RESEARCH: COVID-19
FOLDING PROJECT #16518 PROFILE

Researchers are using computer simulations to study how drugs might stop the SARS-CoV-2 virus from replicating. They're focusing on two viral proteins, nsp14 and nsp12, which are involved in copying the virus's genetic material. The project tests existing FDA-approved drugs like Ribavirin and others to see if they can interfere with these proteins and prevent the virus from spreading.

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. 16517: 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.

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Nonstructural protein 12 (nsp12)

Viral enzyme responsible for RNA replication.

Nonstructural protein 12 (nsp12) is a crucial enzyme found in SARS-CoV-2, the virus that causes COVID-19. It plays a vital role in replicating the virus's genetic material (RNA). Scientists are investigating ways to target nsp12 with antiviral drugs to stop the virus from spreading.

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Nonstructural protein 14 (nsp14)

Viral enzyme involved in RNA proofreading.

Nonstructural protein 14 (nsp14) is another important enzyme found in SARS-CoV-2. It acts like a quality control mechanism, checking and correcting errors made during the replication of the virus's genetic material. This helps ensure accurate viral replication.

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NTP analog

A molecule that resembles a natural nucleoside triphosphate (NTP) used in viral RNA synthesis.

NTP analogs are synthetic molecules designed to mimic the structure of natural building blocks used by viruses to create their genetic material. They can interfere with viral replication by disrupting the process.

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Ribavirin

An antiviral drug used to treat viral infections.

Ribavirin is an antiviral medication approved for treating certain viral infections like hepatitis C and respiratory syncytial virus (RSV). It works by interfering with the replication of the virus.

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Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is an antiviral medication specifically developed to treat COVID-19. It inhibits the activity of the SARS-CoV-2 virus by interfering with its ability to replicate its genetic material.

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SARS-CoV-2

The virus that causes COVID-19.

SARS-CoV-2 stands for Severe Acute Respiratory Syndrome Coronavirus 2. It is a type of coronavirus responsible for causing the disease known as COVID-19. This highly contagious virus spreads primarily through respiratory droplets and can lead to a range of symptoms from mild to severe.

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RNA

A type of genetic material.

RNA (Ribonucleic Acid) is a single-stranded molecule that carries genetic information within cells. It plays a crucial role in protein synthesis and various other cellular processes.

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ATP

Adenosine Triphosphate; the primary energy currency of cells.

ATP (Adenosine Triphosphate) is the main energy source used by cells to power various functions. It's like the 'cellular fuel' that drives processes such as muscle contraction, nerve impulse transmission, and protein synthesis.