References for DNA/RNA interacting proteins for SARS

News Medical Life Sciences

Antiviral inhibitor DDX42 shows broad activity against Chikungunya, HIV and SARS-CoV-2

By Dr. Tomislav Meštrović, MD, Ph.D.Oct 29 2020

By exploiting type 1 interferon’s ability to foster an antagonistic cellular environment for viral replication, a research group from France pinpointed DEAD-box RNA helicase DDX42 as an intrinsic inhibitor of HIV, but also other pathogenic viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Chikungunya virus. This compelling study is currently available on the bioRxiv* preprint server.

During the last 20 years, a myriad of cellular proteins with various functions have been identified as capable of hindering different steps in the HIV life cycle. This effect is particularly strong when human cells are predisposed to interferon.

As expected, the quest was accelerated with the introduction of genome-wide CRISPR/Cas9 knock-out genetic screens, which are touted as extremely steadfast approaches to unveil new regulators of viral infections.

Many RNA helicases from the DEAD box family (found in almost all organisms where they play pivotal roles in RNA metabolism) are well-known to control the HIV life cycle. Some notable examples are DDX3, DDX6, and DDX17; however, the impact of DDX42 on HIV replication had never been studied.

This specific helicase grabbed the attention of a group of scientists from the Université de Montpellier and Montpellier GenomiX in France. They aimed to appraise the impact of endogenous DDX42 on HIV-1 infection, as well as the consequences of enzyme overexpression.



A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor

Boris B, Antoine R, de Gracia Francisco G, Joe M, Marine T, Ana Luiza CV, Valérie C, Eric B, Laurence B, Nathalie G, Wassila D, Mary A, Hugues P, Stéphanie R, Olivier M, Caroline G

Preprint from bioRxiv, 28 Oct 2020. DOI: 10.1101/2020.10.28.359356 PPR: PPR231805


Genome-wide CRISPR/Cas9 knock-out genetic screens are powerful approaches to unravel new regulators of viral infections. Here, we took advantage of the ability of interferon (IFN) to restrict HIV-1 infection, in order to create an environment hostile to replication and reveal new inhibitors through a CRISPR screen. This approach led to the identification of the RNA helicase DDX42 as an intrinsic inhibitor of HIV-1. Depletion of endogenous DDX42 increased HIV-1 DNA accumulation and infection in cell lines and primary cells, irrespectively of IFN treatment. DDX42 overexpression inhibited HIV-1, whereas a dominant-negative mutant of DDX42 increased infection. Importantly, DDX42 impacted retrotransposition of long interspersed elements-1 (LINE-1), infection with other retroviruses and positive-strand RNA viruses, including Chikungunya virus (CHIKV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, DDX42 did not inhibit infection with negative-strand RNA viruses such as influenza A virus (IAV), arguing against a general, unspecific effect on target cells. Proximity ligation assays showed DDX42 in the vicinity of viral elements during infection, and RNA immunoprecipitation confirmed DDX42 interaction with LINE-1 RNAs. This strongly suggested a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Taken together, our results identify DDX42 as a new, broadly active intrinsic antiviral inhibitor.



REVIEW ARTICLE: Front. Microbiol., 14 July 2020 |

Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review

Gi Uk Jeong1†, Hanra Song2†, Gun Young Yoon1, Doyoun Kim2* and Young-Chan Kwon1*

The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies.



Drugs. 2020 May 25 : 1–6. doi: 10.1007/s40265-020-01321-z [Epub ahead of print]

The G-Quadruplex/Helicase World as a Potential Antiviral Approach Against COVID-19

Nadia Panera,1 Alberto Eugenio Tozzi,2 and Anna Alisicorresponding author1


G-Quadruplexes (G4s) are non-canonical secondary structures formed within guanine-rich regions of DNA or RNA. G4 sequences/structures have been detected in human and in viral genomes, including Coronaviruses Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and SARS-CoV-2. Here, we outline the existing evidence indicating that G4 ligands and inhibitors of SARS-CoV-2 helicase may exert some antiviral activity reducing viral replication and can represent a potential therapeutic approach to tackle the COVID-19 pandemic due to SARS-CoV-2 infection. We also discuss how repositioning of FDA-approved drugs against helicase activity of other viruses, could represent a rapid strategy to limit deaths associated with COVID-19 pandemic.



Version 1. bioRxiv. Preprint. 2020 Aug 10.doi: 10.1101/2020.08.09.243246

Discovery of COVID-19 Inhibitors Targeting the SARS-CoV2 Nsp13 Helicase

Mark Andrew White,1,2,* Wei Lin,3,4 and Xiaodong Cheng3,4,*


The raging COVID-19 pandemic caused by SARS-CoV2 has infected millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV2 helicase (Nsp13), which is critical for viral replication and the most conserved non-structural protein within the coronavirus family. Using homology modeling and molecular dynamics approaches, we generated structural models of the SARS-CoV2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ~970,000 chemical compounds against the ATP binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.



Aging (Albany NY). 2021 Jan 11;12. doi: 10.18632/aging.202463. Online ahead of print.

Shorter telomere lengths in patients with severe COVID-19 disease

Raul Sanchez-Vazquez 1, Ana Guío-Carrión 1, Antonio Zapatero-Gaviria 2, Paula Martínez 1, Maria A Blasco 1


The incidence of severe manifestations of COVID-19 increases with age with older patients showing the highest mortality, suggesting that molecular pathways underlying aging contribute to the severity of COVID-19. One mechanism of aging is the progressive shortening of telomeres, which are protective structures at chromosome ends. Critically short telomeres impair the regenerative capacity of tissues and trigger loss of tissue homeostasis and disease. The SARS-CoV-2 virus infects many different cell types, forcing cell turn-over and regeneration to maintain tissue homeostasis. We hypothesize that presence of short telomeres in older patients limits the tissue response to SARS-CoV-2 infection. We measure telomere length in peripheral blood lymphocytes COVID-19 patients with ages between 29 and 85 years-old. We find that shorter telomeres are associated to increased severity of the disease. Individuals within the lower percentiles of telomere length and higher percentiles of short telomeres have higher risk of developing severe COVID-19 pathologies.


Comput Biol Chem. 2005 Jun; 29(3): 212–219.

Structural analysis of inhibition mechanisms of Aurintricarboxylic Acid on SARS-CoV polymerase and other proteins

YeeLeng Yap,a XueWu Zhang,b Anton Andonov,c and RunTao Hec,*


We recently published experimental results that indicated Aurintricarboxylic Acid (ATA) could selectively inhibit SARS-CoV replication inside host cells by greater than 1000 times. This inhibition suggested that ATA could be developed as potent anti-viral drug. Here, to extend our experimental observation, we have incorporated protein structural studies (with positive/negative controls) to investigate the potential binding modes/sites of ATA onto RNA-dependent RNA polymerase (RdRp) from SARS-CoV and other pathogenic positive-strand RNA-viruses, as well as other proteins in SARS-CoV based on the fact that ATA binds to Ca2+-activated neutral protease (m-calpain), the protein tyrosine phosphatase (PTP) and HIV integrase which have existing crystal structures. Eight regions with homologous 3D-conformation were derived for 10 proteins of interest. One of the region, Rbinding (754–766 in SARS-CoV’s RdRp), located in the palm sub-domain mainly constituted of anti-parallel β-strand-turn-β-strand hairpin structures that covers two of the three RdRp catalytic sites (Asp 760, Asp761), was also predicted by molecular docking method (based on free energy of binding ΔG) to be important binding motif recognized by ATA. The existence of this strictly conserved region that incorporated catalytic residues, coupled with the homologous ATA binding pockets and their consistent ΔG values, suggested strongly ATA may be involved in an analogous inhibition mechanism of SARS-COV’s RdRp in concomitant to the case in m-calpain, PTP and HIV integrase.




J Med Microbiol. 2020 Jun;69(6):864-873. doi: 10.1099/jmm.0.001203. Epub 2020 May 29.

Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2

Rudramani Pokhrel 1, Prem Chapagain 2 1, Jessica Siltberg-Liberles 2 3


Introduction. The emergence of SARS-CoV-2 has taken humanity off guard. Following an outbreak of SARS-CoV in 2002, and MERS-CoV about 10 years later, SARS-CoV-2 is the third coronavirus in less than 20 years to cross the species barrier and start spreading by human-to-human transmission. It is the most infectious of the three, currently causing the COVID-19 pandemic. No treatment has been approved for COVID-19. We previously proposed targets that can serve as binding sites for antiviral drugs for multiple coronaviruses, and here we set out to find current drugs that can be repurposed as COVID-19 therapeutics.Aim. To identify drugs against COVID-19, we performed an in silico virtual screen with the US Food and Drug Administration (FDA)-approved drugs targeting the RNA-dependent RNA polymerase (RdRP), a critical enzyme for coronavirus replication.Methodology. Initially, no RdRP structure of SARS-CoV-2 was available. We performed basic sequence and structural analysis to determine if RdRP from SARS-CoV was a suitable replacement. We performed molecular dynamics simulations to generate multiple starting conformations that were used for the in silico virtual screen. During this work, a structure of RdRP from SARS-CoV-2 became available and was also included in the in silico virtual screen.Results. The virtual screen identified several drugs predicted to bind in the conserved RNA tunnel of RdRP, where many of the proposed targets were located. Among these candidates, quinupristin is particularly interesting because it is expected to bind across the RNA tunnel, blocking access from both sides and suggesting that it has the potential to arrest viral replication by preventing viral RNA synthesis. Quinupristin is an antibiotic that has been in clinical use for two decades and is known to cause relatively minor side effects.Conclusion. Quinupristin represents a potential anti-SARS-CoV-2 therapeutic. At present, we have no evidence that this drug is effective against SARS-CoV-2 but expect that the biomedical community will expeditiously follow up on our in silico findings.



Front Chem. 2020 Oct 30;8:584894. doi: 10.3389/fchem.2020.584894. eCollection 2020.

Identification of a New Potential SARS-COV-2 RNA-Dependent RNA Polymerase Inhibitor via Combining Fragment-Based Drug Design, Docking, Molecular Dynamics, and MM-PBSA Calculations

Mahmoud A El Hassab 1, Aly A Shoun 2, Sara T Al-Rashood 3, Tarfah Al-Warhi 4, Wagdy M Eldehna 5


The world has recently been struck by the SARS-Cov-2 pandemic, a situation that people have never before experienced. Infections are increasing without reaching a peak. The WHO has reported more than 25 million infections and nearly 857,766 confirmed deaths. Safety measures are insufficient and there are still no approved drugs for the COVID-19 disease. Thus, it is an urgent necessity to develop a specific inhibitor for COVID-19. One of the most attractive targets in the virus life cycle is the polymerase enzyme responsible for the replication of the virus genome. Here, we describe our Structure-Based Drug Design (SBDD) protocol for designing of a new potential inhibitor for SARS-COV-2 RNA-dependent RNA Polymerase. Firstly, the crystal structure of the enzyme was retrieved from the protein data bank PDB ID (7bv2). Then, Fragment-Based Drug Design (FBDD) strategy was implemented using Discovery Studio 2016. The five best generated fragments were linked together using suitable carbon linkers to yield compound MAW-22. Thereafter, the strength of the binds between compound MAW-22 and the SARS-COV-2 RNA-dependent RNA Polymerase was predicted by docking strategy using docking software. MAW-22 achieved a high docking score, even more so than the score achieved by Remdesivir, indicating very strong binding between MAW-22 and its target. Finally, three molecular dynamic simulation experiments were performed for 150 ns to validate our concept of design. The three experiments revealed that MAW-22 has a great potentiality to inhibit the SARS-COV-2 RNA-dependent RNA Polymerase compared to Remdesivir. Also, it is thought that this study has proven SBDD to be the most suitable avenue for future drug development for the COVID-19 infection.