RESEARCH: COVID-19
FOLDING PROJECT #16513 PROFILE

Scientists are using computer simulations to study how certain COVID-19 proteins interact with existing drugs. They want to find drugs that can block the virus from replicating, potentially leading to new treatments.

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.

---

Nonstructural protein 12

A viral protein involved in RNA replication.

Nonstructural protein 12 (nsp12) is a crucial component of the SARS-CoV-2 virus. It's an enzyme responsible for replicating the virus's RNA genetic material. This process is essential for the virus to spread and cause infection.

---

Nonstructural protein 14

A viral protein involved in RNA proofreading and replication.

Nonstructural protein 14 (nsp14) plays a vital role in the replication process of the SARS-CoV-2 virus. It acts as a 'proofreader,' ensuring that the newly synthesized RNA is accurate. This helps prevent errors that could weaken the virus or make it more susceptible to antiviral drugs.

---

FDA

Food and Drug Administration

The FDA is a federal agency responsible for protecting public health by ensuring the safety, efficacy, and security of human and veterinary drugs, biological products, medical devices, our nation's food supply, cosmetics, and products that emit radiation.

---

NTP

Nucleoside triphosphate

NTPs are the building blocks of DNA and RNA. They are essential for the replication and repair of genetic material.

---

SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2

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

---

Remdesivir

An antiviral medication used to treat COVID-19.

Remdesivir is a drug that interferes with the replication of SARS-CoV-2. It's been shown to reduce the severity and duration of COVID-19 symptoms.

---

Ribavirin

An antiviral medication used to treat various viral infections.

Ribavirin is a broad-spectrum antiviral drug that can be effective against certain RNA viruses, including respiratory syncytial virus (RSV) and hepatitis C.

---

ATP

Adenosine triphosphate

ATP is the primary energy currency of cells. It's used to power various biological processes.