RESEARCH: COVID-19
FOLDING PROJECT #16516 PROFILE

This project uses computer simulations to study how SARS-CoV-2 viruses work and find existing drugs that can stop them. They're focusing on proteins nsp12 and nsp14, which are important for copying the virus's genetic material. Researchers are testing if drugs like Ribavirin and others can block these proteins and slow down the virus.

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

A protein crucial for viral replication.

Nonstructural protein 12 (nsp12) is a vital component of the SARS-CoV-2 virus. It's responsible for replicating the virus's genetic material, RNA. Scientists study nsp12 to develop antiviral drugs that can block its activity and stop the virus from spreading.

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Nonstructural protein 14

A protein involved in proofreading viral RNA replication.

Nonstructural protein 14 (nsp14) is another key player in the SARS-CoV-2 virus. It acts like a 'proofreader' during RNA replication, correcting errors to ensure accurate copies of the virus's genetic material are made.

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SARS-CoV-2

The virus responsible for COVID-19.

SARS-CoV-2 is the official name for the novel coronavirus that causes COVID-19. It's a respiratory virus that spreads easily from person to person through droplets in the air.

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NTP

Nucleoside Triphosphates

NTPs are building blocks used by viruses and cells to create DNA and RNA. They provide the energy needed for these processes. Some drugs work by interfering with NTP metabolism.

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FDA-approved

Drugs that have been reviewed and approved for safety and effectiveness by the U.S. Food and Drug Administration.

FDA-approved drugs are those that have undergone rigorous testing and evaluation by the FDA to ensure they are safe and effective for their intended use. This process ensures public health and patient safety.

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Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is an antiviral medication that has shown effectiveness in treating COVID-19. It works by interfering with the virus's ability to replicate its genetic material.

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Ribavirin

An antiviral drug used to treat various viral infections.

Ribavirin is a broad-spectrum antiviral medication used to treat a range of viral infections, including hepatitis C and respiratory syncytial virus (RSV). It works by interfering with viral replication.

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ATP

Adenosine Triphosphate

ATP is the primary energy currency of cells. It powers many essential cellular processes, including muscle contraction, nerve impulse transmission, and protein synthesis.

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Cladribine

An antiviral and immunosuppressant drug.

Cladribine is a synthetic nucleoside analog used to treat certain types of leukemia and multiple sclerosis. It works by interfering with DNA synthesis in rapidly dividing cells.

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Cordycepin

A natural compound with antiviral and antitumor properties.

Cordycepin is a nucleoside analog derived from the Cordyceps fungus. It has shown promising antiviral activity against various viruses, including HIV and influenza.

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Clofarabine

An antineoplastic drug used to treat certain types of cancer.

Clofarabine is a nucleoside analog that is used in the treatment of acute lymphoblastic leukemia (ALL) and other cancers. It interferes with DNA synthesis, preventing cancer cells from dividing.