Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9

Littler, Dene R.; Mohanty, Biswaranjan; Lowery, Shea A.; Colson, Rhys N.; Gully, Benjamin S.; Perlman, Stanley; Scanlon, M.J.; Rossjohn, Jamie

doi:10.1016/j.jbc.2021.101018

Cited by 10 publications

(13 citation statements)

References 37 publications

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“…A previous study identified the possible RNA-binding sites (Phe40, Val41, and Ile91) by observing the chemical perturbation of Nsp9 titrated with ssRNA using nuclear magnetic resonance (NMR) titration assays. 216 Subsequently, targeted substrates that bind to these sites (or adjacent to these sites) were screened from a small fragment library; the uracil-analog FR6, which has a weak affinity with Nsp9, was obtained. 216 In the Nsp9/FR6 complex, a tetrameric π–π stacking between the pyrimidinedione ring of FR6 and the aromatic ring of Phe40 induces a hexameric form of Nsp9 (a “trimer of dimers”).…”

Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

“… 216 Subsequently, targeted substrates that bind to these sites (or adjacent to these sites) were screened from a small fragment library; the uracil-analog FR6, which has a weak affinity with Nsp9, was obtained. 216 In the Nsp9/FR6 complex, a tetrameric π–π stacking between the pyrimidinedione ring of FR6 and the aromatic ring of Phe40 induces a hexameric form of Nsp9 (a “trimer of dimers”). 216 Changes in the oligomerization state may alter RNA entry channels and thus affect RNA binding.…”

Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

“… 216 In the Nsp9/FR6 complex, a tetrameric π–π stacking between the pyrimidinedione ring of FR6 and the aromatic ring of Phe40 induces a hexameric form of Nsp9 (a “trimer of dimers”). 216 Changes in the oligomerization state may alter RNA entry channels and thus affect RNA binding. In addition to the inhibitors of Nsp9-RNA binding described above, other inhibitors have been identified that target the Nsp9 GXXXG motif to disrupt the dimer interface, affecting RNA binding and viral proliferation.…”

Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

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Structural biology of SARS-CoV-2: open the door for novel therapies

Zheng

Zeng

et al. 2022

Sig Transduct Target Ther

195

149

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Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.

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Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

Section: Nonstructural Proteins Of Sras-cov-2mentioning

confidence: 99%

See 1 more Smart Citation

Structural biology of SARS-CoV-2: open the door for novel therapies

Zheng

Zeng

et al. 2022

Sig Transduct Target Ther

195

149

View full text Add to dashboard Cite

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“…Although NiRAN has no homologs in other RNA viruses, it is present in all nidoviruses and is essential for viral replication [34]. The NiRAN domain is structurally homologous to AM-Pylases [35,36], which catalyze AMP transfer to target proteins [37], and transfers NMPs to several nsps [19][20][21]38]. In contrast to AMPylases, which transfer AMP to hydroxyl groups of Ser, Thr, and Tyr residues to generate stable modifications [37], the NiRAN active site (AS2 in Figure 1) targets primary amines to yield labile adducts [19], which are used as transient catalytic intermediates in other enzymatic systems [39].…”

Section: Sars-cov-2 Niran Domain As a Target For Small-molecule Ligandsmentioning

confidence: 99%

Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19

Wang

Svetlov²,

Bartikofsky

et al. 2022

Molecules

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The severity of the COVID-19 pandemic and the pace of its global spread have motivated researchers to opt for repurposing existing drugs against SARS-CoV-2 rather than discover or develop novel ones. For reasons of speed, throughput, and cost-effectiveness, virtual screening campaigns, relying heavily on in silico docking, have dominated published reports. A particular focus as a drug target has been the principal active site (i.e., RNA synthesis) of RNA-dependent RNA polymerase (RdRp), despite the existence of a second, and also indispensable, active site in the same enzyme. Here we report the results of our experimental interrogation of several small-molecule inhibitors, including natural products proposed to be effective by in silico studies. Notably, we find that two antibiotics in clinical use, fidaxomicin and rifabutin, inhibit RNA synthesis by SARS-CoV-2 RdRp in vitro and inhibit viral replication in cell culture. However, our mutagenesis studies contradict the binding sites predicted computationally. We discuss the implications of these and other findings for computational studies predicting the binding of ligands to large and flexible protein complexes and therefore for drug discovery or repurposing efforts utilizing such studies. Finally, we suggest several improvements on such efforts ongoing against SARS-CoV-2 and future pathogens as they arise.

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“…The 12 kDa nonstructural protein 9 (Nsp9) forms a homodimer that functions as an essential RNA binding subunit of the replication complex (de et al, 2021 ). Because disruption of Nsp9 binding to the replication complex reduces RNA binding and SARS‐CoV proliferation, ligands to Nsp9 are potential anti‐SARS‐CoV‐2 agents (Littler, Mohanty, et al, 2021 ). Native MS screening has been used to discover Nsp9 ligands that can inhibit the replication of SARS‐CoV‐2 (Littler, Liu, et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Affinity selection‐mass spectrometry in the discovery of anti‐SARS‐CoV‐2 compounds

Breemen

Muchiri

2022

Mass Spectrometry Reviews

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Small molecule therapeutic agents are needed to treat or prevent infections by severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2), which is the cause of the COVID‐19 pandemic. To expedite the discovery of lead compounds for development, assays have been developed based on affinity selection‐mass spectrometry (AS‐MS), which enables the rapid screening of mixtures such as combinatorial libraries and extracts of botanicals or other sources of natural products. AS‐MS assays have been used to find ligands to the SARS‐CoV‐2 spike protein for inhibition of cell entry as well as to the 3‐chymotrypsin‐like cysteine protease (3CLpro) and the RNA‐dependent RNA polymerase complex constituent Nsp9, which are targets for inhibition of viral replication. The AS‐MS approach of magnetic microbead affinity selection screening has been used to discover high‐affinity peptide ligands to the spike protein as well as the hemp cannabinoids cannabidiolic acid and cannabigerolic acid, which can prevent cell infection by SARS‐CoV‐2. Another AS‐MS method, native mass spectrometry, has been used to discover that the flavonoids baicalein, scutellarein, and ganhuangenin, can inhibit the SARS‐CoV‐2 protease 3CLpro. Native mass spectrometry has also been used to find an ent ‐kaurane natural product, oridonin, that can bind to the viral protein Nsp9 and interfere with RNA replication. These natural lead compounds are under investigation for the development of therapeutic agents to prevent or treat SARS‐CoV‐2 infection.

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Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9

Cited by 10 publications

References 37 publications

Structural biology of SARS-CoV-2: open the door for novel therapies

Structural biology of SARS-CoV-2: open the door for novel therapies

Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19

Affinity selection‐mass spectrometry in the discovery of anti‐SARS‐CoV‐2 compounds

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