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Qiao Y, Gu M, Wang X, Chen R, Kong L, Li S, Li J, Liu Q, Hou S, Wang Z. Revealing Dynamics of Protein Phosphorylation: A Study on the Cashmere Fineness Disparities in Liaoning Cashmere Goats. Mol Biotechnol 2024:10.1007/s12033-024-01244-0. [PMID: 39117978 DOI: 10.1007/s12033-024-01244-0] [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: 11/24/2023] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
Exploring the landscape of protein phosphorylation, this investigation focuses on skin samples from LCG (Liaoning Cashmere Goats), characterized by different levels of cashmere fineness. Employing LC-MS/MS technology, we meticulously scrutinized FT-LCG (fine-type Liaoning Cashmere Goats) and CT-LCG (coarse-type Liaoning Cashmere Goats). Identifying 512 modified proteins, encompassing 1368 phosphorylated peptide segments and 1376 quantifiable phosphorylation sites, our exploration further revealed consistent phosphorylation sites in both groups. Analysis of phosphorylated peptides unveiled kinase substrates, prominently featuring Protein Kinase C, Protein Kinase B and MAPK3-MAPK1-MAPK7-NLK-group. Differential analysis spotlighted 28 disparate proteins, comprising six upregulated and twenty-two downregulated. Cluster analysis showcased the robust clustering efficacy of the two sample groups. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses underscored the significance of the purine metabolism pathway, suggesting its pivotal role in modulating cashmere fineness in LCG. Notably, through differential protein analysis, two crucial proteins were identified: HSL-X (hormone-sensitive lipase isoform X1) and KPRP (keratinocyte proline-rich protein). Further evidence supports LIPE and KPRP as key genes regulating cashmere fineness, paving the way for promising avenues in further research. These findings not only contribute to a nuanced understanding of protein-level dynamics in cashmere but also provide a theoretical foundation for the selective breeding of superior Liaoning Cashmere Goat strands.
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Affiliation(s)
- Yanjun Qiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaowei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lingchao Kong
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuaitong Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiaqi Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qingkun Liu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Sibing Hou
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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2
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Pan X, Guo X, Shi J. Design of a novel multiepitope vaccine with CTLA-4 extracellular domain against Mycoplasma pneumoniae: A vaccine-immunoinformatics approach. Vaccine 2024; 42:3883-3898. [PMID: 38777697 DOI: 10.1016/j.vaccine.2024.04.098] [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] [Received: 09/17/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Community-acquired pneumonia often stems from the macrolide-resistant strain of Mycoplasma pneumoniae, yet no effective vaccine exists against it. METHODS This study proposes a vaccine-immunoinformatics strategy for Mycoplasma pneumoniae and other pathogenic microbes. Specifically, dominant B and T cell epitopes of the Mycoplasma pneumoniae P30 adhesion protein were identified through immunoinformatics method. The vaccine sequence was then constructed by coupling with CTLA-4 extracellular region, a novel molecular adjuvant for antigen-presenting cells. Subsequently, the vaccine's physicochemical properties, antigenicity, and allergenicity were verified. Molecular dynamics modeling was employed to confirm interaction with TLR-2, TLR-4, B7-1, and B7-2. Finally, the vaccine underwent in silico cloning for expression. RESULTS The vaccine exhibited both antigenicity and non-allergenicity. Molecular dynamics simulation, post-docking with TLR-2, TLR-4, B7-1, and B7-2, demonstrated stable interaction between the vaccine and these molecules. In silico cloning confirmed effective expression of the vaccine gene in insect baculovirus vectors. CONCLUSION This vaccine-immunoinformatics approach holds promise for the development of vaccines against Mycoplasma pneumoniae and other pathogenic non-viral and non-bacterial microbes.
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Affiliation(s)
- Xiaohong Pan
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Xiaomei Guo
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; Kunming Medical University, Kunming, Yunnan, China
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan China.
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3
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Cobre ADF, Maia Neto M, de Melo EB, Fachi MM, Ferreira LM, Tonin FS, Pontarolo R. Naringenin-4'-glucuronide as a new drug candidate against the COVID-19 Omicron variant: a study based on molecular docking, molecular dynamics, MM/PBSA and MM/GBSA. J Biomol Struct Dyn 2024; 42:5881-5894. [PMID: 37394802 DOI: 10.1080/07391102.2023.2229446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
This study aimed to identify natural bioactive compounds (NBCs) as potential inhibitors of the spike (S1) receptor binding domain (RBD) of the COVID-19 Omicron variant using computer simulations (in silico). NBCs with previously proven biological in vitro activity were obtained from the ZINC database and analyzed through virtual screening, molecular docking, molecular dynamics (MD), molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), and molecular mechanics/generalized Born surface area (MM/GBSA). Remdesivir was used as a reference drug in docking and MD calculations. A total of 170,906 compounds were analyzed. Molecular docking screening revealed the top four NBCs with a high affinity with the spike (affinity energy <-7 kcal/mol) to be ZINC000045789238, ZINC000004098448, ZINC000008662732, and ZINC000003995616. In the MD analysis, the four ligands formed a complex with the highest dynamic equilibrium S1 (mean RMSD <0.3 nm), lowest fluctuation of the complex amino acid residues (RMSF <1.3), and solvent accessibility stability. However, the ZINC000045789238-spike complex (naringenin-4'-O glucuronide) was the only one that simultaneously had minus signal (-) MM/PBSA and MM/GBSA binding free energy values (-3.74 kcal/mol and -15.65 kcal/mol, respectively), indicating favorable binding. This ligand (naringenin-4'-O glucuronide) was also the one that produced the highest number of hydrogen bonds in the entire dynamic period (average = 4601 bonds per nanosecond). Six mutant amino acid residues formed these hydrogen bonds from the RBD region of S1 in the Omicron variant: Asn417, Ser494, Ser496, Arg403, Arg408, and His505. Naringenin-4'-O-glucuronide showed promising results as a potential drug candidate against COVID-19. In vitro and preclinical studies are needed to confirm these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Moisés Maia Neto
- Department of Pharmacy, Fametro University Centre (UNIFAMETRO), Fortaleza-Ceará, Brazil
| | - Eduardo Borges de Melo
- Department of Pharmacy, Universidade Estadual do Oeste do Paraná (UNIOESTE), Cascavel-PR, Brazil
| | - Mariana Millan Fachi
- Pharmaceutical Sciences Postgraduate Programme, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Fernanda Stumpf Tonin
- H&TRC - Health & Technology Research Centre, ESTeSL, Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Roberto Pontarolo
- Department of Pharmacy, Universidade Federal do Paraná, Curitiba, Brazil
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4
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Nie J, Wang Q, Li C, Zhou Y, Yao X, Xu L, Chang Y, Ding F, Sun L, Zhan L, Zhu L, Xie K, Wang X, Shi Y, Zhao Q, Shan Y. Self-Assembled Multiepitope Nanovaccine Provides Long-Lasting Cross-Protection against Influenza Virus. Adv Healthc Mater 2024; 13:e2303531. [PMID: 37983728 DOI: 10.1002/adhm.202303531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Indexed: 11/22/2023]
Abstract
Seasonal influenza vaccines typically provide strain-specific protection and are reformulated annually, which is a complex and time-consuming process. Multiepitope vaccines, combining multiple conserved antigenic epitopes from a pathogen, can trigger more robust, diverse, and effective immune responses, providing a potential solution. However, their practical application is hindered by low immunogenicity and short-term effectiveness. In this study, multiple linear epitopes from the conserved stem domain of hemagglutinin and the ectodomain of matrix protein 2 are combined with the Helicobacter pylori ferritin, a stable self-assembled nanoplatform, to develop an influenza multiepitope nanovaccine, named MHF. MHF is prokaryotically expressed in a soluble form and self-assembles into uniform nanoparticles. The subcutaneous immunization of mice with adjuvanted MHF induces cross-reactive neutralizing antibodies, antibody-dependent cell-mediated cytotoxicity, and cellular immunity, offering complete protection against H3N2 as well as partial protection against H1N1. Importantly, the vaccine cargo delivered by ferritin triggers epitope-specific memory B-cell responses, with antibody level persisting for over 6 months post-immunization. These findings indicate that self-assembled multiepitope nanovaccines elicit potent and long-lasting immune responses while significantly reducing the risk of vaccine escape mutants, and offer greater practicality in terms of scalable manufacturing and genetic manipulability, presenting a promising and effective strategy for future vaccine development.
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Affiliation(s)
- Jiaojiao Nie
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau, 519000, China
| | - Qingyu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Chenxi Li
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yongfei Zhou
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xin Yao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Lipeng Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yaotian Chang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Fan Ding
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Lulu Sun
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Li Zhan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Lvzhou Zhu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Kunpeng Xie
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yuhua Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Qi Zhao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau, 519000, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, 519000, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
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5
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Ji H, Wang XX, Zhang Q, Zhang C, Zhang HM. Predicting TCR sequences for unseen antigen epitopes using structural and sequence features. Brief Bioinform 2024; 25:bbae210. [PMID: 38711371 PMCID: PMC11074592 DOI: 10.1093/bib/bbae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
T-cell receptor (TCR) recognition of antigens is fundamental to the adaptive immune response. With the expansion of experimental techniques, a substantial database of matched TCR-antigen pairs has emerged, presenting opportunities for computational prediction models. However, accurately forecasting the binding affinities of unseen antigen-TCR pairs remains a major challenge. Here, we present convolutional-self-attention TCR (CATCR), a novel framework tailored to enhance the prediction of epitope and TCR interactions. Our approach utilizes convolutional neural networks to extract peptide features from residue contact matrices, as generated by OpenFold, and a transformer to encode segment-based coded sequences. We introduce CATCR-D, a discriminator that can assess binding by analyzing the structural and sequence features of epitopes and CDR3-β regions. Additionally, the framework comprises CATCR-G, a generative module designed for CDR3-β sequences, which applies the pretrained encoder to deduce epitope characteristics and a transformer decoder for predicting matching CDR3-β sequences. CATCR-D achieved an AUROC of 0.89 on previously unseen epitope-TCR pairs and outperformed four benchmark models by a margin of 17.4%. CATCR-G has demonstrated high precision, recall and F1 scores, surpassing 95% in bidirectional encoder representations from transformers score assessments. Our results indicate that CATCR is an effective tool for predicting unseen epitope-TCR interactions. Incorporating structural insights enhances our understanding of the general rules governing TCR-epitope recognition significantly. The ability to predict TCRs for novel epitopes using structural and sequence information is promising, and broadening the repository of experimental TCR-epitope data could further improve the precision of epitope-TCR binding predictions.
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MESH Headings
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/genetics
- Humans
- Epitopes/chemistry
- Epitopes/immunology
- Computational Biology/methods
- Neural Networks, Computer
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Antigens/chemistry
- Antigens/immunology
- Amino Acid Sequence
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Affiliation(s)
- Hongchen Ji
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Xiang-Xu Wang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Qiong Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Chengkai Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Hong-Mei Zhang
- Department of Oncology of Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi, China
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6
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Lin Y, Ma J, Yuan H, Chen Z, Xu X, Jiang M, Zhu J, Meng W, Qiu W, Liu Y. Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design. Brief Bioinform 2024; 25:bbae247. [PMID: 38770719 PMCID: PMC11107383 DOI: 10.1093/bib/bbae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Recent advances in cancer immunotherapy have highlighted the potential of neoantigen-based vaccines. However, the design of such vaccines is hindered by the possibility of weak binding affinity between the peptides and the patient's specific human leukocyte antigen (HLA) alleles, which may not elicit a robust adaptive immune response. Triggering cross-immunity by utilizing peptide mutations that have enhanced binding affinity to target HLA molecules, while preserving their homology with the original one, can be a promising avenue for neoantigen vaccine design. In this study, we introduced UltraMutate, a novel algorithm that combines Reinforcement Learning and Monte Carlo Tree Search, which identifies peptide mutations that not only exhibit enhanced binding affinities to target HLA molecules but also retains a high degree of homology with the original neoantigen. UltraMutate outperformed existing state-of-the-art methods in identifying affinity-enhancing mutations in an independent test set consisting of 3660 peptide-HLA pairs. UltraMutate further showed its applicability in the design of peptide vaccines for Human Papillomavirus and Human Cytomegalovirus, demonstrating its potential as a promising tool in the advancement of personalized immunotherapy.
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Affiliation(s)
- Yicheng Lin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Jiakang Ma
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Haozhe Yuan
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Xingyu Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Mengping Jiang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Jialiang Zhu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Wenqing Qiu
- Shanghai Xuhui Central Hospital, 366 North Longchuan Road, Shanghai, 200231, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
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7
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Sura K, Rohilla H, Kumar D, Jakhar R, Ahlawat V, Kaushik D, Dangi M, Chhillar AK. Exploring structural antigens of yellow fever virus to design multi-epitope subunit vaccine candidate by utilizing an immuno-informatics approach. J Genet Eng Biotechnol 2023; 21:161. [PMID: 38051433 DOI: 10.1186/s43141-023-00621-7] [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: 04/21/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Yellow fever is a mosquito-borne viral hemorrhagic disease transmitted by several species of virus-infected mosquitoes endemic to tropical regions of Central and South America and Africa. Earlier in the twentieth century, mass vaccination integrated with mosquito control was implemented to eradicate the yellow fever virus. However, regular outbreaks occur in these regions which pose a threat to travelers and residents of Africa and South America. There is no specific antiviral therapy, but there can be an effective peptide-based vaccine candidate to combat infection caused by the virus. Therefore, the study aims to design a multi-epitope-based subunit vaccine (MESV) construct against the yellow fever virus to reduce the time and cost using reverse vaccinology (RV) approach. METHODS Yellow fever virus contains 10,233 nucleotides that encode for 10 proteins (C, prM, E, NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) including 3 structural and 7 non-structural proteins. Structural proteins-precursor membrane protein (prM) and envelope protein (E)-were taken as a target for B cell and T cell epitope screening. Further, various immunoinformatics approaches were employed to FASTA sequences of structural proteins to retrieve B cell and T cell epitopes. MESV was constructed from these epitopes based on allergenicity, antigenicity and immunogenicity, toxicity, conservancy, and population coverage followed by structure prediction. The efficacy of the MESV construct to bind with human TLR-3, TLR-4, and TLR-8 were evaluated using molecular docking and simulation studies. Finally, in-silico cloning of vaccine construct was performed withpBR322 Escherichia coli expression system using codon optimization. RESULTS Predicted epitopes evaluated and selected for MESV construction were found stable, non-allergenic, highly antigenic, and global population coverage of 68.03% according to in-silico analysis. However, this can be further tested in in-vitro and in-vivo investigations. Epitopes were sequentially merged to construct a MESV consisting of 393 amino acids using adjuvant and linkers. Molecular docking and simulation studies revealed stable and high-affinity interactions. Furthermore, in-silico immune response graphs showed effective immune response generation. Finally, higher CAI value ensured high gene expression of vaccine in the host cell. CONCLUSION The designed MESV construct in the present in-silico study can be effective in generating an immune response against the yellow fever virus. Therefore, to prevent yellow fever, it can be an effective vaccine candidate. However, further downstream, in-vitro study is required.
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Affiliation(s)
- Kiran Sura
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Himanshi Rohilla
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Dev Kumar
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Ritu Jakhar
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
| | - Vaishali Ahlawat
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India
- Centre for Biotechnology, M.D. University, Rohtak, Haryana, India
| | | | - Mehak Dangi
- Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India.
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8
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Chowdhary S, Deka R, Panda K, Kumar R, Solomon AD, Das J, Kanoujiya S, Gupta AK, Sinha S, Ruokolainen J, Kesari KK, Gupta PK. Recent Updates on Viral Oncogenesis: Available Preventive and Therapeutic Entities. Mol Pharm 2023; 20:3698-3740. [PMID: 37486263 PMCID: PMC10410670 DOI: 10.1021/acs.molpharmaceut.2c01080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Human viral oncogenesis is a complex phenomenon and a major contributor to the global cancer burden. Several recent findings revealed cellular and molecular pathways that promote the development and initiation of malignancy when viruses cause an infection. Even, antiviral treatment has become an approach to eliminate the viral infections and prevent the activation of oncogenesis. Therefore, for a better understanding, the molecular pathogenesis of various oncogenic viruses like, hepatitis virus, human immunodeficiency viral (HIV), human papillomavirus (HPV), herpes simplex virus (HSV), and Epstein-Barr virus (EBV), could be explored, especially, to expand many potent antivirals that may escalate the apoptosis of infected malignant cells while sparing normal and healthy ones. Moreover, contemporary therapies, such as engineered antibodies antiviral agents targeting signaling pathways and cell biomarkers, could inhibit viral oncogenesis. This review elaborates the recent advancements in both natural and synthetic antivirals to control viral oncogenesis. The study also highlights the challenges and future perspectives of using antivirals in viral oncogenesis.
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Affiliation(s)
- Shivam Chowdhary
- Department
of Industrial Microbiology, Sam Higginbottom
University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh India
| | - Rahul Deka
- Department
of Bioengineering and Biotechnology, Birla
Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Kingshuk Panda
- Department
of Applied Microbiology, Vellore Institute
of Technology, Vellore 632014, Tamil Nadu, India
| | - Rohit Kumar
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida 201310, Uttar Pradesh, India
| | - Abhishikt David Solomon
- Department
of Molecular & Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India
| | - Jimli Das
- Centre
for
Biotechnology and Bioinformatics, Dibrugarh
University, Assam 786004, India
| | - Supriya Kanoujiya
- School
of
Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashish Kumar Gupta
- Department
of Biophysics, All India Institute of Medical
Sciences, New Delhi 110029, India
| | - Somya Sinha
- Department
of Biotechnology, Graphic Era Deemed to
Be University, Dehradun 248002, Uttarakhand, India
| | - Janne Ruokolainen
- Department
of Applied Physics, School of Science, Aalto
University, 02150 Espoo, Finland
| | - Kavindra Kumar Kesari
- Department
of Applied Physics, School of Science, Aalto
University, 02150 Espoo, Finland
- Division
of Research and Development, Lovely Professional
University, Phagwara 144411, Punjab, India
| | - Piyush Kumar Gupta
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida 201310, Uttar Pradesh, India
- Department
of Biotechnology, Graphic Era Deemed to
Be University, Dehradun 248002, Uttarakhand, India
- Faculty
of Health and Life Sciences, INTI International
University, Nilai 71800, Malaysia
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Raman K, Rajagopal K, Ramesh B, Nallasivan PK, Raja MKMM, Jupudi S, Byran G, Khan SL, Bin Emran T. Drug target of natural products and COVID-19: how far has science progressed? Ann Med Surg (Lond) 2023; 85:2731-2742. [PMID: 37363478 PMCID: PMC10289732 DOI: 10.1097/ms9.0000000000000703] [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: 11/14/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] that caused a viral disease with a high risk of mortality (coronavirus disease 2019) was found toward the end of 2019. This was a significant acute respiratory syndrome. In a brief period, this virus spread throughout the entire planet, causing tremendous loss of life and economic damage. The process of developing new treatments takes time, and there are presently no recognized specific treatments to treat this infection. The most promising participants, who subsequently developed into prospective leads, were dropped from the clinical research in their latter phases. Medication that has previously acquired permission may only be repurposed for use for various medical reasons following a thorough investigation for safety and effectiveness. Because there are now no effective treatments available, natural products are being used haphazardly as antiviral medications and immunity boosters. The fundamental statement that most natural compounds have powerful antiviral action does not apply to SARS-CoV-2. Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus infections are inhibited by natural treatments. According to an in silico study, the virus' nonstructural proteins, including PLpro, Mpro, and RdRp, as well as structural proteins like the spike (S) protein, have been shown to have a strong affinity for several natural products and to be inhibited by them. The virus also suggests that it is a valid candidate for therapeutic research since it utilizes the intracellular angiotensin-converting enzyme 2 receptor of the host cell. In this study, interesting targets for SARS-CoV-2 medication development are explored, as well as the antiviral properties of some well-known natural compounds.
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Affiliation(s)
- Kannan Raman
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Kalirajan Rajagopal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - B. Ramesh
- Kakatiya Government College, Hanumakonda, Telangana India
| | - P. Kumar Nallasivan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore India
| | - M. K. Mohan M. Raja
- Parul Institute of Pharmacy and Research, Parul University, Vadodara, Gujarat India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Gowramma Byran
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu India
| | - Sharuk L. Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa, Maharashtra, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
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10
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Shawan MMAK, Sharma AR, Halder SK, Arian TA, Shuvo MN, Sarker SR, Hasan MA. Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine. Int J Pept Res Ther 2023; 29:60. [PMID: 37251529 PMCID: PMC10203685 DOI: 10.1007/s10989-023-10535-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2023] [Indexed: 05/31/2023]
Abstract
A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens. In silico designing and developing a safe and novel vaccine construct involves knowledge of reverse vaccinology, various vaccine databases, and high throughput techniques. The computational tools and techniques directly associated with vaccine research are extremely effective, economical, precise, robust, and safe for human use. Many vaccine candidates have entered clinical trials instantly and are available prior to schedule. In light of this, the present article provides researchers with up-to-date information on various approaches, protocols, and databases regarding the computational designing and development of potent multi-epitope-based peptide vaccines that can assist researchers in tailoring vaccines more rapidly and cost-effectively.
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Affiliation(s)
- Mohammad Mahfuz Ali Khan Shawan
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| | - Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Tawsif Al Arian
- Department of Pharmacy, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Md. Nazmussakib Shuvo
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Satya Ranjan Sarker
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
| | - Md. Ashraful Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342 Bangladesh
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11
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Bogoyavlenskiy A, Alexyuk M, Alexyuk P, Berezin V, Almalki FA, Ben Hadda T, Alqahtani AM, Ahmed SA, Dall'Acqua S, Jamalis J. Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site. Molecules 2023; 28:molecules28093766. [PMID: 37175179 PMCID: PMC10179817 DOI: 10.3390/molecules28093766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Alaa M Alqahtani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35121 Padova, Italy
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Johor, Malaysia
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12
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Vij S, Thakur R, Kumari L, Suri CR, Rishi P. Potential of a novel flagellin epitope as a broad-spectrum vaccine candidate against enteric fever. Microb Pathog 2023; 174:105936. [PMID: 36494021 DOI: 10.1016/j.micpath.2022.105936] [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] [Received: 10/08/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Relentless emergence of antibiotic resistant Salmonella strains, coupled with the drawbacks associated with currently available vaccines against enteric fever, warrants an urgent need to look for new vaccine candidates. Out of the multiple virulence factors harbored by Salmonella, flagella are regarded as one of the most important targets of innate as well as adaptive immune response. Individual Salmonella serotypes alternate between expression of two different antigenic forms encoded by fliC and fljB genes, respectively thereby employing this as a strategy to escape the host immune response. In the present study, using various immunoinformatic approaches, a flagellin epitope, present in both antigenic forms of typhoidal Salmonellae has been targeted. Following B-cell epitope and B-cell derived T-cell epitope prediction and interaction studies with major histocompatibility complexes using molecular docking, a peptide epitope was selected. Further, it was screened for its presence in majority of typhoidal serovars along with other useful attributes, in silico. Thereafter, safety studies were performed with the synthesized peptide. Subsequently, immunization studies were carried out using S. Typhi as well as S. Paratyphi A induced murine peritonitis model. Active immunization with peptide-BSA conjugate resulted in 75% and 80% mice survival following lethal challenge with S. Typhi and S. Paratyphi A respectively, along with a significant IgG antibody titer, thereby highlighting its immunogenic potential. Reduced bacterial burden in vital organs along with improved histoarchitecture and cytokine levels further substantiated the protective efficacy of the proposed candidate. Passive immunization studies with the candidate verified the protective efficacy of the generated antibodies against lethal challenge of bacteria in mice. Given the endemic nature of enteric fever and the antigenic variability observed in Salmonella serotypes, present study highlights the importance of using a vaccine candidate, which, along with generating a strong immune response, also exhibits a broad coverage against both, S. Typhi as well as S. Paratyphi A strains.
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Affiliation(s)
- Shania Vij
- Department of Microbiology, Basic Medical Sciences, Block I, South Campus, Panjab University, Chandigarh, India
| | - Reena Thakur
- Department of Microbiology, Basic Medical Sciences, Block I, South Campus, Panjab University, Chandigarh, India
| | - Laxmi Kumari
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | | | - Praveen Rishi
- Department of Microbiology, Basic Medical Sciences, Block I, South Campus, Panjab University, Chandigarh, India.
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13
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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14
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Khan I, Rehman W, Rahim F, Hussain R, Khan S, Fazil S, Rasheed L, Taha M, Shah SAA, Abdellattif MH, Farghaly TA. Synthesis, In Vitro α-Glucosidase Inhibitory Activity and Molecular Docking Study of New Benzotriazole-Based Bis-Schiff Base Derivatives. Pharmaceuticals (Basel) 2022; 16:ph16010017. [PMID: 36678514 PMCID: PMC9860641 DOI: 10.3390/ph16010017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
This study was carried out to synthesize benzotriazole-based bis-Schiff base scaffolds (1-20) and assess them in vitro for α-glucosidase inhibitory potentials. All the synthetics analogs based on benzotriazole-based bis-Schiff base scaffolds were found to display an outstanding inhibition profile on screening against the α-glucosidase enzyme. The synthetic scaffolds showed a varied range of inhibition profiles having IC50 values ranging from 1.10 ± 0.05 µM to 28.30 ± 0.60 µM when compared to acarbose as a standard drug (IC50 = 10.30 ± 0.20 µM). Among the series, fifteen scaffolds 1-3, 5, 6, 9-16, 18-20 were identified to be more potent than standard acarbose, while the five remaining scaffolds 4, 7, 8, 16, and 17, also showed potency against the α-glucosidase enzyme but were found to be less potent than standard acarbose. The structure of all the newly synthesized scaffolds was confirmed using different spectroscopic techniques such as HREI-MS and 1H- and 13C- NMR spectroscopy. To find a structure-activity relationship, molecular docking studies were carried out to understand the binding mode of the active inhibitors with the active sites of the enzyme and the results supported the experimental data.
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Affiliation(s)
- Imran Khan
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Wajid Rehman
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
- Correspondence: (W.R.); or (F.R.)
| | - Fazal Rahim
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
- Correspondence: (W.R.); or (F.R.)
| | - Rafaqat Hussain
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Shoaib Khan
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Srosh Fazil
- Department of Chemistry, University of Poonch Rawalakot, Azad Kashmir 12350, Pakistan
| | - Liaqat Rasheed
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdul Rahman Bin Faisal University, P.O. Box 31441, Dammam 34212, Saudi Arabia
| | - Syed Adnan Ali Shah
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdul Rahman Bin Faisal University, P.O. Box 31441, Dammam 34212, Saudi Arabia
| | - Magda H. Abdellattif
- Department of Chemistry, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Thoraya A. Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, P.O. Box 715, Makkah Almukkarramah 24382, Saudi Arabia
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15
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Campos DMDO, Silva MKD, Barbosa ED, Leow CY, Fulco UL, Oliveira JIN. Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants. Comput Biol Chem 2022; 101:107754. [PMID: 36037724 PMCID: PMC9385604 DOI: 10.1016/j.compbiolchem.2022.107754] [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: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
The current COVID-19 pandemic, an infectious disease caused by the novel coronavirus (SARS-CoV-2), poses a threat to global health because of its high rate of spread and death. Currently, vaccination is the most effective method to prevent the spread of this disease. In the present study, we developed a novel multiepitope vaccine against SARS-CoV-2 containing Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (BA.1) variants. To this end, we performed a robust immunoinformatics approach based on multiple epitopes of the four structural proteins of SARS-CoV-2 (S, M, N, and E) from 475 SARS-CoV-2 genomes sequenced from the regions with the highest number of registered cases, namely the United States, India, Brazil, France, Germany, and the United Kingdom. To investigate the best immunogenic epitopes for linear B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL), we evaluated antigenicity, allergenicity, conservation, immunogenicity, toxicity, human population coverage, IFN-inducing, post-translational modifications, and physicochemical properties. The tertiary structure of a vaccine prototype was predicted, refined, and validated. Through docking experiments, we evaluated its molecular coupling to the key immune receptor Toll-Like Receptor 3 (TLR3). To improve the quality of docking calculations, quantum mechanics/molecular mechanics calculations (QM/MM) were used, with the QM part of the simulations performed using the density functional theory formalism (DFT). Cloning and codon optimization were performed for the successful expression of the vaccine in E. coli. Finally, we investigated the immunogenic properties and immune response of our SARS-CoV-2 multiepitope vaccine. The results of the simulations show that administering our prototype three times significantly increases the antibody response and decreases the amount of antigens. The proposed vaccine candidate should therefore be tested in clinical trials for its efficacy in neutralizing SARS-CoV-2.
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Affiliation(s)
- Daniel Melo de Oliveira Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | | | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, 59064-741, Natal/RN, Brazil.
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16
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Parn S, Savsani K, Dakshanamurthy S. SARS-CoV-2 Omicron (BA.1 and BA.2) specific novel CD8+ and CD4+ T cell epitopes targeting spike protein. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2022; 8:100020. [PMID: 36337685 PMCID: PMC9624113 DOI: 10.1016/j.immuno.2022.100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Omicron (BA.1/B.1.1.529) variant of SARS-CoV-2 harbors an alarming 37 mutations on its spike protein, reducing the efficacy of current COVID-19 vaccines. In this study, we identified CD8+ and CD4+ T cell epitopes from SARS-CoV-2 S protein mutants. To identify the highest quality CD8 and CD4 epitopes from the Omicron variant, we selected epitopes with a high binding affinity towards both MHC I and MHC II molecules. We applied other clinical checkpoint predictors, including immunogenicity, antigenicity, allergenicity, instability and toxicity. Subsequently, we found eight Omicron (BA.1/B.1.1.529) specific CD8+ and eleven CD4+ T cell epitopes with a world population coverage of 76.16% and 97.46%, respectively. Additionally, we identified common epitopes across Omicron BA.1 and BA.2 lineages that target mutations critical to SARS-CoV-2 virulence. Further, we identified common epitopes across B.1.1.529 and other circulating SARS-CoV-2 variants, such as B.1.617.2 (Delta). We predicted CD8 epitopes' binding affinity to murine MHC alleles to test the vaccine candidates in preclinical models. The CD8 epitopes were further validated using our previously developed software tool PCOptim. We then modeled the three-dimensional structures of our top CD8 epitopes to investigate the binding interaction between peptide-MHC and peptide-MHC-TCR complexes. Notably, our identified epitopes are targeting the mutations on the RNA-binding domain and the fusion sites of S protein. This could potentially eliminate viral infections and form long-term immune responses compared to relatively short-lived mRNA vaccines and maximize the efficacy of vaccine candidates against the current pandemic and potential future variants.
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Affiliation(s)
- Simone Parn
- University of the District of Columbia, Washington, D.C, USA
| | - Kush Savsani
- Virginia Commonwealth University, Richmond, VA, USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC 20057 USA
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17
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M. A. Kawsar S, Hosen MA, Ahmad S, El Bakri Y, Laaroussi H, Ben Hadda T, Almalki FA, Ozeki Y, Goumri-Said S. Potential SARS-CoV-2 RdRp inhibitors of cytidine derivatives: Molecular docking, molecular dynamic simulations, ADMET, and POM analyses for the identification of pharmacophore sites. PLoS One 2022; 17:e0273256. [PMID: 36441684 PMCID: PMC9704642 DOI: 10.1371/journal.pone.0273256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is one of the optimum targets for antiviral drug design and development. The hydroxyl groups of cytidine structures were modified with different aliphatic and aromatic groups to obtain 5´-O-acyl and 2´,3´-di-O-acyl derivatives, and then, these derivatives were employed in molecular modeling, antiviral prediction, molecular docking, molecular dynamics, pharmacological and POM studies. Density functional theory (DFT) at the B3LYP/6-31G++ level analyzed biochemical behavior and molecular electrostatic potential (MESP) of the modified cytidine derivatives. The antiviral parameters of the mutated derivatives revealed promising drug properties compared with those of standard antiviral drugs. Molecular docking has determined binding affinities and interactions between the cytidine derivatives and SARS-CoV-2 RdRp. The modified derivatives strongly interacted with prime Pro620 and Lys621 residues. The binding conformation and interactions stability were investigated by 200 ns of molecular dynamics simulations and predicted the compounds to firmly dock inside the RdRp binding pocket. Interestingly, the binding residues of the derivatives were revealed in high equilibrium showing an enhanced binding affinity for the molecules. Intermolecular interactions are dominated by both Van der Waals and electrostatic energies. Finally, the pharmacokinetic characterization of the optimized inhibitors confirmed the safety of derivatives due to their improved kinetic properties. The selected cytidine derivatives can be suggested as potential inhibitors against SARS-CoV-2. The POM Theory supports the hypothesis above by confirming the existence of an antiviral (Oδ--O'δ-) pharmacophore site of Hits.
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Affiliation(s)
- Sarkar M. A. Kawsar
- Faculty of Science, Department of Chemistry, Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), University of Chittagong, Chittagong, Bangladesh
- * E-mail: (SMAK); (YEB); (SGS)
| | - Mohammed A. Hosen
- Faculty of Science, Department of Chemistry, Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), University of Chittagong, Chittagong, Bangladesh
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
- * E-mail: (SMAK); (YEB); (SGS)
| | - Hamid Laaroussi
- Faculty of Sciences, Laboratory of Applied Chemistry & Environment, Mohammed Premier University, Oujda, Morocco
| | - Taibi Ben Hadda
- Faculty of Sciences, Laboratory of Applied Chemistry & Environment, Mohammed Premier University, Oujda, Morocco
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Umm AlQura University, Makkah, Saudi Arabia
| | - Faisal A. Almalki
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Umm AlQura University, Makkah, Saudi Arabia
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, Yokohama, Japan
| | - Souraya Goumri-Said
- Physics Department, College of Science, Alfaisal University, Riyadh, Saudi Arabia
- * E-mail: (SMAK); (YEB); (SGS)
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18
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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19
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Augusto DG, Yusufali T, Sabatino JJ, Peyser ND, Murdolo LD, Butcher X, Murray V, Pae V, Sarvadhavabhatla S, Beltran F, Gill G, Lynch K, Yun C, Maguire C, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Viera-Green CA, Spellman SR, Langton DJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Gras S, Maiers M, Hollenbach JA. A common allele of HLA mediates asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.05.13.21257065. [PMID: 34031661 PMCID: PMC8142661 DOI: 10.1101/2021.05.13.21257065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph J. Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Noah D. Peyser
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lawton D. Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victoria Murray
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gurjot Gill
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kara Lynch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Colin Maguire
- University of Utah, Clinical and Translational Science Institute, Salt Lake City, UT
| | - Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A. Goldberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Cynthia A. Viera-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - David J. Langton
- ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK
| | - Sulggi Lee
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gregory M. Marcus
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey E. Olgin
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Pletcher
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
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20
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Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [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: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. METHODS In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS-CoV-2 delta variant performing different computational analysis. RESULTS From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. CONCLUSIONS Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS-CoV-2 delta variant.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular BiologyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Talha Bin Emran
- Department of PharmacyBGC Trust University BangladeshChittagongBangladesh
- Department of PharmacyFaculty of Allied Health Sciences, Daffodil International UniversityDhakaBangladesh
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21
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Identification of Antigenic Properties of Acinetobacter baumannii Proteins as Novel Putative Vaccine Candidates Using Reverse Vaccinology Approach. Appl Biochem Biotechnol 2022; 194:4892-4914. [PMID: 35670904 DOI: 10.1007/s12010-022-03995-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2022] [Indexed: 02/06/2023]
Abstract
Multidrug-resistant Acinetobacter baumannii (A. baumannii) infections are becoming more prevalent all over the world. As a cost-effective and preventative method, vaccination seems to be required against this bacterium. In the present study, subtractive proteomics along with reverse vaccinology approaches was used to predict suitable therapeutics against A. baumannii. Using the Vaxign online tool, we studied over 35 genomes of A. baumannii strains and chose outer membrane and secreted proteins of A. baumannii 1656-2 as possible vaccine candidates. Then, investigations were performed on the immunogenicity, antigenic characteristics, physicochemical properties, B-cell and MHC class I, and MHC class II molecules epitope densities of proteins. After optimizing the codon of the proteins, the pcDNA3.1( +) expression construct was designed and the immunogenicity, allergenicity, and physicochemical properties of the vaccine construct were predicted. Hcp and OmpC proteins were predicted as extracellular and outer membrane proteins, respectively. These proteins interact with 10 other proteins to form a network of protein interactions with virulence properties. Immunoassays of Hcp and OmpC proteins showed antigenicity of 0.88 and 0.79, respectively. These proteins have 5 structural cell epitope points and 5 linear B epitope points. They are also able to bind to different HLA alleles of MCH class I/class II as selected immunogenic proteins and designed non-allergenic structures with solubility of 0.650 and immunogenicity score of 0.91. The results of this "in silico" study indicate high specificity and the development of a significant humoral and cellular immune response. It can be concluded that the Hcp and OmpC dual vaccine construct is one of the promising candidates against A. baumannii. The findings of this "in silico" study show excellent specificity and the emergence of a substantial humoral and cellular immune response. This is a computer-based study that needs to be tested in vitro and in vivo to corroborate the conclusions of the vaccine design procedures.
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22
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da Silva MK, Azevedo AAC, Campos DMDO, de Souto JT, Fulco UL, Oliveira JIN. Computational vaccinology guided design of multi-epitope subunit vaccine against a neglected arbovirus of the Americas. J Biomol Struct Dyn 2022; 41:3321-3338. [PMID: 35285772 DOI: 10.1080/07391102.2022.2050301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mayaro virus (MAYV) is an arbovirus found in the Americas that can cause debilitating arthritogenic disease. Although it is an emerging virus, the only current approach is vector control, as there are no approved vaccines to prevent MAYV infection nor therapeutics to treat it. In search of an effective vaccine candidate against MAYV, we used immunoinformatics and molecular modeling to attempt to identify promiscuous T-cell epitopes of the nonstructural polyproteins (nsP1, nsP2, nsP3, and nsP4) from 127 MAYV genomes sequenced in the Americas (08 Bolivia, 72 Brazil, 04 French Guiana, 05 Haiti, 20 Peru, 04 Trinidad and Tobago, and 14 Venezuela). For this purpose, consensus sequences of 360 proteins were used to identify short protein sequences that can bind to MHC I class (MHC II). Our analysis revealed 56 potential MHC-I/TCD8+ (29 MHC-II/TCD4+) epitopes, but only 6 (16) TCD8+ (TCD4+) epitopes showed high antigenicity and conservation, non-allergenicity, non-toxicity, and excellent population coverage. Finally, classical and quantum mechanical calculations (QM:MM) were used to improve the quality of the docking calculations, with the QM part of the simulations performed using the density functional theory formalism (DFT). These results provide insights for the advancement of diagnostic platforms, vaccine development, and immunotherapeutic interventions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maria Karolaynne da Silva
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | | | - Janeusa Trindade de Souto
- Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
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23
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Soltan MA, Behairy MY, Abdelkader MS, Albogami S, Fayad E, Eid RA, Darwish KM, Elhady SS, Lotfy AM, Alaa Eldeen M. In silico Designing of an Epitope-Based Vaccine Against Common E. coli Pathotypes. Front Med (Lausanne) 2022; 9:829467. [PMID: 35308494 PMCID: PMC8931290 DOI: 10.3389/fmed.2022.829467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium that belongs to the family Enterobacteriaceae. While E. coli can stay as an innocuous resident in the digestive tract, it can cause a group of symptoms ranging from diarrhea to live threatening complications. Due to the increased rate of antibiotic resistance worldwide, the development of an effective vaccine against E. coli pathotypes is a major health priority. In this study, a reverse vaccinology approach along with immunoinformatics has been applied for the detection of potential antigens to develop an effective vaccine. Based on our screening of 5,155 proteins, we identified lipopolysaccharide assembly protein (LptD) and outer membrane protein assembly factor (BamA) as vaccine candidates for the current study. The conservancy of these proteins in the main E. coli pathotypes was assessed through BLASTp to make sure that the designed vaccine will be protective against major E. coli pathotypes. The multitope vaccine was constructed using cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes with suitable linkers and adjuvant. Following that, it was analyzed computationally where it was found to be antigenic, soluble, stable, and non-allergen. Additionally, the adopted docking study, as well as all-atom molecular dynamics simulation, illustrated the promising predicted affinity and free binding energy of this constructed vaccine against the human Toll-like receptor-4 (hTLR-4) dimeric state. In this regard, wet lab studies are required to prove the efficacy of the potential vaccine construct that demonstrated promising results through computational validation.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
| | - Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mennatallah S. Abdelkader
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M. Lotfy
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Muhammad Alaa Eldeen
- Division of Cell Biology, Histology and Genetics, Department of Zoology, Faculty of Science, Zagazig University, Zagazig, Egypt
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24
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Abstract
This review discusses peptide epitopes used as antigens in the development of vaccines in clinical trials as well as future vaccine candidates. It covers peptides used in potential immunotherapies for infectious diseases including SARS-CoV-2, influenza, hepatitis B and C, HIV, malaria, and others. In addition, peptides for cancer vaccines that target examples of overexpressed proteins are summarized, including human epidermal growth factor receptor 2 (HER-2), mucin 1 (MUC1), folate receptor, and others. The uses of peptides to target cancers caused by infective agents, for example, cervical cancer caused by human papilloma virus (HPV), are also discussed. This review also provides an overview of model peptide epitopes used to stimulate non-specific immune responses, and of self-adjuvanting peptides, as well as the influence of other adjuvants on peptide formulations. As highlighted in this review, several peptide immunotherapies are in advanced clinical trials as vaccines, and there is great potential for future therapies due the specificity of the response that can be achieved using peptide epitopes.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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25
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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26
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Rafi MO, Al-Khafaji K, Sarker MT, Taskin-Tok T, Rana AS, Rahman MS. Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. RSC Adv 2022; 12:4288-4310. [PMID: 35425433 PMCID: PMC8981096 DOI: 10.1039/d1ra06532g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/23/2022] [Indexed: 12/17/2022] Open
Abstract
A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, AL-Nisour University College Baghdad Iraq
| | - Md Takim Sarker
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Tugba Taskin-Tok
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University Gaziantep 27310 Turkey
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University Gaziantep Turkey
| | - Abdus Samad Rana
- School of Biotechnology, Jiangnan University Wuxi 214122 PR China
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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27
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Ferreira CS, Martins YC, Souza RC, Vasconcelos ATR. EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes. PeerJ 2021; 9:e12548. [PMID: 34909278 PMCID: PMC8641484 DOI: 10.7717/peerj.12548] [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: 07/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.
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Affiliation(s)
- Cristina S. Ferreira
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Yasmmin C. Martins
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Rangel Celso Souza
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
| | - Ana Tereza R. Vasconcelos
- Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, Brazil
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Sami SA, Marma KKS, Mahmud S, Khan MAN, Albogami S, El-Shehawi AM, Rakib A, Chakraborty A, Mohiuddin M, Dhama K, Uddin MMN, Hossain MK, Tallei TE, Emran TB. Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. ACS OMEGA 2021; 6:32043-32071. [PMID: 34870027 PMCID: PMC8638006 DOI: 10.1021/acsomega.1c04817] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 05/08/2023]
Abstract
Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with infected individuals or animals. Despite being considered to be less threatening in terms of appearances and the number of infected patients, the high fatality rate of this pathogenic virus is a major concern. Until now, no vaccine has been developed to combat this deadly virus. Therefore, vaccination for this virus is necessary to reduce its mortality. Our current investigation focuses on the design and formulation of a multi-epitope vaccine based on the structural proteins of MARV employing immunoinformatics approaches. The screening of potential T-cell and B-cell epitopes from the seven structural proteins of MARV was carried out through specific selection parameters. Afterward, we compiled the shortlisted epitopes by attaching them to an appropriate adjuvant and linkers. Population coverage analysis, conservancy analysis, and MHC cluster analysis of the shortlisted epitopes were satisfactory. Importantly, physicochemical characteristics, human homology assessment, and structure validation of the vaccine construct delineated convenient outcomes. We implemented disulfide bond engineering to stabilize the tertiary or quaternary interactions. Furthermore, stability and physical movements of the vaccine protein were explored using normal-mode analysis. The immune simulation study of the vaccine complexes also exhibited significant results. Additionally, the protein-protein docking and molecular dynamics simulation of the final construct exhibited a higher affinity toward toll-like receptor-4 (TLR4). From simulation trajectories, multiple descriptors, namely, root mean square deviations (rmsd), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), and hydrogen bonds, have been taken into account to demonstrate the inflexible and rigid nature of receptor molecules and the constructed vaccine. Inclusively, our findings suggested the vaccine constructs' ability to regulate promising immune responses against MARV pathogenesis.
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Affiliation(s)
- Saad Ahmed Sami
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kay Kay Shain Marma
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Shafi Mahmud
- Microbiology
Laboratory, Bioinformatics Division, Department of Genetic Engineering
and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asif Nadim Khan
- Department of Biochemistry and Molecular
Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sarah Albogami
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. El-Shehawi
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Rakib
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Agnila Chakraborty
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mostafah Mohiuddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary
Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Kamrul Hossain
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology,
Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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29
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Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins. PLoS One 2021; 16:e0258645. [PMID: 34780495 PMCID: PMC8592446 DOI: 10.1371/journal.pone.0258645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/01/2021] [Indexed: 01/03/2023] Open
Abstract
All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.
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30
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Adji A, Niode NJ, Memah VV, Posangi J, Wahongan GJ, Ophinni Y, Idroes R, Mahmud S, Emran TB, Nainu F, Tallei TE, Harapan H. Designing an epitope vaccine against Dermatophagoides pteronyssinus: An in silico study. Acta Trop 2021; 222:106028. [PMID: 34217726 DOI: 10.1016/j.actatropica.2021.106028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/26/2022]
Abstract
The house dust mite, Dermatophagoides pteronyssinus, is a major source of the inhaled allergen Der p 1, which causes immunoglobulin E (IgE)-mediated hypersensitivity reactions manifesting in allergic diseases. To date, no drugs or vaccines effectively treat or prevent Der p 1 sensitization. We applied in silico immunoinformatics to design T-cell and B-cell epitopes that were specified and developed from the allergen Der p 1 of D. pteronyssinus. We identified the conserved epitope areas by predicting the accessibility and flexibility of B-cell epitopes, and the percentage of human leukocyte antigen representing T cells. Molecular docking using HADDOCK software indicated three optimal clusters: cluster 6 (z-score: -2.1), cluster 1 (z-score: -1.2), and cluster 3 (z-score: -0.6). The most negative Z-score was found in cluster 6, which represented three epitopes. The interaction between A chain proteins (IgE protein residues) and B chains (Der p 1 protein residues) exhibited a knowledge-based FADE and contact value >1, suggesting the best protein interactions occurred in the conserved area. Molecular dynamic simulation further predicted the stable nature of Der p 1 protein. The IQRDNGYQP region is the best candidate to be utilized as a D. pteronyssinus epitope vaccine, which could be used in the development of allergen-specific immunotherapy.
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Rostaminia S, Aghaei SS, Farahmand B, Nazari R, Ghaemi A. Computational Design and Analysis of a Multi-epitope Against Influenza A virus. Int J Pept Res Ther 2021; 27:2625-2638. [PMID: 34539293 PMCID: PMC8435298 DOI: 10.1007/s10989-021-10278-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/28/2022]
Abstract
Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.
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Affiliation(s)
- Samaneh Rostaminia
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | | | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
| | - Raziye Nazari
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
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32
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Dutta M, Tareq AM, Rakib A, Mahmud S, Sami SA, Mallick J, Islam MN, Majumder M, Uddin MZ, Alsubaie A, Almalki ASA, Khandaker MU, Bradley D, Rana MS, Emran TB. Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations. BIOLOGY 2021; 10:789. [PMID: 34440024 PMCID: PMC8389631 DOI: 10.3390/biology10080789] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/05/2021] [Accepted: 08/15/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Jewel Mallick
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Mohuya Majumder
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abdullah Alsubaie
- Department of Physics, College of Khurma, Taif University, Taif 21944, Saudi Arabia;
| | | | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
| | - D.A. Bradley
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
- Department of Physics, University of Surrey, Guilford GU2 7XH, UK
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
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Ghosh N, Sharma N, Saha I. Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 92:104823. [PMID: 33819681 PMCID: PMC8017916 DOI: 10.1016/j.meegid.2021.104823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/23/2022]
Abstract
The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2'-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z-Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. Lessons Learned from Cutting-Edge Immunoinformatics on Next-Generation COVID-19 Vaccine Research. Int J Pept Res Ther 2021; 27:2303-2311. [PMID: 34276266 PMCID: PMC8272614 DOI: 10.1007/s10989-021-10254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2021] [Indexed: 12/23/2022]
Abstract
Presently, immunoinformatics and bioinformatics approaches are contributing actively to COVID-19 vaccine research. The first immunoinformatics-based vaccine construct against SARS-CoV-2 was published in February 2020. Following this, immunoinformatics and bioinformatics approaches have created a new direction in COVID-19 vaccine research. Several researchers have designed the next-generation COVID-19 vaccines using these approaches. Presently, immunoinformatics has accelerated immunology research immensely in the area of COVID-19. Hence, we have tried to depict the current scenario of immunoinformatics and bioinformatics in COVID-19 vaccine research.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Jagannathpur, Kolkata, West Bengal 700126 India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, VyasaVihar, Balasore, Odisha 756020 India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
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Mahmud S, Biswas S, Paul GK, Mita MA, Promi MM, Afrose S, Hasan MR, Zaman S, Uddin MS, Dhama K, Emran TB, Saleh MA, Simal-Gandara J. Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors. BIOLOGY 2021; 10:589. [PMID: 34206970 PMCID: PMC8301192 DOI: 10.3390/biology10070589] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted in a high mortality rate, bringing the world economy to its knees. Thus, mechanistic investigations of drugs capable of counteracting this disease are in high demand. The main protease (Mpro) expressed by SARS-CoV-2 has been targeted for the development of potential drug candidates due to the crucial role played by Mpro in viral replication and transcription. We generated a phytochemical library containing 1672 phytochemicals derived from 56 plants, which have been reported as having antiviral, antibacterial, and antifungal activity. A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate, which had respective binding affinities of -8.4, -8.5, and -8.8 kcal/mol. Several active sites in the targeted protein, including Cys145, His41, Met49, Glu66, and Met165, were found to interact with the top three candidate compounds. The multiple simulation profile, root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and solvent-accessible surface area values supported the inflexible nature of the docked protein-compound complexes. The toxicity and carcinogenicity profiles were assessed, which showed that epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate had favorable pharmacological properties with no adverse effects. These findings suggest that these compounds could be developed as part of an effective drug development pathway to treat COVID-19.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (M.A.M.); (M.M.P.); (S.A.); (M.R.H.)
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
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36
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Sami SA, Marma KKS, Chakraborty A, Singha T, Rakib A, Uddin MG, Hossain MK, Uddin SMN. A comprehensive review on global contributions and recognition of pharmacy professionals amidst COVID-19 pandemic: moving from present to future. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:119. [PMID: 34150911 PMCID: PMC8195448 DOI: 10.1186/s43094-021-00273-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND COVID-19, a respiratory tract infection caused by SARS-CoV-2, is a burning question worldwide as it gives rise to a pandemic situation. No specific medications are still recommended for COVID-19; however, healthcare support is crucial for ameliorating the disease condition. Pharmacists are the frontline fighters who are responsible for providing healthcare support to the COVID-19 infected patients around the world. This review endeavored to briefly rationalize the contributions of several pharmacy professionals in diverse fields along with their collaborative efforts and dedication regarding their limitations during the COVID-19 situation and view the prospects of pharmaceutical care services in the post-pandemic period. MAIN BODY OF THE ABSTRACT Online databases were utilized to search for scholarly articles and organizational websites, to sum up the information about the contemporary and expanded role of pharmacists. Key articles were retrieved from Google Scholar, PubMed, and Science Direct databases using terms: "COVID-19," "novel coronavirus," "community," "industrial," "hospital," "clinical," "recognition," "obstacles," "collaboration," "SARS-CoV-2," "healthcare," and "outbreak" in combination with "pharmacist." The articles were included from the inception of the pandemic to January 25, 2021. The current review found pharmacist's global contributions and involvements with other professionals to provide healthcare services amidst COVID-19. This included testing of suspects, providing medical information, psycho-social support, debunking myths, mitigating drug shortage events, telemedicine, e-prescription, infection control, and controlling the drug supply chain. In many countries, pharmacists' activities were much appreciated but in some countries, they were not properly acknowledged for their contributions amidst COVID-19 outbreak. They played additional roles such as participating in the antimicrobial stewardship team, improving value-added services, conducting clinical data analysis to suppress the outspread of the SARS-CoV-2. SHORT CONCLUSION During the COVID-19 pandemic while the whole world is fighting against an invisible virus, the pharmacists are the earnest hero to serve their responsibilities along with additional activities. They need to be prepared and collaborate with other healthcare professionals further to meet the challenges of post-pandemic circumstances.
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Affiliation(s)
- Saad Ahmed Sami
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Kay Kay Shain Marma
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Agnila Chakraborty
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Tandra Singha
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Ahmed Rakib
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Md. Giash Uddin
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
| | | | - S. M. Naim Uddin
- Department of Pharmacy, University of Chittagong, Chittagong, 4331 Bangladesh
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Cuspoca AF, Díaz LL, Acosta AF, Peñaloza MK, Méndez YR, Clavijo DC, Yosa Reyes J. An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population. Vaccines (Basel) 2021; 9:vaccines9060581. [PMID: 34205992 PMCID: PMC8228945 DOI: 10.3390/vaccines9060581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus pandemic is a major public health crisis affecting global health systems with dire socioeconomic consequences, especially in vulnerable regions such as Latin America (LATAM). There is an urgent need for a vaccine to help control contagion, reduce mortality and alleviate social costs. In this study, we propose a rational multi-epitope candidate vaccine against SARS-CoV-2. Using bioinformatics, we constructed a library of potential vaccine peptides, based on the affinity of the most common major human histocompatibility complex (HLA) I and II molecules in the LATAM population to predict immunological complexes among antigenic, non-toxic and non-allergenic peptides extracted from the conserved regions of 92 proteomes. Although HLA-C, had the greatest antigenic peptide capacity from SARS-CoV-2, HLA-B and HLA-A, could be more relevant based on COVID-19 risk of infection in LATAM countries. We also used three-dimensional structures of SARS-CoV-2 proteins to identify potential regions for antibody production. The best HLA-I and II predictions (with increased coverage in common alleles and regions evoking B lymphocyte responses) were grouped into an optimized final multi-epitope construct containing the adjuvants Beta defensin-3, TpD, and PADRE, which are recognized for invoking a safe and specific immune response. Finally, we used Molecular Dynamics to identify the multi-epitope construct which may be a stable target for TLR-4/MD-2. This would prove to be safe and provide the physicochemical requirements for conducting experimental tests around the world.
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Affiliation(s)
- Andrés Felipe Cuspoca
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Laura Lorena Díaz
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Alvaro Fernando Acosta
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Marcela Katherine Peñaloza
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Yardany Rafael Méndez
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Diana Carolina Clavijo
- Facultad de Ingeniería y Ciencias, Pontificia Universidad Javeriana Cali, Santiago de Cali 760031, Colombia;
| | - Juvenal Yosa Reyes
- Laboratorio de Simulación Molecular, Facultad de Ciencias Básicas y Biomédicas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Correspondence:
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Dutta M, Nezam M, Chowdhury S, Rakib A, Paul A, Sami SA, Uddin MZ, Rana MS, Hossain S, Effendi Y, Idroes R, Tallei T, Alqahtani AM, Emran TB. Appraisals of the Bangladeshi Medicinal Plant Calotropis gigantea Used by Folk Medicine Practitioners in the Management of COVID-19: A Biochemical and Computational Approach. Front Mol Biosci 2021; 8:625391. [PMID: 34124140 PMCID: PMC8187851 DOI: 10.3389/fmolb.2021.625391] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 05/11/2021] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recognized in Wuhan in late 2019 and, since then, had spread globally, eventually culminating in the ongoing pandemic. As there is a lack of targeted therapeutics, there is certain opportunity for the scientific community to develop new drugs or vaccines against COVID-19 and so many synthetic bioactive compounds are undergoing clinical trials. In most of the countries, due to the broad therapeutic spectrum and minimal side effects, medicinal plants have been used widely throughout history as traditional healing remedy. Because of the unavailability of synthetic bioactive antiviral drugs, hence all possible efforts have been focused on the search for new drugs and alternative medicines from different herbal formulations. In recent times, it has been assured that the Mpro, also called 3CLpro, is the SARS-CoV-2 main protease enzyme responsible for viral reproduction and thereby impeding the host's immune response. As such, Mpro represents a highly specified target for drugs capable of inhibitory action against coronavirus disease 2019 (COVID-19). As there continue to be no clear options for the treatment of COVID-19, the identification of potential candidates has become a necessity. The present investigation focuses on the in silico pharmacological activity of Calotropis gigantea, a large shrub, as a potential option for COVID-19 Mpro inhibition and includes an ADME/T profile analysis of that ligand. For this study, with the help of gas chromatography-mass spectrometry analysis of C. gigantea methanolic leaf extract, a total of 30 bioactive compounds were selected. Our analyses unveiled the top four options that might turn out to be prospective anti-SARS-CoV-2 lead molecules; these warrant further exploration as well as possible application in processes of drug development to combat COVID-19.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Nezam
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Subrata Chowdhury
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Arkajyoti Paul
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh
| | | | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Banda Aceh, Indonesia
| | - Trina Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, Indonesia
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
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Ben Hadda T, Berredjem M, Almalki FA, Rastija V, Jamalis J, Emran TB, Abu-Izneid T, Esharkawy E, Rodriguez LC, Alqahtani AM. How to face COVID-19: proposed treatments based on remdesivir and hydroxychloroquine in the presence of zinc sulfate. Docking/DFT/POM structural analysis. J Biomol Struct Dyn 2021; 40:9429-9442. [PMID: 34033727 PMCID: PMC8171014 DOI: 10.1080/07391102.2021.1930161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Remdesivir and hydroxychloroquine derivatives form two important classes of heterocyclic compounds. They are known for their anti-malarial biological activity. This research aims to analyze the physicochemical properties of remdesivir and hydroxychloroquine compounds by the computational approach. DFT, docking, and POM analyses also identify antiviral pharmacophore sites of both compounds. The antiviral activity of hydroxychloroquine compound's in the presence of zinc sulfate and azithromycin is evaluated through its capacity to coordinate transition metals (M = Cu, Ni, Zn, Co, Ru, Pt). The obtained bioinformatic results showed the potent antiviral/antibacterial activity of the prepared mixture (Hydroxychloroquine/Azithromycin/Zinc sulfate) for all the opportunistic Gram-positive, Gram-negative in the presence of coronavirus compared with the complexes Polypyridine-Ruthenium-di-aquo. The postulated zinc(II) complex of hydroxychloroquine derivatives are indeed an effective antibacterial and antiviral agent against coronavirus and should be extended to other pathogens. The combination of a pharmacophore site with a redox [Metal(OH2)2] moiety is of crucial role to fight against viruses and bacteria strains. [Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia,Laboratory of Applied Chemistry & Environment, Faculty of Science, University Mohammed the first, Oujda, Morocco,CONTACT Taibi Ben Hadda Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Almukkarramah 21955, Saudi Arabia; Malika Berredjem Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Box 12, 23000, Annaba, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria,CONTACT Taibi Ben Hadda Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Almukkarramah 21955, Saudi Arabia; Malika Berredjem Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Box 12, 23000, Annaba, Algeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vesna Rastija
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh,Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
| | - Tareq Abu-Izneid
- Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain, UAE
| | - Eman Esharkawy
- Department of Plant Ecology and Range Management, Ecology and Dry Lands Agriculture Division, Desert Research Center, Mathef El-Mataria, Egypt,Department of Chemistry, Science Faculty for Girls, Northern Border University ARAR, North Region, Saudi Arabia
| | - Luis Cruz Rodriguez
- ELIDAN Dynamic LLC, Tampa, FL, USA,ELIDAN Genome SAS, Montereau Fault Yonne, France,Environmental Biotechnology Department, ExCELab Co, Ltd, St Ann, Jamaica
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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Obaidullah AJ, Alanazi MM, Alsaif NA, Albassam H, Almehizia AA, Alqahtani AM, Mahmud S, Sami SA, Emran TB. Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. RSC Adv 2021; 11:18103-18121. [PMID: 35480208 PMCID: PMC9033181 DOI: 10.1039/d1ra02885e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a contagious respiratory tract infection that has become a global burden since the end of 2019. Notably, fewer patients infected with SARS-CoV-2 progress from acute disease onset to death compared with the progression rate associated with two other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Several research organizations and pharmaceutical industries have attempted to develop successful vaccine candidates for the prevention of COVID-19. However, increasing evidence indicates that the SARS-CoV-2 genome undergoes frequent mutation; thus, an adequate analysis of the viral strain remains necessary to construct effective vaccines. The current study attempted to design a multi-epitope vaccine by utilizing an approach based on the SARS-CoV-2 structural proteins. We predicted the antigenic T- and B-lymphocyte responses to four structural proteins after screening all structural proteins according to specific characteristics. The predicted epitopes were combined using suitable adjuvants and linkers, and a secondary structure profile indicated that the vaccine shared similar properties with the native protein. Importantly, the molecular docking analysis and molecular dynamics simulations revealed that the constructed vaccine possessed a high affinity for toll-like receptor 4 (TLR4). In addition, multiple descriptors were obtained from the simulation trajectories, including the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (R g), demonstrating the rigid nature and inflexibility of the vaccine and receptor molecules. In addition, codon optimization, based on Escherichia coli K12, was used to determine the GC content and the codon adaptation index (CAI) value, which further followed for the incorporation into the cloning vector pET28+(a). Collectively, these findings suggested that the constructed vaccine could be used to modulate the immune reaction against SARS-CoV-2.
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Affiliation(s)
- Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hussam Albassam
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University Abha 62529 Saudi Arabia
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi Rajshahi 6205 Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong Chittagong 4331 Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh Chittagong 4381 Bangladesh
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41
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Mahmud S, Paul GK, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Hossain A, Promi MM, Ema FK, Chidambaram K, Chandrasekaran B, Alqahtani AM, Emran TB, Saleh MA. Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2. Front Mol Biosci 2021; 8:628585. [PMID: 34041263 PMCID: PMC8142691 DOI: 10.3389/fmolb.2021.628585] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Fahmida Khan Ema
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Balakumar Chandrasekaran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Philadelphia University-Jordan, Amman, Jordan
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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Rabaan AA, Al-Ahmed SH, Garout MA, Al-Qaaneh AM, Sule AA, Tirupathi R, Mutair AA, Alhumaid S, Hasan A, Dhawan M, Tiwari R, Sharun K, Mohapatra RK, Mitra S, Emran TB, Bilal M, Singh R, Alyami SA, Moni MA, Dhama K. Diverse Immunological Factors Influencing Pathogenesis in Patients with COVID-19: A Review on Viral Dissemination, Immunotherapeutic Options to Counter Cytokine Storm and Inflammatory Responses. Pathogens 2021; 10:565. [PMID: 34066983 PMCID: PMC8150955 DOI: 10.3390/pathogens10050565] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still not fully unraveled. Though preventive vaccines and treatment methods are out on the market, a specific cure for the disease has not been discovered. Recent investigations and research studies primarily focus on the immunopathology of the disease. A healthy immune system responds immediately after viral entry, causing immediate viral annihilation and recovery. However, an impaired immune system causes extensive systemic damage due to an unregulated immune response characterized by the hypersecretion of chemokines and cytokines. The elevated levels of cytokine or hypercytokinemia leads to acute respiratory distress syndrome (ARDS) along with multiple organ damage. Moreover, the immune response against SARS-CoV-2 has been linked with race, gender, and age; hence, this viral infection's outcome differs among the patients. Many therapeutic strategies focusing on immunomodulation have been tested out to assuage the cytokine storm in patients with severe COVID-19. A thorough understanding of the diverse signaling pathways triggered by the SARS-CoV-2 virus is essential before contemplating relief measures. This present review explains the interrelationships of hyperinflammatory response or cytokine storm with organ damage and the disease severity. Furthermore, we have thrown light on the diverse mechanisms and risk factors that influence pathogenesis and the molecular pathways that lead to severe SARS-CoV-2 infection and multiple organ damage. Recognition of altered pathways of a dysregulated immune system can be a loophole to identify potential target markers. Identifying biomarkers in the dysregulated pathway can aid in better clinical management for patients with severe COVID-19 disease. A special focus has also been given to potent inhibitors of proinflammatory cytokines, immunomodulatory and immunotherapeutic options to ameliorate cytokine storm and inflammatory responses in patients affected with COVID-19.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
| | - Shamsah H. Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif 32654, Saudi Arabia;
| | - Mohammed A. Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Ayman M. Al-Qaaneh
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
- Clinical Pharmacy Services Division, Pharmacy Services Department, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
| | - Anupam A Sule
- Department of Informatics and Outcomes, St Joseph Mercy Oakland, Pontiac, MI 48341, USA;
| | - Raghavendra Tirupathi
- Department of Medicine Keystone Health, Penn State University School of Medicine, Hershey, PA 16801, USA;
- Department of Medicine, Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA 16801, USA
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Alahsa 36342, Saudi Arabia;
- College of Nursing, Prince Nora University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Alahsa 31982, Saudi Arabia;
| | - Abdulkarim Hasan
- Department of Pathology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt;
- Prince Mishari Bin Saud Hospital in Baljurashi, Ministry of Health, Baljurash 22888, Saudi Arabia
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India;
- The Trafford Group of Colleges, Manchester WA14 5PQ, UK
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandha Sansthan (DUVASU), Mathura 281001, India;
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India;
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India;
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China;
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India;
| | - Salem A. Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia;
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India;
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Mallavarpu Ambrose J, Priya Veeraraghavan V, Kullappan M, Chellapandiyan P, Krishna Mohan S, Manivel VA. Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach. Antibiotics (Basel) 2021; 10:535. [PMID: 34066389 PMCID: PMC8148159 DOI: 10.3390/antibiotics10050535] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
The current dynamics of the COVID-19 pandemic have become a serious concern with the emergence of a series of mutant variants of the SARS-CoV-2 virus. Unlike the previous strain, it is reported that the descendants are associated with increased risk of transmission yet causing less impact in terms of hospital admission, the severity of illness, or mortality. Moreover, the vaccine efficacy is also not believed to vary among the population depending on the variants of the virus and ethnicity. It has been determined that the mutations recorded in the spike gene and protein of the newly evolved viruses are specificallyresponsible for this transformation in the behavior of the virus and its disease condition. Hence, this study aimed to compare the immunogenic profiles of the spike protein from the latest variants of the SARS-CoV-2 virus concerning the probability of COVID-19 severity. Genome sequences of the latest SARS-CoV-2 variants were obtained from GISAID and NCBI repositories. The translated protein sequences were run against T-cell and B-cell epitope prediction tools. Subsequently, antigenicity, immunogenicity, allergenicity, toxicity, and conservancy of the identified epitopes were ascertained using various prediction servers. Only the non-allergic and non-toxic potential epitopes were matched for population relevance by using the Human Leucocyte Antigen population registry in IEDB. Finally, the selected epitopes were validated by docking and simulation studies. The evaluated immunological parameters would concurrently reveal the severity of COVID-19, determining the infection rate of the pathogen. Our immunoinformatics approach disclosed that spike protein of the five variants was capable of forming potential T and B-cell epitopes with varying immune responses. Although the Wuhan strain showed a high number of epitope/HLA combinations, relatively less antigenicity and higher immunogenicity results in poor neutralizing capacity, which could be associated with increased disease severity. Our data demonstrate that increased viral antigenicity with moderate to high immunogenicity, and several potential epitope/HLA combinations in England strain, the USA, India, and South Africa variants, could possess a high neutralizing ability. Therefore, our findings reinforce that the newly circulating variants of SARS-CoV-2 might be associated with more infectiousness and less severe disease condition despite their greater viremia, as reported in the recent COVID-19 cases, whichconsequently determine their increased epidemiological fitness.
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Affiliation(s)
- Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India; (J.M.A.); (M.K.)
| | - Vishnu Priya Veeraraghavan
- Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Velappanchavadi, Chennai 600 077, Tamil Nadu, India;
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India; (J.M.A.); (M.K.)
| | - Poongodi Chellapandiyan
- Department of Obstetrics & Gynaecological Nursing, Panimalar College of Nursing, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India;
| | - Surapaneni Krishna Mohan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India; (J.M.A.); (M.K.)
- Departments of Biochemistry, Molecular Virology, Clinical Skills and Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India
| | - Vivek Anand Manivel
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600 123, Tamil Nadu, India; (J.M.A.); (M.K.)
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
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Rabaan AA, Al-Ahmed SH, Muhammad J, Khan A, Sule AA, Tirupathi R, Mutair AA, Alhumaid S, Al-Omari A, Dhawan M, Tiwari R, Sharun K, Mohapatra RK, Mitra S, Bilal M, Alyami SA, Emran TB, Moni MA, Dhama K. Role of Inflammatory Cytokines in COVID-19 Patients: A Review on Molecular Mechanisms, Immune Functions, Immunopathology and Immunomodulatory Drugs to Counter Cytokine Storm. Vaccines (Basel) 2021; 9:436. [PMID: 33946736 PMCID: PMC8145892 DOI: 10.3390/vaccines9050436] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a severe pandemic of the current century. The vicious tentacles of the disease have been disseminated worldwide with unknown complications and repercussions. Advanced COVID-19 syndrome is characterized by the uncontrolled and elevated release of pro-inflammatory cytokines and suppressed immunity, leading to the cytokine storm. The uncontrolled and dysregulated secretion of inflammatory and pro-inflammatory cytokines is positively associated with the severity of the viral infection and mortality rate. The secretion of various pro-inflammatory cytokines such as TNF-α, IL-1, and IL-6 leads to a hyperinflammatory response by recruiting macrophages, T and B cells in the lung alveolar cells. Moreover, it has been hypothesized that immune cells such as macrophages recruit inflammatory monocytes in the alveolar cells and allow the production of large amounts of cytokines in the alveoli, leading to a hyperinflammatory response in severely ill patients with COVID-19. This cascade of events may lead to multiple organ failure, acute respiratory distress, or pneumonia. Although the disease has a higher survival rate than other chronic diseases, the incidence of complications in the geriatric population are considerably high, with more systemic complications. This review sheds light on the pivotal roles played by various inflammatory markers in COVID-19-related complications. Different molecular pathways, such as the activation of JAK and JAK/STAT signaling are crucial in the progression of cytokine storm; hence, various mechanisms, immunological pathways, and functions of cytokines and other inflammatory markers have been discussed. A thorough understanding of cytokines' molecular pathways and their activation procedures will add more insight into understanding immunopathology and designing appropriate drugs, therapies, and control measures to counter COVID-19. Recently, anti-inflammatory drugs and several antiviral drugs have been reported as effective therapeutic drug candidates to control hypercytokinemia or cytokine storm. Hence, the present review also discussed prospective anti-inflammatory and relevant immunomodulatory drugs currently in various trial phases and their possible implications.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
| | - Shamsah H. Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif 32654, Saudi Arabia;
| | - Javed Muhammad
- Department of Microbiology, The University of Haripur, Khyber Pakhtunkhwa 22620, Pakistan;
| | - Amjad Khan
- Department of Public Health/Nutrition, The University of Haripur, Khyber Pakhtunkhwa 22620, Pakistan;
| | - Anupam A Sule
- Medical Director of Informatics and Outcomes, St Joseph Mercy Oakland, Pontiac, MI 48341, USA;
| | - Raghavendra Tirupathi
- Department of Medicine Keystone Health, Penn State University School of Medicine, Hershey, PA 16801, USA;
- Department of Medicine, Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA 16801, USA
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Alahsa 36342, Saudi Arabia;
- College of Nursing, Prince Nora University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Ministry of Health, Alahsa 31982, Saudi Arabia;
| | - Awad Al-Omari
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Dr. Sulaiman Al-Habib Medical Group, Critical Care and Infection Control Department, Research Centre, Riyadh 11372, Saudi Arabia
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141027, Punjab, India;
- The Trafford Group of Colleges, Manchester WA14 5PQ, UK
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh; Pandit DeenDayal Upadhyaya PashuChikitsa Vigyan Vishwavidyalaya Evam Go AnusandhaSansthan (DUVASU), Mathura 281001, Uttar Pradesh, India;
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Mathura 281001, Uttar Pradesh, India;
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, Odisha, India;
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh; or
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China;
| | - Salem A. Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, NSW 2052, Australia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
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45
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Sen SR, Sanders EC, Gabriel KN, Miller BM, Isoda HM, Salcedo GS, Garrido JE, Dyer RP, Nakajima R, Jain A, Caldaruse AM, Santos AM, Bhuvan K, Tifrea DF, Ricks-Oddie JL, Felgner PL, Edwards RA, Majumdar S, Weiss GA. Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score. mSphere 2021; 6:e00203-21. [PMID: 33910993 PMCID: PMC8092137 DOI: 10.1128/msphere.00203-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within 6 days post-symptom onset and sometimes within 1 day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patient's comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 likelihood ratio (96.7% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention.IMPORTANCE The COVID-19 pandemic has resulted in over two million deaths worldwide. Despite efforts to fight the virus, the disease continues to overwhelm hospitals with severely ill patients. Diagnosis of COVID-19 is readily accomplished through a multitude of reliable testing platforms; however, prognostic prediction remains elusive. To this end, we identified a short epitope from the SARS-CoV-2 nucleocapsid protein and also a disease risk factor score based upon comorbidities and age. The presence of antibodies specifically binding to this epitope plus a score cutoff can predict severe COVID-19 outcomes with 96.7% specificity.
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Affiliation(s)
- Sanjana R Sen
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Emily C Sanders
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Kristin N Gabriel
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Brian M Miller
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Hariny M Isoda
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Gabriela S Salcedo
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Jason E Garrido
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Rebekah P Dyer
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
| | - Rie Nakajima
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Aarti Jain
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Ana-Maria Caldaruse
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Alicia M Santos
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Keertna Bhuvan
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
| | - Joni L Ricks-Oddie
- Center for Statistical Consulting, Department of Statistics, University of California Irvine, Irvine, California, USA
- Biostatics, Epidemiology and Research Design Unit, Institute for Clinical and Translational Sciences, University of California Irvine, Irvine, California, USA
| | - Philip L Felgner
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
| | - Sudipta Majumdar
- Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - Gregory A Weiss
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, USA
- Department of Chemistry, University of California Irvine, Irvine, California, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
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46
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Maharaj L, Adeleke VT, Fatoba AJ, Adeniyi AA, Tshilwane SI, Adeleke MA, Maharaj R, Okpeku M. Immunoinformatics approach for multi-epitope vaccine design against P. falciparum malaria. INFECTION GENETICS AND EVOLUTION 2021; 92:104875. [PMID: 33905890 DOI: 10.1016/j.meegid.2021.104875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/07/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022]
Abstract
Plasmodium falciparum (P. falciparum) is a leading causative agent of malaria, an infectious disease that can be fatal. Unfortunately, control measures are becoming less effective over time. A vaccine is needed to effectively control malaria and lead towards the total elimination of the disease. There have been multiple attempts to develop a vaccine, but to date, none have been certified as appropriate for wide-scale use. In this study, an immunoinformatics method is presented to design a multi-epitope vaccine construct predicted to be effective against P. falciparum malaria. This was done through the prediction of 12 CD4+ T-cell, 10 CD8+ T-cell epitopes and, 1 B-cell epitope which were assessed for predicted high antigenicity, immunogenicity, and non-allergenicity through in silico methods. The Human Leukocyte Antigen (HLA) population coverage showed that the alleles associated with the epitopes accounted for 78.48% of the global population. The CD4+ and CD8+ T-cell epitopes were docked to HLA-DRB1*07:01 and HLA-A*32:01 successfully. Therefore, the epitopes were deemed to be suitable as components of a multi-epitope vaccine construct. Adjuvant RS09 was added to the construct to generate a stronger immune response, as confirmed by an immune system simulation. Finally, the structural stability of the predicted multi-epitope vaccine was assessed using molecular dynamics simulations. The results show a promising vaccine design that should be further synthesised and assessed for its efficacy in an experimental laboratory setting.
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Affiliation(s)
- Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Victoria T Adeleke
- Discipline of Chemical Engineering, University of KwaZulu-Natal, Howard Campus, Durban 4041, South Africa
| | - Abiodun J Fatoba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Adebayo A Adeniyi
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa; Department of Industrial Chemistry, Federal University Oye Ekiti, Nigeria
| | - Selaelo I Tshilwane
- School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Matthew A Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Rajendra Maharaj
- Office of Malaria Research, Medical Research Council, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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47
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Mahmud S, Paul GK, Afroze M, Islam S, Gupt SBR, Razu MH, Biswas S, Zaman S, Uddin MS, Khan M, Cacciola NA, Emran TB, Saleh MA, Capasso R, Simal-Gandara J. Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study. Molecules 2021; 26:2210. [PMID: 33921289 PMCID: PMC8070553 DOI: 10.3390/molecules26082210] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic is a global threat for healthcare management and the economic system, and effective treatments against the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for this disease have not yet progressed beyond the developmental phases. As drug refinement and vaccine progression require enormously broad investments of time, alternative strategies are urgently needed. In this study, we examined phytochemicals extracted from Avicennia officinalis and evaluated their potential effects against the main protease of SARS-CoV-2. The antioxidant activities of A. officinalis leaf and fruit extracts at 150 µg/mL were 95.97% and 92.48%, respectively. Furthermore, both extracts displayed low cytotoxicity levels against Artemia salina. The gas chromatography-mass spectroscopy analysis confirmed the identifies of 75 phytochemicals from both extracts, and four potent compounds, triacontane, hexacosane, methyl linoleate, and methyl palminoleate, had binding free energy values of -6.75, -6.7, -6.3, and -6.3 Kcal/mol, respectively, in complexes with the SARS-CoV-2 main protease. The active residues Cys145, Met165, Glu166, Gln189, and Arg188 in the main protease formed non-bonded interactions with the screened compounds. The root-mean-square difference (RMSD), root-mean-square fluctuations (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond data from a molecular dynamics simulation study confirmed the docked complexes' binding rigidity in the atomistic simulated environment. However, this study's findings require in vitro and in vivo validation to ensure the possible inhibitory effects and pharmacological efficacy of the identified compounds.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Mirola Afroze
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh; (M.A.); (M.H.R.); (M.K.)
| | - Shirmin Islam
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Swagota Briti Ray Gupt
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.R.G.); (S.B.)
| | - Mamudul Hasan Razu
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh; (M.A.); (M.H.R.); (M.K.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.R.G.); (S.B.)
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements, BRiCM, Bangladesh Council of Scientific and Industrial Research, Dhanmondi, Dhaka 1205, Bangladesh; (M.A.); (M.H.R.); (M.K.)
| | - Nunzio Antonio Cacciola
- Research Institute on Terrestrial Ecosystems (IRET)-UOS Naples, National Research Council of Italy (CNR), via P. Castellino 111, 80131 Naples, Italy;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.I.); (S.Z.); (M.S.U.)
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E32004 Ourense, Spain
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48
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Rakib A, Nain Z, Sami SA, Mahmud S, Islam A, Ahmed S, Siddiqui ABF, Babu SMOF, Hossain P, Shahriar A, Nainu F, Emran TB, Simal-Gandara J. A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation. Brief Bioinform 2021; 22:1476-1498. [PMID: 33623995 PMCID: PMC7929402 DOI: 10.1093/bib/bbab045] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic by the World Health Organization, and the situation worsens daily, associated with acute increases in case fatality rates. The main protease (Mpro) enzyme produced by SARS-CoV-2 was recently demonstrated to be responsible for not only viral reproduction but also impeding host immune responses. The element selenium (Se) plays a vital role in immune functions, both directly and indirectly. Thus, we hypothesised that Se-containing heterocyclic compounds might curb the activity of SARS-CoV-2 Mpro. We performed a molecular docking analysis and found that several of the selected selenocompounds showed potential binding affinities for SARS-CoV-2 Mpro, especially ethaselen (49), which exhibited a docking score of -6.7 kcal/mol compared with the -6.5 kcal/mol score for GC376 (positive control). Drug-likeness calculations suggested that these compounds are biologically active and possess the characteristics of ideal drug candidates. Based on the binding affinity and drug-likeness results, we selected the 16 most effective selenocompounds as potential anti-COVID-19 drug candidates. We also validated the structural integrity and stability of the drug candidate through molecular dynamics simulation. Using further in vitro and in vivo experiments, we believe that the targeted compound identified in this study (ethaselen) could pave the way for the development of prospective drugs to combat SARS-CoV-2 infections and trigger specific host immune responses.
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmaceutical Sciences, College of Pharmacy, 881 Madison Ave, Memphis, TN 38163, USA
| | - Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Saad Ahmed Sami
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Bangladesh
| | - Ashiqul Islam
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Bangladesh
| | - Shahriar Ahmed
- Department of Pharmacy, University of Chittagong, Bangladesh
| | | | | | - Payar Hossain
- Bachelor of Pharmacy professional degree focused in Pharmacy from University of Chittagong, Bangladesh
| | - Asif Shahriar
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, USA
| | - Firzan Nainu
- Faculty of Pharmacy Universitas Hasanuddin, Indonesia
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49
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Fang KY, Cao WC, Xie TA, Lv J, Chen JX, Cao XJ, Li ZW, Deng ST, Guo XG. Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids. Hum Genomics 2021; 15:18. [PMID: 33726831 PMCID: PMC7962432 DOI: 10.1186/s40246-021-00316-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people’s health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein–protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. Results In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. Conclusions In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.
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Affiliation(s)
- Ke-Ying Fang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Wen-Chao Cao
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jie Lv
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Xin Chen
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Xun-Jie Cao
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhong-Wei Li
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shu-Ting Deng
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Sen S, Sanders EC, Gabriel KN, Miller BM, Isoda HM, Salcedo GS, Garrido JE, Dyer RP, Nakajima R, Jain A, Caldaruse AM, Santos AM, Bhuvan K, Tifrea DF, Ricks-Oddie JL, Felgner PL, Edwards RA, Majumdar S, Weiss GA. Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33083803 DOI: 10.1101/2020.10.15.341743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the ICU, requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within six days post-symptom onset and sometimes within one day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patients comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 Likelihood Ratio (96.7% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention.
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