Publications by authors named "Soumya Ranjan Mahapatra"

10 Publications

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Molecular Characterization and Designing of a Novel Multiepitope Vaccine Construct Against .

Int J Pept Res Ther 2022 17;28(2):49. Epub 2022 Jan 17.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India.

Abstract: , an ESKAPE pathogen causes many fatal clinical diseases in humans across the globe. Despite an increase in clinical instances of Pseudomonas infection, there is currently no effective vaccine or treatment available. The major membrane protein candidate of the bacterial cell is known to be a critical component for cellular bacterial susceptibility to antimicrobial peptides and survival inside the host organisms. Therefore, the current computational study aims to examine major membrane protein, OprF, and OprI, in order to design linear B-cell, cytotoxic T-cell, and helper T-cell peptide-based vaccine constructs. Utilizing various immune-informatics tools and databases, a total of two B-cells and twelve T-cells peptides were predicted. The final vaccine design was simulated to generate a high-quality three-dimensional structure, which included epitopes, adjuvant, and linkers. The vaccine was shown to be nonallergenic, antigenic, soluble, and had the best biophysical properties. The vaccine and Toll-like receptor 4 have a strong and stable interaction, according to protein-protein docking and molecular dynamics simulations. Additionally, in silico cloning was employed to see how the developed vaccine expressed in the pET28a (+) vector. Ultimately, an immune simulation was performed to see the vaccine efficacy. In conclusion, the newly developed vaccine appears to be a promising option for a vaccine against infection.

Graphical Abstract:

Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-021-10356-z.
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http://dx.doi.org/10.1007/s10989-021-10356-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8762192PMC
January 2022

Exploring capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia.

Expert Rev Vaccines 2022 Apr 4;21(4):569-587. Epub 2022 Jan 4.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India.

Background: is an emerging human pathogen causing neonatal lung disease, catheter-associated infections, and nosocomial outbreaks with high fatality rates. Capsular polysaccharide (CPS) protein plays a major determinant in virulence and is considered as a promising target for vaccine development.

Research Design And Methods: In this study, we used immunoinformatic approaches to design a multi-peptide vaccine against K. pneumonia. The epitopes were selected through several immune filters, such as antigenicity, conservancy, nontoxicity, non-allergenicity, binding affinity to HLA alleles, overlapping epitopes, and peptides having common epitopes.

Results: Finally, a construct comprising 2 B-Cell, 8 CTL, 2 HTL epitopes, along with adjuvant, linkers was designed. Peptide-HLA interaction analysis showed strong binding of these epitopes with several common HLA molecules. The in silico immune simulation and population coverage analysis of the vaccine showed its potential to evoke strong immune responses.. Further, the interaction between vaccine and immune was evaluated by docking and simulation, revealing high affinity and complex stability. Codon adaptation and in silico cloning revealed higher expression of vaccine in E. coli K12 expression system.

Conclusions: Conclusively, the findings of the present study suggest that the designed novel multi-epitopic vaccine holds potential for further experimental validation against the pathogen.
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http://dx.doi.org/10.1080/14760584.2022.2021882DOI Listing
April 2022

Genome-based identification and comparative analysis of enzymes for carotenoid biosynthesis in microalgae.

World J Microbiol Biotechnol 2021 Nov 27;38(1). Epub 2021 Nov 27.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India.

Microalgae are potential feedstocks for the commercial production of carotenoids, however, the metabolic pathways for carotenoid biosynthesis across algal lineage are largely unexplored. This work is the first to provide a comprehensive survey of genes and enzymes associated with the less studied methylerythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway as well as the carotenoid biosynthetic pathway in microalgae through bioinformatics and comparative genomics approach. Candidate genes/enzymes were subsequently analyzed across 22 microalgae species of lineages Chlorophyta, Rhodophyta, Heterokonta, Haptophyta, Cryptophyta, and known Arabidopsis homologs in order to study the evolutional divergence in terms of sequence-structure properties. A total of 403 enzymes playing a vital role in carotene, lutein, zeaxanthin, violaxanthin, canthaxanthin, and astaxanthin were unraveled. Of these, 85 were hypothetical proteins whose biological roles are not yet experimentally characterized. Putative functions to these hypothetical proteins were successfully assigned through a comprehensive investigation of the protein family, motifs, intrinsic physicochemical features, subcellular localization, pathway analysis, etc. Furthermore, these enzymes were categorized into major classes as per the conserved domain and gene ontology. Functional signature sequences were also identified which were observed conserved across microalgal genomes. Additionally, the structural modeling and active site architecture of three vital enzymes, DXR, PSY, and ZDS catalyzing the vital rate-limiting steps in Dunaliella salina were achieved. The enzymes were confirmed to be stereochemically reliable and stable as revealed during molecular dynamics simulation of 100 ns. The detailed functional information about individual vital enzymes will certainly help to design genetically modified algal strains with enhanced carotenoid contents.
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http://dx.doi.org/10.1007/s11274-021-03188-yDOI Listing
November 2021

Development of a Conserved Chimeric Vaccine for Induction of Strong Immune Response against Using Immunoinformatics Approaches.

Vaccines (Basel) 2021 Sep 18;9(9). Epub 2021 Sep 18.

Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea.

is one of the most notorious Gram-positive bacteria with a very high mortality rate. The WHO has listed as one of the ESKAPE pathogens requiring urgent research and development efforts to fight against it. Yet there is a major layback in the advancement of effective vaccines against this multidrug-resistant pathogen. SdrD and SdrE proteins are attractive immunogen candidates as they are conserved among all the strains and contribute specifically to bacterial adherence to the host cells. Furthermore, these proteins are predicted to be highly antigenic and essential for pathogen survival. Therefore, in this study, using the immunoinformatics approach, a novel vaccine candidate was constructed using highly immunogenic conserved T-cell and B-cell epitopes along with specific linkers, adjuvants, and consequently modeled for docking with human Toll-like receptor 2. Additionally, physicochemical properties, secondary structure, disulphide engineering, and population coverage analysis were also analyzed for the vaccine. The constructed vaccine showed good results of worldwide population coverage and a promising immune response. For evaluation of the stability of the vaccine-TLR-2 docked complex, a molecular dynamics simulation was performed. The constructed vaccine was subjected to in silico immune simulations by C-ImmSim and Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells, and INF-γ. Lastly, upon cloning, the vaccine protein was reverse transcribed into a DNA sequence and cloned into a pET28a (+) vector to ensure translational potency and microbial expression. The overall results of the study showed that the designed novel chimeric vaccine can simultaneously elicit humoral and cell-mediated immune responses and is a reliable construct for subsequent in vivo and in vitro studies against the pathogen.
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http://dx.doi.org/10.3390/vaccines9091038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8470666PMC
September 2021

Immunoinformatics and molecular docking studies reveal a novel Multi-Epitope peptide vaccine against pneumonia infection.

Vaccine 2021 10 21;39(42):6221-6237. Epub 2021 Sep 21.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India. Electronic address:

Pneumonia is a major endemic disease around the world, and an effective vaccine is the need of the hour to fight against the disease. When there are no appropriate antiviral and associated therapies available, vaccine development becomes even more essential. Therefore, in the present study, a variety of immunoinformatics techniques was utilized to develop a novel multi-epitope vaccine that targets the highly immunodominant type 3 fimbrial protein of Klebsiella pneumoniae, the causal organism for pneumonia. The putative B and T cell epitopes were predicted from the protein and screened for antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Subsequently, the selected epitopes were joined with the help of linkers to form a robust vaccine construct. In addition, an adjuvant was applied to the N-terminal of the construct to improve the immunogenicity of the vaccine. The physicochemical properties, solubility, the secondary and tertiary structure of the final vaccine were also established. MD simulations for 100 ns were employed to assess the stability of the vaccine-TLR-2 docked complex. The final vaccine was optimized and cloned in pET28a (+) vector with His-tag to achieve maximum vaccine protein expression for ease of purification. Immune simulation results indicated the potency of this vaccine candidate as a probable therapeutic agent. In conclusion, the overall results of various immunoinformatics tools and methods employed revealed that the constructed multi-epitope vaccine exhibits a high potential for stimulating both B and T-cells immune responses against pneumonia infection. However, experimental immunological studies are required to corroborate the viability of the novel multi-epitope construct as a commercial vaccine.
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http://dx.doi.org/10.1016/j.vaccine.2021.09.025DOI Listing
October 2021

B and T cell epitope-based peptides predicted from clumping factor protein of Staphylococcus aureus as vaccine targets.

Microb Pathog 2021 Nov 2;160:105171. Epub 2021 Sep 2.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India. Electronic address:

Staphylococcus aureus infection is emerging as a global threat because of the highly debilitating nature of the associated disease's unprecedented magnitude of its spread and growing global resistance to antimicrobial medicines. Recently WHO has categorized these bacteria under the high global priority pathogen list and is one of the six nosocomial pathogens termed as ESKAPE pathogens which have emerged as a serious threat to public health worldwide. The development of a specific vaccine can stimulate an optimal antibody response, thus providing immunity against it. Therefore, in the present study efforts have been made to identify potential vaccine candidates from the Clumping factor surface proteins (ClfA and ClfB) of S. aureus. Employing the immunoinformatics approach, fourteen antigenic peptides including T-cell, B-cell epitopes were identified which were non-toxic, non-allergenic, high antigenicity, strong binding efficiency with commonly occurring MHC alleles. Consequently, a multi-epitope vaccine chimera was designed by connecting these epitopes with suitable linkers an adjuvant to enhance immunogenicity. Further, homology modeling and molecular docking were performed to construct the three-dimensional structure of the vaccine and study the interaction between the modeled structure and immune receptor (TLR-2) present on lymphocyte cells. Consequently, molecular dynamics simulation for 100 ns period confirmed the stability of the interaction and reliability of the structure for further analysis. Finally, codon optimization and in silico cloning were employed to ensure the successful expression of the vaccine candidate. As the targeted protein is highly antigenic and conserved, hence the designed novel vaccine construct holds potential against emerging multi-drug-resistant organisms.
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http://dx.doi.org/10.1016/j.micpath.2021.105171DOI Listing
November 2021

Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal serovars.

J Biomol Struct Dyn 2021 Aug 31:1-13. Epub 2021 Aug 31.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.

Overcoming multi drug resistance is one of the crucial challenges to control enteric typhoid fever caused by and Overexpression of efflux pumps predominantly causes drug resistance in microorganisms. Therefore, immunotherapy targeting the various efflux pumps antigens could be a promising strategy to increase the success of vaccines. An immunoinformatic approach was employed to design a Salmonellosis multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of multidrug resistance protein families including ATP Binding Cassette (ABC), major facilitator superfamily (MFS), resistance nodulation cell division (RND), small multidrug resistance (SMR), and multidrug and toxin extrusion (MATE). The selected epitopes exhibited conservation in both and and thus could be helpful for cross-protection. Further, the final vaccine construct encompassing the peptides, adjuvants and specific linker sequences showed high immunogenicity, solubility, non-allergenic, nontoxic, and wide population coverage due to strong binding affinity to maximum HLA alleles. The three-dimensional structure was predicted, and validated using various structure validation tools. Additionally, protein-protein docking of the chimeric vaccine construct with the TLR-2 protein and molecular dynamics demonstrated stable and efficient binding. Conclusively, the immunoinformatic study showed that the novel multi epitopic vaccine construct can simulate the both T-cell and B-cell immune responses in typhoidal Salmonella serovars and could potentially be used for prophylactic or therapeutic applications.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1964600DOI Listing
August 2021

DBCOVP: A database of coronavirus virulent glycoproteins.

Comput Biol Med 2021 02 21;129:104131. Epub 2020 Nov 21.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India. Electronic address:

Since the emergence of SARS-CoV-1 (2002), novel coronaviruses have emerged periodically like the MERS- CoV (2012) and now, the SARS-CoV-2 outbreak which has posed a global threat to public health. Although, this is the third zoonotic coronavirus breakout within the last two decades, there are only a few platforms that provide information about coronavirus genomes. None of them is specific for the virulence glycoproteins and complete sequence-structural features of these virulence factors across the betacoronavirus family including SARS-CoV-2 strains are lacking. Against this backdrop, we present DBCOVP (http://covp.immt.res.in/), the first manually-curated, web-based resource to provide extensive information on the complete repertoire of structural virulent glycoproteins from coronavirus genomes belonging to betacoronavirus genera. The database provides various sequence-structural properties in which users can browse and analyze information in different ways. Furthermore, many conserved T-cell and B-cell epitopes predicted for each protein are present that may perform a significant role in eliciting the humoral and cellular immune response. The tertiary structure of the epitopes together with the docked epitope-HLA binding-complex is made available to facilitate further analysis. DBCOVP presents an easy-to-use interface with in-built tools for similarity search, cross-genome comparison, phylogenetic, and multiple sequence alignment. DBCOVP will certainly be an important resource for experimental biologists engaged in coronavirus research studies and will aid in vaccine development.
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http://dx.doi.org/10.1016/j.compbiomed.2020.104131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679231PMC
February 2021

Designing an efficient multi-epitope vaccine displaying interactions with diverse HLA molecules for an efficient humoral and cellular immune response to prevent COVID-19 infection.

Expert Rev Vaccines 2020 09 24;19(9):871-885. Epub 2020 Sep 24.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India.

Background: The novel SARS-CoV-2 coronavirus, the causative agent of the ongoing pandemic COVID-19 disease continues to infect people globally and has infected millions of humans worldwide. However, no effective vaccine against this virus exists.

Method: Using Immunoinformatics, epitopic sequences from multiple glycoproteins that play crucial role in pathogenesis were identified. Particularly, epitopes were mapped from conserved receptor-binding domain of spike protein which have been experimentally validated in SARS-CoV-1 as a promising target for vaccine development.

Results: A multi-epitopic vaccine construct comprising of B-cell, CTL, HTL epitopes was developed along with fusion of adjuvant and linkers. The epitopes identified herein are reported for the first time and were predicted to be highly antigenic, stable, nonallergen, nontoxic and displayed conservation across several SARS-CoV-2 isolates from different countries. Additionally, the epitopes associated with maximum HLA alleles and population coverage analysis shows the proposed epitopes would be a relevant representative of large proportion of the world population. A reliable three-dimensional structure of the vaccine construct was developed. Consequently, docking and molecular-dynamics simulation ensured the stable interaction between vaccine and innate-immune receptor.
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http://dx.doi.org/10.1080/14760584.2020.1811091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544970PMC
September 2020

dEMBF v2.0: An Updated Database of Enzymes for Microalgal Biofuel Feedstock.

Plant Cell Physiol 2020 May;61(5):1019-1024

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar 751024, India.

In light of increasing algal genomics data and knowledge of biosynthetic pathways responsible for biofuel production, an integrated resource for easy access to all information is essential to improve our understanding of algal lipid metabolism. Against this backdrop, dEMBF v2.0, a significantly updated and improved version of our database of microalgae lipid biosynthetic enzymes for biofuel production, has been developed. dEMBF v2.0 now contains a comprehensive annotation of 2018 sequences encoding 35 enzymes, an increase of over 7-fold as compared with the first version. Other improved features include an increase in species coverage to 32 algal genomes, analysis of additional metabolic pathways, expanded annotation thoroughly detailing sequence and structural features, including enzyme-ligand interactions, and integration of supporting experimental evidence to demonstrate the role of enzymes in increasing lipid content. Along with a complete redesign of the interface, the updated database provides several inbuilt tools and user-friendly functionalities for more interactive and dynamic visualization of data.
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http://dx.doi.org/10.1093/pcp/pcaa015DOI Listing
May 2020
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