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Syed Ali
Center for Biotechnology and Microbiology, University of Swat, Swat 01923, Pakistan

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Journal article
Published: 23 July 2021 in Vaccines
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Pegivirus, HPgV, which was earlier known as Gb virus and hepatitis G virus, is an enveloped, positive-stranded RNA and lymphotropic virus classified into the Flaviviridae family. The transmission routes primarily involve blood products, and infections are worldwide, leading up to 25% of persistent infections. To date, no effective therapeutic means are available to clear Pegivirus infections. Effective vaccine therapeutics is the best alternative to manage this disease and any associated potential pandemic. Thus, whole proteome-based mining of immunogenic peptides, i.e., CTL (cytotoxic T lymphocytes), HTL (helper T lymphocytes), and B cell epitopes, was mapped to design a vaccine ensemble. Our investigation revealed that 29 different epitopes impart a critical role in immune response induction, which was also validated by exploring its physiochemical properties and experimental feasibility. In silico expression and host immune simulation were examined using an agent-based modeling approach and confirmed the induction of both primary and secondary immune factors such as IL, cytokines, and antibodies. The current study warrants further lab experiments to demonstrate its efficacy and safety.

ACS Style

Bowen Zheng; Muhammad Suleman; Zonara Zafar; Syed Ali; Syed Nasir; Namra; Zahid Hussain; Muhammad Waseem; Abbas Khan; Fakhrul Hassan; Yanjing Wang; Dongqing Wei. Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation. Vaccines 2021, 9, 818 .

AMA Style

Bowen Zheng, Muhammad Suleman, Zonara Zafar, Syed Ali, Syed Nasir, Namra, Zahid Hussain, Muhammad Waseem, Abbas Khan, Fakhrul Hassan, Yanjing Wang, Dongqing Wei. Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation. Vaccines. 2021; 9 (8):818.

Chicago/Turabian Style

Bowen Zheng; Muhammad Suleman; Zonara Zafar; Syed Ali; Syed Nasir; Namra; Zahid Hussain; Muhammad Waseem; Abbas Khan; Fakhrul Hassan; Yanjing Wang; Dongqing Wei. 2021. "Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation." Vaccines 9, no. 8: 818.

Journal article
Published: 12 September 2020 in Infection, Genetics and Evolution
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Bartonella bacilliformis a gram-negative facultative aerobe responsible for the Carrion's disease widely distributed in Ecuador, Peru, and Colombia with a high mortality rate when no specific treatment is received. B bacilliformis is transmitted by Sand fly (Lutzomyia verrucarum) to healthy individuals. Immunoinformatic and subtractive proteomics approaches were employed in this study to prioritize the best candidates for vaccine designing. These approaches resulted in five vaccine candidates, flagellar biosynthetic protein (Uniprot ID: A1UTU1), heme exporter protein C (UniProt ID: A1UU82), Cytochrome c-type biogenesis protein (Uniprot ID: A1URZ7), Hemin ABC transporter (Uniprot ID: A1US20) and Phosphatidate cytidylyltransferase (Uniprot ID: A1USE3). The mentioned proteins are antigenic and essential for pathogen survival. A range of immune-informatics tools was applied for the prediction of B and T cell epitopes for the vaccine candidate proteins. In-silico vaccine was constructed using carefully evaluated epitopes and consequently modeled for docking with human Toll-like receptor 4. TLR-4 agonist 50S ribosomal protein L7/L12 (UniproKB ID; P9WHE3) was linked to the vaccine as an adjuvant to boost immune response towards the vaccine. For stability evaluation of the vaccine-TLR-4 docked complex, MD simulations were performed. The final vaccine was back-translated and cloned in Eschericia coli to attain the maximal expression of the vaccine protein. The maximal expression was ensured, and the CAI score of 0.96 was reported. The current vaccine requires future experimental validation to confirm its effectiveness. The vaccine developed will be helpful to protect against B bacilliformis associated infections.

ACS Style

Hina Gul; Syed Shujait Ali; Shoaib Saleem; Shahzeb Khan; Jafar Khan; Abdul Wadood; Ashfaq Ur Rehman; Zia Ullah; Shahid Ali; Haji Khan; Zahid Hussain; Fazal Akbar; Abbas Khan; Dong-Qing Wei. Subtractive proteomics and immunoinformatics approaches to explore Bartonella bacilliformis proteome (virulence factors) to design B and T cell multi-epitope subunit vaccine. Infection, Genetics and Evolution 2020, 85, 104551 .

AMA Style

Hina Gul, Syed Shujait Ali, Shoaib Saleem, Shahzeb Khan, Jafar Khan, Abdul Wadood, Ashfaq Ur Rehman, Zia Ullah, Shahid Ali, Haji Khan, Zahid Hussain, Fazal Akbar, Abbas Khan, Dong-Qing Wei. Subtractive proteomics and immunoinformatics approaches to explore Bartonella bacilliformis proteome (virulence factors) to design B and T cell multi-epitope subunit vaccine. Infection, Genetics and Evolution. 2020; 85 ():104551.

Chicago/Turabian Style

Hina Gul; Syed Shujait Ali; Shoaib Saleem; Shahzeb Khan; Jafar Khan; Abdul Wadood; Ashfaq Ur Rehman; Zia Ullah; Shahid Ali; Haji Khan; Zahid Hussain; Fazal Akbar; Abbas Khan; Dong-Qing Wei. 2020. "Subtractive proteomics and immunoinformatics approaches to explore Bartonella bacilliformis proteome (virulence factors) to design B and T cell multi-epitope subunit vaccine." Infection, Genetics and Evolution 85, no. : 104551.

Research article
Published: 08 September 2020 in Journal of Biomolecular Structure and Dynamics
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The outbreak of the recent coronavirus (SARS-CoV-2), which causes a severe pneumonia infection, first identified in Wuhan, China, imposes significant risks to public health. Around the world, researchers are continuously trying to identify small molecule inhibitors or vaccine candidates by targeting different drug targets. The SARs-CoV-2 macrodomain-I, which helps in viral replication and hijacking the host immune system, is also a potential drug target. Hence, this study targeted viral macrodomain-I by using drug similarity, virtual screening, docking and re-docking approaches. A total of 64,043 compounds were screened, and potential hits were identified based on the docking score and interactions with the key residues. The top six hits were subjected to molecular dynamics simulation and Free energy calculations and repeated three times each. The per-residue energy decomposition analysis reported that these compounds significantly interact with Asp22, Ala38, Asn40, Val44, Phe144, Gly46, Gly47, Leu127, Ser128, Gly130, Ile131, Phe132 and Ala155 which are the critical active site residues. Here, we also used ADPr as a positive control to compare our results. Our results suggest that our identified hits by using such a complicated computational pipeline could inhibit the SARs-CoV-2 by targeting the macrodomain-1. We strongly recommend the experimental testing of these compounds, which could rescue the host immune system and could help to contain the disease caused by SARs-CoV-2. Communicated by Ramaswamy H. Sarma

ACS Style

Zainib Babar; Mazhar Khan; Mubeen Zahra; Munazza Anwar; Kashif Noor; Huma Farooque Hashmi; Muhammad Suleman; Muhammad Waseem; Abdullah Shah; Shahid Ali; Syed Shujait Ali. Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study. Journal of Biomolecular Structure and Dynamics 2020, 1 -15.

AMA Style

Zainib Babar, Mazhar Khan, Mubeen Zahra, Munazza Anwar, Kashif Noor, Huma Farooque Hashmi, Muhammad Suleman, Muhammad Waseem, Abdullah Shah, Shahid Ali, Syed Shujait Ali. Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study. Journal of Biomolecular Structure and Dynamics. 2020; ():1-15.

Chicago/Turabian Style

Zainib Babar; Mazhar Khan; Mubeen Zahra; Munazza Anwar; Kashif Noor; Huma Farooque Hashmi; Muhammad Suleman; Muhammad Waseem; Abdullah Shah; Shahid Ali; Syed Shujait Ali. 2020. "Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study." Journal of Biomolecular Structure and Dynamics , no. : 1-15.

Journal article
Published: 30 March 2020 in Plants
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In current study, the effect of gibberellic acid was tested for production of biomass, polyphenolics and Steviol glycosides in adventitious root cultures of Stevia rebaudiana. Adventitious cultures were induced from the roots of in vitro grown plantlets on Murashige and Skoog (MS) medium containing combination of gibberellic acid (GA3; 0.5, 1.0, 1.5 and 2.0 mg/L) and naphthalene acetic acid (NAA; 0.5 mg/L). Initially, a known mass of inoculum roots were shifted into suspension media augmented with various GA3 concentrations. The growth behavior of adventitious roots was recorded every 3 days for a period of 30 days. Maximum biomass biosynthesis (13.12 g/flask) was noticed in exponential phase on 27th day in the suspension containing 2.0 mg/L of GA3. Other GA3 concentrations also displayed optimum patterns of biomass accumulation as compared to the control. Adventitious roots were investigated for total phenolic content (TPC) and production (TPP), total flavonoid content (TFC) and production (TFP), and 1, 1-diphenyl-2-picrylhydrazyl (DPPH)-based antioxidant potential. Maximum phenolics (TPC 9.84 mg gallic acid equivalent (GAE)/g-dry weight (DW)) and TPP (147.6 mg/L), TFC (5.12 mg Quercitin equivalent (QE)/g-DW) and TFP (76.91 mg/L) were observed in 2.0 mg/L GA3 treated cultures. The same concentration of gibberellic acid enhanced antioxidant activity (77.2%). Furthermore, maximum stevioside (7.13 mg/g-DW), rebaudioside-A (0.27 mg/g-DW) and dulcoside-A (0.001 mg/g-DW) were observed in roots exposed to 2.0 mg/L GA3. This is the first report on the application of GA3 on biomass accumulation and secondary metabolite production in S. rebaudiana. The current study will be helpful to scale up the adventitious root cultures in bioreactors for the production of biomass and pharmaceutically important secondary metabolites.

ACS Style

Ashfaq Ahmad; Haider Ali; Habiba Khan; Almas Begam; Sheraz Khan; Syed Shujait Ali; Naveed Ahmad; Hina Fazal; Mohammad Ali; Christophe Hano; Nisar Ahmad; Bilal Haider Abbasi. Effect of Gibberellic Acid on Production of Biomass, Polyphenolics and Steviol Glycosides in Adventitious Root Cultures of Stevia rebaudiana (Bert.). Plants 2020, 9, 420 .

AMA Style

Ashfaq Ahmad, Haider Ali, Habiba Khan, Almas Begam, Sheraz Khan, Syed Shujait Ali, Naveed Ahmad, Hina Fazal, Mohammad Ali, Christophe Hano, Nisar Ahmad, Bilal Haider Abbasi. Effect of Gibberellic Acid on Production of Biomass, Polyphenolics and Steviol Glycosides in Adventitious Root Cultures of Stevia rebaudiana (Bert.). Plants. 2020; 9 (4):420.

Chicago/Turabian Style

Ashfaq Ahmad; Haider Ali; Habiba Khan; Almas Begam; Sheraz Khan; Syed Shujait Ali; Naveed Ahmad; Hina Fazal; Mohammad Ali; Christophe Hano; Nisar Ahmad; Bilal Haider Abbasi. 2020. "Effect of Gibberellic Acid on Production of Biomass, Polyphenolics and Steviol Glycosides in Adventitious Root Cultures of Stevia rebaudiana (Bert.)." Plants 9, no. 4: 420.

Preprint content
Published: 20 March 2020
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Human Norovirus belong to family Calciviridae, it was identified in the outbreak of gastroenteritis in Norwalk, due to its seasonal prevalence known as “winter vomiting disease”. Treatment of Norovirus infection is still mysterious because there is no effective antiviral drugs or vaccine developed to protect against the infection, to eradicate the infection an effective vaccine should be developed. In this study capsid protein (A7YK10), small protein (A7YK11) and polyprotein (A7YK09) were utilized. These proteins were subjected to B and T cell epitopes prediction by using reliable immunoinformatics tools. The antigenic and non-allergenic epitopes were selected for subunit vaccine, which can activate cellular and humoral immune responses. Linkers joined these epitopes together. The vaccine structure was modelled and validated by using Errat, ProSA and rampage servers. The modelled vaccine was docked with TLR-7. Stability of the docked complex was evaluated by MD simulation. In order to apply the concept in a wet lab, the reverse translated vaccine sequence was cloned in pET28a (+). The vaccine developed in this study requires experimental validation to ensure its effectiveness against the disease.

ACS Style

Irfan Ahmad; Syed Shujait Ali; Ismail Shah; Shahzeb Khan; Mazhar Khan; Saif Ullah; Shahid Ali; Jafar Khan; Mohammad Ali; Abbas Khan; Dong-Qing Wei. Computational vaccinology based development of multi-epitope subunit vaccine for protection against the Norovirus’ infections. 2020, 1 .

AMA Style

Irfan Ahmad, Syed Shujait Ali, Ismail Shah, Shahzeb Khan, Mazhar Khan, Saif Ullah, Shahid Ali, Jafar Khan, Mohammad Ali, Abbas Khan, Dong-Qing Wei. Computational vaccinology based development of multi-epitope subunit vaccine for protection against the Norovirus’ infections. . 2020; ():1.

Chicago/Turabian Style

Irfan Ahmad; Syed Shujait Ali; Ismail Shah; Shahzeb Khan; Mazhar Khan; Saif Ullah; Shahid Ali; Jafar Khan; Mohammad Ali; Abbas Khan; Dong-Qing Wei. 2020. "Computational vaccinology based development of multi-epitope subunit vaccine for protection against the Norovirus’ infections." , no. : 1.

Journal article
Published: 04 June 2019 in Infection, Genetics and Evolution
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The Mayaro virus (MAYV) belongs to genus “Alphavirus” and family “Togaviridae”. MAYV has distribution in the Amazonia, Central and Northeastern regions of Brazil. The abundance of mosquito vector Haemagogus janthinomys has major role in the outbreaks of arthralgia disease in Brazil. Vaccination or immunization is an alternative approach for the protection against this disease. To search the effective candidate for vaccine against Mayaro virus, various immunoinformatics tools were used to predict both the B and T cell epitopes from five structural polyproteins (capsid, E2, 6K, E3and E1). A multi subunit vaccine was designed and the final sequence was modeled for docking with TLR-3. Human b defensin based on previous studies was used as linker. The docked complexes of vaccine-TLR-3 were then subjected to dynamics stability and RMSD and RMSF results suggested that the complexes are stable. Further, to validate our final vaccine construct, in silico cloning was carried out using E. coli as host. The CAI value of 0.96 suggests that the vaccine construct properly expresses in the host. The current findings will be useful for the future experimental validations to ratify the immunogenicity and safety of the supposed structure of vaccine, and ultimately to treat the Mayaro virus, associated infections.

ACS Style

Shahzeb Khan; Abbas Khan; Ashfaq Ur Rehman; Irfan Ahmad; Saif Ullah; Abdul Aziz Khan; Syed Shujait Ali; Sahib Gul Afridi; Dong-Qing Wei. Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression. Infection, Genetics and Evolution 2019, 73, 390 -400.

AMA Style

Shahzeb Khan, Abbas Khan, Ashfaq Ur Rehman, Irfan Ahmad, Saif Ullah, Abdul Aziz Khan, Syed Shujait Ali, Sahib Gul Afridi, Dong-Qing Wei. Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression. Infection, Genetics and Evolution. 2019; 73 ():390-400.

Chicago/Turabian Style

Shahzeb Khan; Abbas Khan; Ashfaq Ur Rehman; Irfan Ahmad; Saif Ullah; Abdul Aziz Khan; Syed Shujait Ali; Sahib Gul Afridi; Dong-Qing Wei. 2019. "Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression." Infection, Genetics and Evolution 73, no. : 390-400.

Journal article
Published: 01 June 2018 in Journal of Molecular Graphics and Modelling
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Dengue virus belongs to a group of human pathogens, which causes different diseases, dengue hemorrhagic fever and dengue shock syndrome in humans. It possesses RNA as a genetic material and is replicated with the aid of NS5 protein. RNA-dependent RNA polymerase (RdRp) is an important domain of NS5 in the replication of that virus. The catalytic process activity of RdRp is making it an important target for antiviral chemical therapy. To date, No FDA drug has been approved and marketed for the treatment of diseases caused by Dengue virus. So, there is a dire need to advance an area of active antiviral inhibitors that is safe, less expensive and widely available. An experimentally validated complex of Dengue NS5 and compound 27 (6LS) were used as pharmacophoric input and hits were identified. We also used Molecular dynamics (MD) simulations alongside free energy and dynamics of the internal residues of the apo and holo systems to understand the binding mechanism. Our analysis resulted that the three inhibitors (ZINC72070002, ZINC6551486, and ZINC39588257) greatly affected the interior dynamics and residual signaling to dysfunction the replicative role of NS5. The interaction of these inhibitors caused the loss of the correlated motion of NS5 near to the N terminus and helped the stability of the binding complex. This investigation provided a methodological route to discover allosteric inhibitors against the epidemics of this Flaviviruses. Allosteric inhibitors are important and major assets in considering the development of the competitive and robust antiviral agents such as against Dengue viral infection.

ACS Style

Abbas Khan; Shoaib Saleem; Muhammad Idrees; Syed Shujait Ali; Muhammad Junaid; Aman Chandra Kaushik; Dong-Qing Wei. Allosteric ligands for the pharmacologically important Flavivirus target (NS5) from ZINC database based on pharmacophoric points, free energy calculations and dynamics correlation. Journal of Molecular Graphics and Modelling 2018, 82, 37 -47.

AMA Style

Abbas Khan, Shoaib Saleem, Muhammad Idrees, Syed Shujait Ali, Muhammad Junaid, Aman Chandra Kaushik, Dong-Qing Wei. Allosteric ligands for the pharmacologically important Flavivirus target (NS5) from ZINC database based on pharmacophoric points, free energy calculations and dynamics correlation. Journal of Molecular Graphics and Modelling. 2018; 82 ():37-47.

Chicago/Turabian Style

Abbas Khan; Shoaib Saleem; Muhammad Idrees; Syed Shujait Ali; Muhammad Junaid; Aman Chandra Kaushik; Dong-Qing Wei. 2018. "Allosteric ligands for the pharmacologically important Flavivirus target (NS5) from ZINC database based on pharmacophoric points, free energy calculations and dynamics correlation." Journal of Molecular Graphics and Modelling 82, no. : 37-47.