4.7 Article

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants

Toluwase Hezekiah Fatoki et al.

Summary: This study aimed to investigate potential therapeutic compounds from medicinal plants for COVID-19 treatment, identifying key proteins involved in the virus lifecycle, and predicting high-binding compounds. DNA-dependent protein kinase and CK2 were found to play important roles, while compounds like caffeine, ellagic acid, and quercetin were suggested for COVID-19 remediation.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Chemistry, Medicinal

QSAR Modeling of SARS-CoV MproInhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and Other Drugs as Candidates for Repurposing against SARS-CoV-2

Vinicius M. Alves et al.

Summary: The researchers conducted virtual screening of inhibitors of the M-protease using QSAR models, and validated the effectiveness of some compounds in subsequent experiments. The results demonstrate that the models effectively guided experimental investigations of potential anti-COVID-19 drug candidates.

MOLECULAR INFORMATICS (2021)

Review Chemistry, Medicinal

COVID-19 drug repurposing: A review of computational screening methods, clinical trials, and protein interaction assays

Xueqing Wang et al.

Summary: Researchers worldwide are actively seeking cures for COVID-19, with drug repurposing being an important method. This review categorizes COVID-19 drug repurposing research into clinical trials, computational research, and in vitro experiments, organizing drugs by mechanisms of action and efficacy measured by clinical trials to guide future drug discovery efforts.

MEDICINAL RESEARCH REVIEWS (2021)

Review Chemistry, Medicinal

Review of registered clinical trials for the treatment of COVID-19

Fatemeh Babaei et al.

Summary: COVID-19, caused by SARS-CoV-2, was first reported in Wuhan, China in December 2019, but now more than 200 countries are affected. Treatments such as remdesivir are being explored, with antiviral, anti-inflammatory, and immunomodulatory properties considered important mechanisms against COVID-19.

DRUG DEVELOPMENT RESEARCH (2021)

Article Biochemistry & Molecular Biology

Open Targets Platform: supporting systematic drug-target identification and prioritisation

David Ochoa et al.

Summary: The Open Targets Platform provides a queryable knowledgebase and user interface for systematic target identification and prioritization for drug discovery, continuously improving evidence for target-disease relationships from various data sources. They have developed a new evidence scoring framework, added evaluation of post-marketing adverse drug reactions and target tractability, and optimized user interface and backend technologies to address the challenge of developing effective and safe drugs.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment

Alisa Pavel et al.

Summary: The ongoing COVID-19 pandemic has created an urgent need to understand the host response to the SARS-CoV-2 virus. By integrating data and developing a Unified Knowledge Space, new genes associated with the virus's effects have been identified, with functional analysis revealing potential long-term systemic impacts of the infection. Additionally, potentially relevant drugs targeting proteins involved in the host response have been identified to aid in combating the virus.

BRIEFINGS IN BIOINFORMATICS (2021)

Correction Biochemistry & Molecular Biology

Syncytia formation by SARS-CoV-2-infected cells (vol 39, e106267, 2020)

Julian Buchrieser et al.

EMBO JOURNAL (2021)

Article Multidisciplinary Sciences

Drugs that inhibit TMEM16 proteins block SARS-CoV-2 spike-induced syncytia

Luca Braga et al.

Summary: COVID-19 patients' lungs contain infected pneumocytes with abnormal morphology and frequent multinucleation, leading to the formation of syncytia driven by the activation of the SARS-CoV-2 spike protein. The antihelminthic drug niclosamide has shown to effectively inhibit cell fusion, potentially providing a new therapeutic approach for COVID-19 disease pathogenesis.

NATURE (2021)

Article Multidisciplinary Sciences

Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway

Andrea R. Daamen et al.

Summary: Analysis of gene expression data from COVID-19 patients revealed that the inflammatory response is mainly driven by populations of myeloid-lineage cells. Delayed virus clearance may lead to exaggerated activation of these cells, contributing to disease pathogenesis through the production of inflammatory mediators.

SCIENTIFIC REPORTS (2021)

Review Biochemistry & Molecular Biology

Neutralizing monoclonal antibodies for COVID-19 treatment and prevention

Juan Pablo Jaworski

Summary: The SARS-CoV-2 pandemic has caused unprecedented global health and economic crises. Various vaccine approaches and repurposed drugs are being evaluated, while nMAbs targeting the virus spike glycoprotein show promise. Large-scale production and high costs are key limitations for their clinical use. Collaboration, rapid development, safety evaluation, and production planning are crucial for controlling the COVID-19 pandemic.

BIOMEDICAL JOURNAL (2021)

Article Virology

Synergistic Block of SARS-CoV-2 Infection by Combined Drug Inhibition of the Host Entry Factors PIKfyve Kinase and TMPRSS2 Protease

Alex J. B. Kreutzberger et al.

Summary: Repurposing FDA-approved inhibitors can effectively prevent SARS-CoV-2 infection, with the combined use of apilimod, camostat mesylate, and nafamostat mesylate showing unexpected synergistic effects, which may serve as a plausible treatment strategy.

JOURNAL OF VIROLOGY (2021)

Article Multidisciplinary Sciences

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2

Nir Drayman et al.

Summary: This study identified a drug called masitinib that can inhibit the replication of both SARS-CoV-2 and OC43 virus, and acts by competitively inhibiting 3CLpro. The drug showed strong antiviral effects in in vivo experiments on mice infected with SARS-CoV-2, and was effective against multiple variants in vitro.

SCIENCE (2021)

Article Multidisciplinary Sciences

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19

Brian L. Le et al.

Summary: Researchers utilized a computational drug repositioning pipeline to predict potential antiviral drugs for SARS-CoV-2 based on gene expression differences. In validation experiments, 11 out of 16 tested compounds showed measurable antiviral activity against SARS-CoV-2, offering promising potential therapeutic options for treating COVID-19.

SCIENTIFIC REPORTS (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Petra Mlcochova et al.

Summary: The B.1.617.2 (Delta) variant of SARS-CoV-2 has lower sensitivity to antibodies and higher replication efficiency compared to other lineages, which may contribute to its dominance and reduced vaccine effectiveness, highlighting the need for continued infection control measures post-vaccination.

NATURE (2021)

Article Biochemistry & Molecular Biology

WADDAICA: A webserver for aiding protein drug design by artificial intelligence and classical algorithm

Qifeng Bai et al.

Summary: WADDAICA is a webserver that integrates deep learning models and classical algorithms for drug design, with good scoring power based on the PDBbind database. It provides a user-friendly web interface for drug design jobs submission.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Cathepsin L plays a key role in SARS-CoV-2 infection in humans and humanized mice and is a promising target for new drug development

Miao-Miao Zhao et al.

Summary: CTSL plays a crucial role in COVID-19 patients, with its levels positively correlated with disease severity. Research showed that CTSL promotes SARS-CoV-2 virus entry into cells, and the CTSL inhibitor amantadine can inhibit this process, providing a direction for the development of new anti-COVID-19 drugs.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

Review Biochemical Research Methods

A review on drug repurposing applicable to COVID-19

Serena Dotolo et al.

Summary: Drug repurposing involves finding new uses for existing drugs at a lower cost and in a shorter time period. Different computational drug-repurposing strategies, including network-based models, structure-based approaches, and artificial intelligence (AI) approaches, have been applied to COVID-19. Network-based clustering and propagation approaches have been used to identify proteins associated with COVID-19, while structure-based approaches have focused on discovering new applications for existing drugs through interactions with biological targets. AI-based networks, however, require more data before becoming relevant in this context.

BRIEFINGS IN BIOINFORMATICS (2021)

Review Public, Environmental & Occupational Health

Antivirals for COVID-19: A critical review

Andri Frediansyah et al.

Summary: No specific drugs have been approved for COVID-19 to date, so evaluating and utilizing currently available antiviral drugs is crucial. Research includes assessments of efficacy, in vitro studies, and clinical use results of these antivirals against the COVID-19 pandemic.

CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH (2021)

Article Biochemical Research Methods

BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data

Angela Serra et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Daniel Blanco-Melo et al.

Editorial Material Immunology

COVID-19: A New Virus, but a Familiar Receptor and Cytokine Release Syndrome

Toshio Hirano et al.

IMMUNITY (2020)

Article Biology

TinderMIX: Time-dose integrated modelling of toxicogenomics data

Angela Serra et al.

GIGASCIENCE (2020)

Article Multidisciplinary Sciences

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

David E. Gordon et al.

NATURE (2020)

Editorial Material Biotechnology & Applied Microbiology

The COVID-19 vaccine development landscape

Tung Thanh Le et al.

NATURE REVIEWS DRUG DISCOVERY (2020)

Review Pharmacology & Pharmacy

A comprehensive review on drug repositioning against coronavirus disease 2019 (COVID19)

Maryam Rameshrad et al.

NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY (2020)

Editorial Material Medicine, Research & Experimental

Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19?

Irene Karampela et al.

ARCHIVES OF MEDICAL RESEARCH (2020)

Editorial Material Oncology

Repurposing anticancer drugs for COVID-19-induced inflammation, immune dysfunction, and coagulopathy

Kamal S. Saini et al.

BRITISH JOURNAL OF CANCER (2020)

Article Biochemistry & Molecular Biology

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Mehdi Bouhaddou et al.

Article Immunology

Transcriptome-based drug repositioning for coronavirus disease 2019 (COVID-19)

Zhilong Jia et al.

PATHOGENS AND DISEASE (2020)

Review Pharmacology & Pharmacy

COVID-19 Therapeutic Options Under Investigation

Malak Kaddoura et al.

FRONTIERS IN PHARMACOLOGY (2020)

Review Public, Environmental & Occupational Health

Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review

Shahamah Jomah et al.

JOURNAL OF INFECTION AND PUBLIC HEALTH (2020)

Article Immunology

Inhibition of Bruton tyrosine kinase in patients with severe COVID-19

Mark Roschewski et al.

SCIENCE IMMUNOLOGY (2020)

Review Chemistry, Multidisciplinary

Repurposing of Kinase Inhibitors for Treatment of COVID-19

Ellen Weisberg et al.

PHARMACEUTICAL RESEARCH (2020)

Article Biochemistry & Molecular Biology

Syncytia formation by SARS-CoV-2-infected cells

Julian Buchrieser et al.

EMBO JOURNAL (2020)

Review Multidisciplinary Sciences

Array programming with NumPy

Charles R. Harris et al.

NATURE (2020)

Article Multidisciplinary Sciences

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

Ludovico Cantuti-Castelvetri et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Sofosbuvir terminated RNA is more resistant to SARS-CoV-2 proofreader than RNA terminated by Remdesivir

Steffen Jockusch et al.

SCIENTIFIC REPORTS (2020)

Article Cell Biology

Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19

Paola Stolfi et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2020)

Article Infectious Diseases

A connectivity map-based drug repurposing study and integrative analysis of transcriptomic profiling of SARS-CoV-2 infection

Seyedeh Zahra Mousavi et al.

INFECTION GENETICS AND EVOLUTION (2020)

Editorial Material Public, Environmental & Occupational Health

COVID-19 pneumonia and the appropriate use of antibiotics

Amy Sarah Ginsburg et al.

LANCET GLOBAL HEALTH (2020)

Review Critical Care Medicine

Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19

Wentao Ni et al.

CRITICAL CARE (2020)

Review Chemistry, Medicinal

Repurposing Anti-Cancer Drugs for COVID-19 Treatment

Nicholas Borcherding et al.

DRUG DESIGN DEVELOPMENT AND THERAPY (2020)

Review Respiratory System

COVID-19 and coagulative axis: review of emerging aspects in a novel disease

Matilde Boccia et al.

MONALDI ARCHIVES FOR CHEST DISEASE (2020)

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

INfORM: Inference of NetwOrk Response Modules

Veer Singh Marwah et al.

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Coronavirus S protein-induced fusion is blocked prior to hemifusion by Abl kinase inhibitors

Jeanne M. Sisk et al.

JOURNAL OF GENERAL VIROLOGY (2018)

Article Multidisciplinary Sciences

Network-based approach to prediction and population-based validation of in silico drug repurposing

Feixiong Cheng et al.

NATURE COMMUNICATIONS (2018)

Review Biochemical Research Methods

A review of network-based approaches to drug repositioning

Maryam Lotfi Shahreza et al.

BRIEFINGS IN BIOINFORMATICS (2018)

Proceedings Paper Computer Science, Artificial Intelligence

Mask R-CNN

Kaiming He et al.

2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION (ICCV) (2017)

Article Biochemistry & Molecular Biology

PubChem Substance and Compound databases

Sunghwan Kim et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists

Michael G. Schimek et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2015)

Article Chemistry, Multidisciplinary

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

David Bajusz et al.

JOURNAL OF CHEMINFORMATICS (2015)

Article Biochemistry & Molecular Biology

TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists

Michael G. Schimek et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Open TG-GATEs: a large-scale toxicogenomics database

Yoshinobu Igarashi et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Chemistry, Multidisciplinary

Drug repositioning: a machine-learning approach through data integration

Francesco Napolitano et al.

JOURNAL OF CHEMINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Differential expression in RNA-seq: A matter of depth

Sonia Tarazona et al.

GENOME RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Differential expression analysis for sequence count data

Simon Anders et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Steffen Durinck et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

Patrick E. Meyer et al.

BMC BIOINFORMATICS (2008)

Article Biotechnology & Applied Microbiology

BMDExpress: a software tool for the benchmark dose analyses of genomic data

Longlong Yang et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

DrugBank: a comprehensive resource for in silico drug discovery and exploration

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramanian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemical Research Methods

affy -: analysis of Affymetrix GeneChip data at the probe level

L Gautier et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Summaries of affymetrix GeneChip probe level data

RA Irizarry et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Statistics & Probability

Greedy function approximation: A gradient boosting machine

JH Friedman

ANNALS OF STATISTICS (2001)