RESEARCH: COVID-19
FOLDING PROJECT #16551 PROFILE

This project uses computer simulations to study how viruses work and find new ways to fight them. Scientists are looking at drugs that can block the activity of important proteins in the SARS-CoV-2 virus, like nsp12 and nsp14. They're testing if these drugs can stop the virus from making copies of itself.

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. 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 16554: Liquid-liquid Phase separation simulation for condensate containing peptide ADMA and RNA 16555: Liquid-liquid Phase separation simulation for condensate containing peptide ARG and RNA 16556: Liquid-liquid Phase separation simulation for condensate containing peptide LYS and RNA 16557: Liquid-liquid Phase separation simulation for condensate containing peptide ADMA and RNA, concentration 3.7 mM 16558: Liquid-liquid Phase separation simulation for condensate containing peptide ARG and RNA, concentration 3.7 mM 16559: Liquid-liquid Phase separation simulation for condensate containing peptide LYS and RNA, concentration 3.7 mM.

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Nonstructural protein 12

A protein essential for viral replication.

Nonstructural protein 12 (nsp12) is a key enzyme in the SARS-CoV-2 virus that replicates its genetic material. This process allows the virus to create copies of itself, spreading infection.

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Nonstructural protein 14

A protein involved in proofreading viral RNA.

Nonstructural protein 14 (nsp14) acts as a quality control mechanism during viral replication. It corrects errors in the copied viral RNA, ensuring accurate replication.

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NTP analog

A molecule that resembles a natural building block of RNA and DNA.

NTP analogs are chemical compounds designed to mimic natural nucleotides. They can interfere with viral replication by disrupting the process of copying RNA or DNA.

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FDA-approved

Drugs that have met safety and efficacy standards set by the FDA.

FDA-approved drugs have undergone rigorous testing and review by the U.S. Food and Drug Administration to ensure they are safe and effective for treating specific conditions.

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Ribirine

An antiviral drug used to treat infections.

Ribirine is a medication that inhibits viral replication. It is used to treat various viral infections, including those caused by RNA viruses.

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Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is an antiviral medication specifically developed for treating severe cases of COVID-19. It interferes with the replication process of the SARS-CoV-2 virus.

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SARS-CoV-2

The virus responsible for COVID-19.

SARS-CoV-2 is a coronavirus that causes the respiratory illness known as COVID-19. It spreads through respiratory droplets released when an infected person coughs, sneezes, or talks.

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RNA

A nucleic acid that carries genetic information.

RNA (ribonucleic acid) is a molecule essential for various cellular processes. It plays a crucial role in protein synthesis and can also serve as genetic material in some viruses.

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ATP

The primary energy currency of cells.

ATP (adenosine triphosphate) is a molecule that stores and releases energy within cells. It powers various cellular processes, including muscle contraction, nerve impulse transmission, and protein synthesis.

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Cordycepin

An antiviral and antifungal compound derived from fungi.

Cordycepin is a natural product with antiviral and antifungal properties. It has been investigated for its potential therapeutic applications.