4.6 Article

Interactome-Based Machine Learning Predicts Potential Therapeutics for COVID-19

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Inhibitory mechanism of Ambroxol and Bromhexine Hydrochlorides as potent blockers of molecular interaction between SARS-CoV-2 spike protein and human angiotensin-converting Enzyme-2

Idowu A. Kehinde et al.

Summary: This study analyzed the inhibitory potentials of two mucolytic drugs, AMB and BHH, on the molecular interactions between SARS-CoV-2 spike protein and hACE-2. The results showed that the binding of these drugs at the exopeptidase site of hACE-2 reduced the binding affinity and molecular interaction between the proteins, suggesting their potential as inhibitors of hACE-2 and viral attachment.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2022)

Article Biology

Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19

Enrique J. deAndres-Galiana et al.

Summary: This study provides insights into the transcriptomic response and potential side effects of SARS-CoV-2 infection. It suggests that drug repositioning based on transcriptome analysis could be a fast-track antiviral therapy for COVID-19 patients.

COMPUTERS IN BIOLOGY AND MEDICINE (2022)

Article Infectious Diseases

In silico drug repurposing against SARS-CoV-2 using an integrative transcriptomic profiling approach: Hydrocortisone and Benzhydrocodone as potential drug candidates against COVID-19

SeyedehMozhdeh Mirmohammadi et al.

Summary: The pathogenesis of COVID-19 is mainly caused by dysregulated immune response. Repurposing existing drugs may hold promise for the treatment of COVID-19. By analyzing the transcriptomic profile of human alveolar cells infected with SARS-CoV-2, researchers identified up-regulated genes specific to COVID-19 and several antiviral proteins and pro-viral proteins. Molecular docking experiments showed that Hydrocortisone and Benzhydrocodone have high binding affinity for all pro-viral proteins. Further in vitro and in vivo experiments are needed to evaluate the potential of these repurposed drugs for the treatment of COVID-19.

INFECTION GENETICS AND EVOLUTION (2022)

Article Medicine, General & Internal

Favipiravir, camostat, and ciclesonide combination therapy in patients with moderate COVID-19 pneumonia with/without oxygen therapy: An open- label, single-center phase 3 randomized clinical trial

Jiro Terada et al.

Summary: This study evaluated the effectiveness of combination therapy with favipiravir, camostat, and ciclesonide in patients with moderate COVID-19 pneumonia. The combination therapy was found to reduce the length of hospital stay without safety concerns. However, the study had limitations due to the lack of a hard clinical primary outcome.

ECLINICALMEDICINE (2022)

Article Biochemistry & Molecular Biology

Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

Mubarak A. Alamri et al.

Summary: The study identifies potential covalent inhibitors through a structure-based approach and repurposes FDA-approved drugs against SARS-CoV-2 3CLpro. Molecular dynamics simulations characterize the binding mechanism and dynamic stability between the compounds and the protease. Identified compounds show promise as potential inhibitors for further development as COVID-19 drugs, including FDA-approved anti-hepatitis-C virus drugs paritaprevir and simeprevir.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Biochemistry & Molecular Biology

Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

Chandrabose Selvaraj et al.

Summary: This study focuses on screening for antiviral inhibitors targeting guanine-N7 methyltransferase (N7-MTase), a key drug target in the first methylation step of the SARS-CoV-2 RNA capping mechanism. Compounds binding the substrate-binding site can disrupt enzyme catalysis and hinder 5'-end cap formation, crucial for mimicking host RNA and evading host immune responses. Our research suggests potential compounds from the Traditional Chinese Medicine (TCM) database through a combination of computational approaches.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Biochemical Research Methods

MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs

Zhiwei Feng et al.

Summary: In response to the scale and rapid spread of COVID-19 caused by SARS-CoV-2, novel strategies are needed for drug discovery due to the limitations of traditional research methods. Our new in silico approach overcomes these limitations and provides a way to quickly evaluate potential therapeutics for COVID-19 before vaccines are available.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Cell & Tissue Engineering

Structure-Based Design of Novel Peptidomimetics Targeting the SARS-CoV-2 Spike Protein

Manikandan Alagumuthu et al.

Summary: SARS-CoV-2 spike protein plays a critical role in the pathogenesis of COVID-19 by interacting with the host cell ACE2 PD domain. Efforts are being made worldwide to combat COVID-19, and this study identified potential peptidomimetics against the SARS-CoV-2 spike protein.

CELLULAR AND MOLECULAR BIOENGINEERING (2021)

Review Pharmacology & Pharmacy

Can N-3 polyunsaturated fatty acids be considered a potential adjuvant therapy for COVID-19-associated cardiovascular complications?

Ahmed M. Darwesh et al.

Summary: The global COVID-19 pandemic caused by SARS-CoV-2 has led to millions of confirmed cases worldwide. The exaggerated immune response, hypercoagulation, and oxidative stress triggered by viral infection significantly impact the cardiovascular health of COVID-19 patients. n-3 polyunsaturated fatty acids (n-3 PUFAs) may serve as potential adjuvant therapies for COVID-19 management, with demonstrated beneficial effects on controlling inflammation, reducing oxidative stress, and mitigating coagulopathy.

PHARMACOLOGY & THERAPEUTICS (2021)

Article Computer Science, Artificial Intelligence

A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing

K. Deepthi et al.

Summary: In response to the COVID-19 pandemic, this study presents a deep learning ensemble model to prioritize clinically validated antiviral drugs for potential efficacy against SARS-CoV-2. The method extracts deep features through a convolutional neural network and classifies them using an extreme gradient boosting classifier to infer potential virus-drug associations.

APPLIED SOFT COMPUTING (2021)

Article Biology

Interactome of human and SARS-CoV-2 proteins to identify human hub proteins associated with comorbidities

Nimisha Ghosh et al.

Summary: SARS-CoV-2 has a higher chance of progression in adults with certain underlying health conditions or comorbidities, possibly leading to death. Understanding host-virus protein interactions can aid in designing effective antiviral drugs. Identifying hub proteins connected to most human proteins helps predict potential diseases and comorbidities.

COMPUTERS IN BIOLOGY AND MEDICINE (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)

Article Biochemical Research Methods

HVIDB: a comprehensive database for human-virus protein-protein interactions

Xiaodi Yang et al.

Summary: The study introduces a database called HVIDB that provides comprehensive annotated data on human-virus protein-protein interactions and integrates online PPI prediction tools. Users can easily access reliable information on various human virus PPIs and conduct in-depth analysis through this database.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

Leveraging publicly available coronavirus data to identify new therapeutic targets for COVID-19

Stacy L. Sell et al.

Summary: There are many unanswered questions regarding SARS-CoV-2, including the high percentage of asymptomatic but highly infectious individuals, wide variability in disease susceptibility, and long-lasting debilitating effects. Bioinformatic analysis has identified diverse host factors involved in virus-induced immune suppression, viral replication, and evasion of antiviral immune surveillance, which deserve further investigation for their roles in COVID-19-related symptoms and organ dysfunctions.

PLOS ONE (2021)

Article Multidisciplinary Sciences

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

Emanuel Wyler et al.

Summary: Detailed analysis of SARS-CoV-2 infection in comparison with SARS-CoV reveals a stronger induction of innate immune response, including the upregulation of miRNA-155. Infected cells show broad upregulation of genes, while interferon beta/lambda genes and pro-inflammatory cytokines like IL-6 are expressed in only a small subset of cells. Time analysis suggests that interferon regulatory factors are activated before nuclear factor kappa B in response to infection, with heat shock protein 90 (HSP90) identified as a relevant protein for viral replication and inflammatory cytokine expression.

ISCIENCE (2021)

Article Infectious Diseases

Methylprednisolone or dexamethasone, which one is superior corticosteroid in the treatment of hospitalized COVID-19 patients: a triple-blinded randomized controlled trial

Keivan Ranjbar et al.

Summary: The study demonstrated that methylprednisolone was more effective than dexamethasone in hospitalized hypoxic COVID-19 patients, with better clinical status, shorter hospital stay, and lower need for a ventilator in the intervention group.

BMC INFECTIOUS DISEASES (2021)

Article Biochemistry & Molecular Biology

Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2

Thirumal D. Kumar et al.

Summary: The increasing number of confirmed COVID-19 cases is highlighting the need for effective treatments. Repurposed drugs are being tested against SARS-CoV-2, with a focus on identifying alternative compounds to combat potential drug-resistant mutations. Further research and validation are required to confirm the efficacy of these lead compounds in inhibiting SARS-CoV-2.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

Article Engineering, Biomedical

Automatic detection of coronavirus disease (COVID-19) in X-ray and CT images: A machine learning based approach

Sara Hosseinzadeh Kassani et al.

Summary: COVID-19 is highly transmittable and pathogenic, with no approved antiviral drug or vaccine for treatment. Computer-aided diagnosis systems can assist in early detection of COVID-19 abnormalities. Different deep learning-based feature extraction frameworks were compared for automatic COVID-19 classification in this study.

BIOCYBERNETICS AND BIOMEDICAL ENGINEERING (2021)

Article Multidisciplinary Sciences

Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization

Gita A. Pathak et al.

Summary: This study integrates genome-wide association study data with mRNA expression, splicing, and protein levels to identify genes and pathways related to COVID-19 hospitalization, highlighting putative causal genes impacting disease severity and symptomology.

NATURE COMMUNICATIONS (2021)

Article Computer Science, Artificial Intelligence

A machine learning platform to estimate anti-SARS-CoV-2 activities

Govinda B. KC et al.

Summary: REDIAL-2020 is a suite of computational models for estimating small molecule activities in a range of SARS-CoV-2-related assays, available as a web application through the DrugCentral web portal. It provides similarity search results and experimental data, serving as a rapid online tool for identifying active molecules for COVID-19 treatment.

NATURE MACHINE INTELLIGENCE (2021)

Article Biochemistry & Molecular Biology

An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

Yiyue Ge et al.

Summary: A drug repositioning framework was developed to identify CVL218 as a potential treatment for COVID-19, with in vitro assays showing its inhibitory effect on SARS-CoV-2 replication and interaction with viral proteins, as well as suppression of inflammatory cytokines relevant to immunopathology induced by the virus.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

Article Biochemistry & Molecular Biology

In silico identification of novel SARS-COV-2 2′-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches

Mahmoud A. El Hassab et al.

Summary: This study aimed to identify a potential inhibitor for SARS CoV-2 nsp16, an important target in the virus life cycle. Through virtual screening and molecular dynamics simulations, compound 11 was identified as the best potential nsp16 inhibitor with improved stability and binding free energy compared to Sinefungin.

JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY (2021)

Article Genetics & Heredity

Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data

Jianchang Hu et al.

Summary: This study identified 8 super variants associated with susceptibility to COVID-19 mortality through a genome-wide association study. These variants are related to cilia dysfunctions, cardiovascular diseases, thromboembolic disease, and other conditions, providing potential directions for understanding the molecular pathogenesis of COVID-19 and the genetic basis of heterogeneous susceptibility.

HUMAN GENOMICS (2021)

Article Medicine, Research & Experimental

Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis

Jingjiao Li et al.

Summary: This study provides insights into the molecular mechanisms of SARS-CoV-2 pathogenesis by identifying host proteins targeted by the virus and perturbed in COVID-19 patients. The findings suggest a potential link between the upregulation of cellular proteins related to neutrophil activation, blood coagulation, and downregulation of proteins mediating T cell receptor signaling in severe COVID-19 patients. The interactome analysis further reveals the potential mechanisms by which SARS-CoV-2 triggers cytokine storms through the induction of interleukin-8 and the facilitation of neutrophil chemotaxis.
Article Biochemistry & Molecular Biology

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

Daniel Blanco-Melo et al.

Article Multidisciplinary Sciences

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

David E. Gordon et al.

NATURE (2020)

Article Infectious Diseases

Nutritional status of patients with COVID-19

Jae Hyoung Im et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

Article Immunology

COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning

Edison Ong et al.

FRONTIERS IN IMMUNOLOGY (2020)

Review Multidisciplinary Sciences

Current Status of COVID-19 Therapies and Drug Repositioning Applications

Ozlem Altay et al.

ISCIENCE (2020)

Article Chemistry, Physical

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

Rohit Batra et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

Article Biochemistry & Molecular Biology

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

Aaron J. Wilk et al.

NATURE MEDICINE (2020)

Editorial Material Pharmacology & Pharmacy

Ongoing Clinical Trials for the Management of the COVID-19 Pandemic

Mark P. Lythgoe et al.

TRENDS IN PHARMACOLOGICAL SCIENCES (2020)

Article Biochemical Research Methods

DeepPurpose: a deep learning library for drug-target interaction prediction

Kexin Huang et al.

BIOINFORMATICS (2020)

Article Computer Science, Artificial Intelligence

Mapping the landscape of Artificial Intelligence applications against COVID-19

Joseph Bullock et al.

JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH (2020)

Article Computer Science, Artificial Intelligence

COVID-19 Outbreak Prediction with Machine Learning

Sina F. Ardabili et al.

ALGORITHMS (2020)

Article Biochemistry & Molecular Biology

Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model

Bo Ram Beck et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Biochemistry & Molecular Biology

The ChEMBL database in 2017

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Mathematical & Computational Biology

A two-step framework for inferring direct protein-protein interaction network from AP-MS data

Bo Tian et al.

BMC SYSTEMS BIOLOGY (2017)

Article Biochemistry & Molecular Biology

ChEMBL: a large-scale bioactivity database for drug discovery

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Chemistry, Multidisciplinary

PaDEL-Descriptor: An Open Source Software to Calculate Molecular Descriptors and Fingerprints

Chun Wei Yap

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemical Research Methods

Precision and recall estimates for two-hybrid screens

Hailiang Huang et al.

BIOINFORMATICS (2009)

Review Cell Biology

Analysis of protein complexes using mass spectrometry

Anne-Claude Gingras et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

Article Biochemical Research Methods

An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

Tilmann Buerckstuemmer et al.

NATURE METHODS (2006)

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 Mathematical & Computational Biology

Molecular drug targets and structure based drug design: A holistic approach

Shailza Singh et al.

BIOINFORMATION (2006)

Review Biochemistry & Molecular Biology

New methodologies for measuring protein interactions in vivo and in vitro

J Piehler

CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)

Review Biotechnology & Applied Microbiology

Docking and scoring in virtual screening for drug discovery: Methods and applications

DB Kitchen et al.

NATURE REVIEWS DRUG DISCOVERY (2004)

Article Multidisciplinary Sciences

Systematic genetic analysis with ordered arrays of yeast deletion mutants

AHY Tong et al.

SCIENCE (2001)

Article Multidisciplinary Sciences

A comprehensive two-hybrid analysis to explore the yeast protein interactome

T Ito et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)