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Bernardo-Menezes LC, Agrelli A, Oliveira ASLED, Azevedo EDAN, Morais CNLD. Zika virus: Critical crosstalk between pathogenesis, cytopathic effects, and macroautophagy. J Cell Biochem 2023. [PMID: 37334850 DOI: 10.1002/jcb.30438] [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: 02/23/2023] [Revised: 05/06/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Zika virus (ZIKV) is a re-emerging positive-sense RNA arbovirus. Its genome encodes a polyprotein that is cleaved by proteases into three structural proteins (Envelope, pre-Membrane, and Capsid) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). These proteins have essential functions in viral replication cycle, cytopathic effects, and host cellular response. When infected by ZIKV, host cells promote macroautophagy, which is believed to favor virus entry. Although several authors have attempted to understand this link between macroautophagy and viral infection, little is known. Herein, we performed a narrative review of the molecular connection between macroautophagy and ZIKV infection while focusing on the roles of the structural and nonstructural proteins. We concluded that ZIKV proteins are major virulence factors that modulate host-cell machinery to its advantage by disrupting and/or blocking specific cellular systems and organelles' function, such as endoplasmic reticulum stress and mitochondrial dysfunction.
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Affiliation(s)
- Lucas Coêlho Bernardo-Menezes
- Laboratory of Virology and Experimental Therapeutics (LaViTE), Aggeu Magalhães Institute, Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Almerinda Agrelli
- Laboratory of Nanostructured Materials (LMNANO), Strategic Technologies Center of Northeast (CETENE), Recife, Pernambuco, Brazil
| | | | - Elisa de Almeida Neves Azevedo
- Laboratory of Virology and Experimental Therapeutics (LaViTE), Aggeu Magalhães Institute, Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Clarice Neuenschwander Lins de Morais
- Laboratory of Virology and Experimental Therapeutics (LaViTE), Aggeu Magalhães Institute, Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
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A Combined Approach for Detection of Ovine Small Ruminant Retrovirus Co-Infections. Viruses 2023; 15:v15020376. [PMID: 36851589 PMCID: PMC9958757 DOI: 10.3390/v15020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Jaagsiekte retrovirus (JSRV)-induced ovine pulmonary adenocarcinoma (OPA) is an important ovine respiratory disease in Switzerland. Furthermore, ovine lungs with OPA frequently exhibited lesions suggestive of maedi-visna virus (MVV) or caprine arthritis encephalitis virus (CAEV) infection, indicating that co-morbidities might occur. Lungs and pulmonary lymph nodes were sampled from suspected OPA cases, inflammatory lung lesions and control lungs (total of 110 cases). Tissues were (a) processed for histology and immunohistochemistry (IHC), and (b) underwent DNA extraction and real-time PCR for JSRV, MVV and CAEV. Peptide sequences were used to generate virus-specific customized polyclonal antibodies. PCR-positive OPA cases and formalin-fixed and paraffin-embedded MVV- and CAEV-infected synovial cell pellets served as positive controls. Fifty-two lungs were histologically diagnosed with OPA. Histological evidence of MVV/CAEV infection was detected in 25 lungs. JSRV was detected by PCR in 84% of the suspected OPA cases; six were co-infected with MVV and one with CAEV. MVV was detected by PCR in 14 cases, and four lungs were positive for CAEV. Three lungs had MVV/CAEV co-infection. In IHC, JSRV was detected in 91% of the PCR-positive cases, whereas MVV and CAEV immunoreactivity was seen in all PCR-positive lungs. Although PCR showed a higher sensitivity compared to IHC, the combined approach allows for investigations on viral cell tropism and pathogenic processes in co-morbidities, including their potential interdependency. Furthermore, an immunohistochemical tool for specific differentiation of MVV and/or CAEV infection was implemented.
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Sola L, Brambilla D, Mussida A, Damin F, Chiari M. A Bifunctional Polymeric Coating for the Co-Immobilization of Proteins and Peptides on Microarray Substrates. Methods Mol Biol 2023; 2578:27-39. [PMID: 36152278 DOI: 10.1007/978-1-0716-2732-7_3] [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: 06/16/2023]
Abstract
The analytical performance of the microarray technique in screening the affinity and reactivity of molecules toward a specific target is highly affected by the coupling chemistry adopted to bind probes to the surface. However, the surface functionality limits the biomolecules that can be attached to the surface to a single type of molecule, thus forcing the execution of separate analyses to compare the performance of different species in recognizing their targets. Here, we introduce a new N,N-dimethylacrylamide-based polymeric coating, bearing simultaneously different functionalities (N-acryloyloxysuccinimide and azide groups) to allow an easy and straightforward method to co-immobilize proteins and oriented peptides on the same substrate. The bifunctional copolymer has been obtained by partial post-polymerization modification of the functional groups of a common precursor. This strategy represents a convenient method to reduce the number of analyses, therefore possible systematic or random errors, besides offering a drastic shortage in time, reagents, and costs.
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Affiliation(s)
- Laura Sola
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy.
| | - Dario Brambilla
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Alessandro Mussida
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Dipartimento di Scienze Farmaceutiche (DISFARM), Università degli Studi di Milano, Milan, Italy
| | - Francesco Damin
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
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Piedimonte P, Sola L, Chiari M, Ferrari G, Sampietro M. Peptide-Based Sensor and Microfluidic Platform for IgG Antibody Detection by Differential Impedance Sensing. Methods Mol Biol 2023; 2578:191-198. [PMID: 36152288 DOI: 10.1007/978-1-0716-2732-7_13] [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: 06/16/2023]
Abstract
Serological assays enable infection screening as relatively easy-to-operate approaches compared with standard methods. In addition, to be relevant for early diagnosis, specific antibody detection is important for epidemiological surveillance and quantitative detection has potential significance for evaluating the severity and prognosis of different diseases.Here, we describe the detection process based on differential impedance sensing of IgG antibodies labeled with polystyrene nanoparticles. The electrode differential configuration, the amplification with nanoparticle functionalization, the electronic reading, and the microfluidic protocol allow to reach a limit of detection below 100 pg/mL for commercial IgG antibody spiked in buffer.
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Affiliation(s)
- Paola Piedimonte
- Department of Electronics Information and Bioengineering, Politecnico di Milano, Milan, Italy.
| | - Laura Sola
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Giorgio Ferrari
- Department of Electronics Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Marco Sampietro
- Department of Electronics Information and Bioengineering, Politecnico di Milano, Milan, Italy
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Strada A, Frigerio R, Bergamaschi G, Gagni P, Cretich M, Gori A. Membrane-Sensing Peptides for Extracellular Vesicle Analysis. Methods Mol Biol 2023; 2578:249-257. [PMID: 36152293 DOI: 10.1007/978-1-0716-2732-7_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: 06/16/2023]
Abstract
Analytical platforms for small extracellular vesicle (sEV) high-throughput analysis are highly desirable. These bionanoparticles present fairly distinctive lipid membrane features including high curvature, lipid-packing defects, and a relative abundance in lipids. sEV membrane could be considered as a "universal" marker, complementary or alternative to traditional surface-associated proteins. Here, we describe the use of membrane-sensing peptides as a new, highly efficient ligand to directly integrate sEV capturing and analysis on a microarray platform.
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Affiliation(s)
- Alessandro Strada
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy.
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Milan, Italy.
| | - Roberto Frigerio
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Greta Bergamaschi
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Paola Gagni
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Marina Cretich
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
| | - Alessandro Gori
- National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Milan, Italy
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Ranaudo A, Cosentino U, Greco C, Moro G, Bonardi A, Maiocchi A, Moroni E. Evaluation of docking procedures reliability in affitins-partners interactions. Front Chem 2022; 10:1074249. [DOI: 10.3389/fchem.2022.1074249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
Affitins constitute a class of small proteins belonging to Sul7d family, which, in microorganisms such as Sulfolobus acidocaldarius, bind DNA preventing its denaturation. Thanks to their stability and small size (60–66 residues in length) they have been considered as ideal candidates for engineering and have been used for more than 10 years now, for different applications. The individuation of a mutant able to recognize a specific target does not imply the knowledge of the binding geometry between the two proteins. However, its identification is of undoubted importance but not always experimentally accessible. For this reason, computational approaches such as protein-protein docking can be helpful for an initial structural characterization of the complex. This method, which produces tens of putative binding geometries ordered according to a binding score, needs to be followed by a further reranking procedure for finding the most plausible one. In the present paper, we use the server ClusPro for generating docking models of affitins with different protein partners whose experimental structures are available in the Protein Data Bank. Then, we apply two protocols for reranking the docking models. The first one investigates their stability by means of Molecular Dynamics simulations; the second one, instead, compares the docking models with the interacting residues predicted by the Matrix of Local Coupling Energies method. Results show that the more efficient way to deal with the reranking problem is to consider the information given by the two protocols together, i.e. employing a consensus approach.
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Zhou J, Chen J, Peng Y, Xie Y, Xiao Y. A Promising Tool in Serological Diagnosis: Current Research Progress of Antigenic Epitopes in Infectious Diseases. Pathogens 2022; 11:1095. [PMID: 36297152 PMCID: PMC9609281 DOI: 10.3390/pathogens11101095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 07/30/2023] Open
Abstract
Infectious diseases, caused by various pathogens in the clinic, threaten the safety of human life, are harmful to physical and mental health, and also increase economic burdens on society. Infections are a complex mechanism of interaction between pathogenic microorganisms and their host. Identification of the causative agent of the infection is vital for the diagnosis and treatment of diseases. Etiological laboratory diagnostic tests are therefore essential to identify pathogens. However, due to its rapidity and automation, the serological diagnostic test is among the methods of great significance for the diagnosis of infections with the basis of detecting antigens or antibodies in body fluids clinically. Epitopes, as a special chemical group that determines the specificity of antigens and the basic unit of inducing immune responses, play an important role in the study of immune responses. Identifying the epitopes of a pathogen may contribute to the development of a vaccine to prevent disease, the diagnosis of the corresponding disease, and the determination of different stages of the disease. Moreover, both the preparation of neutralizing antibodies based on useful epitopes and the assembly of several associated epitopes can be used in the treatment of disease. Epitopes can be divided into B cell epitopes and T cell epitopes; B cell epitopes stimulate the body to produce antibodies and are therefore commonly used as targets for the design of serological diagnostic experiments. Meanwhile, epitopes can fall into two possible categories: linear and conformational. This article reviews the role of B cell epitopes in the clinical diagnosis of infectious diseases.
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Piedimonte P, Sola L, Cretich M, Gori A, Chiari M, Marchisio E, Borga P, Bertacco R, Melloni A, Ferrari G, Sampietro M. Differential Impedance Sensing platform for high selectivity antibody detection down to few counts: A case study on Dengue Virus. Biosens Bioelectron 2022; 202:113996. [DOI: 10.1016/j.bios.2022.113996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 11/02/2022]
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Bergamaschi G, Musicò A, Frigerio R, Strada A, Pizzi A, Talone B, Ghezzi J, Gautieri A, Chiari M, Metrangolo P, Vanna R, Baldelli Bombelli F, Cretich M, Gori A. Composite Peptide-Agarose Hydrogels for Robust and High-Sensitivity 3D Immunoassays. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4811-4822. [PMID: 35060693 DOI: 10.1021/acsami.1c18466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Canonical immunoassays rely on highly sensitive and specific capturing of circulating biomarkers by interacting biomolecular baits. In this frame, bioprobe immobilization in spatially discrete three-dimensional (3D) spots onto analytical surfaces by hydrogel encapsulation was shown to provide relevant advantages over conventional two-dimensional (2D) platforms. Yet, the broad application of 3D systems is still hampered by hurdles in matching their straightforward fabrication with optimal functional properties. Herein, we report on a composite hydrogel obtained by combining a self-assembling peptide (namely, Q3 peptide) with low-temperature gelling agarose that is proved to have simple and robust application in the fabrication of microdroplet arrays, overcoming hurdles and limitations commonly associated with 3D hydrogel assays. We demonstrate the real-case scenario feasibility of our 3D system in the profiling of Covid-19 patients' serum IgG immunoreactivity, which showed remarkably improved signal-to-noise ratio over canonical assays in the 2D format and exquisite specificity. Overall, the new two-component hydrogel widens the perspectives of hydrogel-based arrays and represents a step forward towards their routine use in analytical practices.
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Affiliation(s)
- Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Angelo Musicò
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Roberto Frigerio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Strada
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Benedetta Talone
- Physics Department, Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Jacopo Ghezzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Renzo Vanna
- Istituto di Fotonica e Nanotecnologie─National Research Council of Italy (IFN-CNR), 20133 Milan, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
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Vengesai A, Kasambala M, Mutandadzi H, Mduluza-Jokonya TL, Mduluza T, Naicker T. Scoping review of the applications of peptide microarrays on the fight against human infections. PLoS One 2022; 17:e0248666. [PMID: 35077448 PMCID: PMC8789108 DOI: 10.1371/journal.pone.0248666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 01/11/2022] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION This scoping review explores the use of peptide microarrays in the fight against infectious diseases. The research domains explored included the use of peptide microarrays in the mapping of linear B-cell and T cell epitopes, antimicrobial peptide discovery, immunosignature characterisation and disease immunodiagnostics. This review also provides a short overview of peptide microarray synthesis. METHODS Electronic databases were systematically searched to identify relevant studies. The review was conducted using the Joanna Briggs Institute methodology for scoping reviews and data charting was performed using a predefined form. The results were reported by narrative synthesis in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews guidelines. RESULTS Ninety-five articles from 103 studies were included in the final data charting process. The majority (92. 0%) of the articles were published during 2010-2020 and were mostly from Europe (44.2%) and North America (34.7%). The findings were from the investigation of viral (45.6%), bacterial (32. 0%), parasitic (23.3%) and fungal (2. 0%) infections. Out of the serological studies, IgG was the most reported antibody type followed by IgM. The largest portion of the studies (77.7%) were related to mapping B-cell linear epitopes, 5.8% were on diagnostics, 5.8% reported on immunosignature characterisation and 8.7% reported on viral and bacterial cell binding assays. Two studies reported on T-cell epitope profiling. CONCLUSION The most important application of peptide microarrays was found to be B-cell epitope mapping or antibody profiling to identify diagnostic and vaccine targets. Immunosignatures identified by random peptide microarrays were found to be applied in the diagnosis of infections and interrogation of vaccine responses. The analysis of the interactions of random peptide microarrays with bacterial and viral cells using binding assays enabled the identification of antimicrobial peptides. Peptide microarray arrays were also used for T-cell linear epitope mapping which may provide more information for the design of peptide-based vaccines and for the development of diagnostic reagents.
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Affiliation(s)
- Arthur Vengesai
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
| | - Maritha Kasambala
- Department of Biology, Faculty of Science and Agriculture, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Hamlet Mutandadzi
- Faculty of Medicine and Health Sciences, Parirenyatwa Hospital, University of Zimbabwe, Harare, Zimbabwe
| | - Tariro L. Mduluza-Jokonya
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Takafira Mduluza
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
| | - Thajasvarie Naicker
- Optics & Imaging, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
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Sola L, Brambilla D, Mussida A, Consonni R, Damin F, Cretich M, Gori A, Chiari M. A bi-functional polymeric coating for the co-immobilization of proteins and peptides on microarray substrates. Anal Chim Acta 2021; 1187:339138. [PMID: 34753566 DOI: 10.1016/j.aca.2021.339138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
The analytical performance of the microarray technique in screening the affinity and reactivity of molecules towards a specific target, is highly affected by the coupling chemistry adopted to bind probes to the surface. However, the surface functionality limits the biomolecules that can be attached to the surface to a single type of molecule, thus forcing the execution of separate analyses to compare the performance of different species in recognizing their targets. Here we introduce a new N, N-dimethylacrylamide-based polymeric coating, bearing simultaneously different functionalities (N-acryloyloxysuccinimide and azide groups) to allow an easy and straightforward method to co-immobilize proteins and oriented peptides on the same substrate. The bi-functional copolymer has been obtained by partial post polymerization modification of the functional groups of a common precursor. A NMR characterization of the copolymer was conducted to quantify the percentage of NAS that has been transformed into azido groups. The polymer was used to coat surfaces onto which both native antibodies and alkyne modified peptides were immobilized, to perform the phenotype characterization of extracellular vesicles (EVs). This strategy represents a convenient method to reduce the number of analysis, thus possible systematic or random errors, besides offering a drastic shortage in time, reagents and costs.
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Affiliation(s)
- Laura Sola
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy.
| | - Dario Brambilla
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Alessandro Mussida
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Roberto Consonni
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "G.Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milan, Italy
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Fumagalli MJ, Figueiredo LTM, Aquino VH. Linear and Continuous Flavivirus Epitopes From Naturally Infected Humans. Front Cell Infect Microbiol 2021; 11:710551. [PMID: 34458161 PMCID: PMC8387565 DOI: 10.3389/fcimb.2021.710551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/15/2021] [Indexed: 12/27/2022] Open
Abstract
This manuscript is an up-to-date review of experimentally validated linear and continuous epitopes identified from arbovirus members of the Flavivirus genus. We summarized 153 immunoreactive peptides from the Dengue virus, Zika virus, Japanese encephalitis virus, West Nile virus, and tick-borne encephalitis virus described in studies published from 1989 to 2020. We included peptides from structural (envelope, capsid, and pre-membrane) and nonstructural (Ns1–5) viral proteins that demonstrated relevant immunoreactivity with antibodies from naturally infected or vaccinated humans. We included peptides that demonstrated relevant reactivity features, such as indicators of disease severity related to immunological or immunopathological outcomes, differential or group diagnostic markers, immunotherapy candidates, and potential for vaccine formulation. The majority of immunoreactive peptides were described for DENV probably due to its long-lasting impact on human health and the lack of efficient vaccines and therapeutic methods. Immune landscape data regarding linear immunoreactive and continuous flavivirus peptides are still scarce, and a complete and more detailed map remains to be elucidated. Therefore, this review provides valuable data for those investigating the antibody response against flavivirus infection.
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Affiliation(s)
- Marcilio Jorge Fumagalli
- Virology Research Center, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Epitope mapping from Mycobacterium leprae proteins: Convergent data from in silico and in vitro approaches for serodiagnosis of leprosy. Mol Immunol 2021; 138:48-57. [PMID: 34343723 DOI: 10.1016/j.molimm.2021.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023]
Abstract
Knowledge of immunodominant B-cell epitopes is essential to design powerful diagnostic strategies aiming for antibody detection. Outstanding progress in computational prediction has achieved a significant contribution to the biomedical fields, including immunodiagnosis. In silico analysis may have an even more important role when information concerning antigens from etiologic agents of neglected diseases, such as leprosy, is scarce. The aim of this study was to provide mapping of B-cell epitopes from two Mycobacterium leprae-derived antigens (Ag85B and ML2055), confirm their antigenicity, and to assess the ability of in silico immunoinformatics tools to accurately predict them. Linear B-cell epitopes predicted by ABCpred and SVMTrip servers were compared to antigenic regions of synthetic overlapping peptides that exhibited reactivity to antibodies from patients with leprosy. Our in vitro results identified several immunodominant regions that had also been indicated by in silico prediction, providing agreement between experimental and simulated data. After chemical synthesis, we used enzyme-linked immunosorbent assays to determine the effectiveness of the first identified sequence (GTNVPAEFLENFVHG) which had 72 % sensitivity and 78 % specificity (AUC = 0.79) while the second one (PVSSEAQPGDPNAPS) had 72 % sensitivity and 93.8 % specificity (AUC = 0.85). Using dot blotting, an easy-to-read visual test, both peptides could distinguish sera from patients with leprosy from those with tuberculosis and from sera of healthy volunteers. Our findings suggest that these synthetic peptides, with some refinement, may be useful as serological diagnostic antigens for leprosy. In addition, it was displayed that immunoinformatics provides reliable information for mapping potential B-cell epitopes for development of peptide-based diagnostic assays for neglected diseases.
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14
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Vengesai A, Naicker T, Kasambala M, Midzi H, Mduluza-Jokonya T, Rusakaniko S, Mduluza T. Clinical utility of peptide microarrays in the serodiagnosis of neglected tropical diseases in sub-Saharan Africa: protocol for a diagnostic test accuracy systematic review. BMJ Open 2021; 11:e042279. [PMID: 34330850 PMCID: PMC8327806 DOI: 10.1136/bmjopen-2020-042279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION Neglected tropical diseases tend to cluster in the same poor populations and, to make progress with their control, they will have to be dealt with in an integrated manner. Peptide microarrays may be a solution to these problems, where diagnosis for co-infection can be detected simultaneously using the one tool. A meta-analysis using hierarchical models will be performed to assess the diagnostic accuracy of peptide microarrays for detecting schistosomiasis (Schistosoma mansoni and S. haematobium), soil-transmitted helminths (Trichuris trichiura, Ascaris lumbricoides and Necator americanus), trachoma (Chlamydia trachomatis), lymphatic filariasis (Wuchereria bancrofti) and onchocerciasis (Onchocerca volvulus) in people residing in sub-Saharan Africa. METHODS AND ANALYSIS A comprehensive search of the following databases will be performed: Cochrane Infectious Diseases Group Specialised Register, PubMed, EMBASE and The Web of Science. Studies comparing peptide microarrays with a reference standard from a random or consecutive series of patients will be included in the study. Two review authors will independently screen titles and abstracts for relevance, assess full-text articles for inclusion and carry out data extraction using a tailored data extraction form. The quality Assessment of Diagnostic Accuracy Studies-2 tool will be used to assess the quality of the selected studies. The bivariate model and the hierarchical summary receiver operating characteristic curve model will be performed to evaluate the diagnostic accuracy of the peptide microarrays. Meta-regression analyses will be performed to investigate heterogeneity across studies. ETHICS AND DISSEMINATION There is no requirement for ethical approval because the work will be carried out using previously published data, without human beings involvement. Findings will be disseminated through peer-reviewed publication and in conference presentations. PROSPERO REGISTRATION NUMBER CRD42020175145.
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Affiliation(s)
- Arthur Vengesai
- Biotechnology and Biochemistry, University of Zimbabwe Faculty of Science, Harare, Zimbabwe
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thajasvarie Naicker
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maritha Kasambala
- Faculty of Science and Agriculture, University of KwaZulu-Natal, Durban, South Africa
| | - Herald Midzi
- Biotechnology and Biochemistry, University of Zimbabwe Faculty of Science, Harare, Zimbabwe
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Takafira Mduluza
- Biotechnology and Biochemistry, University of Zimbabwe Faculty of Science, Harare, Zimbabwe
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15
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Kabir MA, Zilouchian H, Younas MA, Asghar W. Dengue Detection: Advances in Diagnostic Tools from Conventional Technology to Point of Care. BIOSENSORS 2021; 11:206. [PMID: 34201849 PMCID: PMC8301808 DOI: 10.3390/bios11070206] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 06/02/2023]
Abstract
The dengue virus (DENV) is a vector-borne flavivirus that infects around 390 million individuals each year with 2.5 billion being in danger. Having access to testing is paramount in preventing future infections and receiving adequate treatment. Currently, there are numerous conventional methods for DENV testing, such as NS1 based antigen testing, IgM/IgG antibody testing, and Polymerase Chain Reaction (PCR). In addition, novel methods are emerging that can cut both cost and time. Such methods can be effective in rural and low-income areas throughout the world. In this paper, we discuss the structural evolution of the virus followed by a comprehensive review of current dengue detection strategies and methods that are being developed or commercialized. We also discuss the state of art biosensing technologies, evaluated their performance and outline strategies to address challenges posed by the disease. Further, we outline future guidelines for the improved usage of diagnostic tools during recurrence or future outbreaks of DENV.
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Affiliation(s)
- Md Alamgir Kabir
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Hussein Zilouchian
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | | | - Waseem Asghar
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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16
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Sánchez-González G, Belak ZR, Lozano L, Condé R. Probability of consolidation constrains novel serotype emergence in dengue fever virus. PLoS One 2021; 16:e0248765. [PMID: 33819302 PMCID: PMC8021166 DOI: 10.1371/journal.pone.0248765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
Since their first sequencing 40 years ago, Dengue virus (DENV) genotypes have shown extreme coherence regarding the serotype class they encode. Considering that DENV is a ribonucleic acid (RNA) virus with a high mutation rate, this behavior is intriguing. Here, we explore the effect of various parameters on likelihood of new serotype emergence. In order to determine the time scales of such an event, we used a Timed Markov Transmission Model to explore the influences of sylvatic versus peri-urban transmission, viral mutation rate, and vertical transmission on the probabilities of novel serotype emergence. We found that around 1 000 years are required for a new serotype to emerge, consistent with phylogenetic analysis of extant dengue serotypes. Furthermore, we show that likelihood of establishing chains of mosquito-human-mosquito infection, known as consolidation, is the primary factor which constrains novel serotype emergence. Our work illustrates the restrictions on and provides a mechanistic explanation for the low probability of novel dengue virus serotype emergence and the low number of observed DENV serotypes.
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Affiliation(s)
- Gilberto Sánchez-González
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | | | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Renaud Condé
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
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17
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De Benedetti S, Di Pisa F, Fassi EMA, Cretich M, Musicò A, Frigerio R, Mussida A, Bombaci M, Grifantini R, Colombo G, Bolognesi M, Grande R, Zanchetta N, Gismondo MR, Mileto D, Mancon A, Gourlay LJ. Structure, Immunoreactivity, and In Silico Epitope Determination of SmSPI S. mansoni Serpin for Immunodiagnostic Application. Vaccines (Basel) 2021; 9:vaccines9040322. [PMID: 33915716 PMCID: PMC8066017 DOI: 10.3390/vaccines9040322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
The human parasitic disease Schistosomiasis is caused by the Schistosoma trematode flatworm that infects freshwaters in tropical regions of the world, particularly in Sub-Saharan Africa, South America, and the Far-East. It has also been observed as an emerging disease in Europe, due to increased immigration. In addition to improved therapeutic strategies, it is imperative to develop novel, rapid, and sensitive diagnostic tests that can detect the Schistosoma parasite, allowing timely treatment. Present diagnosis is difficult and involves microscopy-based detection of Schistosoma eggs in the feces. In this context, we present the 3.22 Å resolution crystal structure of the circulating antigen Serine protease inhibitor from S. mansoni (SmSPI), and we describe it as a potential serodiagnostic marker. Moreover, we identify three potential immunoreactive epitopes using in silico-based epitope mapping methods. Here, we confirm effective immune sera reactivity of the recombinant antigen, suggesting the further investigation of the protein and/or its predicted epitopes as serodiagnostic Schistosomiasis biomarkers.
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Affiliation(s)
- Stefano De Benedetti
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
| | - Flavio Di Pisa
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
| | - Enrico Mario Alessandro Fassi
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Angelo Musicò
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Roberto Frigerio
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Alessandro Mussida
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.B.); (R.G.)
| | - Renata Grifantini
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.B.); (R.G.)
| | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy;
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milano, Italy
| | - Romualdo Grande
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Nadia Zanchetta
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Maria Rita Gismondo
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
- Clinical Microbiology, Virology and Bioemergency Unit, Department of Biomedical and Clinical Sciences, Luigi Sacco Hospital, University of Milan, 20157 Milan, Italy
| | - Davide Mileto
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Alessandro Mancon
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Louise Jane Gourlay
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
- Correspondence: ; Tel.: +39-(0)2-5031-4914
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18
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Serapian S, Marchetti F, Triveri A, Morra G, Meli M, Moroni E, Sautto GA, Rasola A, Colombo G. The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations May Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein. J Phys Chem Lett 2020; 11:8084-8093. [PMID: 32885971 PMCID: PMC7491317 DOI: 10.1021/acs.jpclett.0c02341] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 is a health threat with dire socioeconomical consequences. As the crucial mediator of infection, the viral glycosylated spike protein (S) has attracted the most attention and is at the center of efforts to develop therapeutics and diagnostics. Herein, we use an original decomposition approach to identify energetically uncoupled substructures as antibody binding sites on the fully glycosylated S. Crucially, all that is required are unbiased MD simulations; no prior knowledge of binding properties or ad hoc parameter combinations is needed. Our results are validated by experimentally confirmed structures of S in complex with anti- or nanobodies. We identify poorly coupled subdomains that are poised to host (several) epitopes and potentially involved in large functional conformational transitions. Moreover, we detect two distinct behaviors for glycans: those with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes, and those with weaker coupling could themselves be prone to antibody recognition.
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Affiliation(s)
- Stefano
A. Serapian
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
- Department
of Chemistry, University of Milan, via Venezian 21, 20133 Milano, Italy
| | - Alice Triveri
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Giulia Morra
- SCITEC−CNR, via Mario Bianco 9, 20131 Milano, Italy
| | | | | | - Giuseppe A. Sautto
- Center
for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602, United States
| | - Andrea Rasola
- Dipartimento
di Scienze Biomediche, Università
di Padova, viale G. Colombo
3, 35131 Padova, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
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19
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Meli M, Morra G, Colombo G. Simple Model of Protein Energetics To Identify Ab Initio Folding Transitions from All-Atom MD Simulations of Proteins. J Chem Theory Comput 2020; 16:5960-5971. [PMID: 32693598 PMCID: PMC8009504 DOI: 10.1021/acs.jctc.0c00524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A fundamental
requirement to predict the native conformation, address
questions of sequence design and optimization, and gain insights into
the folding mechanisms of proteins lies in the definition of an unbiased
reaction coordinate that reports on the folding state without the
need to compare it to reference values, which might be unavailable
for new (designed) sequences. Here, we introduce such a reaction coordinate,
which does not depend on previous structural knowledge of the native
state but relies solely on the energy partition within the protein:
the spectral gap of the pair nonbonded energy matrix (ENergy Gap,
ENG). This quantity can be simply calculated along unbiased MD trajectories.
We show that upon folding the gap increases significantly, while its
fluctuations are reduced to a minimum. This is consistently observed
for a diverse set of systems and trajectories. Our approach allows
one to promptly identify residues that belong to the folding core
as well as residues involved in non-native contacts that need to be
disrupted to guide polypeptides to the folded state. The energy gap
and fluctuations criteria are then used to develop an automatic detection
system which allows us to extract and analyze folding transitions
from a generic MD trajectory. We speculate that our method can be
used to detect conformational ensembles in dynamic and intrinsically
disordered proteins, revealing potential preorganization for binding.
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Affiliation(s)
| | - Giulia Morra
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,Weill-Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Giorgio Colombo
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,University of Pavia, Department of Chemistry, Viale Taramelli 12, Pavia 27100, Italy
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20
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Saranya V, Radhika R, Shankar R, Vijayakumar S. In silico studies of the inhibition mechanism of dengue with papain. J Biomol Struct Dyn 2020; 39:1912-1927. [PMID: 32249700 DOI: 10.1080/07391102.2020.1742205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.
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21
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Houen G, Trier N. Molecular Recognition and Advances in Antibody Design and Antigenic Peptide Targeting. Int J Mol Sci 2020; 21:ijms21041405. [PMID: 32092996 PMCID: PMC7073054 DOI: 10.3390/ijms21041405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 12/16/2022] Open
Abstract
Molecular recognition, the specific interaction between molecules by a combination of physical forces, has been a subject of scientific investigation for decades [...].
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22
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Kerkhof K, Falconi-Agapito F, Van Esbroeck M, Talledo M, Ariën KK. Reliable Serological Diagnostic Tests for Arboviruses: Feasible or Utopia? Trends Microbiol 2019; 28:276-292. [PMID: 31864844 DOI: 10.1016/j.tim.2019.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023]
Abstract
Infections with arthropod-borne viruses are increasing globally as a result of climate and demographic changes, global dispersion of insect vectors, and increased air travel. The similar symptomatology of arboviral diseases and the cocirculation of different arboviruses in Africa, Asia, and South America complicate diagnosis. Despite the high sensitivity and specificity of molecular diagnostic tests, their utility is limited to the short viremic phase of arbovirus infections, and therefore the diagnosis of infection is frequently missed in clinical practice. Conversely, the duration of antibody responses provides a wider window of opportunity, making diagnosis more dependent on IgM/IgG detection. This review discusses the issues underlying the low specificity of antibody-detection assays, and addresses the challenges and strategies for discovering more specific biomarkers to enable a more accurate diagnosis.
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Affiliation(s)
- Karen Kerkhof
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Francesca Falconi-Agapito
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium; Molecular Epidemiology Laboratory, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, National Reference Center for Arboviruses, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michael Talledo
- Molecular Epidemiology Laboratory, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kevin K Ariën
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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23
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Barbosa MDS, de Sousa IBA, Simionatto S, Borsuk S, Marchioro SB. Recombinant polypeptide of Mycobacterium leprae as a potential tool for serological detection of leprosy. AMB Express 2019; 9:201. [PMID: 31848766 PMCID: PMC6917672 DOI: 10.1186/s13568-019-0928-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022] Open
Abstract
Current prevention methods for the transmission of Mycobacterium leprae, the causative agent of leprosy, are inadequate as suggested by the rate of new leprosy cases reported. Simple large-scale detection methods for M. leprae infection are crucial for early detection of leprosy and disease control. The present study investigates the production and seroreactivity of a recombinant polypeptide composed of various M. leprae protein epitopes. The structural and physicochemical parameters of this construction were assessed using in silico tools. Parameters like subcellular localization, presence of signal peptide, primary, secondary, and tertiary structures, and 3D model were ascertained using several bioinformatics tools. The resultant purified recombinant polypeptide, designated rMLP15, is composed of 15 peptides from six selected M. leprae proteins (ML1358, ML2055, ML0885, ML1811, ML1812, and ML1214) that induce T cell reactivity in leprosy patients from different hyperendemic regions. Using rMLP15 as the antigen, sera from 24 positive patients and 14 healthy controls were evaluated for reactivity via ELISA. ELISA-rMLP15 was able to diagnose 79.17% of leprosy patients with a specificity of 92.86%. rMLP15 was also able to detect the multibacillary and paucibacillary patients in the same proportions, a desirable addition in the leprosy diagnosis. These results summarily indicate the utility of the recombinant protein rMLP15 in the diagnosis of leprosy and the future development of a viable screening test.
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24
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Peptides, Antibodies, Peptide Antibodies and More. Int J Mol Sci 2019; 20:ijms20246289. [PMID: 31847088 PMCID: PMC6941022 DOI: 10.3390/ijms20246289] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
The applications of peptides and antibodies to multiple targets have emerged as powerful tools in research, diagnostics, vaccine development, and therapeutics. Antibodies are unique since they, in theory, can be directed to any desired target, which illustrates their versatile nature and broad spectrum of use as illustrated by numerous applications of peptide antibodies. In recent years, due to the inherent limitations such as size and physical properties of antibodies, it has been attempted to generate new molecular compounds with equally high specificity and affinity, albeit with relatively low success. Based on this, peptides, antibodies, and peptide antibodies have established their importance and remain crucial reagents in molecular biology.
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