4.6 Article

In Silico Prediction of Novel Inhibitors of SARS-CoV-2 Main Protease through Structure-Based Virtual Screening and Molecular Dynamic Simulation

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Anti-Coronavirus Vaccines: Past Investigations on SARS-CoV-1 and MERS-CoV, the Approved Vaccines from BioNTech/Pfizer, Moderna, Oxford/AstraZeneca and others under Development Against SARS-CoV-2 Infection

Michele Costanzo et al.

Summary: The aim of this review article is to provide an overview of the current knowledge about prophylaxis achievements in the fight against Coronaviruses. The article summarizes the recent literature on vaccines effective against the most pathogenic Coronaviruses and focuses on the development and use of vaccines in combating the COVID-19 pandemic. The main objective is to understand the molecular level of anti-SARS-CoV-2 prophylactic intervention and provide an overall picture of innovative approaches for vaccine development against the most pathogenic Coronaviruses.

CURRENT MEDICINAL CHEMISTRY (2022)

Review Immunology

Review Article Genotype and phenotype of COVID-19: Their roles in pathogenesis

Leila Mousavizadeh et al.

Summary: COVID-19 is a novel coronavirus belonging to the Betacoronavirus genus, with similarities and differences in genomic structure compared to other human Betacoronaviruses. It contains at least six open reading frames and important structural proteins are encoded near the one-third of the genome.

JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION (2021)

Review Pharmacology & Pharmacy

Chloroquine and hydroxychloroquine for COVID-19:Perspectives on their failure in repurposing

Rashmi R. Shah

Summary: Current evidence suggests that chloroquine and hydroxychloroquine are not effective in treating COVID-19 infection, and may cause adverse effects such as QT interval prolongation in some patients. Despite concerns about QT liability, the risk of proarrhythmia is low and manageable with careful monitoring. Efforts to repurpose these drugs for COVID-19 treatment have largely failed due to safety concerns.

JOURNAL OF CLINICAL PHARMACY AND THERAPEUTICS (2021)

Article Biochemistry & Molecular Biology

SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging

Wioletta Rut et al.

Summary: A team of researchers synthesized a new type of antiviral agent, demonstrating through experiments its high efficacy in inhibiting SARS-CoV-2 with a low effective concentration, providing new insights for antiviral treatment. By observing the active SARS-CoV-2 M-pro in the cells of patients infected with COVID-19, important clues were provided for the design of antiviral drugs and diagnostic tests.

NATURE CHEMICAL BIOLOGY (2021)

Editorial Material Biochemistry & Molecular Biology

Analyzing FDA-approved drugs for compliance of pharmacokinetic principles: should there be a critical screening parameter in drug designing protocols?

Shelly Pathania et al.

EXPERT OPINION ON DRUG METABOLISM & TOXICOLOGY (2021)

Article Biochemistry & Molecular Biology

Evidence of Protein Binding by a Nucleopeptide Based on a Thymine-decorated L-Diaminopropanoic Acid through CD and In Silico Studies

Valentina Roviello et al.

Summary: The study aims to explore novel features of a thymine-bearing nucleopeptide based on L-diaminopropanoic acid through spectroscopic methods, and found that the modified peptide bound the albumin target by inducing significant changes to the protein secondary structure. In silico studies also suggested the potential ability of the nucleopeptide to bind with good affinity the main protease of SARS-CoV-2 and other relevant targets.

CURRENT MEDICINAL CHEMISTRY (2021)

Article Chemistry, Medicinal

Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Arkajyoti Sengupta et al.

Summary: The new water models and ion parameter sets accurately reproduce experimental data, demonstrating improved performance.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Medicine, General & Internal

Tocilizumab in Hospitalized Patients with Severe Covid-19 Pneumonia

I. O. Rosas et al.

Summary: In this randomized trial involving hospitalized patients with severe Covid-19 pneumonia, the use of tocilizumab did not result in significantly better clinical status or lower mortality than placebo at 28 days.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

Caterina Vicidomini et al.

Summary: Opuntia ficus-indica, a cactaceous plant, has been investigated for its potential as a source of antiviral drugs for COVID-19. In silico docking experiments revealed several flavonols and flavonol glucosides from Opuntia ficus-indica with strong binding affinities for the main protease of SARS-CoV-2, suggesting astragalin as a promising protease inhibitor candidate for anti-COVID-19 strategies.

SYMMETRY-BASEL (2021)

Review Infectious Diseases

Understanding the Molecular Biology of SARS-CoV2 and the COVID-19 Pandemic: A Review

Sarah Alsobaie

Summary: Coronaviruses, responsible for 15-30% of atypical pneumonia cases globally, have caused the COVID-19 pandemic with the newest SARS virus, SARS-CoV-2, resulting in over 3 million deaths and over 140 million infections as of April 2021. Understanding the molecular biology and infection process of coronaviruses is crucial for developing therapeutic drugs and vaccines.

INFECTION AND DRUG RESISTANCE (2021)

Review Microbiology

Coronavirus biology and replication: implications for SARS-CoV-2

Philip V'kovski et al.

Summary: This review discusses key aspects of coronavirus biology and their implications for SARS-CoV-2 infections, treatment, and prevention strategies. Understanding virus-host interactions at the molecular level is crucial for developing effective intervention strategies. Summarizing the discoveries of SARS-CoV-2 infection and comparing it with other coronaviruses will support future preparedness and combat strategies.

NATURE REVIEWS MICROBIOLOGY (2021)

Article Chemistry, Physical

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Review Virology

Emerging coronaviruses: Genome structure, replication, and pathogenesis

Yu Chen et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

Editorial Material Medicine, General & Internal

A novel coronavirus outbreak of global health concern

Chen Wang et al.

LANCET (2020)

Letter Infectious Diseases

An interactive web-based dashboard to track COVID-19 in real time

Ensheng Dong et al.

LANCET INFECTIOUS DISEASES (2020)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Medicine, General & Internal

A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Medicine, General & Internal

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

Qun Li et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Editorial Material Medicine, General & Internal

Chloroquine and hydroxychloroquine in covid-19

Robin E. Ferner et al.

BMJ-BRITISH MEDICAL JOURNAL (2020)

Article Multidisciplinary Sciences

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Zhenming Jin et al.

NATURE (2020)

Article Medicine, General & Internal

Remdesivir for the Treatment of Covid-19-Final Report

John H. Beigel et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Medicine, General & Internal

A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19

B. Cao et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Biochemistry & Molecular Biology

The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options

Arghavan Asghari et al.

DNA AND CELL BIOLOGY (2020)

Review Medicine, General & Internal

Treatment Options for COVID-19: A Review

Mukarram Jamat Ali et al.

FRONTIERS IN MEDICINE (2020)

Article Chemistry, Medicinal

The SARS-CoV-2 main protease as drug target

Sven Ullrich et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2020)

Article Immunology

Tocilizumab for treatment patients with COVID-19: Recommended medication for novel disease

Hamidreza Samaee et al.

INTERNATIONAL IMMUNOPHARMACOLOGY (2020)

Review Medicine, General & Internal

severe Acute Respiratory Syndrome Coronavirus-2 SARS-CoV-2 An Update

Mahendra Pal et al.

CUREUS JOURNAL OF MEDICAL SCIENCE (2020)

Article Biochemistry & Molecular Biology

Developing degraders: principles and perspectives on design and chemical space

Hannah J. Maple et al.

MEDCHEMCOMM (2019)

Review Virology

Structure, Function, and Evolution of Coronavirus Spike Proteins

Fang Li

ANNUAL REVIEW OF VIROLOGY, VOL 3 (2016)

Article Chemistry, Physical

Building Water Models: A Different Approach

Saeed Izadi et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Computer Science, Interdisciplinary Applications

A mesh evolution algorithm based on the level set method for geometry and topology optimization

Gregoire Allaire et al.

STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION (2013)

Article Chemistry, Medicinal

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

Feixiong Cheng et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Multidisciplinary

Quantifying the chemical beauty of drugs

G. Richard Bickerton et al.

NATURE CHEMISTRY (2012)

Article Chemistry, Physical

Langevin thermostat for rigid body dynamics

Ruslan L. Davidchack et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Medicinal

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space

Marwen Naim et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Medicinal

Molecular properties that influence the oral bioavailability of drug candidates

DF Veber et al.

JOURNAL OF MEDICINAL CHEMISTRY (2002)

Article Chemistry, Medicinal

Simple selection criteria for drug-like chemical matter

I Muegge et al.

JOURNAL OF MEDICINAL CHEMISTRY (2001)