scholarly journals A Candidate Multi-Epitope Vaccine Against Pathogenic Chandipura Vesiculovirus Identified using Immunoinformatics.

2020 ◽  
Author(s):  
Debashrito Deb ◽  
Srijita Basak ◽  
Tamalika Kar ◽  
Utkarsh Narsaria ◽  
Filippo Castiglione ◽  
...  
Keyword(s):  
Immune Responses ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Peptide Fragments ◽  
African Countries ◽  
Epitope Vaccine ◽  
Widespread Occurrence ◽  
Computer Aided Analysis ◽  
Global Threat ◽  
Antigenic Load

Abstract Chandipura vesiculovirus (CHPV) is a rapidly emerging pathogen responsible for causing acute encephalitis. Due to its widespread occurrence in Asian and African countries, this has become a global threat, and there is an urgent need to design an effective and non-allergenic vaccine against this pathogen. The conventional method of vaccine design involves large proteins or whole organism which leads to unnecessary antigenic load with increased chances of allergenic reactions. In addition, the process is also very time consuming and labour intensive. These limitations can be overcome by peptide-based vaccines comprising of short immunogenic peptide fragments that can elicit highly targeted immune responses, avoiding the chances of allergenic reactions, in a relatively shorter time span. The multi-epitope vaccine constructed using CTL, HTL and IFN-γ epitopes was able to elicit specific immune responses when exposed to the pathogen, in-silico. Not only that, Molecular Docking and Molecular Dynamics Simulation studies confirmed a stable interaction of the vaccine with the immune receptors. Several physicochemical analyses of the designed vaccine candidate confirmed it to be highly immunogenic and non-allergic. The computer-aided analysis performed in this study suggests that the designed multi-epitope vaccine can elicit specific immune responses and can be a potential candidate against CHPV.

scholarly journals A Candidate multi-epitope vaccine against SARS-CoV-2

2020 ◽  
Author(s):  
Tamalika Ka ◽  
Utkarsh Narsaria ◽  
Srijita Basak ◽  
Debashrito De ◽  
Filippo Castiglion ◽  
...  
Keyword(s):  
In Silico ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Candidate Vaccine ◽  
Antigenic Determinants ◽  
Potential Candidate ◽  
Spike Glycoprotein ◽  
Epitope Vaccine ◽  
K 12 ◽  
Computational Analyses

Abstract In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stabilityof the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll Like Receptors and MHC Receptors. Codon optimization was used to optimize high expression of the vaccine in E.coli K-12 strain. In silico cloning suggested efficient expression in pET-28a (+) vector. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.Authors Tamalika Kar, Utkarsh Narsaria, Srijita Basak, and Debashrito Deb contributed equally to this work.

scholarly journals Treatment of Rheumatoid Arthritis with Traditional Chinese Medicine

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Wen-Yuan Lee ◽  
Hsin-Yi Chen ◽  
Kuan-Chung Chen ◽  
Calvin Yu-Chian Chen
Keyword(s):  
Rheumatoid Arthritis ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Protein Complex ◽  
Chronic Inflammatory Disease ◽  
Dynamics Simulation ◽  
Current Therapy ◽  
Potential Candidate ◽  
Interleukin 6 Receptor ◽  
The Stability

Rheumatoid arthritis (RA) is a chronic inflammatory disease that will affect quality of life and, working efficiency, and produce negative thoughts for patients. Current therapy of RA is treated with disease-modifying antirheumatic drugs (DMARDs). Although most of these treatment methods are effective, most patients still have a pleasant experience either due to poor efficacy or side effects or both. Interleukin-6 receptor (IL6R) is important in the pathogenesis of RA. In this study, we would like to detect the potential candidates which inhibit IL6R against RA from traditional Chinese medicine (TCM). We use TCM compounds from the TCM Database@Taiwan for virtually screening the potential IL6R inhibitors. The TCM candidate compound, calycosin, has potent binding affinity with IL6R protein. The molecular dynamics simulation was employed to validate the stability of interaction in the protein complex with calycosin. The analysis indicates that protein complex with calycosin is more stable. In addition, calycosin is known to be one of the components ofAngelica sinensis, which has been indicated to have an important role in the treatment of rheumatoid arthritis. Therefore, calycosin is a potential candidate as lead compounds for further study in drug development process with IL6R protein against rheumatoid arthritis.

scholarly journals A Novel Recombinant Fcγ Receptor-Targeted Survivin Combines with Chemotherapy for Efficient Cancer Treatment

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 806
Author(s):  
Chiao-Chieh Wu ◽  
Chen-Yi Chiang ◽  
Shih-Jen Liu ◽  
Hsin-Wei Chen
Keyword(s):  
Immune Responses ◽  
Fusion Protein ◽  
Human Cancer ◽  
Formyl Peptide Receptor ◽  
Antigen Delivery ◽  
Potential Candidate ◽  
Fcγ Receptor ◽  
Formyl Peptide ◽  
Efficient Uptake

Formyl peptide receptor-like 1 inhibitor (FLIPr), an Fcγ receptor (FcγR) antagonist, can be used as a carrier to guide antigen-FLIPr fusion protein to FcγR then enhances antigen-specific immune responses. Survivin, a tumor-associated antigen, is over-expressed in various types of human cancer. In this study, we demonstrate that recombinant survivin-FLIPr fusion protein (rSur-FLIPr) binds to FcγRs, and efficient uptake by dendritic cells in vivo. In addition, rSur-FLIPr alone stimulates survivin-specific immune responses, which effectively suppresses the tumor growth. The antitumor immunities are through TAP-mediated and CD8-dependent pathways. Furthermore, preexisting anti-FLIPr antibody does not abolish antitumor responses induced by rSur-FLIPr immunization. These results suggest that FLIPr is an effective antigen delivery vector and can be repeatedly used. Combination of chemotherapy with rSur-FLIPr treatment reveals a great benefit to tumor-bearing mice. Altogether, these findings suggest that rSur-FLIPr is a potential candidate for efficient cancer therapy.

scholarly journals Pharmacophore Modelling-Based Drug Repurposing Approaches for SARS-CoV-2 Therapeutics

2021 ◽  
Vol 9 ◽  
Author(s):  
Shailima Rampogu ◽  
Keun Woo Lee
Keyword(s):  
Effective Treatment ◽  
Pharmacophore Model ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Binding Mode ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Pharmacophore Modelling ◽  
Discovery Studio

The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to repurpose the approved drugs. In this pursuit, an exhaustive computational method has been used on the DrugBank compounds targeting nsp16/nsp10 complex (PDB code: 6W4H). A structure-based pharmacophore model was generated, and the selected model was escalated to screen DrugBank database, resulting in three compounds. These compounds were subjected to molecular docking studies at the protein-binding pocket employing the CDOCKER module available with the Discovery Studio v18. In order to discover potential candidate compounds, the co-crystallized compound S-adenosyl methionine (SAM) was used as the reference compound. Additionally, the compounds remdesivir and hydroxycholoroquine were employed for comparative docking. The results have shown that the three compounds have demonstrated a higher dock score than the reference compounds and were upgraded to molecular dynamics simulation (MDS) studies. The MDS results demonstrated that the three compounds, framycetin, kanamycin, and tobramycin, are promising candidate compounds. They have represented a stable binding mode at the targets binding pocket with an average protein backbone root mean square deviation below 0.3 nm. Additionally, they have prompted the hydrogen bonds during the entire simulations, inferring that the compounds have occupied the active site firmly. Taken together, our findings propose framycetin, kanamycin, and tobramycin as potent putative inhibitors for COVID-19 therapeutics.

scholarly journals Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae

Vaccines ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 88 ◽  
Author(s):  
Dar ◽  
Zaheer ◽  
Shehroz ◽  
Ullah ◽  
Naz ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
High Morbidity ◽  
T Cell Epitopes ◽  
Toll Like Receptor ◽  
Epitope Vaccine ◽  
The Core ◽  
Core Proteins

Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.

FbaA- and M protein-based multi-epitope vaccine elicits strong protective immune responses against group A streptococcus in mouse model

2014 ◽  
Vol 16 (5) ◽  
pp. 409-418 ◽  
Author(s):  
Cuiqing Ma ◽  
Zheng Liu ◽  
Wenjian Li ◽  
Xuesong Qian ◽  
Song Zhang ◽  
...  
Keyword(s):  
Mouse Model ◽  
Immune Responses ◽  
Group A Streptococcus ◽  
M Protein ◽  
Epitope Vaccine ◽  
Group A

Behavioral pattern exploration of single guest, hexadecane-1,16-diol and hexadecane in urea inclusion compounds via molecular dynamics simulation

2016 ◽  
Vol 15 (06) ◽  
pp. 1650047 ◽  
Author(s):  
Siti Fatimah Zaharah Mustafa ◽  
Hasmerya Maarof ◽  
Mohammed Abu Naser ◽  
Hassan H. Abdallah ◽  
Ahmad Irfan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Inclusion Compounds ◽  
Behavioral Pattern ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Urea Inclusion Compounds ◽  
High Interaction ◽  
Restricted Environment ◽  
Rotational Orientation ◽  
Urea Inclusion

The urea inclusion compounds, a unique polar organic crystalline complex, are considered as a potential candidate for a molecular separator of long chain alkane molecule. A well-defined structure of the crystalline channel systems constructed from hydrogen bonding arrangement of the urea molecules, can be used to understand the fundamental aspects of the processes involving ions or molecules transportation. To do so, in our work, molecular dynamics approach is implemented to understand the behavioral pattern of the hexadecane-1,16-diol and hexadecane guests’ related to translational and rotational orientation along the urea tunnel. Our obtained results reveal that high interaction of hexadecane-1,16-diol with urea host molecules offers a restricted environment inside urea tunnel, resulting in slowing down the guest movement. Hexadecane guest system, on the contrary, exhibits lower interaction whereby the translational and rotational movement is faster. Moreover, as the distance increases (along [Formula: see text]-axis) in the urea tunnel, both guest systems favor a clockwise rotational orientation. Preference of the respected orientation indicates the influence of chiral urea tunnel on achiral guests that is clathrate inside the tunnel structure.

scholarly journals Inhibition of Innate Immune Responses Is Key to Pathogenesis by Arenaviruses

2016 ◽  
Vol 90 (8) ◽  
pp. 3810-3818 ◽  
Author(s):  
Bjoern Meyer ◽  
Hinh Ly
Keyword(s):  
Immune Responses ◽  
Immune Evasion ◽  
Molecular Mechanisms ◽  
Multiorgan Failure ◽  
Hemorrhagic Fever ◽  
Innate Immune ◽  
Lassa Virus ◽  
Immune Recognition ◽  
African Countries ◽  
Host Immune Responses

Mammalian arenaviruses are zoonotic viruses that cause asymptomatic, persistent infections in their rodent hosts but can lead to severe and lethal hemorrhagic fever with bleeding and multiorgan failure in human patients. Lassa virus (LASV), for example, is endemic in several West African countries, where it is responsible for an estimated 500,000 infections and 5,000 deaths annually. There are currently no FDA-licensed therapeutics or vaccines available to combat arenavirus infection. A hallmark of arenavirus infection (e.g., LASV) is general immunosuppression that contributes to high viremia. Here, we discuss the early host immune responses to arenavirus infection and the recently discovered molecular mechanisms that enable pathogenic viruses to suppress host immune recognition and to contribute to the high degree of virulence. We also directly compare the innate immune evasion mechanisms between arenaviruses and other hemorrhagic fever-causing viruses, such as Ebola, Marburg, Dengue, and hantaviruses. A better understanding of the immunosuppression and immune evasion strategies of these deadly viruses may guide the development of novel preventative and therapeutic options.

scholarly journals Phloroglucinol as a Potential Candidate against Trypanosoma congolense Infection: Insights from In Vivo, In Vitro, Molecular Docking and Molecular Dynamic Simulation Analyses

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 469
Author(s):  
Nasirudeen Idowu Abdulrashid ◽  
Suleiman Aminu ◽  
Rahma Muhammad Adamu ◽  
Nasir Tajuddeen ◽  
Murtala Bindawa Isah ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Binding Energies ◽  
Sub Saharan Africa ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Inhibitory Effects ◽  
Hydrogen Bond Interaction

Sub-Saharan Africa is profoundly challenged with African Animal Trypanosomiasis and the available trypanocides are faced with drawbacks, necessitating the search for novel agents. Herein, the chemotherapeutic potential of phloroglucinol on T. congolense infection and its inhibitory effects on the partially purified T. congolense sialidase and phospholipase A2 (PLA2) were investigated. Treatment with phloroglucinol for 14 days significantly (p < 0.05) suppressed T. congolense proliferation, increased animal survival and ameliorated anemia induced by the parasite. Using biochemical and histopathological analyses, phloroglucinol was found to prevent renal damages and splenomegaly, besides its protection against T. congolense-associated increase in free serum sialic acids in infected animals. Moreover, the compound inhibited bloodstream T. congolense sialidase via mixed inhibition pattern with inhibition binding constant (Ki) of 0.181 µM, but a very low uncompetitive inhibitory effects against PLA2 (Ki > 9000 µM) was recorded. Molecular docking studies revealed binding energies of −4.9 and −5.3 kcal/mol between phloroglucinol with modeled sialidase and PLA2 respectively, while a 50 ns molecular dynamics simulation using GROMACS revealed the sialidase-phloroglucinol complex to be more compact and stable with higher free binding energy (−67.84 ± 0.50 kJ/mol) than PLA2-phloroglucinol complex (−77.17 ± 0.52 kJ/mol), based on MM-PBSA analysis. The sialidase-phloroglucinol complex had a single hydrogen bond interaction with Ser453 while none was observed for the PLA2-phloroglucinol complex. In conclusion, phloroglucinol showed moderate trypanostatic activity with great potential in ameliorating some of the parasite-induced pathologies and its anti-anemic effects might be linked to inhibition of sialidase rather than PLA2.

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