1
|
Wiśniewski M, Babirye P, Musubika C, Papakonstantinou E, Kirimunda S, Łaźniewski M, Szczepińska T, Joloba ML, Eliopoulos E, Bongcam-Rudloff E, Vlachakis D, Kumar Halder A, Plewczyński D, Wayengera M. Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies. Brief Funct Genomics 2024:elae012. [PMID: 38605526 DOI: 10.1093/bfgp/elae012] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Intermolecular interactions of protein-protein complexes play a principal role in the process of discovering new substances used in the diagnosis and treatment of many diseases. Among such complexes of proteins, we have to mention antibodies; they interact with specific antigens of two genera of single-stranded RNA viruses belonging to the family Filoviridae-Ebolavirus and Marburgvirus; both cause rare but fatal viral hemorrhagic fever in Africa, with pandemic potential. In this research, we conduct studies aimed at the design and evaluation of antibodies targeting the filovirus glycoprotein precursor GP-1,2 to develop potential targets for the pan-filovirus easy-to-use rapid diagnostic tests. The in silico research using the available 3D structure of the natural antibody-antigen complex was carried out to determine the stability of individual protein segments in the process of its formation and maintenance. The computed free binding energy of the complex and its decomposition for all amino acids allowed us to define the residues that play an essential role in the structure and indicated the spots where potential antibodies can be improved. Following that, the study involved targeting six epitopes of the filovirus GP1,2 with two polyclonal antibodies (pABs) and 14 monoclonal antibodies (mABs). The evaluation conducted using Enzyme Immunoassays tested 62 different sandwich combinations of monoclonal antibodies (mAbs), identifying 10 combinations that successfully captured the recombinant GP1,2 (rGP). Among these combinations, the sandwich option (3G2G12* - (rGP) - 2D8F11) exhibited the highest propensity for capturing the rGP antigen.
Collapse
Affiliation(s)
- Maciej Wiśniewski
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Peace Babirye
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Carol Musubika
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Eleni Papakonstantinou
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology,Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Samuel Kirimunda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Michal Łaźniewski
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Teresa Szczepińska
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| | - Elias Eliopoulos
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology,Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics section, Swedish University for Agricultural Sciences, Ulls väg 26, PO Box 7023, S-750 07 Uppsala, Sweden
| | - Dimitrios Vlachakis
- Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology, Agricultural University of Athens, Iera Odos 7511855 Athens, Greece
| | - Anup Kumar Halder
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Dariusz Plewczyński
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Old Mulago Hill Road P.O. Box 7072, Kampala, Uganda
| |
Collapse
|
2
|
de Puig H, Bosch I, Salcedo N, Collins JJ, Hamad-Schifferli K, Gehrke L. Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness. NANO TODAY 2022; 47:101669. [PMID: 36348742 PMCID: PMC9632299 DOI: 10.1016/j.nantod.2022.101669] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/09/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Global public health infrastructure is unprepared for emerging pathogen epidemics, in part because diagnostic tests are not developed in advance. The recent Zika, Ebola, and SARS-CoV-2 virus epidemics are cases in point. We demonstrate here that multicolored gold nanoparticles, when coupled to cross-reactive monoclonal antibody pairs generated from a single immunization regimen, can be used to create multiple diagnostics that specifically detect and distinguish related viruses. The multiplex approach for specific detection centers on immunochromatography with pairs of antibody-conjugated red and blue gold nanoparticles, coupled with clustering algorithms to detect and distinguish related pathogens. Cross-reactive antibodies were used to develop rapid tests for i) Dengue virus serotypes 1-4, ii) Zika virus, iii) Ebola and Marburg viruses, and iv) SARS-CoV and SARS-CoV-2 viruses. Multiplexed rapid antigen tests based on multicolored nanoparticles and cross-reactive antibodies and can be developed prospectively at low cost to improve preparedness for epidemic outbreaks.
Collapse
Affiliation(s)
- Helena de Puig
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, United States
| | - Irene Bosch
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, United States
- IDx20, Newton, MA, United States
| | | | - James J Collins
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge MA, United States
- Broad Institute of MIT and Harvard, Cambridge MA, United States
| | - Kimberly Hamad-Schifferli
- Department of Engineering, University of Massachusetts Boston, Boston, MA, United States
- School for the Environment, University of Massachusetts Boston, Boston, MA, United States
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, United States
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
Collapse
|
5
|
Jain S, Baranwal M. Conserved immunogenic peptides of Ebola glycoprotein elicit immune response in human peripheral blood mononuclear cells. Microbiol Immunol 2021; 65:505-511. [PMID: 34343363 DOI: 10.1111/1348-0421.12935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/24/2021] [Accepted: 08/01/2021] [Indexed: 11/30/2022]
Abstract
In the past 45 years, ebolaviruses have periodically caused epidemics on the African continent. In December 2019, approval of a recombinant vector-based EBOV vaccine, named Ervebo, came as encouraging news; still, there is a long way to go in the development of an accessible, global, and pan-ebolavirus vaccine. The current study expanded our previous in silico work which was conducted on ebolavirus glycoprotein and this resulted in the identification of three potentially immunogenic peptides (P1 - FKRTSFFLWVIILFQRTFSIPL, P2 - LANETTQALQLF, and P3 - RATTELRTFSILNRKAIDF). An analysis to estimate the number of expected human leukocyte antigen (HLA) responders revealed that P1, P2, and P3 can potentially interact with 2540, 2150, and 2802 HLA alleles, respectively. Further, these peptides were subject to in vitro analysis wherein the human peripheral blood mononuclear cell proliferation and interferon-gamma (IFN-γ) production by peptide stimulated cells was studied in 10 healthy human blood samples with the help of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and a sandwich enzyme-linked immunosorbent assay (ELISA) respectively. P3 presented the best results, a significant (P < 0.05) peptide induced cell proliferation and IFN-γ stimulation for 8 and 10 samples, respectively, followed by P1 (5 and 6) and P2 (5 and 7). The in silico and in vitro results obtained in this study indicate the immunogenic potential of these peptides and warrant exploration of the effects on other cytokines as well as in vivo experimental validation.
Collapse
Affiliation(s)
- Sahil Jain
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.,University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| |
Collapse
|
6
|
First Evidence of Antibodies Against Lloviu Virus in Schreiber's Bent-Winged Insectivorous Bats Demonstrate a Wide Circulation of the Virus in Spain. Viruses 2019; 11:v11040360. [PMID: 31010201 PMCID: PMC6521100 DOI: 10.3390/v11040360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022] Open
Abstract
Although Lloviu virus (LLOV) was discovered in the carcasses of insectivorous Schreiber’s Bent-winged bats in the caves of Northern Spain in 2002, its infectivity and pathogenicity remain unclear. We examined the seroprevalence of LLOV in potentially exposed Schreiber’s Bent-winged bats (n = 60), common serotine bats (n = 10) as controls, and humans (n = 22) using an immunoblot assay. We found antibodies against LLOV GP2 in all of Schreiber’s Bent-winged bats serum pools, but not in any of the common serotine bats and human pools tested. To confirm this seroreactivity, 52 serums were individually tested using Domain Programmable Arrays (DPA), a phage display based-system serology technique for profiling filovirus epitopes. A serological signature against different LLOV proteins was obtained in 19/52 samples tested (36.5%). The immunodominant response was in the majority specific to LLOV-unique epitopes, confirming that the serological response detected was to LLOV. To our knowledge, this is the first serological evidence of LLOV exposure in live captured Schreiber’s Bent-winged bats, dissociating LLOV circulation as the cause of the previously reported die-offs.
Collapse
|