RESEARCH: COVID-19
FOLDING PROJECT #16517 PROFILE

This project uses computer simulations to study how certain drugs might stop the SARS-CoV-2 virus from replicating. They're looking at how drugs like Ribavirin and Cladribine affect two key viral proteins, nsp12 and nsp14, which are involved in copying the virus's genetic material.

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. 16517: 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.

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Nonstructural protein 12

Viral protein essential for replication.

Nonstructural protein 12 (nsp12) is a key protein found in coronaviruses like SARS-CoV-2. It acts as the main enzyme responsible for replicating the virus's genetic material, making it a crucial target for antiviral drugs.

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Nonstructural protein 14

Viral protein involved in proofreading RNA replication.

Nonstructural protein 14 (nsp14) is another important protein found in coronaviruses. It acts as a proofreader during the virus's replication process, correcting any errors made by nsp12. This ensures accurate viral genetic material production.

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FDA

Food and Drug Administration

The FDA is a federal agency in the United States responsible for ensuring the safety and efficacy of drugs, medical devices, and other products.

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NTP analog

A molecule structurally similar to a natural nucleotide triphosphate (NTP).

NTP analogs are molecules that resemble the building blocks of genetic material. They can be used as antiviral drugs because they interfere with viral replication.

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Ribirine

An antiviral drug used to treat hepatitis B.

Ribirine is a medication that inhibits the replication of viruses like Hepatitis B. It is being investigated for its potential use against coronaviruses.

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SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 is the virus that causes COVID-19. It is a type of coronavirus that spreads easily through respiratory droplets.

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Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is a medication that inhibits the replication of SARS-CoV-2. It has been shown to be effective in treating hospitalized patients with COVID-19.

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ATP

Adenosine Triphosphate

ATP is the primary energy currency of cells, providing energy for various cellular processes.

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Cladribine

An antiviral drug used to treat multiple sclerosis.

Cladribine is a medication that suppresses the immune system. It is being investigated for its potential use against coronaviruses.

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Cordycepin

A nucleoside analog with antiviral and anticancer properties.

Cordycepin is a natural compound derived from mushrooms. It has shown promise as an antiviral and anticancer agent.

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Clofarabine

An antiviral drug used to treat certain types of leukemia.

Clofarabine is a medication that inhibits the growth of cancer cells. It is being investigated for its potential use against coronaviruses.