Article
Medicine, General & Internal
Supriya Ravichandran, Surender Khurana
Summary: A serodiagnostic test has been developed to differentiate between individuals with EBOV infection-induced antibodies and those with EBOV vaccine-induced antibodies. This test can accurately detect Ebola virus infections and could be implemented as a robust diagnostic tool for epidemiology and surveillance during and after outbreaks, especially in countries with mass Ebola vaccinations.
Article
Biochemical Research Methods
Priyank Shukla, Preeti Pandey, Bodhayan Prasad, Tony Robinson, Rituraj Purohit, Leon G. D'Cruz, Murtaza M. Tambuwala, Ankur Mutreja, Jim Harkin, Taranjit Singh Rai, Elaine K. Murray, David S. Gibson, Anthony J. Bjourson
Summary: This study utilizes immuno-informatics tools and bioinformatics databases to identify potential immunogenic epitopes of SARS-CoV-2 and validates their binding and interaction with HLA proteins. These findings have significant implications for the development of globally effective SARS-CoV-2 vaccines.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Immunology
Alexandra Kupke, Asisa Volz, Erik Dietzel, Astrid Freudenstein, Joerg Schmidt, Hosam Shams-Eldin, Sylvia Jany, Lucie Sauerhering, Verena Kraehling, Michelle Gellhorn Serra, Christiane Herden, Markus Eickmann, Stephan Becker, Gerd Sutter
Summary: This study tested two recombinant MVA-based Ebola virus vaccine candidates in mice and found that vaccination generated virus-neutralizing antibodies and specific CD8+ T cell response. Vaccinated mice survived Ebola virus infection and had significantly reduced viral loads compared to mock-vaccinated mice.
Article
Biochemistry & Molecular Biology
Aditi Bhardwaj, Ritika Sharma, Abhinav Grover
Summary: This study developed a multi-epitope, multi-pathogenic vaccine against Dengue and Zika viruses using immuno-informatics. The vaccine, incorporating salivary proteins from Aedes aegypti along with viral proteins, showed potential to provide protection against both viruses. In-silico modeling, molecular docking, and immune simulation studies supported the effectiveness of the designed vaccine.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Microbiology
Dustin M. McCraw, Mallory L. Myers, Neetu M. Gulati, Madhu Prabhakaran, Joshua Brand, Sarah Andrews, John R. Gallagher, Samantha Maldonado-Puga, Alexander J. Kim, Udana Torian, Hubza Syeda, Seyhan Boyoglu-Barnum, Masaru Kanekiyo, Adrian B. McDermott, Audray K. Harris
Summary: Structure-guided design of nanoparticles displaying conserved regions of influenza virus has the potential to develop more efficacious and universal vaccines. This design concept provides a new approach to universal influenza vaccine development strategies and opens opportunities for the development of nanoparticles with broad coverage over many antigenically diverse influenza HA subtypes.
Article
Biochemistry & Molecular Biology
Wahiba Ezzemani, Ahd Ouladlahsen, Haya Altawalah, Rachid Saile, M'hammed Sarih, Anass Kettani, Sayeh Ezzikouri
Summary: The researchers used in silico structural biology and advanced immunoinformatics to design a multi-epitope subunit vaccine against monkeypox virus (MPV) infection. The modified vaccine showed strong interaction with Toll-like receptor 9 (TLR9) and demonstrated stability through molecular dynamics simulation and normal mode analysis. While additional in vitro and in vivo studies are needed, the promising data suggest the effectiveness of this vaccine against MPV.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Immunology
Peter A. Barry, Smita S. Iyer, Laura Gibson
Summary: Traditionally, vaccine development for Human cytomegalovirus (HCMV) has focused on viral antigens that are identified as key targets of neutralizing antibody and/or T cell responses in healthy adults. However, there is currently no licensed HCMV vaccine that reduces the risk of infection in pregnant women. This study suggests that HCMV proteins recognized by only a small minority of participants may contain important vaccine antigens.
Article
Cell Biology
Saskia Meyer, Isaac Blaas, Ravi Chand Bollineni, Marina Delic-Sarac, Trung T. Tran, Cathrine Knetter, Ke-Zheng Dai, Torfinn Stove Madssen, John T. Vaage, Alice Gustavsen, Weiwen Yang, Lise Sofie Haug Nissen-Meyer, Karolos Douvlataniotis, Maarja Laos, Morten Milek Nielsen, Bernd Thiede, Arne Soraas, Fridtjof Lund-Johansen, Even H. Rustad, Johanna Olweus
Summary: Research shows that mutations in the coronavirus can lead to escape from neutralizing antibodies and loss of T cell epitopes. Previous studies on viral escape from T cell immunity have been hindered by uncertain estimates of epitope prevalence. This study maps and quantifies CD8 T cell responses to specific minimal epitopes of SARS-CoV-2 in COVID-19 convalescent individuals. It finds that mutations in variants of concern (VOC) are present in some epitopes but does not provide evidence that the mutations are driven by escape from T cell immunity.
Article
Immunology
Saskia V. Vijver, Sarah Danklmaier, Lisa Pipperger, Raphael Gronauer, Gabriel Floriani, Hubert Hackl, Krishna Das, Guido Wollmann
Summary: This study aimed to identify the anti-viral T cells raised by VSV-GP virotherapy in C57BL/6J mice using a multi-level adapted bioinformatics approach. The top-ranked viral epitopes triggering IFN-gamma secretion due to T cell activation were identified and validated. Overall, this identification of VSV-GP T cell epitopes enables comprehensive monitoring of anti-viral T cell responses and supports the development of novel VSV-GP variants.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Daniela Manno, Philip Ayieko, David Ishola, Muhammed O. Afolabi, Baimba Rogers, Frank Baiden, Alimamy Serry-Bangura, Osman M. Bah, Brian Kohn, Ibrahim Swaray, Kwabena Owusu-Kyei, Godfrey T. Otieno, Dickens Kowuor, Daniel Tindanbil, Elizabeth Smout, Cynthia Robinson, Babajide Keshinro, Julie Foster, Katherine Gallagher, Brett Lowe, Macaya Douoguih, Bailah Leigh, Brian Greenwood, Deborah Watson-Jones
Summary: This study investigated the association between Ebola virus antibody seropositivity and concentration, and potential risk factors for infection. Among 1,282 adults and children from a community affected by the 2014-2016 Ebola outbreak in Sierra Leone, 8% tested positive for virus antibodies without experiencing any disease symptoms. Antibody concentration was found to increase with age.
EMERGING INFECTIOUS DISEASES
(2022)
Review
Virology
Toufik Abdul-Rahman, Lukman Lawal, Emily Meale, Oyinbolaji A. Ajetunmobi, Soyemi Toluwalashe, Uthman Hassan Alao, Shankhaneel Ghosh, Neil Garg, Abdullahi Tunde Aborode, Andrew Awuah Wireko, Aashna Mehta, Kateryna Sikora
Summary: The Ebola virus has caused multiple outbreaks in Africa with high fatality rates. Social factors such as human mobility, behavior, and cultural norms contribute to the transmission risk. However, challenges including lagging vaccine production pose a risk of another outbreak.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Eva Mittler, Tanwee Alkutkar, Rohit K. Jangra, Kartik Chandran
Summary: Researchers introduced a novel in situ assay to monitor the binding of GPCL-NPC1 in intact, infected cells. This assay, based on DNA-assisted, antibody-mediated proximity ligation, allows for visualization of binding complexes and helps dissect the interaction between the Ebola virus glycoprotein and its receptor NPC1.
Article
Biology
Muhammad Tahir ul Qamar, Sajjad Ahmad, Israr Fatima, Faisal Ahmad, Farah Shahid, Anam Naz, Sumra Wajid Abbasi, Abbas Khan, Muhammad Usman Mirza, Usman Ali Ashfaq, Ling-Ling Chen
Summary: This study used subtractive proteomics assisted reverse vaccinology-based immunoinformatics pipeline to target antigenic proteins for developing a multi-epitope vaccine (MEV) against Staphylococcus aureus infections. Immunoinformatics tools were used to predict T-cell and B-cell epitopes, and a MEV construct with CTL, HTL, and LBL epitopes was designed. Molecular docking and dynamics simulations were performed to validate the interaction of MEV with TLR4 and MHC molecules, showing high antigenicity and stability. Further experimental validations are needed to confirm the effectiveness of the proposed MEV vaccine candidate.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Marta Gomez-Perosanz, Jose L. Sanchez-Trincado, Miguel Fernandez-Arquero, John Sidney, Alessandro Sette, Esther M. Lafuente, Pedro A. Reche
Summary: This study identified and characterized 23 conserved HRV-specific CD8 T cell epitopes on PBMCs from 14 HLA I typed subjects, confirming peptide-specific IFN gamma production and binding to the relevant HLA I for nine of these epitopes. The study also validated cytotoxicity mediated by A*02:01-restricted epitopes and discovered an unusually long 16-mer epitope peptide restricted by A*02:01. These HRV-specific CD8 T cell epitopes are expected to elicit CD8 T cell responses in up to 87% of the population and could be crucial for developing an HRV vaccine.
Review
Biotechnology & Applied Microbiology
Maddy L. Newby, Joel D. Allen, Max Crispin
Summary: A key aspect of successful viral vaccine design is the elicitation of neutralizing antibodies targeting viral attachment and fusion glycoproteins. Glycosylation can influence the antigenicity and immunogenicity of vaccines, with native-like glycosylation potentially enhancing immunogenicity. Understanding viral glycosylation can guide the development of future vaccines in various enveloped viruses.
BIOTECHNOLOGY ADVANCES
(2024)
Review
Biotechnology & Applied Microbiology
Iqra Kamal, Usman Ali Ashfaq, Sumreen Hayat, Bilal Aslam, Muhammad Hassan Sarfraz, Hamna Yaseen, Muhammad Shahid Riaz Rajoka, Asad Ali Shah, Mohsin Khurshid
Summary: Antimicrobial peptides (AMPs) have significant potential for inhibiting bacterial pathogens and can inhibit microbial growth through various mechanisms. They are biocompatible and biodegradable, making them a good alternative to antimicrobial agents and chemical preservatives in food preservation. However, their vulnerability to external environmental factors limits their practical applications in this field.
BIOTECHNOLOGY LETTERS
(2023)
Article
Biology
Muhammad Qasim, Muhammad Abdullah, Usman Ali Ashfaq, Fatima Noor, Nazia Nahid, Ahmad Alzamami, Norah A. Alturki, Mohsin Khurshid
Summary: Asthma is a challenging and costly health issue, and the therapeutic efficacy of Ferula asafoetida in treating asthma is yet to be fully understood. This study used network pharmacology and molecular docking to identify the bioactive compounds of F. asafoetida and reveal its mechanism in preventing asthma.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Gul Bushra Khan, Muhammad Qasim, Azhar Rasul, Usman Ali Ashfaq, Abdullah M. Alnuqaydan
Summary: In this study, virtual screening tools were used for structure-based drug discovery and 115 inhibitors with higher selectivity and binding affinity were identified for the enzyme 6-phosphogluconate dehydrogenase. Molecular dynamics simulations revealed three potential hits with stable confirmation. In vitro assays and cytotoxicity assays demonstrated the anticancer activity of these compounds against various cancer cell lines, particularly lung cancer.
Article
Multidisciplinary Sciences
Laraib Zara, Rizwana Hussain, Muhammad Shareef Masoud, Nadia Naseem, Hafiz Usman Ahmad, Usman Ali Ashfaq, Saba Khaliq
Summary: The PI3K/AKT/mTOR signaling pathway plays a crucial role in ovarian cancer. This study found that the gene expression of the PTEN/AKT pathway is deregulated in ovarian cancer patients. The phosphorylated level of AKT, expression of mTOR, and miRNAs may serve as markers for the disease.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2023)
Article
Biochemical Research Methods
Fatima Noor, Muhammad Asif, Usman Ali Ashfaq, Muhammad Qasim, Muhammad Tahir ul Qamar
Summary: Network pharmacology is an emerging field that aims to understand drug actions and interactions through multiple targets. The paradigm has shifted from 'one-target one-drug' to 'multi-target drug'. However, mining effective information from massive, heterogeneous data remains a challenge. Computational algorithms, especially machine learning (ML) and deep learning (DL), have shown great potential in analyzing big data in network pharmacology. ML can improve discovery and decision making at various stages of network pharmacology research. This review summarizes the algorithmic concepts and applications of ML in network pharmacology, highlighting the opportunities and challenges in implementing ML in the pharmaceutical industry.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Ayesha Rafiq, Tooba Jabeen, Sana Aslam, Matloob Ahmad, Usman Ali Ashfaq, Noor ul Amin Mohsin, Magdi E. A. Zaki, Sami A. Al-Hussain
Summary: The ongoing COVID-19 pandemic has caused global panic due to its continuous evolution and recurring spikes. This article summarizes the literature reports to date on natural products showing inhibitory activity towards the SARS-CoV-2 virus through various approaches, such as in vivo, in vitro, and in silico studies. These natural compounds, mainly extracted from plants, have the potential to combat the deadly viral disease.
Article
Microbiology
Fatima Noor, Usman Ali Ashfaq, Abu Bakar, Waqar ul Haq, Khaled S. S. Allemailem, Basmah F. F. Alharbi, Wafa Abdullah I. Al-Megrin, Muhammad Tahir ul Qamar
Summary: Recent studies have found that patients with Hantavirus-caused hemorrhagic fever with renal syndrome (HFRS) are at risk of contracting SARS-CoV-2. By analyzing gene expression and using bioinformatics and machine learning approaches, common dysregulated genes in HFRS and COVID-19 have been identified, which could be used for the design of personalized treatment to prevent the linked attacks of COVID-19 and HFRS.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Shumaila Mehdi, Malik Hassan Mehmood, Mobeen Ghulam Ahmed, Usman Ali Ashfaq
Summary: This study evaluates the antidiabetic activity of B. brandisiana in a high fat diet and streptozotocin-induced diabetes animal model. The results show that B. brandisiana and berbamine have antidiabetic activity, possibly through their effects on oxidative stress, glucose metabolism, inflammatory biomarkers, and adipocytokine levels.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Chemistry, Analytical
Zilwa Mumtaz, Zubia Rashid, Ashaq Ali, Afsheen Arif, Fuad Ameen, Mona S. AlTami, Muhammad Zubair Yousaf
Summary: Conventional diagnostic techniques require separate platforms for sample collection, sensing, and signaling, which can be integrated into point of care (POC) testing devices. Microfluidic systems made of polymers or glass offer specific and sensitive detection of diseases and have advantages such as low cost, good biological affinity, strong capillary action, and simple fabrication process. Challenges in nucleic acid detection, such as cellular lysis, isolation, and amplification, have been addressed by advances in on-chip sample preparation and detection through modular microfluidics. This review highlights the importance of microfluidic technology in nucleic acid detection of infectious and non-infectious diseases.
Article
Biology
Muhammad Sadaqat, Muhammad Qasim, Muhammad Tahir ul Qamar, Muhammad Shareef Masoud, Usman Ali Ashfaq, Fatima Noor, Kinza Fatima, Khaled S. Allemailem, Faris Alrumaihi, Ahmad Almatroudi
Summary: This study identifies effective phytochemicals from Bacopa monnieri that can inhibit liver cancer growth by targeting key genes. Quercetin, luteolin, apigenin, catechin, epicatechin, stigmasterol, beta-sitosterol, celastrol, and betulic acid were found to affect the occurrence and development of liver cancer through the modulation of multiple key genes.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Mamoona Sarfaraz, Faiqa Anjum, Duaa Zahra, Ayesha Maqsood, Usman Ali Ashfaq
Summary: Peptides play a crucial role in drug and vaccine development due to their ability to act as drug carriers, generate an immune response, and their stability in blood serum. They are cost-effective, easy to administer, and have target specificity, making them effective for pharmaceutical companies. Branched peptides are preferred for drug development as they are resistant to proteolytic enzymes.
CURRENT PHARMACEUTICAL DESIGN
(2023)
Article
Agronomy
Fatima Ahmadzai, Kanval Shaukat, Hafiz Mohammad Akram, Mahmood ur Rehman Ansari, Noreen Zahra, Abdul Samad, Mereen Nizar, Muhammad Bilal Hafeez, Ali Raza
Summary: This study assessed the effects of different plant growth promoters on stevia seedlings under drought stress. The findings showed that these promoters can improve the growth and physiological characteristics of stevia under drought stress, including root length, dry weight, and photosynthetic pigment content.
Article
Chemistry, Applied
Aqsa Asghar, Muhammad Qasim, Fatima Noor, Usman Ali Ashfaq, Muhammad Tahir ul Qamar, Muhammad Shareef Masoud, Rashid Bhatti, Ahmad Almatroudi, Faris Alrumaihi, Khaled S. Allemailem
Summary: Oleanolic acid, arjunolic acid, luteolin, kaempferol, cholesterol, ellagic acid 4-O-xylopyranoside 3,3'-dimethyl ether, and cyclohexyl (2,4-dimethyl phenyl) methanone were found to significantly contribute to the development of CCF by affecting AKT1, MAPK14, TNF, IL6, ESR1, and HSP90AA1 genes. Integrated network pharmacology and docking analysis revealed the molecular mechanism of T. arjuna in CCF and highlighted its potential as a promising preventive treatment for this condition.
NATURAL PRODUCT RESEARCH
(2023)
Article
Immunology
Fatima Noor, Usman Ali Ashfaq, Abu Bakar, Muhammad Qasim, Muhammad Shareef Masoud, Abdulrahman Alshammari, Metab Alharbi, Muhammad Shahid Riaz
Summary: Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis transmitted by infected rodents. The complex etiology of HFRS hinders the development of therapeutic solutions.
FRONTIERS IN IMMUNOLOGY
(2023)