RNA dependent RNA polymerase (RdRp) as a drug target for SARS-CoV2

The flaviviral RNA-dependent RNA polymerase (RdRp) is an attractive drug target. To discover new inhibitors of dengue virus RdRp, the authors have developed a fluorescence-based alkaline phosphatase–coupled polymerase assay (FAPA) for high-throughput screening (HTS). A modified nucleotide analogue (2′-[2-benzothiazoyl]-6′-hydroxybenzothiazole) conjugated adenosine triphosphate (BBT-ATP) and 3′UTR-U30 RNA were used as substrates. After the polymerase reaction, treatment with alkaline phosphatase liberates the BBT fluorophore from the polymerase reaction by-product, BBTPPi, which can be detected at excitation and emission wavelengths of 422 and 566 nm, respectively. The assay was evaluated by examining the time dependency, assay reagent effects, reaction kinetics, and signal stability and was validated with 3′dATP and an adenosine-nucleotide triphosphate inhibitor, giving IC50 values of 0.13 µM and 0.01 µM, respectively. A pilot screen of a diverse compound library of 40,572 compounds at 20 µM demonstrated good performance with an average Z factor of 0.81. The versatility and robustness of FAPA were evaluated with another substrate system, BBT-GTP paired with 3′UTR-C30 RNA. The FAPA method presented here can be readily adapted for other nucleotide-dependent enzymes that generate PPi.

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In Silico Discovery of Natural Products Against Dengue RNA-Dependent RNA Polymerase Drug Target

Chem-Bio Informatics Journal ◽

10.1273/cbij.21.11 ◽

2021 ◽

Vol 21 (0) ◽

pp. 11-27

Author(s):

Junie B. Billones ◽

Nina Abigail B. Clavio

Keyword(s):

Natural Products ◽

Rna Polymerase ◽

In Silico ◽

Drug Target ◽

Rna Dependent Rna Polymerase

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Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target

10.1101/2020.03.16.993386 ◽

2020 ◽

Cited By ~ 19

Author(s):

Yan Gao ◽

Liming Yan ◽

Yucen Huang ◽

Fengjiang Liu ◽

Yao Zhao ◽

...

Keyword(s):

Rna Polymerase ◽

Drug Target ◽

Antiviral Drug ◽

Central Component ◽

Rna Dependent Rna Polymerase ◽

Transcription Machinery ◽

Global Pandemic ◽

Novel Coronavirus ◽

Key Residues ◽

Insight Into

AbstractA novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified β-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp.One Sentence SummaryStructure of 2019-nCov RNA polymerase.

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STRUKTUR PROTEOMIK VIRUS DENGUE DAN MANFAATNYA SEBAGAI TARGET ANTIVIRUS

Majalah Kedokteran Andalas ◽

10.22338/mka.v37.i2.p136-142.2014 ◽

2015 ◽

Vol 37 (2) ◽

pp. 136

Author(s):

Novia Rachmayanti

Keyword(s):

Protein Structure ◽

Rna Polymerase ◽

Drug Target ◽

Rna Dependent Rna Polymerase ◽

Methyl Transferase ◽

Ns3 Protease

AbstrakVirus dengue (DENV) telah menyebabkan sekitar 50 juta kasus infeksi demam berdarah setiap tahunnya, akan tetapi hingga saat ini belum terdapat vaksin maupun antivirus yang mampu mencegah atau mengobati penyakit tersebut. Selama pengembangan vaksin dan antivirus, diperoleh berbagai informasi tentang struktur protein DENV yang dapat dimanfaatkan sebagai target obat. Makalah membahas tentang struktur proteomik pada DENV, yaitu glikoprotein pada envelope, NS3 protease, NS3 helikase, NS5 metiltransferase, dan NS5 RNA-dependent RNA polimerase.AbstractDengue virus (DENV) has caused over 50 millions infection every year. However, to date neither vaccine nor medicine could be used to prevent or cure the illness. During researches in finding the vaccine or antiviral for DENV, information on DENV protein structure has been obtained which is potentially used as drug target. This paper disscuss DENV proteomic structure that consist of envelope glicoprotein, NS3 protease, NS3 helicase, NS5 methyl-transferase, and NS5 RNA-dependent RNA polymerase.

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