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Dhulipala S, Uversky VN. Looking at the Pathogenesis of the Rabies Lyssavirus Strain Pasteur Vaccins through a Prism of the Disorder-Based Bioinformatics. Biomolecules 2022; 12:1436. [PMID: 36291645 PMCID: PMC9599798 DOI: 10.3390/biom12101436] [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] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Rabies is a neurological disease that causes between 40,000 and 70,000 deaths every year. Once a rabies patient has become symptomatic, there is no effective treatment for the illness, and in unvaccinated individuals, the case-fatality rate of rabies is close to 100%. French scientists Louis Pasteur and Émile Roux developed the first vaccine for rabies in 1885. If administered before the virus reaches the brain, the modern rabies vaccine imparts long-lasting immunity to the virus and saves more than 250,000 people every year. However, the rabies virus can suppress the host's immune response once it has entered the cells of the brain, making death likely. This study aimed to make use of disorder-based proteomics and bioinformatics to determine the potential impact that intrinsically disordered protein regions (IDPRs) in the proteome of the rabies virus might have on the infectivity and lethality of the disease. This study used the proteome of the Rabies lyssavirus (RABV) strain Pasteur Vaccins (PV), one of the best-understood strains due to its use in the first rabies vaccine, as a model. The data reported in this study are in line with the hypothesis that high levels of intrinsic disorder in the phosphoprotein (P-protein) and nucleoprotein (N-protein) allow them to participate in the creation of Negri bodies and might help this virus to suppress the antiviral immune response in the host cells. Additionally, the study suggests that there could be a link between disorder in the matrix (M) protein and the modulation of viral transcription. The disordered regions in the M-protein might have a possible role in initiating viral budding within the cell. Furthermore, we checked the prevalence of functional disorder in a set of 37 host proteins directly involved in the interaction with the RABV proteins. The hope is that these new insights will aid in the development of treatments for rabies that are effective after infection.
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Affiliation(s)
- Surya Dhulipala
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
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Lian M, Hueffer K, Weltzin MM. Interactions between the rabies virus and nicotinic acetylcholine receptors: A potential role in rabies virus induced behavior modifications. Heliyon 2022; 8:e10434. [PMID: 36091963 PMCID: PMC9450143 DOI: 10.1016/j.heliyon.2022.e10434] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/06/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Marianne Lian
- University of Alaska Fairbanks, Department of Veterinary Medicine, 2141 Koyukuk Drive, Fairbanks, AK, 99775, USA
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Koppang, NO-2480, Norway
| | - Karsten Hueffer
- University of Alaska Fairbanks, Department of Veterinary Medicine, 2141 Koyukuk Drive, Fairbanks, AK, 99775, USA
| | - Maegan M. Weltzin
- University of Alaska Fairbanks, Department of Chemistry and Biochemistry, 1930 Yukon Dr. Fairbanks, AK, 99775, USA
- Corresponding author.
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Bhat RAH, Thakuria D, Tandel RS, Khangembam VC, Dash P, Tripathi G, Sarma D. Tools and techniques for rational designing of antimicrobial peptides for aquaculture. FISH & SHELLFISH IMMUNOLOGY 2022; 127:1033-1050. [PMID: 35872334 DOI: 10.1016/j.fsi.2022.07.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Fisheries and aquaculture industries remain essential sources of food and nutrition for millions of people worldwide. Indiscriminate use of antibiotics has led to the emergence of antimicrobial-resistant bacteria and posed a severe threat to public health. Researchers have opined that antimicrobial peptides (AMPs) can be the best possible alternative to curb the rising tide of antimicrobial resistance in aquaculture. AMPs may also help to achieve the objectives of one health approach. The natural AMPs are associated with several shortcomings, like less in vivo stability, toxicity to host cell, high cost of production and low potency in a biological system. In this review, we have provided a comprehensive outline about the strategies for designing synthetic mimics of natural AMPs with high potency. Moreover, the freely available AMP databases and the information about the molecular docking tools are enlisted. We also provided in silico template for rationally designing the AMPs from fish piscidins or other peptides. The rationally designed piscidin (rP1 and rp2) may be used to tackle microbial infections in aquaculture. Further, the protocol can be used to develop the truncated mimics of natural AMPs having more potency and protease stability.
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Affiliation(s)
| | - Dimpal Thakuria
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | | | - Victoria C Khangembam
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Pragyan Dash
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Gayatri Tripathi
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, Maharashtra, India
| | - Debajit Sarma
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
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Novel peptide (RATH) mediated delivery of peptide nucleic acids for antiviral interventions. Appl Microbiol Biotechnol 2021; 105:6669-6677. [PMID: 34427763 DOI: 10.1007/s00253-021-11502-9] [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] [Received: 05/10/2021] [Revised: 07/20/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
The peptide nucleic acid (PNA) is a chimeric molecule with the nucleobases connected by peptide bonds. This chimeric nature gives the PNA certain therapeutic advantages over natural antisense nucleic acid molecules. The PNA probes are known for its better and stronger complementation with target nucleic acids. However, cellular delivery of PNA is a major hurdle due to the charge-neutral nature of the PNA. For cellular delivery of PNA, peptide-PNA conjugates are used. This approach may face some practical limitation in terms of PNA antisense activity. In this study, we propose a novel RATH-2 peptide-based non-covalent PNA delivery mechanism. We observed RATH-2 shows a favorable molecular interaction with PNA at 16:1 (peptide:PNA) molar ratio resulting in co-centric nanoparticle formation. With this combination, we could achieve as high as 93% cellular delivery of the PNA. The proposed non-covalent RATH:PNA delivery model showed endocytic entrapment free delivery of PNA. The study further demonstrated the therapeutic application of PNA with in vitro antiviral intervention model. Using RATH-2 non-covalent PNA delivery system, we could inhibit 69.5% viral load. The present study demonstrates a cell-penetrating peptide:PNA interaction can lead to nanoparticle formations that facilitated cellular delivery of PNA.Key points• A novel cell-penetrating peptide (RATH-2) was identified for non-covalent delivery of PNA.• RATH-2 and PNA formed co-centric nanoparticles at appropriate molar combination.• PNA delivered through the RATH-2 inhibited the viral gene expression and reduced the viral load.
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Research progress on coronavirus S proteins and their receptors. Arch Virol 2021; 166:1811-1817. [PMID: 33778918 PMCID: PMC8005323 DOI: 10.1007/s00705-021-05008-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/22/2020] [Indexed: 01/19/2023]
Abstract
Coronaviruses are a large family of important pathogens that cause human and animal diseases. At the end of 2019, a pneumonia epidemic caused by a novel coronavirus brought attention to coronaviruses. Exploring the interaction between the virus and its receptor will be helpful in developing preventive vaccines and therapeutic drugs. The coronavirus spike protein (S) plays an important role in both binding to receptors on host cells and fusion of the viral membrane with the host cell membrane. This review introduces the structure and function of the S protein and its receptor, focusing on the binding mode and binding region of both.
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Bourhy H, de Melo GD, Tarantola A. [New aspects of rabies control]. BULLETIN DE L'ACADEMIE NATIONALE DE MEDECINE 2020; 204:1000-1009. [PMID: 32981935 PMCID: PMC7500396 DOI: 10.1016/j.banm.2020.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022]
Abstract
Rabies still causes about 60,000 human deaths per year, mainly in poor populations in Africa and Asia. However, since Louis Pasteur developed the first vaccine 130 years ago, prophylactic measures have been considerably improved and simplified. They now consist of the vaccine combined with purified rabies immunoglobulins of equine or human origin. In general, however, post-exposure prophylaxis protocols are long and expensive. Furthermore, the immunoglobulins used for associated serotherapy are costly and not widely available in developing countries. Approaches have been developed to deal with these two issues that offer hope for a paradigm shift for the benefit of exposed populations. Finally, mass rabies vaccination in dogs, which are the most cost-effective measure for preventing rabies in humans, are difficult to implement and sometimes have moderate effectiveness. The identification and analysis of the epidemiological drivers conditioning the circulation of the virus in dog populations allow a better understanding of the key control points that need to be associated with these campaigns for a better efficacy.
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Affiliation(s)
- H Bourhy
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
| | - G D de Melo
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
| | - A Tarantola
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
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Zhou J, Ren M, Wang W, Huang L, Lu Z, Song Z, Foda MF, Zhao L, Han H. Pomegranate-Inspired Silica Nanotags Enable Sensitive Dual-Modal Detection of Rabies Virus Nucleoprotein. Anal Chem 2020; 92:8802-8809. [PMID: 32450687 DOI: 10.1021/acs.analchem.0c00200] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The outbreak of rabies virus (RABV) in Asia and Africa has attracted widespread concern due to its 100% mortality rate, and RABV detection is crucial to its diagnosis and treatment. Herein, we report a sensitive and reliable strategy for the dual-modal RABV detection using pomegranate-shaped dendritic silica nanospheres fabricated with densely incorporated quantum dots (QDs) and horseradish peroxidase (HRP)-labeled antibody. The immunoassay involves the specific interaction between virus and nanospheres-conjugated antibody coupled with robust fluorescence signal originating from QDs and naked-eye discernible colorimetric signal on the oxTMB. The ultrahigh loading capacity of QDs enables the detection limit down to 8 pg/mL via fluorescence modality, a 348-fold improvement as compared with conventional enzyme-linked immunosorbent assay (ELISA). In addition, the detection range was from 1.20 × 102 to 2.34 × 104 pg/mL by plotting the absorbance at 652 nm with RABV concentrations with a detection limit of 91 pg/mL, which is nearly 2 order of magnitude lower than that of the conventional ELISA. Validated with 12 brain tissue samples, our immunoassay results are completely consistent with polymerase chain reaction (PCR) results. Compared with the PCR assay, our approach requires no complex sample pretreatments or expensive instruments. This is the first report on RABV diagnosis using nanomaterials for colorimetry-based prescreening and fluorescence-based quantitative detection, which may pave the way for virus-related disease diagnosis and clinical analysis.
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Affiliation(s)
- Jiaojiao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Meishen Ren
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Huang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhicheng Lu
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Song
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Mohamed F Foda
- Department of Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Toukh, 13736, Egypt.,State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Heyou Han
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
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Yang F, Lin S, Ye F, Yang J, Qi J, Chen Z, Lin X, Wang J, Yue D, Cheng Y, Chen Z, Chen H, You Y, Zhang Z, Yang Y, Yang M, Sun H, Li Y, Cao Y, Yang S, Wei Y, Gao GF, Lu G. Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody. Cell Host Microbe 2020; 27:441-453.e7. [DOI: 10.1016/j.chom.2019.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/06/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
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Agnihotry S, Dhusia K, Srivastav AK, Upadhyay J, Verma V, Shukla PK, Ramteke PW, Gautam B. Biochemical regulation and structural analysis of copper‐transporting ATPase in a human hepatoma cell line for Wilson disease. J Cell Biochem 2019; 120:18826-18844. [DOI: 10.1002/jcb.29199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shikha Agnihotry
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Kalyani Dhusia
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Ajeet K. Srivastav
- Photobiology Laboratory, System Toxicology and Health Risk Assessment GroupCSIR‐Indian Institute of Toxicology Research (CSIR‐IITR) Lucknow Uttar Pradesh India
| | - Jaya Upadhyay
- Department of GastroenterologySanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow Uttar Pradesh India
| | - Vinod Verma
- Department of Hematology, Stem Cell Research CentreSanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow Uttar Pradesh India
| | - Pradeep K. Shukla
- Department of Biological Sciences, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Pramod W. Ramteke
- Department of Biological Sciences, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
| | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio‐Engineering, Sam Higginbottom University of AgricultureTechnology and Sciences Allahabad Uttar Pradesh India
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Dhusia K, Raja K, Thomas PPM, Yadav PK, Ramteke PW. Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcescens. INFECTION GENETICS AND EVOLUTION 2018; 67:101-111. [PMID: 30396000 DOI: 10.1016/j.meegid.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/02/2018] [Accepted: 11/01/2018] [Indexed: 10/27/2022]
Abstract
Ornithine decarboxylase (ODC) is an immediate precursor of polyamine biosynthesis in Serratia marcescens and a potential target for inhibition of its growth. We predicted the 3D structural conformation of ODC enzyme and validated it using MDS in our previous study. In this current study, the potential inhibitors of ODC were obtained by virtual screening of potential inhibitors from ZINC database and studied in depth for their different binding pose. Among the ten virtually screened inhibitors, Conessine exhibited the best binding with ODC and its inhibition property was studied further by MDS studies. The natural compound conessine is isolated from plant Holarrhena antidysenterica and it is studied against ODC of Serratia marcenses for its inhibitory potentials. This revealed unforeseen twisted position in root mean square fluctuation (RMSF) and ODC modelled conformation that influenced ligand binding. Both predicted model and ligand bound model were compared and found to be stable with Root Mean Square Deviation (RMSD) of approximately 7 nm and 0.25 nm to that of crystallographic structure over simulation time of 55 ns and 70 ns respectively. This work paves the way for future development of new drugs against nosocomial diseases caused by Serratia marcescens.
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Affiliation(s)
- Kalyani Dhusia
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Kalpana Raja
- Department of Dermatology, University of Michigan Medical School, Ann arbor, MI 48109, USA
| | - Pierre Paul Michel Thomas
- Institute of Public Health Genomics, Genetics and Cell Biology cluster, GROW Research School for Oncology and Developmental Biology, Maastricht University, the Netherlands
| | - Pramod K Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Pramod W Ramteke
- Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India.
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