequences, amino acids, and constructing phylogenetic trees. The other three articles used molecular modeling and docking of receptors such as GABA and TRP with plant-derived and synthetic compounds to study intermolecular interactions. However, we identified gaps in these studies that could lead to further research in the biorational development of biopesticides using bioinformatics tools.
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Affiliation(s)
- Tarcisio Silva Melo
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil.
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
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3
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Vats S, Bobrovs R, Söderhjelm P, Bhakat S. AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics. PLoS One 2024; 19:e0307226. [PMID: 39190764 DOI: 10.1371/journal.pone.0307226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/02/2024] [Indexed: 08/29/2024] Open
Abstract
Sampling rare events in proteins is crucial for comprehending complex phenomena like cryptic pocket opening, where transient structural changes expose new binding sites. Understanding these rare events also sheds light on protein-ligand binding and allosteric communications, where distant site interactions influence protein function. Traditional unbiased molecular dynamics simulations often fail to sample such rare events, as the free energy barrier between metastable states is large relative to the thermal energy. This renders these events inaccessible on the timescales typically simulated by unbiased molecular dynamics, limiting our understanding of these critical processes. In this paper, we proposed a novel unsupervised learning approach termed as slow feature analysis (SFA) which aims to extract slowly varying features from high-dimensional temporal data. SFA trained on small unbiased molecular dynamics simulations launched from AlphaFold generated conformational ensembles manages to capture rare events governing cryptic pocket opening, protein-ligand binding, and allosteric communications in a kinase. Metadynamics simulations using SFA as collective variables manage to sample 'deep' cryptic pocket opening within a few hundreds of nanoseconds which was beyond the reach of microsecond long unbiased molecular dynamics simulations. SFA augmented metadynamics also managed to capture conformational plasticity of protein upon ligand binding/unbinding and provided novel insights into allosteric communication in receptor-interacting protein kinase 2 (RIPK2) which dictates protein-protein interaction. Taken together, our results show how SFA acts as a dimensionality reduction tool which bridges the gap between AlphaFold, molecular dynamics simulation and metadynamics in context of capturing rare events in biomolecules, extending the scope of structure-based drug discovery in the era of AlphaFold.
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Affiliation(s)
- Shray Vats
- Department of Computer Science, University of Texas at Austin, Austin, TX, United States of America
| | | | - Pär Söderhjelm
- Division of Biophysical Chemistry, Chemical Center, Lund University, Lund, Sweden
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4
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Nayak S, Regati DR, Sowdhamini R. Computational analysis of human gut microbial prolyl oligopeptidases (POPs) reveal candidate genes as therapeutics for celiac disease. Sci Rep 2024; 14:19641. [PMID: 39179709 PMCID: PMC11343888 DOI: 10.1038/s41598-024-70079-1] [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: 02/20/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024] Open
Abstract
Celiac disease (CD) is a common autoimmune disorder in which the patients are unable to digest gluten, which is present in foods made up of wheat, barley and rye. Whilst diagnosis happens late in 80% of the cases, avoidance of such foods appears to be the common solution. Alternative management strategies are required for the patients and their families since CD is also genetically carried over. Probiotic therapeutics and the consumption of appropriate enzymes, such as prolyloligopeptidases (POPs), from gut-friendly bacteria could reduce the disease burden and provide a better lifestyle for CD patients. We have examined around 5000 gut bacterial genomes and identified nearly 4000 non-redundant putative POPs. A select set of 10 gut bacterial POP sequences were subject to three-dimensional modelling, ligand docking and molecular dynamics simulations where stable interactions were observed between the POPs and gluten peptides. Our study provides sequence and structural analysis of potential POP enzymes in gut bacterial genomes, which form a strong basis to offer probiotic solutions to CD patients. In particular, these enzymes could be lead future therapeutics for this disease.
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Affiliation(s)
- Soumya Nayak
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India
| | - Dheemanth Reddy Regati
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.
- Molecular Biophysics Unit, Indian Institute of Science, C V Raman Avenue, Bangalore, Karnataka, 560012, India.
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, GN Ramachandran Rd, Electronics City Phase 1, Electronic City, Bangalore, Karnataka, 560100, India.
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5
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Baños-Jaime B, Corrales-Guerrero L, Pérez-Mejías G, Rejano-Gordillo CM, Velázquez-Campoy A, Martínez-Cruz LA, Martínez-Chantar ML, De la Rosa MA, Díaz-Moreno I. Phosphorylation at the disordered N-end makes HuR accumulate and dimerize in the cytoplasm. Nucleic Acids Res 2024; 52:8552-8565. [PMID: 38966993 PMCID: PMC11317137 DOI: 10.1093/nar/gkae564] [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: 10/24/2023] [Revised: 05/30/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024] Open
Abstract
Human antigen R (HuR) is an RNA binding protein mainly involved in maintaining the stability and controlling the translation of mRNAs, critical for immune response, cell survival, proliferation and apoptosis. Although HuR is a nuclear protein, its mRNA translational-related function occurs at the cytoplasm, where the oligomeric form of HuR is more abundant. However, the regulation of nucleo-cytoplasmic transport of HuR and its connection with protein oligomerization remain unclear. In this work, we describe the phosphorylation of Tyr5 as a new hallmark for HuR activation. Our biophysical, structural and computational assays using phosphorylated and phosphomimetic HuR proteins demonstrate that phosphorylation of Tyr5 at the disordered N-end stretch induces global changes on HuR dynamics and conformation, modifying the solvent accessible surface of the HuR nucleo-cytoplasmic shuttling (HNS) sequence and releasing regions implicated in HuR dimerization. These findings explain the preferential cytoplasmic accumulation of phosphorylated HuR in HeLa cells, aiding to comprehend the mechanisms underlying HuR nucleus-cytoplasm shuttling and its later dimerization, both of which are relevant in HuR-related pathogenesis.
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Affiliation(s)
- Blanca Baños-Jaime
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Laura Corrales-Guerrero
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Gonzalo Pérez-Mejías
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Claudia M Rejano-Gordillo
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura; University Institute of Biosanitary Research of Extremadura (INUBE), Badajoz 06071, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, Zaragoza 50018, Spain
- Departament of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza 50009, Spain
- Institute for Health Research of Aragón (IIS Aragon), Zaragoza 50009, Spain
| | - Luis Alfonso Martínez-Cruz
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - María Luz Martínez-Chantar
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - Miguel A De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
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6
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Pietrafesa D, Napoli A, Iacovelli F, Romeo A, Tucci FG, Billi D, Falconi M. Deciphering the Role of Trehalose in Chroococcidiopsis sp. 029's High-Desiccation Resistance: Sequence Determination, Structural Modelling and Simulative Analysis of the 30S Ribosomal Subunit. Molecules 2024; 29:3486. [PMID: 39124891 PMCID: PMC11314286 DOI: 10.3390/molecules29153486] [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: 05/15/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Desert strains of the genus Chroococcidiopsis are among the most desiccation-resistant cyanobacteria capable of anhydrobiosis. The accumulation of two sugars, sucrose and trehalose, facilitates the entrance of anhydrobiotes into a reversible state of dormancy by stabilizing cellular components upon water removal. This study aimed to evaluate, at the atomistic level, the role of trehalose in desiccation resistance by using as a model system the 30S ribosomal subunit of the desert cyanobacterium Chroococcidiopsis sp. 029. Molecular dynamic simulations provided atomistic evidence regarding its protective role on the 30S molecular structure. Trehalose forms an enveloping shell around the ribosomal subunit and stabilizes the structures through a network of direct interactions. The simulation confirmed that trehalose actively interacts with the 30S ribosomal subunit and that, by replacing water molecules, it ensures ribosomal structural integrity during desiccation, thus enabling protein synthesis to be carried out upon rehydration.
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Affiliation(s)
| | | | | | | | | | | | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (D.P.); (A.N.); (F.I.); (A.R.); (F.G.T.); (D.B.)
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7
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Le Meur RA, Pecen TJ, Le Meur KV, Nagel ZD, Chazin WJ. Molecular basis and functional consequences of the interaction between the base excision repair DNA glycosylase NEIL1 and RPA. J Biol Chem 2024; 300:107579. [PMID: 39025455 PMCID: PMC11387677 DOI: 10.1016/j.jbc.2024.107579] [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: 12/29/2023] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024] Open
Abstract
NEIL1 is a DNA glycosylase that recognizes and initiates base excision repair of oxidized bases. The ubiquitous ssDNA binding scaffolding protein, replication protein A (RPA), modulates NEIL1 activity in a manner that depends on DNA structure. Interaction between NEIL1 and RPA has been reported, but the molecular basis of this interaction has yet to be investigated. Using a combination of NMR spectroscopy and isothermal titration calorimetry (ITC), we show that NEIL1 interacts with RPA through two contact points. An interaction with the RPA32C protein recruitment domain was mapped to a motif in the common interaction domain (CID) of NEIL1 and a dissociation constant (Kd) of 200 nM was measured. A substantially weaker secondary interaction with the tandem RPA70AB ssDNA binding domains was also mapped to the CID. Together these two contact points reveal NEIL1 has a high overall affinity (Kd ∼ 20 nM) for RPA. A homology model of the complex of RPA32C with the NEIL1 RPA binding motif in the CID was generated and used to design a set of mutations in NEIL1 to disrupt the interaction, which was confirmed by ITC. The mutant NEIL1 remains catalytically active against a thymine glycol lesion in duplex DNA in vitro. Testing the functional effect of disrupting the NEIL1-RPA interaction in vivo using a Fluorescence Multiplex-Host Cell Reactivation (FM-HCR) reporter assay revealed an unexpected role for NEIL1 in nucleotide excision repair. These findings are discussed in the context of the role of NEIL1 in replication-associated repair.
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Affiliation(s)
- Rémy A Le Meur
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Turner J Pecen
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kateryna V Le Meur
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
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8
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Montalvão RW, Pitt WR, Pinheiro VB, Blundell TL. Melodia: A Python Library for Protein Structure Analysis. Bioinformatics 2024; 40:btae468. [PMID: 39037932 PMCID: PMC11290362 DOI: 10.1093/bioinformatics/btae468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/21/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024] Open
Abstract
SUMMARY Analysing protein structure similarities is an important step in protein engineering and drug discovery. Methodologies that are more advanced than simple RMSD are available but often require extensive mathematical or computational knowledge for implementation. Grouping and optimising such tools in an efficient open-source library increases accessibility and encourages the adoption of more advanced metrics. Melodia is a Python library with a complete set of components devised for describing, comparing and analysing the shape of protein structures using differential geometry of three-dimensional curves and knot theory. It can generate robust geometric descriptors for thousands of shapes in just a few minutes. Those descriptors are more sensitive to structural feature variation than RMSD deviation. Melodia also incorporates sequence structural annotation and three-dimensional visualisations. AVAILABILITY AND IMPLEMENTATION Melodia is an open-source Python library freely available on https://github.com/rwmontalvao/Melodia_py, along with interactive Jupyter Notebook tutorials. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rinaldo W Montalvão
- Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49, Leuven 3000, Belgium
| | - William R Pitt
- Evotec (UK), 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, United Kingdom
| | - Vitor B Pinheiro
- Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49, Leuven 3000, Belgium
| | - Tom L Blundell
- Heart and Lung Research Institute, University of Cambridge, Biomedical Campus, Trumpington, Cambridgeshire CB2 0BB, United Kingdom
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9
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Matsubara M, Muraki Y, Suzuki H, Hatano N, Muraki K. Critical amino acid residues regulating TRPA1 Zn 2+ response: A comparative study across species. J Biol Chem 2024; 300:107302. [PMID: 38642892 PMCID: PMC11134551 DOI: 10.1016/j.jbc.2024.107302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024] Open
Abstract
Cellular zinc ions (Zn2+) are crucial for signal transduction in various cell types. The transient receptor potential (TRP) ankyrin 1 (TRPA1) channel, known for its sensitivity to intracellular Zn2+ ([Zn2+]i), has been a subject of limited understanding regarding its molecular mechanism. Here, we used metal ion-affinity prediction, three-dimensional structural modeling, and mutagenesis, utilizing data from the Protein Data Bank and AlphaFold database, to elucidate the [Zn2+]i binding domain (IZD) structure composed by specific AAs residues in human (hTRPA1) and chicken TRPA1 (gTRPA1). External Zn2+ induced activation in hTRPA1, while not in gTRPA1. Moreover, external Zn2+ elevated [Zn2+]i specifically in hTRPA1. Notably, both hTRPA1 and gTRPA1 exhibited inherent sensitivity to [Zn2+]i, as evidenced by their activation upon internal Zn2+ application. The critical AAs within IZDs, specifically histidine at 983/984, lysine at 711/717, tyrosine at 714/720, and glutamate at 987/988 in IZD1, and H983/H984, tryptophan at 710/716, E854/E855, and glutamine at 979/980 in IZD2, were identified in hTRPA1/gTRPA1. Furthermore, mutations, such as the substitution of arginine at 919 (R919) to H919, abrogated the response to external Zn2+ in hTRPA1. Among single-nucleotide polymorphisms (SNPs) at Y714 and a triple SNP at R919 in hTRPA1, we revealed that the Zn2+ responses were attenuated in mutants carrying the Y714 and R919 substitution to asparagine and proline, respectively. Overall, this study unveils the intrinsic sensitivity of hTRPA1 and gTRPA1 to [Zn2+]i mediated through IZDs. Furthermore, our findings suggest that specific SNP mutations can alter the responsiveness of hTRPA1 to extracellular and intracellular Zn2+.
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Affiliation(s)
- Masaki Matsubara
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Yukiko Muraki
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Hiroka Suzuki
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Noriyuki Hatano
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Katsuhiko Muraki
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan.
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10
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Yuan L, Liang X, He L. Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex. ACS OMEGA 2024; 9:20819-20831. [PMID: 38764655 PMCID: PMC11097150 DOI: 10.1021/acsomega.3c09433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/27/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage repair responses. For this process to occur, it is necessary for PHF8 to dissociate from Topbp1. Topbp1 binds to the acidic patch sequence (APS) of PHF8 through its C-terminal BRCT7/8 domain, and disrupting this interaction could be a promising strategy for cancer treatment. To investigate the dissociation process and binding pattern of BRCT7/8-PHF8, we employed enhanced sampling techniques, such as steered molecular dynamics (SMD) simulations and accelerated molecular dynamics (aMD) simulations, along with self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. Our results demonstrate that the dissociation of PHF8 from BRCT7/8 starts from the N-terminus, leading to the unfolding of the N-terminal helix. Additionally, we identified critical residues that play a pivotal role in this dissociation process. These findings provide valuable insights into the disassociation of PHF8 from BRCT7/8, which could potentially guide the development of novel drugs targeting Topbp1 for cancer therapy.
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Affiliation(s)
- Longxiao Yuan
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Xiaodan Liang
- School
of Computer Sciences and Technology, Tiangong
University, Tianjin 300387, China
| | - Lei He
- Institute
for Fetology, The First Affiliated Hospital
of Soochow University, Suzhou 215006, China
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11
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Abdullahi AD, Unban K, Saenjum C, Kodchasee P, Kangwan N, Thananchai H, Shetty K, Khanongnuch C. Antibacterial activities of Miang extracts against selected pathogens and the potential of the tannin-free extracts in the growth inhibition of Streptococcus mutans. PLoS One 2024; 19:e0302717. [PMID: 38718045 PMCID: PMC11078415 DOI: 10.1371/journal.pone.0302717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Bacterial pathogens have remained a major public health concern for several decades. This study investigated the antibacterial activities of Miang extracts (at non-neutral and neutral pH) against Bacillus cereus TISTR 747, Escherichia coli ATCC 22595, Salmonella enterica serovar Typhimurium TISTR 292 and Streptococcus mutans DMST 18777. The potential of Polyvinylpolypyrrolidone (PVPP)-precipitated tannin-free Miang extracts in growth-inhibition of the cariogenic Streptococcus mutans DMST 18777 and its biofilms was also evaluated. The tannin-rich fermented extracts had the best bacterial growth inhibition against S. mutans DMST 18777 with an MIC of 0.29 and 0.72 mg/mL for nonfilamentous fungi (NFP) Miang and filamentous-fungi-processed (FFP) Miang respectively. This observed anti-streptococcal activity still remained after PVPP-mediated precipitation of bioactive tannins especially, in NFP and FFP Miang. Characterization of the PVPP-treated extracts using High performance liquid chromatography quadrupole-time of flight-mass spectrometry (HPLC-QToF-MS) analysis, also offered an insight into probable compound classes responsible for the activities. In addition, Crystal violet-staining also showed better IC50 values for NFP Miang (4.30 ± 0.66 mg/mL) and FFP Miang (12.73 ± 0.11 mg/mL) against S. mutans DMST 18777 biofilms in vitro. Homology modeling and molecular docking analysis using HPLC-MS identified ligands in tannin-free Miang supernatants, was performed against modelled S. mutans DMST 18777 sortase A enzyme. The in silico analysis suggested that the inhibition by NFP and FFP Miang might be attributed to the presence of ellagic acid, flavonoid aglycones, and glycosides. Thus, these Miang extracts could be optimized and explored as natural active pharmaceutical ingredients (NAPIs) for applications in oral hygienic products.
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Affiliation(s)
- Aliyu Dantani Abdullahi
- Interdisciplinary Program in Biotechnology, The Graduate School, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Kridsada Unban
- Faculty of Agro-Industry, Division of Food Science and Technology, School of Agro-Industry, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Chalermpong Saenjum
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pratthana Kodchasee
- Research Center for Multidisciplinary Approaches to Miang, Multidisciplinary Research Institute (MDRI), Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Napapan Kangwan
- Division of Physiology, School of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Hathairat Thananchai
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Kalidas Shetty
- Faculty of Agriculture, Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Chartchai Khanongnuch
- Research Center for Multidisciplinary Approaches to Miang, Multidisciplinary Research Institute (MDRI), Chiang Mai University, Muang, Chiang Mai, Thailand
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
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12
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Virgens GS, Oliveira J, Cardoso MIO, Teodoro JA, Amaral DT. BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration. J Mol Graph Model 2024; 128:108721. [PMID: 38308972 DOI: 10.1016/j.jmgm.2024.108721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as blind docking or site-specific targeting, which are invaluable in applications ranging from drug repositioning to the exploration of new allosteric binding sites and toxicity assessments. BioProtIS has been designed with modularity at its core. This inherent flexibility empowers users to make custom modifications directly within the source code, tailoring the pipeline to their specific research needs. Moreover, it lays the foundation for seamless integration of diverse docking algorithms in future iterations, promising ongoing advancements in the field of computational biology. This pipeline is available for free distribution and can be download at: https://github.com/BBMDO/BioProtIS.
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Affiliation(s)
- Graziela Sória Virgens
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Júlia Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | | | - João Alfredo Teodoro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil.
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13
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Wang K, Cui H, Liu K, He Q, Fu X, Li W, Han W. Exploring the anti-gout potential of sunflower receptacles alkaloids: A computational and pharmacological analysis. Comput Biol Med 2024; 172:108252. [PMID: 38493604 DOI: 10.1016/j.compbiomed.2024.108252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Gout, a painful condition marked by elevated uric acid levels often linked to the diet's high purine and alcohol content, finds a potential treatment target in xanthine oxidase (XO), a crucial enzyme for uric acid production. This study explores the therapeutic properties of alkaloids extracted from sunflower (Helianthus annuus L.) receptacles against gout. By leveraging computational chemistry and introducing a novel R-based clustering algorithm, "TriDimensional Hierarchical Fingerprint Clustering with Tanimoto Representative Selection (3DHFC-TRS)," we assessed 231 alkaloid molecules from sunflower receptacles. Our clustering analysis pinpointed six alkaloids with significant gout-targeting potential, particularly emphasizing the fifth cluster's XO inhibition capabilities. Through molecular docking and the BatchDTA prediction model, we identified three top compounds-2-naphthylalanine, medroxalol, and fenspiride-with the highest XO affinity. Further molecular dynamics simulations assessed their enzyme active site interactions and binding free energies, employing MM-PBSA calculations. This investigation not only highlights the discovery of promising compounds within sunflower receptacle alkaloids via LC-MS but also introduces medroxalol as a novel gout treatment candidate, showcasing the synergy of computational techniques and LC-MS in drug discovery.
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Affiliation(s)
- Kaiyu Wang
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China
| | - Huizi Cui
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China
| | - Qizheng He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, Qianjin road 2699, China.
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14
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Panda SP, Roy P, Soren D, Ranjan Sahoo D, Dehury B, Rout AK, Behera BK, Das BK. Structural insights of Labeo catla (catla) myxovirus resistance protein,GTP binding recognition and constitutive expression induced with Poly I:C. J Biomol Struct Dyn 2024; 42:3520-3534. [PMID: 37227778 DOI: 10.1080/07391102.2023.2213345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The Myxovirus resistance (Mx) proteins are critical effectors belonging to the super-family of guanidine triphosphatase, often stimulated by type I interferon (IFN) and mediates antiviral responses to restrict the replication of numerous viral genes in fishes. In teleosts, Mx proteins display diverse and complicated antiviral activity in different species. The present investigation seeks to characterize the Mx gene from Labeo catla upon induction by double-stranded (ds) RNA, polyinosinic-polycytidylic acid, (poly I: C). Molecular modeling and all-atoms molecular dynamics (MD) simulations were employed to understand the architecture of the GTPase domain and its plausible mode of GTP recognition in Mx protein. The full-length L. catla Mx (LcMx) gene sequence (1821 bp nucleotides) encodes an open reading frame of 606 amino acids. Domain search indicated conserved tripartite domain architecture of LcMx and forms a major cluster with the Mx from other teleosts. The positively charged Arginine and polar Glutamine residues from helix 3 and 4 of stalk region LcMx aid in homo-oligomerization. MD simulation portrayed the role of conserved critical residues aid in GTP recognition by the GTPase domain which perfectly corroborates with experimental findings and prior MD studies. After injection of poly I:C, the temporal mRNA profile showed that LcMx expression was significantly elevated in the spleen, brain, kidney, liver, muscle, heart, intestine, and gill tissues. Collectively, these results suggest that the elevated expression of the major innate immune defense gene Mx was able to inhibit the poly I: C mediated virulence in fish.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | - Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Dhananjay Soren
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | | | - Budheswar Dehury
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
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15
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 PMCID: PMC11314541 DOI: 10.1016/j.slast.2023.10.005] [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: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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16
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Costanzi S, Stahr LG, Trivellin G, Stratakis CA. GPR101: Modeling a constitutively active receptor linked to X-linked acrogigantism. J Mol Graph Model 2024; 127:108676. [PMID: 38006624 PMCID: PMC10843723 DOI: 10.1016/j.jmgm.2023.108676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
GPR101 is a G protein-coupled receptor (GPCR) implicated in a rare form of genetic gigantism known as X-linked acrogigantism, or X-LAG. In particular, X-LAG patients harbor microduplications in the long arm of the X-chromosome that invariably include the GPR101 gene. Duplications of the GPR101 gene lead to the formation of a new chromatin domain that causes over-expression of the receptor in the pituitary tumors of the patients. Notably, GPR101 is a constitutively active receptor, which stimulates cells to produce the second messenger cyclic AMP (cAMP) in the absence of ligands. Moreover, GPR101 was recently reported to constitutively activate not only the cAMP pathway via Gs, but also other G protein subunits (Gq/11 and G12/13). Hence, chemicals that block the constitutive activity of GPR101, known as inverse agonists, have the potential to be useful for the development of pharmacological tools for the treatment of X-LAG. In this study, we provide structural insights into the putative structure of GPR101 based on in-house built homology models, as well as third party models based on the machine learning methods AlphaFold and AlphaFold-Multistate. Moreover, we report a molecular dynamics study, meant to further probe the constitutive activity of GPR101. Finally, we provide a structural comparison with the closest GPCRs, which suggests that GPR101 does not share their natural ligands. While this manuscript was under review, cryo-electron microscopy structures of GPR101 were reported. These structures are expected to enable computer-aided ligand discovery efforts targeting GPR101.
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Affiliation(s)
- Stefano Costanzi
- American University, Department of Chemistry, Washington, DC, USA.
| | - Lea G Stahr
- American University, Department of Chemistry, Washington, DC, USA
| | - Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
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17
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Philippe GJB, Huang YH, Mittermeier A, Brown CJ, Kaas Q, Ramlan SR, Wang CK, Lane D, Loewer A, Troeira Henriques S, Craik DJ. Delivery to, and Reactivation of, the p53 Pathway in Cancer Cells Using a Grafted Cyclotide Conjugated with a Cell-Penetrating Peptide. J Med Chem 2024; 67:1197-1208. [PMID: 38174919 DOI: 10.1021/acs.jmedchem.3c01682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Peptides are promising drug modalities that can modulate protein-protein interactions, but their application is hampered by their limited ability to reach intracellular targets. Here, we improved the cytosolic delivery of a peptide blocking p53:MDM2/X interactions using a cyclotide as a stabilizing scaffold. We applied several design strategies to improve intracellular delivery and found that the conjugation of the lead cyclotide to the cyclic cell-penetrating peptide cR10 was the most effective. Conjugation allowed cell internalization at micromolar concentration and led to elevated intracellular p53 levels in A549, MCF7, and MCF10A cells, as well as inducing apoptosis in A549 cells without causing membrane disruption. The lead peptide had >35-fold improvement in inhibitory activity and increased cellular uptake compared to a previously reported cyclotide p53 activator. In summary, we demonstrated the delivery of a large polar cyclic peptide in the cytosol and confirmed its ability to modulate intracellular protein-protein interactions involved in cancer.
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Affiliation(s)
- Grégoire Jean-Baptiste Philippe
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anna Mittermeier
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Christopher J Brown
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siti Radhiah Ramlan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David Lane
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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18
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Basu S, Veeraraghavan B, Anbarasu A. Impact of PmrB mutations on clinical Klebsiella pneumoniae with variable colistin-susceptibilities: Structural insights and potent therapeutic solutions. Chem Biol Drug Des 2024; 103:e14381. [PMID: 37875387 DOI: 10.1111/cbdd.14381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections continue to impose high morbidity threats to hospitalized patients worldwide, limiting therapeutic options to last-resort antibiotics like colistin. However, the dynamic genomic landscape of colistin-resistant K. pneumoniae (COLR-Kp) invoked ardent exploration of underlying molecular signatures for therapeutic propositions/designs. We unveiled the structural impact of the widespread and emerging PmrB mutations involved in colistin resistance (COLR) in K. pneumoniae. In the present study, clinical isolates of K. pneumoniae expressed variable susceptibilities to colistin (>0.5 μg/mL for resistant and ≤0.25 μg/mL for susceptible) despite mutations such as T157P, G207D and T246A. The protein sequences extracted from in-house sequenced genomes were used to model mutant PmrB proteins and analyze the underlying structural alterations. The mutations were contrasted based on molecular dynamics simulation trajectories, free-energy landscapes and structural flexibility profiles. The altered backbone flexibilities can be an essential factor for mutant selection by COLR K. pneumoniae and can provide clues to deal with emerging mutants. Furthermore, PmrB having high druggability confidence (>0.99), was explored as a potential target for 1396 virtually screened FDA-approved drug candidates. Among the top-10 compounds (scores >70), amphotericin B was found to be potential candidate with high affinity (Binding energy <-8 kcal/mol) and stable interactions (RMSF <0.7 Å) against PmrB druggable pockets, despite the mutations, which encourages future adjunct therapeutic research against COLR-Kp.
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Affiliation(s)
- Soumya Basu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College (CMC), Vellore, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
- Department of Biotechnology, SBST, VIT, Vellore, India
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19
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Xu Y, Zhang F, Mu G, Zhu X. Effect of lactic acid bacteria fermentation on cow milk allergenicity and antigenicity: A review. Compr Rev Food Sci Food Saf 2024; 23:e13257. [PMID: 38284611 DOI: 10.1111/1541-4337.13257] [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: 03/02/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
Cow milk is a major allergenic food. The potential prevention and treatment effects of lactic acid bacteria (LAB)-fermented dairy products on allergic symptoms have garnered considerable attention. Cow milk allergy (CMA) is mainly attributed to extracellular and/or cell envelope proteolytic enzymes with hydrolysis specificity. Numerous studies have demonstrated that LAB prevents the risk of allergies by modulating the development and regulation of the host immune system. Specifically, LAB and its effectors can enhance intestinal barrier function and affect immune cells by interfering with humoral and cellular immunity. Fermentation hydrolysis of allergenic epitopes is considered the main mechanism of reducing CMA. This article reviews the linear epitopes of allergens in cow milk and the effect of LAB on these allergens and provides insight into the means of predicting allergenic epitopes by conventional laboratory analysis methods combined with molecular simulation. Although LAB can reduce CMA in several ways, the mechanism of action remains partially clarified. Therefore, this review additionally attempts to summarize the main mechanism of LAB fermentation to provide guidance for establishing an effective preventive and treatment method for CMA and serve as a reference for the screening, research, and application of LAB-based intervention.
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Affiliation(s)
- Yunpeng Xu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, P. R. China
| | - Feifei Zhang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, P. R. China
| | - Guangqing Mu
- Dalian Key Laboratory of Functional Probiotics, Dalian, Liaoning, P. R. China
| | - Xuemei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, P. R. China
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20
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Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc Natl Acad Sci U S A 2023; 120:e2312057120. [PMID: 38085776 PMCID: PMC10742377 DOI: 10.1073/pnas.2312057120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.
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Affiliation(s)
- Jean M. Custodio
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Tatiana J. Rosales
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Chad A. Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Alyssa G. Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Lauren M. Landau
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Grant L. J. Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Pramod K. Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT06030
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
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21
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Shiryaev SA, Cieplak P, Cheltsov A, Liddington RC, Terskikh AV. Dual function of Zika virus NS2B-NS3 protease. PLoS Pathog 2023; 19:e1011795. [PMID: 38011215 PMCID: PMC10723727 DOI: 10.1371/journal.ppat.1011795] [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: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro binds single-stranded RNA with a Kd of ~0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered "super-open" conformation do not bind RNA. Likewise, stabilizing NS2B-NS3pro in the "closed" (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the "open" conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved across Flaviviridae family and could be aligned with the positively charged grove on NS3hel, providing a contiguous binding surface for the negative RNA strand exiting helicase. We propose a "reverse inchworm" model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that NS2B-NS3pro cycles between open and super-open conformations to bind and release RNA enabling long-range NS3hel processivity. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.
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Affiliation(s)
- Sergey A. Shiryaev
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Anton Cheltsov
- Q-mol LLC, San Diego, California, United States of America
| | - Robert C. Liddington
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Alexey V. Terskikh
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
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22
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Chi YI, Jorge SD, Jensen DR, Smith BC, Volkman BF, Mathison AJ, Lomberk G, Zimmermann MT, Urrutia R. A multi-layered computational structural genomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1. Comput Struct Biotechnol J 2023; 21:5249-5258. [PMID: 37954151 PMCID: PMC10632586 DOI: 10.1016/j.csbj.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
This study investigates the functional significance of assorted variants of uncertain significance (VUS) in euchromatic histone lysine methyltransferase 1 (EHMT1), which is critical for early development and normal physiology. EHMT1 mutations cause Kleefstra syndrome and are linked to various human cancers. However, accurate functional interpretations of these variants are yet to be made, limiting diagnoses and future research. To overcome this, we integrate conventional tools for variant calling with computational biophysics and biochemistry to conduct multi-layered mechanistic analyses of the SET catalytic domain of EHMT1, which is critical for this protein function. We use molecular mechanics and molecular dynamics (MD)-based metrics to analyze the SET domain structure and functional motions resulting from 97 Kleefstra syndrome missense variants within the domain. Our approach allows us to classify the variants in a mechanistic manner into SV (Structural Variant), DV (Dynamic Variant), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). Our findings reveal that the damaging variants are mostly mapped around the active site, substrate binding site, and pre-SET regions. Overall, we report an improvement for this method over conventional tools for variant interpretation and simultaneously provide a molecular mechanism for variant dysfunction.
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Affiliation(s)
- Young-In Chi
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Salomão D. Jorge
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Davin R. Jensen
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C. Smith
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F. Volkman
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J. Mathison
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T. Zimmermann
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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23
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Chi YI, Jorge SD, Jensen DR, Smith BC, Volkman BF, Mathison AJ, Lomberk G, Zimmermann MT, Urrutia R. A Multi-Layered Computational Structural Genomics Approach Enhances Domain-Specific Interpretation of Kleefstra Syndrome Variants in EHMT1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556558. [PMID: 37786696 PMCID: PMC10541560 DOI: 10.1101/2023.09.06.556558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
This study investigates the functional significance of assorted variants of uncertain significance (VUS) in euchromatic histone lysine methyltransferase 1 (EHMT1), which is critical for early development and normal physiology. EHMT1 mutations cause Kleefstra syndrome and are linked to various human cancers. However, accurate functional interpretation of these variants are yet to be made, limiting diagnoses and future research. To overcome this, we integrate conventional tools for variant calling with computational biophysics and biochemistry to conduct multi-layered mechanistic analyses of the SET catalytic domain of EHMT1, which is critical for this protein function. We use molecular mechanics and molecular dynamics (MD)-based metrics to analyze the SET domain structure and functional motions resulting from 97 Kleefstra syndrome missense variants within this domain. Our approach allows us to classify the variants in a mechanistic manner into SV (Structural Variant), DV (Dynamic Variant), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). Our findings reveal that the damaging variants are mostly mapped around the active site, substrate binding site, and pre-SET regions. Overall, we report an improvement for this method over conventional tools for variant interpretation and simultaneously provide a molecular mechanism of variant dysfunction.
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24
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Scarpa F, Azzena I, Ciccozzi A, Giovanetti M, Locci C, Casu M, Fiori PL, Borsetti A, Cella E, Quaranta M, Pascarella S, Sanna D, Ciccozzi M. Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant. Int J Mol Sci 2023; 24:13573. [PMID: 37686383 PMCID: PMC10487968 DOI: 10.3390/ijms241713573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The XBB.1.16 SARS-CoV-2 variant, also known as Arcturus, is a recent descendant lineage of the recombinant XBB (nicknamed Gryphon). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the immune response compared to other circulating lineages. In this context, we conducted a comprehensive genome-based survey to gain a detailed understanding of the evolution and potential dangers of the XBB.1.16 variant, which became dominant in late June. Genetic data indicates that the XBB.1.16 variant exhibits an evolutionary background with limited diversification, unlike dangerous lineages known for rapid changes. The evolutionary rate of XBB.1.16, which amounts to 3.95 × 10-4 subs/site/year, is slightly slower than that of its direct progenitors, XBB and XBB.1.5, which have been circulating for several months. A Bayesian Skyline Plot reconstruction suggests that the peak of genetic variability was reached in early May 2023, and currently, it is in a plateau phase with a viral population size similar to the levels observed in early March. Structural analyses indicate that, overall, the XBB.1.16 variant does not possess structural characteristics markedly different from those of the parent lineages, and the theoretical affinity for ACE2 does not seem to change among the compared variants. In conclusion, the genetic and structural analyses of SARS-CoV-2 XBB.1.16 do not provide evidence of its exceptional danger or high expansion capability. Detected differences with previous lineages are probably due to genetic drift, which allows the virus constant adaptability to the host, but they are not necessarily connected to a greater danger. Nevertheless, continuous genome-based monitoring is essential for a better understanding of its descendants and other lineages.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-009, MG, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), National Institute of Health, 00161 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
| | - Miriana Quaranta
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
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25
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Aldakhil T, Alshammari SO, Siraj B, El-Aarag B, Zarina S, Salehi D, Ahmed A. The structural characterization and bioactivity assessment of nonspecific lipid transfer protein 1 (nsLTP1) from caraway (Carum carvi) seeds. BMC Complement Med Ther 2023; 23:254. [PMID: 37474939 PMCID: PMC10357877 DOI: 10.1186/s12906-023-04083-9] [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: 02/08/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Carum carvi (caraway) of the Apiaceae family has been used in many cultures as a cooking spice and part of the folk medicine. Previous reports primarily focus on the medicinal properties of caraway seed essential oil and the whole seeds extract. However, no effort has been made to study caraway proteins and their potential pharmacological properties, including nonspecific lipid transfer protein (nsLTP), necessitating further research. The current study aimed to characterize nonspecific lipid transfer protein 1 (nsLTP1) from caraway seed, determine its three-dimensional structure, and analyze protein-ligand complex interactions through docking studies. We also evaluated nsLTP1 in vitro cytotoxic effect and antioxidant capacity. Additionally, nsLTP1 thermal- and pH- stability were investigated. METHODS Caraway nsLTP1 was purified using two-dimensional chromatography. The complete amino acid sequence of nsLTP1 was achieved by intact protein sequence for the first 20 residues and the overlapping digested peptides. The three-dimensional structure was predicted using MODELLER. Autodock Vina software was employed for docking fatty acids against caraway nsLTP1. Assessment of nsLTP1 cytotoxic activity was achieved by MTS assay, and the Trolox equivalent antioxidant capacity (TAC) was determined. Thermal and pH stability of the nsLTP1 was examined by circular dichroism (CD) spectroscopy. RESULTS Caraway nsLTP1 is composed of 91 residues and weighs 9652 Da. The three-dimensional structure of caraway nsLTP1 sequence was constructed based on searching known structures in the PDB. We chose nsLTP of Solanum melongena (PDB ID: 5TVI) as the modeling template with the highest identity among all other homologous proteins. Docking linolenic acid with caraway protein showed a maximum binding score of -3.6 kcal/mol. A preliminary screening of caraway nsLTP1 suppressed the proliferation of human breast cancer cell lines MDA-MB-231 and MCF-7 in a dose‑dependent manner with an IC50 value of 52.93 and 44.76 μM, respectively. Also, nsLTP1 (41.4 μM) showed TAC up to 750.4 μM Trolox equivalent. Assessment of nsLTP1 demonstrated high thermal/pH stability. CONCLUSION To the best of our knowledge, this is the first study carried out on nsLTP1 from caraway seeds. We hereby report the sequence of nsLTP1 from caraway seeds and its possible interaction with respective fatty acids using in silico approach. Our data indicated that the protein had anticancer and antioxidant activities and was thermally stable.
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Affiliation(s)
- Taibah Aldakhil
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 16278, Saudi Arabia
| | - Saud O Alshammari
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Department of Plant Chemistry and Natural Products, Faculty of Pharmacy, Northern Border University, Arar, 91431, Saudi Arabia
| | - Bushra Siraj
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - Bishoy El-Aarag
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Biochemistry Division, Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Koom, 32512, Egypt
| | - Shamshad Zarina
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - David Salehi
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Aftab Ahmed
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA.
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26
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Scarpa F, Locci C, Azzena I, Casu M, Fiori PL, Ciccozzi A, Giovanetti M, Quaranta M, Ceccarelli G, Pascarella S, Ciccozzi M, Sanna D. SARS-CoV-2 Recombinants: Genomic Comparison between XBF and Its Parental Lineages. Microorganisms 2023; 11:1824. [PMID: 37512996 PMCID: PMC10383834 DOI: 10.3390/microorganisms11071824] [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: 05/31/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Recombination events are very common and represent one of the primary drivers of RNA virus evolution. The XBF SARS-CoV-2 lineage is one of the most recently generated recombinants during the COVID-19 pandemic. It is a recombinant of BA.5.2.3 and BA.2.75.3, both descendants of lineages that caused many concerns (BA.5 and BA.2.75, respectively). Here, we performed a genomic survey focused on comparing the recombinant XBF with its parental lineages to provide a comprehensive assessment of the evolutionary potential, epidemiological trajectory, and potential risks. Genetic analyses indicated that although XBF initially showed the typical expansion depicted by a steep curve, causing several concerns, currently there is no indication of significant expansion potential or a contagion rate surpassing that of other currently active or previously prevalent lineages. BSP indicated that the peak has been reached around 19 October 2022 and then the genetic variability suffered slight oscillations until early 5 March 2023 when the population size reduced for the last time starting its last plateau that is still lasting. Structural analyses confirmed its reduced potential, also indicating that properties of NTDs and RBDs of XBF and its parental lineages present no significant difference. Of course, cautionary measures must still be taken and genome-based monitoring remains the best tool for detecting any important changes in viral genome composition.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
- Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
| | - Miriana Quaranta
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Campus Bio-Medico, Fondazione Policlinico Universitario, 00128 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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Scarpa F, Imperia E, Ciccozzi A, Pascarella S, Quaranta M, Giovanetti M, Borsetti A, Petrosillo N, Ciccozzi M. Khosta: A Genetic and Structural Point of View of the Forgotten Virus. Infect Dis Rep 2023; 15:307-318. [PMID: 37367190 DOI: 10.3390/idr15030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Bats are well-known to be natural reservoirs of various zoonotic coronaviruses, which have caused outbreaks of severe acute respiratory syndrome (SARS) and the COVID-19 pandemic in 2002 and 2019, respectively. In late 2020, two new Sarbecoviruses were found in Russia, isolated in Rhinolophus bats, i.e., Khosta-1 in R. ferrumequinum and Khosta-2 in R. hipposideros. The potential danger associated with these new species of Sarbecovirus is that Khosta-2 has been found to interact with the same entry receptor as SARS-CoV-2. Our multidisciplinary approach in this study demonstrates that Khosta-1 and -2 currently appear to be not dangerous with low risk of spillover, as confirmed by prevalence data and by phylogenomic reconstruction. In addition, the interaction between Khosta-1 and -2 with ACE2 appears weak, and furin cleavage sites are absent. While the possibility of a spillover event cannot be entirely excluded, it is currently highly unlikely. This research further emphasizes the importance of assessing the zoonotic potential of widely distributed batborne CoV in order to monitor changes in genomic composition of viruses and prevent spillover events (if any).
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico, 00128 Rome, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico, 00128 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", 00185 Rome, Italy
| | - Miriana Quaranta
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", 00185 Rome, Italy
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
- Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30.190-009, Minas Gerais, Brazil
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control-Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University of Campus Bio-Medico, 00128 Rome, Italy
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28
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Fei H, Li W, Lu N, Liu Q, Zhang Y. Molecular dynamic simulation reveals the molecular interactions of epidermal growth factor receptor with musk xylene are involved in the carcinogenicity. RSC Adv 2023; 13:16311-16320. [PMID: 37266509 PMCID: PMC10230269 DOI: 10.1039/d2ra07552k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/24/2023] [Indexed: 06/03/2023] Open
Abstract
Musk xylene (MX), a kind of personal care product, has become a new type of environmental contaminant in recent years. Long-term exposure to MX is associated with a variety of cancers, but the mechanism is still unclear. Meanwhile, our previous research showed that MX exposure could lead to malignant transformation of human liver cells L02 and up-regulation of multi genes which are involved in the MAPK signaling pathway, such as the epidermal growth factor receptor (EGFR). These findings indicated that the MAPK signaling pathway might be involved in the malignant transformation caused by MX, but the mechanism is also unclear. In this study, the underlying interaction mechanisms between EGFR and MX were investigated using molecular dynamics (MD) simulation. Results revealed that MX bound to the ECD of EGFR in four binding sites, which was mainly driven by van der Waals and nonpolar interactions, and the affinity of MX toward ECD was sIII > sI > sII > sIV. Further analysis through MD simulation found that s III, the site with the strongest binding, was coincidentally located at the binding area of EGF, which is the natural ligand of EGFR. Therefore, we speculated that MX may activate the MAPK signaling pathway by binding to EGFR in a similar way to EGF, and finally lead to tumorigenesis. In addition, the MM/PBSA method could also be utilized to calculate the hot residues in each binding site. The prediction of hot residues would provide some theoretical guidance for further study of the carcinogenesis mechanisms of MX both in MD simulation and experimental research.
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Affiliation(s)
- Huaxing Fei
- Institute of Electromagnetics and Acoustics, Department of Electronic Science, Xiamen University Xiamen 361005 P. R. China
- Fujian Engineering Research Center for EDA, Fujian Provincial Key Laboratory of Electromagnetic Wave Science and Detection Technology, Xiamen Key Laboratory of Multiphysics Electronic Information, Institute of Electromagnetics and Acoustics, Xiamen University Xiamen 361005 P. R. China
| | - Wen Li
- Institute of Electromagnetics and Acoustics, Department of Electronic Science, Xiamen University Xiamen 361005 P. R. China
- Fujian Engineering Research Center for EDA, Fujian Provincial Key Laboratory of Electromagnetic Wave Science and Detection Technology, Xiamen Key Laboratory of Multiphysics Electronic Information, Institute of Electromagnetics and Acoustics, Xiamen University Xiamen 361005 P. R. China
| | - Nan Lu
- Institute of Electromagnetics and Acoustics, Department of Electronic Science, Xiamen University Xiamen 361005 P. R. China
- Fujian Engineering Research Center for EDA, Fujian Provincial Key Laboratory of Electromagnetic Wave Science and Detection Technology, Xiamen Key Laboratory of Multiphysics Electronic Information, Institute of Electromagnetics and Acoustics, Xiamen University Xiamen 361005 P. R. China
| | - Qinghuo Liu
- Institute of Electromagnetics and Acoustics, Department of Electronic Science, Xiamen University Xiamen 361005 P. R. China
- EIT Eastern Institute for Advanced Study Ningbo China
| | - Youyu Zhang
- Institute of Electromagnetics and Acoustics, Department of Electronic Science, Xiamen University Xiamen 361005 P. R. China
- Fujian Engineering Research Center for EDA, Fujian Provincial Key Laboratory of Electromagnetic Wave Science and Detection Technology, Xiamen Key Laboratory of Multiphysics Electronic Information, Institute of Electromagnetics and Acoustics, Xiamen University Xiamen 361005 P. R. China
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29
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Bazzani L, Imperia E, Scarpa F, Sanna D, Casu M, Borsetti A, Pascarella S, Petrosillo N, Cella E, Giovanetti M, Ciccozzi M. SARS-CoV CH.1.1 Variant: Genomic and Structural Insight. Infect Dis Rep 2023; 15:292-298. [PMID: 37367188 DOI: 10.3390/idr15030029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
In early February 2023, the Omicron subvariant XBB.1.5, also known as "Kraken", accounted for more than 44% of new COVID-19 cases worldwide, whereas a relatively new Omicron subvariant named CH.1.1, deemed "Orthrus", accounted for less than 6% of new COVID-19 cases during the subsequent weeks. This emerging variant carries a mutation, L452R, previously observed in the highly pathogenic Delta and the highly transmissible BA.4 and BA.5 variants, necessitating a shift to active surveillance to assure adequate preparedness for likely future epidemic peaks. We provide a preliminary understanding of the global distribution of this emerging SARS-CoV-2 variant by combining genomic data with structural molecular modeling. In addition, we shield light on the number of specific point mutations in this lineage that may have functional significance, thereby increasing the risk of disease severity, vaccine resistance, and increased transmission. This variant shared about 73% of the mutations with Omicron-like strains. Our homology modeling analysis revealed that CH.1.1 may have a weakened interaction with ACE2 and that its electrostatic potential surface appears to be more positive than that of the reference ancestral virus. Finally, our phylogenetic analysis revealed that this likely-emerging variant was already cryptically circulating in European countries prior to its first detection, highlighting the importance of having access to whole genome sequences for detecting and controlling emerging viral strains.
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Affiliation(s)
- Liliana Bazzani
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center (CNAIDS), National Institute of Health, 00161 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control-Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
| | - Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30190-002, MG, Brazil
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
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Debroy R, Ramaiah S. Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study. World J Microbiol Biotechnol 2023; 39:187. [PMID: 37150764 PMCID: PMC10164620 DOI: 10.1007/s11274-023-03634-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023]
Abstract
The pathogenic Enterobacter cloacae subsp. cloacae str. ATCC 13047 has contemporarily emerged as a multi-drug resistant strain. To formulate an effective treatment option, alternative therapeutic methods need to be explored. The present study focused on Gene Interaction Network study of 46 antimicrobial resistance genes to reveal the densely interconnecting and functional hub genes in E. cloacae ATCC 13047. The AMR genes were subjected to clustering, topological and functional enrichment analysis, revealing rpsE (RpsE), acrA (AcrA) and arnT (ArnT) as novel therapeutic drug targets for hindering drug resistance in the pathogenic strain. Network topology further indicated translational protein RpsE to be exploited as a promising drug-target candidate for which the structure was predicted, optimized and validated through molecular dynamics simulations (MDS). Absorption, distribution, metabolism and excretion screening recognized ZINC5441082 (N-Isopentyladenosine) (Lead_1) and ZINC1319816 (cyclopentyl-aminopurinyl-hydroxymethyl-oxolanediol) (Lead_2) as orally bioavailable compounds against RpsE. Molecular docking and MDS confirmed the binding efficacy and protein-ligand complex stability. Furthermore, binding free energy (Gbind) calculations, principal component and free energy landscape analyses affirmed the predicted nucleoside analogues against RpsE protein to be comprehensively examined as a potential treatment strategy against E. cloacae ATCC 13047.
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Affiliation(s)
- Reetika Debroy
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
- Department of Bio-Medical Sciences, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
- Department of Bio-Sciences, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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Moreno-Cabezuelo JÁ, Del Carmen Muñoz-Marín M, López-Lozano A, Athayde D, Simón-García A, Díez J, Archer M, Issoglio FM, García-Fernández JM. Production, homology modeling and mutagenesis studies on GlcH glucose transporter from Prochlorococcus sp. strain SS120. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148954. [PMID: 36563737 DOI: 10.1016/j.bbabio.2022.148954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The marine cyanobacterium Prochlorococcus is one of the main primary producers on Earth, which can take up glucose by using the high affinity, multiphasic transporter GlcH. We report here the overexpression of glcH from Prochlorococcus marinus strain SS120 in Escherichia coli. Modeling studies of GlcH using the homologous MelB melibiose transporter from Salmonella enterica serovar Typhimurium showed high conservation at the overall fold. We observed that an important structural interaction, mediated by a strong hydrogen bond between D8 and R141, is conserved in Prochlorococcus, although the corresponding amino acids in MelB from Salmonella are different. Biased docking studies suggested that when glucose reaches the pocket of the transporter and interacts with D8 and R141, the hydrogen bond network in which these residues are involved could be disrupted, favoring a conformational change with the subsequent translocation of the glucose molecule towards the cytoplasmic region of the pmGlcH structure. Based on these theoretical predictions and on the conservation of N117 and W348 in other MelB structures, D8, N117, R141 and W348 were mutated to glycine residues. Their key role in glucose transport was evaluated by glucose uptake assays. N117G and W348G mutations led to 17 % decrease in glucose uptake, while D8G and R141G decreased the glucose transport by 66 % and 92 % respectively. Overall, our studies provide insights into the Prochlorococcus 3D-structure of GlcH, paving the way for further analysis to understand the features which are involved in the high affinity and multiphasic kinetics of this transporter.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Ana Simón-García
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Federico M Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain.
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Scarpa F, Azzena I, Locci C, Casu M, Fiori PL, Ciccozzi A, Angeletti S, Imperia E, Giovanetti M, Maruotti A, Borsetti A, Cauda R, Cassone A, Via A, Pascarella S, Sanna D, Ciccozzi M. Molecular In-Depth on the Epidemiological Expansion of SARS-CoV-2 XBB.1.5. Microorganisms 2023; 11:microorganisms11040912. [PMID: 37110335 PMCID: PMC10142263 DOI: 10.3390/microorganisms11040912] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Since the beginning of the pandemic, the generation of new variants periodically recurs. The XBB.1.5 SARS-CoV-2 variant is one of the most recent. This research was aimed at verifying the potential hazard of this new subvariant. To achieve this objective, we performed a genome-based integrative approach, integrating results from genetic variability/phylodynamics with structural and immunoinformatic analyses to obtain as comprehensive a viewpoint as possible. The Bayesian Skyline Plot (BSP) shows that the viral population size reached the plateau phase on 24 November 2022, and the number of lineages peaked at the same time. The evolutionary rate is relatively low, amounting to 6.9 × 10−4 subs/sites/years. The NTD domain is identical for XBB.1 and XBB.1.5 whereas their RBDs only differ for the mutations at position 486, where the Phe (in the original Wuhan) is replaced by a Ser in XBB and XBB.1, and by a Pro in XBB.1.5. The variant XBB.1.5 seems to spread more slowly than sub-variants that have caused concerns in 2022. The multidisciplinary molecular in-depth analyses on XBB.1.5 performed here does not provide evidence for a particularly high risk of viral expansion. Results indicate that XBB.1.5 does not possess features to become a new, global, public health threat. As of now, in its current molecular make-up, XBB.1.5 does not represent the most dangerous variant.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (F.S.); (M.C.)
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, Department of Medicine and Surgery, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Research Unit of Laboratory, University Hospital Campus Bio-Medico, 00128 Rome, Italy
| | - Elena Imperia
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Unit of Gastroenterology, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil
- Science and Technology for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
| | | | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- Correspondence: (F.S.); (M.C.)
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Książek M, Goulas T, Mizgalska D, Rodríguez-Banqueri A, Eckhard U, Veillard F, Waligórska I, Benedyk-Machaczka M, Sochaj-Gregorczyk AM, Madej M, Thøgersen IB, Enghild JJ, Cuppari A, Arolas JL, de Diego I, López-Pelegrín M, Garcia-Ferrer I, Guevara T, Dive V, Zani ML, Moreau T, Potempa J, Gomis-Rüth FX. A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia. Chem Sci 2023; 14:869-888. [PMID: 36755705 PMCID: PMC9890683 DOI: 10.1039/d2sc04166a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Periodontopathogenic Tannerella forsythia uniquely secretes six peptidases of disparate catalytic classes and families that operate as virulence factors during infection of the gums, the KLIKK-peptidases. Their coding genes are immediately downstream of novel ORFs encoding the 98-132 residue potempins (Pot) A, B1, B2, C, D and E. These are outer-membrane-anchored lipoproteins that specifically and potently inhibit the respective downstream peptidase through stable complexes that protect the outer membrane of T. forsythia, as shown in vivo. Remarkably, PotA also contributes to bacterial fitness in vivo and specifically inhibits matrix metallopeptidase (MMP) 12, a major defence component of oral macrophages, thus featuring a novel and highly-specific physiological MMP inhibitor. Information from 11 structures and high-confidence homology models showed that the potempins are distinct β-barrels with either a five-stranded OB-fold (PotA, PotC and PotD) or an eight-stranded up-and-down fold (PotE, PotB1 and PotB2), which are novel for peptidase inhibitors. Particular loops insert like wedges into the active-site cleft of the genetically-linked peptidases to specifically block them either via a new "bilobal" or the classic "standard" mechanism of inhibition. These results discover a unique, tightly-regulated proteolytic armamentarium for virulence and competence, the KLIKK-peptidase/potempin system.
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Affiliation(s)
- Mirosław Książek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly Temponera str. Karditsa 43100 Greece
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Arturo Rodríguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Irena Waligórska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Małgorzata Benedyk-Machaczka
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Alicja M. Sochaj-Gregorczyk
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityGronostajowa 7Kraków 30-387Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Ida B. Thøgersen
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Joan L. Arolas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
| | - Iñaki de Diego
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Sample Environment and Characterization Group, European XFEL GmbH Holzkoppel 4 Schenefeld 22869 Germany
| | - Mar López-Pelegrín
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Irene Garcia-Ferrer
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), ERL CNRS 9004Gif-sur-Yvette 91191France
| | - Marie-Louise Zani
- Departement de Biochimie, Université de Tours10 Bd. TonelléTours Cedex 37032France
| | | | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
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Lee FS, Anderson AG, Olafson BD. Benchmarking TriadAb using targets from the second antibody modeling assessment. Protein Eng Des Sel 2023; 36:gzad013. [PMID: 37864287 DOI: 10.1093/protein/gzad013] [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: 05/05/2023] [Revised: 08/10/2023] [Indexed: 10/22/2023] Open
Abstract
Computational modeling and design of antibodies has become an integral part of today's research and development in antibody therapeutics. Here we describe the Triad Antibody Homology Modeling (TriadAb) package, a functionality of the Triad protein design platform that predicts the structure of any heavy and light chain sequences of an antibody Fv domain using template-based modeling. To gauge the performance of TriadAb, we benchmarked against the results of the Second Antibody Modeling Assessment (AMA-II). On average, TriadAb produced main-chain carbonyl root-mean-square deviations between models and experimentally determined structures at 1.10 Å, 1.45 Å, 1.41 Å, 3.04 Å, 1.47 Å, 1.27 Å, 1.63 Å in the framework and the six complementarity-determining regions (H1, H2, H3, L1, L2, L3), respectively. The inaugural results are comparable to those reported in AMA-II, corroborating with our internal bench-based experiences that models generated using TriadAb are sufficiently accurate and useful for antibody engineering using the sequence design capabilities provided by Triad.
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Choudhary P, Waseem M, Kumar S, Subbarao N, Srivastava S, Chakdar H. Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study. World J Microbiol Biotechnol 2023; 39:75. [PMID: 36637534 DOI: 10.1007/s11274-023-03518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023]
Abstract
Appropriate amino acid substitutions are critical for protein engineering to redesign catalytic properties of industrially important enzymes like lipases. The present study aimed for improving the environmental stability of lipase from Pseudomonas plecoglossicida S7 through site-directed mutagenesis driven by computational studies. lipA gene was amplified and sequenced. Both wild type (WT) and mutant type (MT) lipase genes were expressed into the pET SUMO system. The expressed proteins were purified and characterized for pH and thermostability. The lipase gene belonged to subfamily I.1 lipase. Molecular dynamics revealed that Y12F-palmitic acid complex had a greater binding affinity (-6.3 Kcal/mol) than WT (-6.0 Kcal/mol) complex. Interestingly, MDS showed that the binding affinity of WT-complex (-130.314 ± 15.11 KJ/mol) was more than mutant complex (-108.405 ± 69.376 KJ/mol) with a marked increase in the electrostatic energy of mutant (-26.969 ± 12.646 KJ/mol) as compared to WT (-15.082 ± 13.802 KJ/mol). Y12F mutant yielded 1.27 folds increase in lipase activity at 55 °C as compared to the purified WT protein. Also, Y12F mutant showed increased activity (~ 1.2 folds each) at both pH 6 and 10. P. plecoglossicida S7. Y12F mutation altered the kinetic parameters of MT (Km- 1.38 mM, Vmax- 22.32 µM/min) as compared to WT (Km- 1.52 mM, Vmax- 29.76 µM/min) thus increasing the binding affinity of mutant lipase. Y12F mutant lipase with better pH and thermal stability can be used in biocatalysis.
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Affiliation(s)
- Prassan Choudhary
- Microbial Technology Unit-II, ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Maunath Bhanjan, India
- Amity Institute of Biotechnology, Amity University, 226010, Lucknow, India
| | - Mohd Waseem
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, 110012, New Delhi, India
| | - Sunil Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, 110012, Pusa, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, 110012, New Delhi, India
| | - Shilpi Srivastava
- Amity Institute of Biotechnology, Amity University, 226010, Lucknow, India
| | - Hillol Chakdar
- Microbial Technology Unit-II, ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Maunath Bhanjan, India.
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Cetintas VB, Duzgun Z, Akalin T, Ozgiray E, Dogan E, Yildirim Z, Akinturk N, Biceroglu H, Ertan Y, Kosova B. Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma. J Biomol Struct Dyn 2023; 41:11471-11483. [PMID: 36591942 DOI: 10.1080/07391102.2022.2162582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023]
Abstract
PTEN, a dual-phosphatase and scaffold protein, is one of the most commonly mutated tumour suppressor gene across various cancer types in human. The aim of this study therefore was to investigate the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations (R15S, E18G, G36R, N49I, Y68H, I101T, C105F, D109N, V133I, C136Y, R173C and N276S) found by next generation sequencing of the PTEN gene in tissue samples obtained from glioblastoma patients. Computational tools and molecular dynamic simulation programs were used to identify the deleterious effects of these mutations. Furthermore, PTEN mRNA and protein expression levels were evaluated by qRT-PCR, Western Blot, and immunohistochemistry staining methods. Various computational tools predicted strong deleterious effects for the G36R, C105F, C136Y and N276S mutations. Molecular dynamic simulation revealed a significant decrease in protein stability for the Y68H and N276S mutations when compared with the wild type protein; whereas, C105F, D109N, V133I and R173C showed partial stability reduction. Significant residual fluctuations were observed in the R15S, N49I and C136Y mutations and radius of gyration graphs revealed the most compact structure for D109N and least for C136Y. In summary, our study is the first one to show the presence of PTEN E18G, N49I, D109N and N276S mutations in glioblastoma patients; where, D109N is neutral and N276S is a damaging and disease-associated mutation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Zekeriya Duzgun
- Department of Medical Biology, Giresun University Faculty of Medicine, Giresun, Turkey
| | - Taner Akalin
- Department of Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Erkin Ozgiray
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Eda Dogan
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Zafer Yildirim
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nevhis Akinturk
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Huseyin Biceroglu
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Yesim Ertan
- Department of Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Buket Kosova
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
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Bota PM, Oliva B, Fernandez-Fuentes N. Theoretical 3D Modeling of NLRP3 Inflammasome Complex. Methods Mol Biol 2023; 2696:269-280. [PMID: 37578729 DOI: 10.1007/978-1-0716-3350-2_18] [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: 08/15/2023]
Abstract
The NOD-like receptor pyrin domain containing 3 (NLRP3) is a multidomain protein that plays a key role in innate immune response. Structures of NLRP3 in different conformational states and bound to cognate partners are available. In this chapter we present an approach to model the oligomeric structure of NLRP3 by homology modeling using multiple templates, symmetry, and refinement. The overall process presented here represents advanced exercise in structural modeling that provides unique insights into the biological role and activation of NLRP3 oligomer. Finally, the same approach can be easily adapted to the rest of the members of the NLRP family.
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Affiliation(s)
- Patricia Mirela Bota
- Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Baldo Oliva
- Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Gniado N, Krawczyk-Balska A, Mehta P, Miszta P, Filipek S. Protein Homology Modeling for Effective Drug Design. Methods Mol Biol 2023; 2627:329-337. [PMID: 36959456 DOI: 10.1007/978-1-0716-2974-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The effective drug design, especially for combating the multi-drug-resistant bacterial pathogens, requires more and more sophisticated procedures to obtain novel lead-like compounds. New classes of enzymes should be explored, especially those that help bacteria overcome existing treatments. The homology modeling is useful in obtaining the models of new enzymes; however, the active sites of them are sometimes present in closed conformations in the crystal structures, not suitable for drug design purposes. In such difficult cases, the combination of homology modeling, molecular dynamics simulations, and fragment screening can give satisfactory results.
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Affiliation(s)
- Natalia Gniado
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agata Krawczyk-Balska
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pakhuri Mehta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Przemysław Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
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Marzella DF, Crocioni G, Parizi FM, Xue LC. The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling. Methods Mol Biol 2023; 2673:251-271. [PMID: 37258920 DOI: 10.1007/978-1-0716-3239-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Major histocompatibility complexes (MHC) play a key role in the immune surveillance system in all jawed vertebrates. MHC class I molecules randomly sample cytosolic peptides from inside the cell, while MHC class II sample exogenous peptides. Both types of peptide:MHC complex are then presented on the cell surface for recognition by αβ T cells (CD8+ and CD4+, respectively). The three-dimensional structure of such complexes can give crucial insights in the presentation and recognition mechanisms. For this reason, softwares like PANDORA have been developed to rapidly and accurately generate peptide:MHC (pMHC) 3D structures. In this chapter, we describe the protocol of PANDORA. PANDORA exploits the structural knowledge on anchor pockets that MHC molecules use to dock peptides. PANDORA provides anchor positions as restraints to guide the modeling process. This allows PANDORA to generate twenty 3D models in just about 5 min. PANDORA is highly customizable, easy to install, supports parallel processing, and is suitable to provide large datasets for deep learning algorithms.
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Affiliation(s)
- Dario F Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | | | - Farzaneh M Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Li C Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.
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40
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Jakowiecki J, Orzeł U, Gliździnska A, Możajew M, Filipek S. Specificities of Protein Homology Modeling for Allosteric Drug Design. Methods Mol Biol 2023; 2627:339-348. [PMID: 36959457 DOI: 10.1007/978-1-0716-2974-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The allosteric binding sites are usually located in the flexible areas of proteins, which are hardly visible in the crystal structures. However, there are notable exceptions like allosteric sites in receptors in class B and C of GPCRs, which are located within a well-defined bundle of transmembrane helices. Class B and C evolved from class A and even after swapping of orthosteric and allosteric sites the central binding site persisted and it can be used for easy design of allosteric drugs. However, studying the ligand binding to the allosteric sites in the most populated class A of GPCRs is still a challenge, since they are located mostly in unresolved parts of the receptor's structure, and especially N-terminus. This chapter provides an example of cannabinoid CB1 receptor N-terminal homology modeling, ligand-guided modeling of the allosteric site in GABA receptor, as well as C-linker modeling in the potassium ion channels where the allosteric phospholipid ligand PIP2 is bound.
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Affiliation(s)
- Jakub Jakowiecki
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Urszula Orzeł
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Aleksandra Gliździnska
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Mariusz Możajew
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
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Thiour-Mauprivez C, Dayan FE, Terol H, Devers M, Calvayrac C, Martin-Laurent F, Barthelmebs L. Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9932-9944. [PMID: 36068455 DOI: 10.1007/s11356-022-22801-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.
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Affiliation(s)
- Clémence Thiour-Mauprivez
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Franck Emmanuel Dayan
- Agricultural Biology Department, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hugo Terol
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Marion Devers
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Christophe Calvayrac
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Lise Barthelmebs
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France.
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Scarpa F, Sanna D, Benvenuto D, Borsetti A, Azzena I, Casu M, Fiori PL, Giovanetti M, Maruotti A, Ceccarelli G, Caruso A, Caccuri F, Cauda R, Cassone A, Pascarella S, Ciccozzi M. Genetic and Structural Data on the SARS-CoV-2 Omicron BQ.1 Variant Reveal Its Low Potential for Epidemiological Expansion. Int J Mol Sci 2022; 23:15264. [PMID: 36499592 PMCID: PMC9739521 DOI: 10.3390/ijms232315264] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 has some additional spike mutations in some key antigenic sites, which confer further immune escape ability over other circulating lineages. In such a context, here, we perform a genome-based survey aimed at obtaining a complete-as-possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggest that BQ.1 represents an evolutionary blind background, lacking the rapid diversification that is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 × 10-4 and 7 × 10-4 subs/site/year, respectively), which has been circulating for several months. The Bayesian Skyline Plot reconstruction indicates a low level of genetic variability, suggesting that the peak was reached around 3 September 2022. Concerning the affinity for ACE2, structure analyses (also performed by comparing the properties of BQ.1 and BA.5 RBD) indicate that the impact of the BQ.1 mutations may be modest. Likewise, immunoinformatic analyses showed moderate differences between the BQ.1 and BA5 potential B-cell epitopes. In conclusion, genetic and structural analyses on SARS-CoV-2 BQ.1 suggest no evidence of a particularly dangerous or high expansion capability. Genome-based monitoring must continue uninterrupted for a better understanding of its descendants and all other lineages.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy
| | | | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, 00161 Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, 25123 Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, 25123 Brescia, Italy
| | - Roberto Cauda
- UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences “A Rossi Fanelli”, Sapienza Università di Roma, 00161 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
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43
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Potent Activation of Human but Not Mouse TRPA1 by JT010. Int J Mol Sci 2022; 23:ijms232214297. [PMID: 36430781 PMCID: PMC9695908 DOI: 10.3390/ijms232214297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Transient receptor potential (TRP) ankyrin repeat 1 (TRPA1), which is involved in inflammatory pain sensation, is activated by endogenous factors, such as intracellular Zn2+ and hydrogen peroxide, and by irritant chemical compounds. The synthetic compound JT010 potently and selectively activates human TRPA1 (hTRPA1) among the TRPs. Therefore, JT010 is a useful tool for analyzing TRPA1 functions in biological systems. Here, we show that JT010 is a potent activator of hTRPA1, but not mouse TRPA1 (mTRPA1) in human embryonic kidney (HEK) cells expressing hTRPA1 and mTRPA1. Application of 0.3-100 nM of JT010 to HEK cells with hTRPA1 induced large Ca2+ responses. However, in HEK cells with mTRPA1, the response was small. In contrast, both TRPA1s were effectively activated by allyl isothiocyanate (AITC) at 10-100 μM. Similar selective activation of hTRPA1 by JT010 was observed in electrophysiological experiments. Additionally, JT010 activated TRPA1 in human fibroblast-like synoviocytes with inflammation, but not TRPA1 in mouse dorsal root ganglion cells. As cysteine at 621 (C621) of hTRPA1, a critical cysteine for interaction with JT010, is conserved in mTRPA1, we applied JT010 to HEK cells with mutations in mTRPA1, where the different residue of mTRPA1 with tyrosine at 60 (Y60), with histidine at 1023 (H1023), and with asparagine at 1027 (N1027) were substituted with cysteine in hTRPA1. However, these mutants showed low sensitivity to JT010. In contrast, the mutation of hTRPA1 at position 669 from phenylalanine to methionine (F669M), comprising methionine at 670 in mTRPA1 (M670), significantly reduced the response to JT010. Moreover, the double mutant at S669 and M670 of mTRPA1 to S669E and M670F, respectively, induced slight but substantial sensitivity to 30 and 100 nM JT010. Taken together, our findings demonstrate that JT010 potently and selectively activates hTRPA1 but not mTRPA1.
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Kumari A, Zeng XA, Rahaman A, Farooq MA, Huang Y, Alee M, Yao R, Ali M, Khalifa I, Badr O. Phenotype-based drug screening: An in vivo strategy to classify and identify the chemical compounds modulating zebrafish M-cell regeneration. Front Mol Biosci 2022; 9:984461. [PMID: 36353729 PMCID: PMC9637979 DOI: 10.3389/fmolb.2022.984461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/20/2022] [Indexed: 02/03/2023] Open
Abstract
Several disease-modulatory FDA-approved drugs are being used in patients with neurodegenerative diseases. However, information on their toxicity-related profiles is very limited. Therefore, measurement of drug toxicity is essential to increase the knowledge of their side effects. This study aimed to identify compounds that can modulate M-cell regeneration by causing neuro-protection and -toxicity. Here, we developed a simple and efficient in vivo assay using Tg (hsp: Gal4FF62A; UAS: nfsB-mCherry) transgenic zebrafish larvae. Interestingly, via the phenotype-based drug screening approach, we rapidly investigated 1,260 compounds from the United States drug collection and validated these in large numbers, including 14 compounds, that were obstructing this regeneration process. Next, 4 FDA-approved drugs out of 14 compounds were selected as the lead hits for in silico analysis to clarify their binding patterns with PTEN and SOCS3 signaling due to their significant potential in the inhibition of axon regeneration. Molecular docking studies indicated good binding affinity of all 4 drugs with the respective signaling molecules. This may point to PTEN and SOCS3 as the signaling molecules responsible for reducing axon regeneration. Moreover, the acute effect of compounds in reducing M-cell regeneration delineated their toxic effect. In conclusion, our in vivo along with in silico screening strategy will promote the rapid translation of new therapeutics to improve knowledge of the toxicity profile of approved/non-approved drugs efficiently.
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Affiliation(s)
- Ankita Kumari
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China,Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China,Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China,Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China,Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China,*Correspondence: Xin-An Zeng, ; Abdul Rahaman, ; Ibrahim Khalifa,
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China,Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China,Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China,*Correspondence: Xin-An Zeng, ; Abdul Rahaman, ; Ibrahim Khalifa,
| | - Muhammad Adil Farooq
- Department of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahimyar Khan, Punjab, Pakistan
| | - Yanyan Huang
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China
| | - Mahafooj Alee
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China,Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Murtaza Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China,Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China,Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| | - Ibrahim Khalifa
- Department of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahimyar Khan, Punjab, Pakistan,Food Technology Department, Faculty of Agriculture, Benha University, Qalyubia, Egypt,*Correspondence: Xin-An Zeng, ; Abdul Rahaman, ; Ibrahim Khalifa,
| | - Omnia Badr
- Department of Food Science and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahimyar Khan, Punjab, Pakistan,Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Qalyubia, Egypt
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In Vitro Rescue of the Bile Acid Transport Function of ABCB11 Variants by CFTR Potentiators. Int J Mol Sci 2022; 23:ijms231810758. [PMID: 36142670 PMCID: PMC9502978 DOI: 10.3390/ijms231810758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
ABCB11 is responsible for biliary bile acid secretion at the canalicular membrane of hepatocytes. Variations in the ABCB11 gene cause a spectrum of rare liver diseases. The most severe form is progressive familial intrahepatic cholestasis type 2 (PFIC2). Current medical treatments have limited efficacy. Here, we report the in vitro study of Abcb11 missense variants identified in PFIC2 patients and their functional rescue using cystic fibrosis transmembrane conductance regulator potentiators. Three ABCB11 disease-causing variations identified in PFIC2 patients (i.e., A257V, T463I and G562D) were reproduced in a plasmid encoding an Abcb11-green fluorescent protein. After transfection, the expression and localization of the variants were studied in HepG2 cells. Taurocholate transport activity and the effect of potentiators were studied in Madin–Darby canine kidney (MDCK) clones coexpressing Abcb11 and the sodium taurocholate cotransporting polypeptide (Ntcp/Slc10A1). As predicted using three-dimensional structure analysis, the three variants were expressed at the canalicular membrane but showed a defective function. Ivacaftor, GLP1837, SBC040 and SBC219 potentiators increased the bile acid transport of A257V and T463I and to a lesser extent, of G562D Abcb11 missense variants. In addition, a synergic effect was observed when ivacaftor was combined with SBC040 or SBC219. Such potentiators could represent new pharmacological approaches for improving the condition of patients with ABCB11 deficiency due to missense variations affecting the function of the transporter.
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46
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T. G. S, Siddiqui SA, Dubey KD. Unraveling key interactions and the mechanism of demethylation during hAGT-mediated DNA repair via simulations. Front Mol Biosci 2022; 9:975046. [PMID: 36188219 PMCID: PMC9515978 DOI: 10.3389/fmolb.2022.975046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Alkylating agents pose the biggest threat to the genomic integrity of cells by damaging DNA bases through regular alkylation. Such damages are repaired by several automated types of machinery inside the cell. O6-alkylguanine-DNA alkyltransferase (AGT) is an enzyme that performs the direct repair of an alkylated guanine base by transferring the alkyl group to a cysteine residue. In the present study, using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of the damaged base as a three-step process in a thermodynamically feasible and irreversible manner. Our calculations show that the final product forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.
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Affiliation(s)
- Shruti T. G.
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
| | - Shakir Ali Siddiqui
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, Uttar Pradesh, India
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Romsuk J, Yasumoto S, Seki H, Fukushima EO, Muranaka T. Identification of key amino acid residues toward improving the catalytic activity and substrate specificity of plant-derived cytochrome P450 monooxygenases CYP716A subfamily enzyme for triterpenoid production in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:955650. [PMID: 36061436 PMCID: PMC9437279 DOI: 10.3389/fbioe.2022.955650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022] Open
Abstract
Triterpenoids constitute a group of specialized plant metabolites with wide structural diversity and high therapeutic value for human health. Cytochrome P450 monooxygenases (CYP) are a family of enzymes important for generating the structural diversity of triterpenoids by catalyzing the site-specific oxidization of the triterpene backbone. The CYP716 enzyme family has been isolated from various plant families as triterpenoid oxidases; however, their experimental crystal structures are not yet available and the detailed catalytic mechanism remains elusive. Here, we address this challenge by integrating bioinformatics approaches with data from other CYP families. Medicago truncatula CYP716A12, the first functionally characterized CYP716A subfamily enzyme, was chosen as the model for this study. We performed homology modeling, structural alignment, in silico site-directed mutagenesis, and molecular docking analysis to search and screen key amino acid residues relevant to the catalytic activity and substrate specificity of the CYP716A subfamily enzyme in triterpenoid biosynthesis. An in vivo functional analysis using engineered yeast that endogenously produced plant-derived triterpenes was performed to elucidate the results. When the amino acids in the signature region and substrate recognition sites (SRSs) were substituted, the product profile of CYP716A12 was modified. We identified amino acid residues that control the substrate contraction of the enzyme (D292) and engineered the enzyme to improve its catalytic activity and substrate specificity (D122, I212, and Q358) for triterpenoid biosynthesis. In addition, we demonstrated the versatility of this strategy by changing the properties of key residues in SRSs to improve the catalytic activity of Arabidopsis thaliana CYP716A1 (S356) and CYP716A2 (M206, F210) at C-28 on the triterpene backbone. This research has the potential to help in the production of desired triterpenoids in engineered yeast by increasing the catalytic activity and substrate specificity of plant CYP716A subfamily enzymes.
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Affiliation(s)
- Jutapat Romsuk
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Shuhei Yasumoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Ery Odette Fukushima
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Plant Traslational Research Group, Universidad Regional Amazónica IKIAM, Tena, Ecuador
- *Correspondence: Ery Odette Fukushima, ; Toshiya Muranaka,
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- *Correspondence: Ery Odette Fukushima, ; Toshiya Muranaka,
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48
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Ruggiero A, Choi HG, Barra G, Squeglia F, Back YW, Kim HJ, Berisio R. Structure based design of effective HtpG-derived vaccine antigens against M. tuberculosis. Front Mol Biosci 2022; 9:964645. [PMID: 36032688 PMCID: PMC9403545 DOI: 10.3389/fmolb.2022.964645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/15/2022] [Indexed: 12/03/2022] Open
Abstract
Vaccine development against Tuberculosis is a strong need, given the low efficacy of the sole vaccine hitherto used, the Bacillus Calmette–Guérin (BCG) vaccine. The chaperone-like protein HtpGMtb of M. tuberculosis is a large dimeric and multi-domain protein with promising antigenic properties. We here used biophysical and biochemical studies to improve our understanding of the structural basis of HtpGMtb functional role and immunogenicity, a precious information to engineer improved antigens. We showed that HtpGMtb is a dimeric nucleotide-binding protein and identified the dimerisation interface on the C-terminal domain of the protein. We also showed that the most immunoreactive regions of the molecule are located on the C-terminal and middle domains of the protein, whereas no role is played by the catalytic N-terminal domain in the elicitation of the immune response. Based on these observations, we experimentally validated our predictions in mice, using a plethora of immunological assays. As an outcome, we designed vaccine antigens with enhanced biophysical properties and ease of production, albeit conserved or enhanced antigenic properties. Our results prove the efficacy of structural vaccinology approaches in improving our understanding of the structural basis of immunogenicity, a precious information to engineer more stable, homogeneous, efficiently produced, and effective vaccine antigens.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Han-Gyu Choi
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Giovanni Barra
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Young Woo Back
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hwa-Jung Kim
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
- *Correspondence: Hwa-Jung Kim, ; Rita Berisio,
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
- *Correspondence: Hwa-Jung Kim, ; Rita Berisio,
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Yang ZK, Li DW, Peng L, Liu CF, Wang ZY. Transcriptomic responses of the zearalenone (ZEN)-detoxifying yeast Apiotrichum mycotoxinivorans to ZEN exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113756. [PMID: 35691196 DOI: 10.1016/j.ecoenv.2022.113756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Zearalenone (ZEN) is a potent oestrogenic mycotoxin that is mainly produced by Fusarium species and is a serious environmental pollutant in animal feeds. Apiotrichum mycotoxinivorans has been widely used as a feed additive to detoxify ZEN. However, the effects of ZEN on A. mycotoxinivorans and its detoxification mechanisms remain unclear. In this study, transcriptomic and bioinformatic analyses were used to investigate the molecular responses of A. mycotoxinivorans to ZEN exposure and the genetic basis of ZEN detoxification. We detected 1424 significantly differentially expressed genes (DEGs), of which 446 were upregulated and 978 were downregulated. Functional and enrichment analyses showed that ZEN-induced genes were significantly associated with xenobiotic metabolism, oxidative stress response, and active transport systems. However, ZEN-inhibited genes were mainly related to cell division, cell cycle, and fungal development. Subsequently, bioinformatic analysis identified candidate ZEN-detoxification enzymes. The Baeyer-Villiger monooxygenases and carboxylesterases, which are responsible for the formation and subsequent hydrolysis of a new ZEN lactone, respectively, were significantly upregulated. In addition, the expression levels of genes related to conjugation and transport involved in the xenobiotic detoxification pathway were significantly upregulated. Moreover, the expression levels of genes encoding enzymatic antioxidants and those related to growth and apoptosis were significantly upregulated and downregulated, respectively, which made it possible for A. mycotoxinivorans to survive in a highly toxic environment and efficiently detoxify ZEN. This is the first systematic report of ZEN tolerance and detoxification in A. mycotoxinivorans. We identified the metabolic enzymes that were potentially involved in detoxifying ZEN in the GMU1709 strain and found that ZEN-induced transcriptional regulation of genes is key to withstanding highly toxic environments. Hence, our results provide valuable information for developing enzymatic detoxification systems or engineering this detoxification pathway in other species.
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Affiliation(s)
- Zhi-Kai Yang
- Innovation centre for Advanced Interdisciplinary Medicine, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Da-Wei Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liang Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chen-Fei Liu
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yuan Wang
- Innovation Centre for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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50
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Characterization of SARS-CoV-2 Escape Mutants to a Pair of Neutralizing Antibodies Targeting the RBD and the NTD. Int J Mol Sci 2022; 23:ijms23158177. [PMID: 35897753 PMCID: PMC9332373 DOI: 10.3390/ijms23158177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023] Open
Abstract
Mutations in the spike protein of SARS-CoV-2 can lead to evasion from neutralizing antibodies and affect the efficacy of passive and active immunization strategies. Immunization of mice harboring an entire set of human immunoglobulin variable region gene segments allowed to identify nine neutralizing monoclonal antibodies, which either belong to a cluster of clonally related RBD or NTD binding antibodies. To better understand the genetic barrier to emergence of SARS-CoV-2 variants resistant to these antibodies, escape mutants were selected in cell culture to one antibody from each cluster and a combination of the two antibodies. Three independently derived escape mutants to the RBD antibody harbored mutations in the RBD at the position T478 or S477. These mutations impaired the binding of the RBD antibodies to the spike protein and conferred resistance in a pseudotype neutralization assay. Although the binding of the NTD cluster antibodies were not affected by the RBD mutations, the RBD mutations also reduced the neutralization efficacy of the NTD cluster antibodies. The mutations found in the escape variants to the NTD antibody conferred resistance to the NTD, but not to the RBD cluster antibodies. A variant resistant to both antibodies was more difficult to select and only emerged after longer passages and higher inoculation volumes. VOC carrying the same mutations as the ones identified in the escape variants were also resistant to neutralization. This study further underlines the rapid emergence of escape mutants to neutralizing monoclonal antibodies in cell culture and indicates the need for thorough investigation of escape mutations to select the most potent combination of monoclonal antibodies for clinical use.
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