Article
Biochemical Research Methods
Ranjan Kumar Barman, Anirban Mukhopadhyay, Ujjwal Maulik, Santasabuj Das
Summary: The ongoing global pandemic of COVID-19, caused by SARS-CoV-2, has resulted in over 5.9 million deaths and around 43 million confirmed infections. Mass vaccination has started in many countries, but the availability is limited. Therefore, repurposing existing drugs has become a focus for finding immediate solutions. A recent study used affinity-purification mass spectrometry to map the physical interactions between SARS-CoV-2 and human proteins, identifying 332 high-confidence protein-protein interactions. Using a network biology approach, the study constructed a human protein-protein interaction network (PPIN) and identified four human proteins as the best therapeutic targets. Additionally, several candidate drugs/compounds were found to bind to these target proteins. The study suggests that repurposing drugs for host targeting therapy may be an effective strategy for treating SARS-CoV-2 infection.
Article
Biochemistry & Molecular Biology
Samaneh Maleknia, Mohammad Javad Tavassolifar, Faezeh Mottaghitalab, Mohammad Reza Zali, Anna Meyfour
Summary: This study utilized bioinformatics and machine learning algorithms to investigate RNA-Seq datasets of COVID-19 patients' whole blood and nasopharyngeal samples, revealing distinct host gene meta-signatures and immune cell landscape, and ultimately identifying optimal diagnostic biomarker panels.
MOLECULAR MEDICINE
(2022)
Article
Medicine, General & Internal
Eugenia Z. Ong, Shirin Kalimuddin, Wen Chong Chia, Sarah H. Ooi, Clara Wt Koh, Hwee Cheng Tan, Summer L. Zhang, Jenny G. Low, Eng Eong Ooi, Kuan Rong Chan
Summary: Neutrophil activation was found to be closely associated with respiratory dysfunction in severe COVID-19 patients, while type I interferon signaling transcripts were not. Transcripts encoding for protein phosphorylation, especially serine-threonine kinases, increased after respiratory function declined, potentially contributing to its recovery.
Review
Public, Environmental & Occupational Health
Jivan Qasim Ahmed, Sazan Qadir Maulud, Manish Dhawan, Priyanka, Om Prakash Choudhary, Paywast Jamal Jalal, Rezhna Kheder Ali, Gahin Abdulraheem Tayib, Dlshad Abdullah Hasan
Summary: miRNAs have potential therapeutic targets in combating COVID-19, reducing viral load, and mitigating the deleterious consequences of excessive cytokine secretion.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2022)
Article
Biology
Taehwan Oh, Green Kim, Seung Ho Baek, Youngmin Woo, Bon-Sang Koo, Eun-Ha Hwang, Kyuyoung Shim, You Jung An, Yujin Kim, Jinyoung Won, Youngjeon Lee, Kyung Seob Lim, Jae-Hak Park, Jung Joo Hong
Summary: We utilized a spatial transcriptome atlas to identify specific gene expression profiles of acute lung injury during SARS-CoV-2 infection. The alveolar regions showed activation of genes related to virus-induced cell death and the innate immune response, while inflamed vascular regions exhibited upregulation of interferon and complement pathway genes. Known biomarker genes were expressed in specific pulmonary microstructures, highlighting the importance of identifying key drivers of disease progression and clinically applicable biomarkers during SARS-CoV-2 infection.
COMMUNICATIONS BIOLOGY
(2023)
Review
Virology
Brandon Bautista-Becerril, Guillermo Perez-Dimas, Paola C. Sommerhalder-Nava, Alejandro Hanono, Julio A. Martinez-Cisneros, Barbara Zarate-Maldonado, Evangelina Munoz-Soria, Arnoldo Aquino-Galvez, Manuel Castillejos-Lopez, Armida Juarez-Cisneros, Jose S. Lopez-Gonzalez, Angel Camarena
Summary: The COVID-19 pandemic has highlighted the importance of prognostic predictors and therapeutic targets in the disease. miRNA biomolecules have been shown to play a vital role in regulating genes associated with the pathophysiology of COVID-19 and can be used as predictors of complications and potential targets for treatment. However, further studies are needed to confirm these findings.
Article
Medicine, Research & Experimental
Nahid Arghiani, Tracy Nissan, Maryam M. Matin
Summary: COVID-19 is a pneumonia-like disease caused by a coronavirus, and changes in miRNAs are associated with disease severity, targeting these small noncoding-RNAs could potentially alleviate complications.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Immunology
Aijaz Parray, Fayaz Ahmad Mir, Asmma Doudin, Ahmad Iskandarani, Ibn Mohammed Masud Danjuma, Rahim Ayadathil Thazhhe Kuni, Alaaedin Abdelmajid, Ibrahim Abdelhafez, Rida Arif, Mohammad Mulhim, Mohammad Abukhattab, Shoukat Rashhid Dar, Ala-Eddin Al Moustafa, Eyad Elkord, Abdul Latif Al Khal, Abdel-Naser Elzouki, Farhan Cyprian
Summary: This study identified microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) as potential biomarkers of COVID-19 severity through differential expression analysis of microarray data, and found that they are significantly correlated with white blood cell count, neutrophil count, lymphocyte count, red blood cell count, hemoglobin, etc. The study provides a unique miRNA and snoRNA profile associated with a higher risk of severity in SARS-CoV-2 infected patients, highlighting the importance of these molecules in SARS-CoV-2 infection.
Review
Immunology
Lianpan Dai, George F. Gao
Summary: The urgent need for vaccines to control the COVID-19 pandemic has led to the rapid development of multiple vaccine candidates, with some showing positive results in late-stage clinical trials. This article discusses the viral elements used in these candidates, the reasons why they are good targets for the immune system, and their implications for protective immunity. Dai and Gao highlight the importance of selecting the right viral targets in vaccine development to ensure an effective immune response and the overall safety and efficacy of the vaccine.
NATURE REVIEWS IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Margherita Galli, Agnese Zardini, Worku Nigussa Gamshie, Stefano Santini, Ademe Tsegaye, Filippo Trentini, Valentina Marziano, Giorgio Guzzetta, Mattia Manica, Valeria d'Andrea, Giovanni Putoto, Fabio Manenti, Marco Ajelli, Piero Poletti, Stefano Merler
Summary: The inequitable access to vaccination globally calls for a re-evaluation of policies to reduce the COVID-19 burden in low-income countries. In Ethiopia, only 3.4% of the population received two doses of the COVID-19 vaccine after nine months of the national vaccination program. Using a transmission model, it was found that prioritizing vaccination for the elderly remained the best strategy to minimize the disease burden caused by the Delta variant, regardless of the available doses.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Lukas van de Sand, Peer Brass, Jonas Gregorius, Kevin Pattberg, Andrea Engler, Ulf Dittmer, Christian Taube, Stephan Brock, Marc Moritz Berger, Thorsten Brenner, Oliver Witzke, Adalbert Krawczyk
Summary: The COVID-19 pandemic has caused millions of deaths worldwide and remains a significant health issue. Infection by SARS-CoV-2 can be categorized into different phases, and hyperinflammation during the acute pneumonia phase is a major cause of disease progression and death. Early initiation of treatment is crucial for optimal patient care.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Medicine, General & Internal
Dan H. Barouch
Summary: This article reviews the protective effects of vaccination and prior infection on severe Covid-19, and proposes future research directions.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Multidisciplinary Sciences
Qin Liu, Qi Su, Fen Zhang, Hein M. Tun, Joyce Wing Yan Mak, Grace Chung-Yan Lui, Susanna So Shan Ng, Jessica Y. L. Ching, Amy Li, Wenqi Lu, Chenyu Liu, Chun Pan Cheung, David S. C. Hui, Paul K. S. Chan, Francis Ka Leung Chan, Siew C. Ng
Summary: By integrating clinical features and multi-omics data, the authors identified specific gut microbiome patterns associated with disease severity and development of post-acute COVID-19 syndrome. These findings highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Immunology
Rustom Antia, M. Elizabeth Halloran
Summary: The article discusses the basic concepts underlying the transition from an epidemic to an endemic state, as well as the implications of this transition for COVID-19.
Review
Biochemistry & Molecular Biology
Sabrina Esposito, Gianluca D'Abrosca, Anna Antolak, Paolo Vincenzo Pedone, Carla Isernia, Gaetano Malgieri
Summary: An unprecedented effort is being made by the global scientific community to tackle COVID-19 and understand the role of zinc finger proteins in the disease. This understanding could lead to important therapeutic developments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
M. Sudhan, V. Janakiraman, Rajesh Patil, Atif Abdulwahab A. Oyouni, Ahmad Mufti, Shiek S. S. J. Ahmed
Summary: This study investigates the impact of Asn215Ser, Ala143Thr and Arg112Cys variants on the structure and function of alpha-GalA protein, and finds that these variants may contribute to Fabry disease.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Genetics & Heredity
V. Janakiraman, M. Sudhan, Shankargouda Patil, Khalid J. Alzahrani, Fuad M. Alzahrani, Ibrahim F. Halawani, Shiek S. S. J. Ahmed
Summary: This study constructed a protein-protein interaction network of rheumatoid arthritis (RA) genes and identified STAT3 and IL2 as potential drug targets. The drug docking and molecular dynamics simulations showed that zoledronic acid had the lowest binding energy and exhibited notable differences in conformational changes. In vitro assessment confirmed the potential of zoledronic acid as an inhibitor for these targets, benefiting patients with RA.
Article
Pharmacology & Pharmacy
Thrinayan Moorthy, B. Mohamed Hathim, C. H. Murali NagaMahesh, G. Anburaj, Shiek S. S. J. Ahmed, V. Gopinath, Ganesh Munuswamy-Ramanujam, Subha Krishna Rao, Manjunath Srinivas Kamath
Summary: Bone tissue engineering (BTE) aims to treat bone abnormalities by using a porous polymer matrix that hosts cells, promotes proliferation, and releases drugs/growth factors. This study developed a 3D porous scaffold releasing kaempferol through kaempferol-entrapped albumin nanoparticles (KaeNP) and polycaprolactone (PCL). The scaffolds possessed porous structures with pore diameters essential for cell penetration and angiogenesis.
JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
V. Janakiraman, M. Sudhan, Khalid J. Alzahrani, Saleh Alshammeri, Shiek S. S. J. Ahmed, Shankargouda Patil
Summary: The study evaluated the pathogenic variants of TUBB protein and found that Q15K, Y222F, M299V, and E401K have detrimental effects on cortical dysplasia. Modeling and assessment of variant structures and their affinity with the cofactor GTP revealed different binding energies compared to the wild-type. Molecular dynamics simulation showed trajectory differences between pathogenic and non-pathogenic variants. These findings highlight the impact of amino acid residue changes in TUBB structure on protein flexibility and interactions with cofactors.
JOURNAL OF MOLECULAR MODELING
(2023)
Article
Plant Sciences
Almendra Reyes-Calderon, Claudia Gutierrez-Garcia, Andrea G. Uriostegui-Pena, Aashish Srivastava, Liliana Aguilar-Marcelino, Hafiz M. N. Iqbal, Shiek S. S. J. Ahmed, Sujay Paul, Ashutosh Sharma
Summary: The pharmacological properties of plants depend on their secondary metabolites, which are classified based on biosynthesis, structures, and functions. MicroRNAs (miRNAs) are small non-coding RNA molecules that play important roles in post-transcriptional regulation in plants. This study investigated the miRNA profile of Cumin and its association with secondary metabolite biosynthesis, identifying conserved and novel miRNAs targeting enzymes involved in terpenoid, flavonoid, and lipid/fatty acid pathways.
Article
Clinical Neurology
Pallavi Kesavan, Aiswarya Padmaja Satheesh, Akram Husain Rehman Syed Rasheed, Umamaheshwari Veerappan, Subramaniyan Kannaian, Ramakrishnan Veerabathiran
Summary: This study aimed to investigate the genetic association of serotonin transporter (SERT) 5-hydroxytryptamine transporter-linked promoter region (5-HTTLPR) polymorphism and migraine risk in South-Indian population. The genotyping analysis revealed no significant relationship between the polymorphism and migraine subjects when compared with controls. Further clinical studies are required to validate these results in diverse ethnic descents.
CURRENT JOURNAL OF NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jency Roshni, Mahema Sivakumar, Fuad M. M. Alzahrani, Ibrahim F. F. Halawani, Khalid J. J. Alzahrani, Shankargouda Patil, Shiek S. S. J. Ahmed
Summary: TRPV1 gene polymorphisms are susceptible to multiple diseases and considered a therapeutic target for various inflammatory conditions. In this study, suitable TRPV1 protein structures were constructed and 3363 anti-inflammatory compounds were screened. C18H15F3N4O showed potential as a potential analgesic for inflammatory conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Neurosciences
Athira Anirudhan, George Chandy Mattethra, Khalid J. Alzahrani, Hamsa Jameel Banjer, Fuad M. Alzahrani, Ibrahim F. Halawani, Shankargouda Patil, Ashutosh Sharma, Prabu Paramasivam, Shiek S. S. J. Ahmed
Summary: Pesticides kill neurons, but the mechanism leading to selective dopaminergic loss in Parkinson's disease (PD) is unknown. Understanding the pesticide's effect on dopaminergic neurons (DA) can help to screen and treat PD. Through molecular docking, protein networks, regulatory pathways, and prioritization of key pesticide-regulating proteins, the study reveals the mechanisms of eleven crucial pesticides and their impact on gene expression in pesticide-exposed PD patients.
Article
Biochemistry & Molecular Biology
K. Monisha, S. Mahema, M. Chokkalingam, Sheikh F. Ahmad, Talha Bin Emran, Paramasivam Prabu, Shiek S. S. J. Ahmed
Summary: This study aimed to investigate the expression of HDAC genes in coronary artery disease (CAD) and evaluate their impact on hematological, biochemical, and echocardiographic indices. The researchers found that certain HDACs were upregulated in CAD patients and significantly associated with various physiological parameters. Additionally, a diagnostic model using key HDACs showed excellent accuracy in distinguishing CAD from the control group.
Article
Genetics & Heredity
Ramakrishnan Veerabathiran, Keerthana Srinivasan, Prema Jayaprasad, B. K. Iyshwarya, R. S. Akram Husain
Summary: This study aims to examine the impact of specific methylation within the MTHFR gene polymorphisms on the occurrence of preeclampsia and recurrent miscarriages in the South Indian population. The findings suggest that the variant allele of the MTHFR gene (rs1801133) is associated with an increased risk of preeclampsia and recurrent pregnancies.
Article
Biotechnology & Applied Microbiology
V Janakiraman, M. Sudhan, Khalaf F. Alsharif, Ibrahim F. Halawani, Shiek S. S. J. Ahmed, Shankargouda Patil
Summary: In this study, the three-dimensional structures of NUDT15 and its common variants were docked with anti-cancer drugs. Azathioprine showed the highest affinity for NUDT15 structures and demonstrated stability in the molecular dynamics simulation. These findings suggest that azathioprine could be an effective anti-cancer drug for individuals with NUDT15 variants.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Gastroenterology & Hepatology
Vasanthakumar Sekar, Ramakrishnan Veerabathiran, Arjun Pandian, Ganesan Sivamani
Summary: This study investigates the effectiveness of targeting liver cancer stem cells through EpCAM gene therapy combined with chemotherapy. The results show that silencing the EpCAM gene and treating cells with XAV939 can decrease the expression of liver cancer stem cell marker CD133 and reduce chemoresistance marker ABCG2. The cells also showed reduced ability to form colonies and spheroids. These findings support the potential of EpCAM-targeted therapy to improve prognosis in hepatocellular carcinoma patients.
EGYPTIAN LIVER JOURNAL
(2023)
Review
Oncology
Iyshwarya Bhaskar Kalarani, Ganesan Sivamani, Ramakrishnan Veerabathiran
Summary: This study aimed to identify a specific gene as a key candidate for thyroid cancer progression in order to better understand the inheritance of thyroid cancer.
JOURNAL OF THE EGYPTIAN NATIONAL CANCER INSTITUTE
(2023)
Article
Biotechnology & Applied Microbiology
Jency Roshni, Mahema Sivakumar, Faris Ahmed Bahammam, Shilpa Bhandi, Shankargouda Patil, Manjunath Kamath, Ali Abusharha, Shiek S. S. J. Ahmed
Summary: COVID-19 is a systemic disease caused by SARS-CoV-2 infection, affecting multiple organs, biological pathways, and cell types. A systems biology approach was used to investigate the impact of lung microbiome-derived metabolites on the host immune system during COVID-19. The study identified overlapping genes and a key transcriptional regulator in the immune network, as well as the high affinity of a metabolite derived from the lung microbiome with the regulator. The findings provide new insights into the importance of lung microbiome metabolites in regulating the host immune system during COVID-19.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Microbiology
Kalaivani Manokaran, Saritha U. Kamath, Aneena Varghese, Ravi N. Shankar, Siddharth Kaushik, Shiek Fareeth Ahmed, Robert Selvam, Prabu Paramasivam, M. Anju
Summary: This study assessed the knowledge, attitude, and practice of the Indian population towards COVID-19. The results showed an average KAP score of 16.92. Interventional programs and adherence to precautionary measures are necessary to prevent disease spread.
REVIEWS AND RESEARCH IN MEDICAL MICROBIOLOGY
(2023)
