4.7 Review

Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery

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Exploring Phytochemicals of Traditional Medicinal Plants Exhibiting Inhibitory Activity Against Main Protease, Spike Glycoprotein, RNA-dependent RNA Polymerase and Non-Structural Proteins of SARS-CoV-2 Through Virtual Screening

Saranya Nallusamy et al.

Summary: The study explores the potential of phytochemicals and antiviral molecules from various plant species in inhibiting SARS-CoV-2, highlighting the need for discovering novel drugs. Some plant compounds, such as cyanin from ginger, showed promising inhibitory activity against main proteases of SARS-CoV-2, SARS-CoV, and MERS-CoV. Identified herbal plants, including Mangifera indica and Vitex negundo, were suggested as potential sources of phytochemicals for combating COVID-19. Overall, the study emphasizes the importance of herbal medicines in drug discovery and development for treating viral diseases.

FRONTIERS IN PHARMACOLOGY (2021)

Article Pharmacology & Pharmacy

Remdesivir Strongly Binds to RNA-Dependent RNA Polymerase, Membrane Protein, and Main Protease of SARS-CoV-2: Indication From Molecular Modeling and Simulations

Faez Iqbal Khan et al.

Summary: The global efforts are underway to find therapeutics against SARS-CoV-2, with remdesivir identified as more effective in treatment and potentially inhibiting multiple targets to demonstrate antiviral activity.

FRONTIERS IN PHARMACOLOGY (2021)

Article Biochemistry & Molecular Biology

Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp

Mitul Srivastava et al.

Summary: The study explores the inhibitory mechanism of Remdesivir (RDV) derivatives, particularly RDV triphosphate (RTP), on SARS-CoV-2 RdRp activity. RTP was found to interact with key residues and destabilize the catalytic site, potentially leading to the discovery of potent inhibitors against RNA viruses.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

Review Biochemistry & Molecular Biology

Natural Products, Alone or in Combination with FDA-Approved Drugs, to Treat COVID-19 and Lung Cancer

Liyan Yang et al.

Summary: The COVID-19 pandemic and lung cancer have posed serious threats to global public health, and recent studies have shown that natural products may serve as effective treatments for lung diseases, particularly in combination therapy and with the assistance of nanotechnology.

BIOMEDICINES (2021)

Article Biochemistry & Molecular Biology

Transcriptomic signatures and repurposing drugs for COVID-19 patients: findings of bioinformatics analyses

Guobing Li et al.

Summary: The study systematically evaluated the impact of SARS-CoV-2 on gene expression in COVID-19 patients, revealing potential mechanisms of COVID-19-induced pneumonia and suggesting anti-inflammatory therapies as promising regimens. Drug repurposing analysis identified potential candidates such as etanercept and baclofen for COVID-19 treatment, while traditional drugs like chloroquine, hydroxychloroquine, and interferons showed limited efficacy. Further clinical trials are needed to validate these findings and search for effective treatments for the current crisis.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Dissecting nucleotide selectivity in viral RNA polymerases

Chunhong Long et al.

Summary: This article reviews the structural biology and computational clues of representative single-subunit viral polymerases related to the SARS-CoV-2 RdRp. It compares the nucleotide selectivity among different viruses' RdRps and explores the structural and biochemical characteristics of SARS-CoV-2 RdRp. Additionally, the article discusses computational findings on phage T7 RNA polymerase and human mitochondria RNAP, highlighting the importance of proofreading strategies in synthesizing large viral genomes.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning

Gaspar P. Pinto et al.

Summary: The study utilized virtual screening with CaverDock to identify potential drugs for the spike glycoprotein of the new coronavirus, providing new treatment options using approved drugs worldwide. By using molecular dynamics simulations and statistical methods, top candidate drugs were selected, revealing new applications for globally approved drugs.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Chemistry, Medicinal

dIdentification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

Maria Kuzikov et al.

Summary: Compound repurposing is a crucial strategy for identifying effective treatments against SARS-CoV-2 infection and COVID-19. The SARS-CoV-2 main protease, 3CL-Pro, is a promising drug target due to its central role in viral replication. This study identified multiple compounds with potential inhibitory effects on 3CL-Pro, including the compound myricetin which was found to covalently bind to the enzyme and inhibit its activity.

ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE (2021)

Article Biochemistry & Molecular Biology

Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises

Natesh Singh et al.

Summary: New therapies are urgently needed to prevent SARS-CoV-2 infection and improve outcomes for COVID-19 patients. While several vaccines have been developed, there is ongoing research on other types of therapeutic agents. This article introduces databases and online tools for discovering anti-SARS-CoV-2 compounds and highlights the lack of discussion and planning in academic research during the crisis.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Chemistry, Physical

1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication

Lu Zhang et al.

Summary: Remdesivir effectively inhibits SARS-CoV-2 viral RNA replication by interfering with nucleotide addition and proofreading mechanisms, reducing the likelihood of viral replication. The molecular dynamics simulations provide insights into the inhibitory mechanisms of Remdesivir, guiding potential rational designs for new COVID-19 treatments targeting viral replication.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (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 Biochemistry & Molecular Biology

Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics

Rick Oerlemans et al.

Summary: The rapid growth of COVID-19 cases leads to increasing deaths and economic paralysis. Drug repurposing is a potential short-term solution, while vaccination is a middle-term solution. Research suggests that the HCV drug boceprevir may be repurposed for COVID-19 and other coronaviral infections.

RSC MEDICINAL CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity

Kemel Arafet et al.

Summary: By simulating the inhibition process of SARS-CoV-2 main protease, researchers have identified two potential drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor. These findings suggest promising candidates for drug development.

CHEMICAL SCIENCE (2021)

Article Multidisciplinary Sciences

Identification of SARS-CoV-2 inhibitors using lung and colonic organoids

Yuling Han et al.

Summary: Researchers have developed lung and colonic organoid models using human pluripotent stem cells, which demonstrate susceptibility to SARS-CoV-2 infection. These models are valuable for studying the infection of the virus and screening drugs, with potential therapeutic implications for COVID-19.

NATURE (2021)

Article Chemistry, Medicinal

The Exploration of Chirality for Improved Druggability within the Human Kinome

Debasmita Saha et al.

JOURNAL OF MEDICINAL CHEMISTRY (2020)

Review Pharmacology & Pharmacy

Favipiravir, an anti-influenza drug against life-threatening RNA virus infections

Kimiyasu Shiraki et al.

PHARMACOLOGY & THERAPEUTICS (2020)

Article Multidisciplinary Sciences

Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection

Emmie de Wit et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

Qihui Wang et al.

Article Multidisciplinary Sciences

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

Yan Gao et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Structure of replicating SARS-CoV-2 polymerase

Hauke S. Hillen et al.

NATURE (2020)

Article Multidisciplinary Sciences

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

Zhenming Jin et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur

Zhenming Jin et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Engineering, Multidisciplinary

Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study

Qingxian Cai et al.

ENGINEERING (2020)

Article Medicine, General & Internal

Remdesivir for 5 or 10 Days in Patients with Severe Covid-19

Jason D. Goldman et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Chemistry, Multidisciplinary

Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients

Hai-xia Su et al.

ACTA PHARMACOLOGICA SINICA (2020)

Article Microbiology

Suramin Inhibits SARS-CoV-2 Infection in Cell Culture by Interfering with Early Steps of the Replication Cycle

Clarisse Salgado-Benvindo et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2020)

Review Chemistry, Medicinal

The development of Coronavirus 3C-Like protease (3CLpro) inhibitors from 2010 to 2020

Yuzhi Liu et al.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike

Joao Trigueiro-Louro et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Chemistry, Medicinal

COVID-19: Drug Targets and Potential Treatments

Carmen Gil et al.

JOURNAL OF MEDICINAL CHEMISTRY (2020)

Article Chemistry, Physical

Michael Acceptors Tuned by the Pivotal Aromaticity of Histidine to Block COVID-19 Activity

Albert Poater

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

Article Chemistry, Multidisciplinary

Catalytic Asymmetric Synthesis of the anti-COVID-19 Drug Remdesivir

Mo Wang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Editorial Material Microbiology

Favipiravir and the Need for Early Ambulatory Treatment of SARS-CoV-2 Infection (COVID-19)

Peter A. McCullough

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2020)

Review Pharmacology & Pharmacy

Candidate drugs against SARS-CoV-2 and COVID-19

Dwight L. McKee et al.

PHARMACOLOGICAL RESEARCH (2020)

Article Biochemistry & Molecular Biology

Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2

Theresa Klemm et al.

EMBO JOURNAL (2020)

Review Oncology

Repurposing anticancer drugs for the management of COVID-19

Khalid El Bairi et al.

EUROPEAN JOURNAL OF CANCER (2020)

Article Chemistry, Medicinal

Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment

Victoria C. Yan et al.

ACS MEDICINAL CHEMISTRY LETTERS (2020)

Article Multidisciplinary Sciences

Structural basis of RNA cap modification by SARS-CoV-2

Thiruselvam Viswanathan et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin

Petra Krafcikova et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

Daniel W. Kneller et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

Tai-Sung Lee et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Review Pharmacology & Pharmacy

The strategies and techniques of drug discovery from natural products

Li Zhang et al.

PHARMACOLOGY & THERAPEUTICS (2020)

Article Multidisciplinary Sciences

Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein

Christine Toelzer et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals

Daniel W. Kneller et al.

STRUCTURE (2020)

Article Chemistry, Medicinal

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2

Mohammad M. Ghahremanpour et al.

ACS MEDICINAL CHEMISTRY LETTERS (2020)

Article Multidisciplinary Sciences

Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease

Lifeng Fu et al.

NATURE COMMUNICATIONS (2020)

Editorial Material Multidisciplinary Sciences

Many small steps towards a COVID-19 drug

Daniel A. Erlanson

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication

Wayne Vuong et al.

NATURE COMMUNICATIONS (2020)

Review Pharmacology & Pharmacy

Current Prevention of COVID-19: Natural Products and Herbal Medicine

Junqing Huang et al.

FRONTIERS IN PHARMACOLOGY (2020)

Article Genetics & Heredity

Underlying Mechanisms and Candidate Drugs for COVID-19 Based on the Connectivity Map Database

Zhonglin Li et al.

FRONTIERS IN GENETICS (2020)

Review Biochemistry & Molecular Biology

Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge

Francesca Picarazzi et al.

MOLECULES (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

Lizhou Zhang et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Chinese herbal compounds against SARS-CoV-2: Puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor

Boyu Pan et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Biochemistry & Molecular Biology

Structural insight into the recognition of S-adenosyl-L-homocysteine and sinefungin in SARS-CoV-2 Nsp16/Nsp10 RNA cap 2′-O-Methyltransferase

Panupong Mahalapbutr et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Chemistry, Medicinal

Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors

Chunlong Ma et al.

ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE (2020)

Article Biochemistry & Molecular Biology

An Overview of the Crystallized Structures of the SARS-CoV-2

Mihaela Ileana Ionescu

PROTEIN JOURNAL (2020)

Review Chemistry, Multidisciplinary

GS-5734: a potentially approved drug by FDA against SARS-Cov-2

Zhonglei Wang et al.

NEW JOURNAL OF CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

Mutations in the SARS-CoV-2 spike RBD are responsible for stronger ACE2 binding and poor anti-SARS-CoV mAbs cross-neutralization

Masaud Shah et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Review Chemistry, Medicinal

Strategies to diversify natural products for drug discovery

Gang Li et al.

MEDICINAL RESEARCH REVIEWS (2018)

Article Multidisciplinary Sciences

Recombinant RNA-Dependent RNA Polymerase Complex of Ebola Virus

Egor P. Tchesnokov et al.

SCIENTIFIC REPORTS (2018)

Article Chemistry, Medicinal

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

Zoe Cournia et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

Article Cell Biology

Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses

Timothy P. Sheahan et al.

SCIENCE TRANSLATIONAL MEDICINE (2017)

Article Integrative & Complementary Medicine

Differences in anti-inflammatory effects between two specifications of Scutellariae Radix in LPS-induced macrophages in vitro

Chen Qian-Yu et al.

CHINESE JOURNAL OF NATURAL MEDICINES (2017)

Article Medicine, General & Internal

Late Ebola virus relapse causing meningoencephalitis: a case report

Michael Jacobs et al.

LANCET (2016)

Article Multidisciplinary Sciences

Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys

Travis K. Warren et al.

NATURE (2016)

Review Biotechnology & Applied Microbiology

The re-emergence of natural products for drug discovery in the genomics era

Alan L. Harvey et al.

NATURE REVIEWS DRUG DISCOVERY (2015)

Article Chemistry, Organic

Practical synthesis of 1′-substituted Tubercidin C-nucleoside analogs

Sammy E. Metobo et al.

TETRAHEDRON LETTERS (2012)