We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL ) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes. How to cite this article:Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL ) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates [version 1; peer review: 2 F1000Research 2020, :129 ( ) approved] 9 https://doi.PubMed Abstract | Publisher Full Text 2. Muramatsu T, Takemoto C, Kim YT, et al.: SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc Natl Acad Sci U S A. 2016; 113(46): 12997-13002. PubMed Abstract | Publisher Full Text | Free Full Text 3. Krivov GG, Shapovalov MV, Dunbrack RL Jr: Improved prediction of protein side-chain conformations with SCWRL4. Proteins. 2009; 77(4): 778-795. PubMed Abstract | Publisher Full Text | Free Full Text 4. Labbé CM, Rey J, Lagorce D, et al.: MTiOpenScreen: a web server for structure-based virtual screening. Nucleic Acids Res. 2015; 43(W1): W448-W454. PubMed Abstract | Publisher Full Text | Free Full Text 5. Trott O, Olson AJ: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010; 31(2): 455-461. PubMed Abstract | Publisher Full Text | Free Full Text The PyMOL molecular graphics system (Schrödinger, LLC). Reference Source 7. Chen YW: SARS-CoV-2 (2019-nCoV) 3CLpro Model & Screening. 2020. http://www.doi.org/10.17605/OSF.IO/HCU8X 8. Huang C, Wei P, Fan K, et al.: 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry. 2004; 43(15): 4568-4574. PubMed Abstract | Publisher Full Text 9. Hsu MF, Kuo CJ, Chang KT, et al.: Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem. 2005; 280(35): 31257-31266. PubMed Abstract | Publisher Full Text 10. Barrila J, Bacha U, Freire E: Long-range cooperative interactions modulate dimerization in SARS 3CL pro . Biochemistry. 2006...

We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL ) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes. pro 1. Chan JF, Yuan S, Kok KH, et al.: A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020; 395(10223): 514-523.PubMed Abstract | Publisher Full Text 2. Muramatsu T, Takemoto C, Kim YT, et al.: SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc Natl Acad Sci U S A. 2016; 113(46): 12997-13002. PubMed Abstract | Publisher Full Text | Free Full Text 3. Krivov GG, Shapovalov MV, Dunbrack RL Jr: Improved prediction of protein sidechain conformations with SCWRL4. Proteins. 2009; 77(4): 778-795. PubMed Abstract | Publisher Full Text | Free Full Text 4. Labbé CM, Rey J, Lagorce D, et al.: MTiOpenScreen: a web server for structurebased virtual screening. Nucleic Acids Res. 2015; 43(W1): W448-W454. PubMed Abstract | Publisher Full Text | Free Full Text 5. Trott O, Olson AJ: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010; 31(2): 455-461. PubMed Abstract | Publisher Full Text | Free Full Text 6. Huang C, Wei P, Fan K, et al.: 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry. 2004; 43(15): 4568-4574. PubMed Abstract | Publisher Full Text 7. Hsu MF, Kuo CJ, Chang KT, et al.: Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem. 2005; 280(35): 31257-31266. PubMed Abstract | Publisher Full Text 8. Barrila J, Bacha U, Freire E: Long-range cooperative interactions modulate dimerization in SARS 3CL pro . Biochemistry. 2006; 45(50): 14908-14916. PubMed Abstract | Publisher Full Text | Free Full Text 9. Barrila J, Gabelli SB, Bacha U, et al.: Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL pro . Biochemistry. 2010; 49(20): ...

Structural and biochemical study of urease accessory protein complex provides mechanistic insights into the delivery of nickel to metalloenzyme urease, an enzyme enabling the survival of Helicobacter pylori in the human stomach.

Spinocerebellar ataxia type 1 is a late-onset neurodegenerative disease caused by the expansion of a CAG triplet repeat in the SCA1 gene. This results in the lengthening of a polyglutamine tract in the gene product ataxin-1. This produces a toxic gain of function that results in specific neuronal death. A region in ataxin-1, the AXH domain, exhibits significant sequence similarity to the transcription factor HBP1. This region of the protein has been implicated in RNA binding and selfassociation. We have determined the crystal structure of the AXH domain of ataxin-1. The AXH domain is dimeric and contains an OB-fold, a structural motif found in many oligonucleotide-binding proteins, supporting its proposed role in RNA binding. By structure comparison with other proteins that contain an OB-fold, a putative RNA-binding site has been identified. We also identified a cluster of charged surface residues that are well conserved among AXH domains. These residues may constitute a second ligand-binding surface, suggesting that all AXH domains interact with a common yet unidentified partner.Spinocerebellar ataxia type 1 (SCA1) 1 is an autosomal dominant neurodegenerative disorder characterized by the loss of Purkinje's cells in the cerebellar cortex. It is a member of the polyglutamine expansion disease family. These diseases are caused by the abnormal lengthening of a CAG triplet repeat in the coding region of the respective gene. In normal individuals, the triplet repeat translates into a polymorphic glutamine tract of fewer than 35ϳ40 residues. In patients with these diseases, the length of the polyglutamine tract exceeds the 35ϳ40-residue threshold. This results in a toxic gain of function that leads to tissue-specific neuronal loss. In most cases, nuclear ubiquitinated aggregates of the pathogenic proteins are observed in affected neurons (1). The relationship between the polyglutamine tract and disease pathology is unclear and has been the subject of much interest (2). In some cases, overexpression of even the normal protein can lead to mild disease phenotypes (3), suggesting that protein misfolding or turnover may play a role in the disease process.SCA1 is caused by polyglutamine expansion in ataxin-1, a nuclear protein of ϳ800 residues. Transgenic animal models for this disease have contributed significantly to our understanding of polyglutamine expansion diseases in general. The areas addressed have included the role of protein aggregates in neural toxicity, the effects of chaperones and the proteasome in neuropathology, and the role of post-translational modification and protein-protein interactions in disease progression (4). Recently, it has been shown that neurodegeneration is mediated by the interaction of ataxin-1 with the 14-3-3 proteins (5). This finding has emphasized the importance of understanding the normal function of the protein. Ataxin-1 appears to be involved in the regulation of gene expression. It has been shown to associate with several proteins involved in controlling transcription, and an expa...

A rational design strategy was used to construct a sensitive "turn-on" biosensor for beta-lactam antibiotics and beta-lactamase inhibitors from a class A beta-lactamase mutant with suppressed hydrolytic activity. A fluorescein molecule was attached to the 166 position on the Omega-loop of the E166C mutant close to the active site of the beta-lactamase. Upon binding with antibiotics or inhibitors, the flexibility of the Omega-loop allows the fluorescein molecule to move out from the active site and be more exposed to solvent. This process is accompanied by an increase in the fluorescence of the labeled enzyme. The fluorescence intensity of the biosensor increases with the concentration of antibiotics or inhibitors, which can detect penicillin G at concentrations as low as 50 nM in water. This approach opens a possibility for converting highly active and nonallosteric enzymes into substrate-binding proteins for biosensing purposes.

Background: Maturation of urease is assisted by urease accessory proteins UreE, UreF, UreG, and UreH. Results: Crystal structure of UreF-UreH complex revealed conformational changes of UreF upon complex formation. Conclusion: Mutagenesis study confirmed that the conformational changes in UreF are essential for recruitment of UreG to the heterotrimeric complex of UreG-UreF-UreH. Significance: Our results provide a structural basis for understanding urease maturation.

Ataxin-1 is a human protein responsible for spinocerebellar ataxia type 1, a hereditary disease associated with protein aggregation and misfolding. Essential for ataxin-1 aggregation is the anomalous expansion of a polyglutamine tract near the protein N-terminus, but the sequence-wise distant AXH domain modulates and contributes to the process. The AXH domain is also involved in the nonpathologic functions of the protein, including a variety of intermolecular interactions with other cellular partners. The domain forms a globular dimer in solution and displays a dimer of dimers arrangement in the crystal asymmetric unit. Here, we have characterized the domain further by studying its behavior in the crystal and in solution. We solved two new structures of the domain crystallized under different conditions that confirm an inherent plasticity of the AXH fold. In solution, the domain is present as a complex equilibrium mixture of monomeric, dimeric, and higher molecular weight species. This behavior, together with the tendency of the AXH fold to be trapped in local conformations, and the multiplicity of protomer interfaces, makes the AXH domain an unusual example of a chameleon protein whose properties bear potential relevance for the aggregation properties of ataxin-1 and thus for disease.

One Sentence SummaryDiscovery of simeprevir as a potent suppressor of SARS-CoV-2 viral replication that synergizes remdesivir. AbstractThe recent outbreak of coronavirus disease 2019 , caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, is a global threat to human health. By in vitro screening and biochemical characterization, we identified the hepatitis C virus (HCV) protease inhibitor simeprevir as an especially promising repurposable drug for treating COVID-19. We also revealed that simeprevir synergizes with the RNA-dependent RNA polymerase (RdRP) inhibitor remdesivir to suppress the replication of SARS-CoV-2 in vitro. Our results provide preclinical rationale for the combination treatment of simeprevir and remdesivir for the pharmacological management of COVID-19 patients.