RESEARCH: COVID-19
FOLDING PROJECT #16553 PROFILE

Scientists are using computer simulations to study how COVID-19's proteins work and how existing drugs might stop them. They're looking at proteins that help the virus copy its genetic material and see if common antiviral drugs can block this process.

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. 16518: 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. 16519: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and GTP. 16520: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and ATP. 16521: Nonstructural protein 12 (nsp12-RdRp & nsp7 & nsp8) of the SARS-CoV-2 in complex with the RNA template, a short nascent RNA, and GTP. 16550: Liquid-liquid Phase separation simulation for condensate and added peptide ADMA 16551: Liquid-liquid Phase separation simulation for condensate and added peptide ADMA 16552: Liquid-liquid Phase separation simulation for condensate and added peptide ARG 16553: Liquid-liquid Phase separation simulation for condensate and added peptide LYS.

Nonstructural protein 12

A viral protein essential for RNA replication.

Nonstructural protein 12 (nsp12) is a key enzyme found in coronaviruses like SARS-CoV-2. It's responsible for making copies of the virus's RNA genetic material, which is crucial for its ability to spread and infect cells.

Nonstructural protein 14

A viral protein involved in proofreading RNA replication.

Nonstructural protein 14 (nsp14) acts like a quality control mechanism during RNA replication in coronaviruses. It removes incorrect nucleotides from the newly synthesized RNA strands, ensuring the genetic information is accurate.

FDA-approved

Drugs cleared by the U.S. Food and Drug Administration for medical use.

FDA-approved drugs have gone through rigorous testing and evaluation by the U.S. Food and Drug Administration to ensure they are safe and effective for treating specific diseases or conditions.

NTP analog

Molecules that mimic natural nucleoside triphosphates (NTPs) used in viral replication.

NTP analogs are a class of antiviral drugs that interfere with the ability of viruses to replicate their genetic material. They resemble the building blocks of viral RNA and DNA, but they disrupt the replication process.

Ribavirin

An antiviral drug used to treat certain viral infections.

Ribavirin is a broad-spectrum antiviral medication used to combat various viral diseases, including hepatitis C and respiratory syncytial virus (RSV). It interferes with viral replication by disrupting the synthesis of RNA.

Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is an experimental antiviral medication specifically developed to target and inhibit the replication of SARS-CoV-2, the virus responsible for COVID-19. It works by interfering with the virus's ability to create new genetic material.

SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. It's a type of coronavirus that primarily affects the respiratory system and can cause a range of symptoms from mild to severe.