RESEARCH: COVID-19
FOLDING PROJECT #16520 PROFILE

Scientists are using computer simulations to study how COVID-19's proteins interact with antiviral drugs. They want to see if existing medications, like Ribavirin, can block the virus from replicating and potentially be repurposed as effective 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. 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.

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Nonstructural protein 12

A viral protein essential for replication.

Nonstructural protein 12 (nsp12), also known as RNA-dependent RNA polymerase, is a crucial enzyme in coronaviruses like SARS-CoV-2. It plays a vital role in replicating the virus's genetic material (RNA) and spreading the infection.

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Nonstructural protein 14

A viral protein involved in proofreading and replication.

Nonstructural protein 14 (nsp14) is another important protein found in coronaviruses. It acts as a proofreader during RNA replication, correcting errors made by nsp12 to ensure accurate virus reproduction.

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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, causing symptoms like fever, cough, and difficulty breathing.

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NTP analog

A molecule structurally similar to a natural nucleotide triphosphate (NTP) used in RNA synthesis.

NTP analogs are synthetic compounds that resemble the building blocks of RNA. They can interfere with viral replication by acting as false nucleotides, disrupting the process.

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Ribirine

An antiviral drug used to treat hepatitis C.

Ribirine is a medication originally developed to combat hepatitis C. Research suggests it might also have activity against coronaviruses by interfering with their replication.

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Remdesivir

An antiviral drug used to treat COVID-19.

Remdesivir is a nucleotide analog antiviral medication approved for treating severe cases of COVID-19. It works by inhibiting the replication of the SARS-CoV-2 virus.

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Ribavirin Triphosphate

A nucleoside analog used in antiviral therapy.

Ribavirin triphosphate is a synthetic nucleoside analog used as an antiviral agent. It interferes with viral RNA synthesis and has been effective against various viruses, including some coronaviruses.

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Cladribine

An antiviral drug used to treat multiple sclerosis.

Cladribine is a nucleoside analog primarily used to treat relapsing-remitting multiple sclerosis. It has also been investigated for its potential antiviral activity against various viruses.

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Clofarabine

An antiviral drug used to treat acute lymphoblastic leukemia.

Clofarabine is a nucleoside analog used in chemotherapy to treat certain types of leukemia, particularly acute lymphoblastic leukemia. It also shows potential as an antiviral agent.

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Cordycepin

A nucleoside analog with antiviral and antifungal properties.

Cordycepin is a naturally occurring nucleoside analog extracted from certain fungi. It possesses antiviral and antifungal activity and has been studied for its potential therapeutic applications.