RESEARCH: COVID-19
FOLDING PROJECT #16514 PROFILE

This project uses computer simulations to study how certain drugs might block the replication of the SARS-CoV-2 virus. The focus is on proteins called nsp12, nsp14, and their interactions with viral RNA and potential drug molecules. Researchers are exploring if existing FDA-approved drugs could be repurposed as treatments for COVID-19.

Note: This TLDR is a simplication and may not be 100% accurate.

This series of CPU projects to simulation the Nonstructural protein 12 (nsp12) and Nonstructural protein 14 (nsp14) complexes.

We will screen existing FDA-approved NTP analog drugs (e.g.

Ribirine).

We aim to repurpose drugs that can inhibit SARS-CoV-2 replication 16500: This project contains simulations of nsp14-ExoN and nsp10 of the SARS-CoV-2 in complex with a short nascent RNA.

Nsp14 is in charge of proofeading of the replication SARS-CoV-2 by removing mis-incoproated nucleotides including drugs, so that it is important that NTP analog drugs (e.g.

Remdesivir) added to the nascent RNA do not get cleaved by nsp14. 16501: This project contains simulations of nsp12, nsp7, and nsp8 of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and Ribavirin Triphosphate in the active site.

We aim to examine if the drug Ribirine can inhibite the viral replicaiton of SARS-CoV-2. 16502: This project contains simulations of nsp12, nsp7 and nsp8 of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA with Ribavirin as the 3’ terminal nucleotide. 16503: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA and Cladribine Triphosphate in the active site. 16504: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA and Clofarabine Triphosphate in the active site. 16505: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA and Cordycepin Triphosphate in the active site.

16506: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA(Cladribine at 3'-terminal), and ATP in the active site.

16507: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA(Clofarabine at 3'-terminal), and ATP in the active site. 16508: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA(Cordycepin at 3'-terminal), and ATP in the active site. 16509: Nonstructural protein 14 and 10 (nsp14-ExoN & nsp 10) of the SARS-CoV-2 in complex with a short nascent RNA containing Cordycepin at 3'-terminal. 16510: Nonstructural protein 14 and 10 (nsp14-ExoN & nsp 10) of the SARS-CoV-2 in complex with a short nascent RNA containing Clofarabine at 3'-terminal. 16513: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and ATP in the active site. 16514: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and GTP in the active site. 16515: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and GTP in the active site with nonbonded dummy ion model. 16516: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and ATP in the active site with nonbonded dummy ion model.

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Nonstructural protein 12

Protein essential for viral RNA replication.

Nonstructural protein 12 (nsp12), also known as RdRp, is a vital enzyme in the SARS-CoV-2 virus. It helps replicate the virus's RNA genome by adding nucleotides to the growing RNA chain.

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Nonstructural protein 14

Protein involved in proofreading viral RNA replication.

Nonstructural protein 14 (nsp14) is another crucial enzyme in the SARS-CoV-2 virus. It acts as a proofreader during RNA replication, ensuring accuracy by removing incorrectly incorporated nucleotides.

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NTP analog

Molecule resembling a natural nucleoside triphosphate, interfering with viral replication.

NTP analogs are drugs that mimic the structure of nucleotides used by viruses to build their RNA. They can disrupt viral replication by interfering with the enzymes responsible for copying the viral genome.

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FDA-approved

Approved for use by the US Food and Drug Administration.

FDA-approved drugs have undergone rigorous testing and review by the US Food and Drug Administration to ensure their safety and effectiveness for treating specific medical conditions.

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Remdesivir

An antiviral medication used to treat COVID-19.

Remdesivir is an antiviral drug that has been shown to be effective in treating COVID-19. It works by interfering with the replication of the SARS-CoV-2 virus.

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Ribavirin

An antiviral medication used to treat respiratory viral infections.

Ribavirin is a broad-spectrum antiviral drug that has been used to treat a range of viral infections, including hepatitis C and respiratory syncytial virus (RSV).

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SARS-CoV-2

The virus that causes COVID-19.

SARS-CoV-2 is a novel coronavirus responsible for the global pandemic known as COVID-19. It primarily affects the respiratory system and can lead to severe illness.

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RdRp

RNA-dependent RNA polymerase.

RdRp is the enzyme responsible for replicating the RNA genome of certain viruses, including SARS-CoV-2.