Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses

Giri, Rajanish; Bhardwaj, Taniya; Shegane, Meenakshi; Gehi, Bhuvaneshwari R.; Kumar, Prateek; Gadhave, Kundlik; Oldfield, Christopher J.; Uversky, Vladimir N.

doi:10.1007/s00018-020-03603-x

Cited by 109 publications

(167 citation statements)

References 157 publications

(199 reference statements)

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“…The 4 structural and 9-10 accessory proteins are translated from subgenomic RNAs produced from (–) sense ssRNA 2 . To reach the replication stage, the CoV-2 genomic (+) sense ssRNA is used as mRNA to ultimately produce 15 non-structural proteins (Nsps) from two large polyproteins, Pp1a (4,405 amino acids) and Pp1ab (7,096 amino acids) 3 . Pp1a is cleaved into the first 10 Nsps (Nsp11 is just a 7 residue peptide) and Pp1ab, which is made through a –1 ribosomal frame-shifting mechanism 4 .…”

Section: Introductionmentioning

confidence: 99%

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

Osipiuk

Azizi

Dvorkin

et al. 2020

Preprint

124

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The number of new cases world-wide for the COVID-19 disease is increasing dramatically, while efforts to contain Severe Acute Respiratory Syndrome Coronavirus 2 is producing varied results in different countries. There are three key SARS-CoV-2 enzymes potentially targetable with antivirals: papain-like protease (PLpro), main protease (Mpro), and RNA-dependent RNA polymerase. Of these, PLpro is an especially attractive target because it plays an essential role in several viral replication processes, including cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex (RTC), and disruption of host viral response machinery to facilitate viral proliferation and replication. Moreover, this enzyme is conserved across different coronaviruses and promising inhibitors have already been discovered for its SARS-CoV variant. Here we report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the enzyme from SARS-CoV-2 in both wild-type and mutant forms. These efforts include the first structures of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors, determined at 1.60–2.70 Angstroms. This collection of structures provides fundamental molecular and mechanistic insight to PLpro, and critically, illustrates details for inhibitors recognition and interactions. All presented compounds inhibit the peptidase activity of PLpro in vitro, and some molecules block SARS-CoV-2 replication in cell culture assays. These collated findings will accelerate further structure-based drug design efforts targeting PLpro, with the ultimate goal of identifying high-affinity inhibitors of clinical value for SARS-CoV-2.

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Section: Introductionmentioning

confidence: 99%

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

Osipiuk

Azizi

Dvorkin

et al. 2020

Preprint

124

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“…The sequence of NSP1 C-terminal (residues 130-180) "NH2-AGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG-COOH" was retrieved from the UniProt (ID: P0DTC1.1). As described earlier by our group, protein intrinsic disorder predictor, PONDR® VSL2 was used for analysis of intrinsic disorder properties of NSP1-CTR (2,13,14,19,26,27). The secondary structure predisposition analysis for NSP1-CTR was performed with several different web-servers pep2d, Jpred4, and PSIPRED (28-30).…”

Section: Phylogenetic Analysis Of Sars-cov-2 On the Basis Of Nsp1mentioning

confidence: 99%

“…CoVs have single-stranded positive-sense RNA genome, of which, the two-third part (~20kb) is translated into two large polyproteins named pp1a and pp1ab. These two polyproteins encode sixteen non-structural proteins (NSP1-NSP16), which make up the viral replication-transcription complex (1,2). The very interesting feature among the four CoVs genera is presence of NSP1, which is present only in alpha-and beta-genera of CoVs (3).…”

Section: Introductionmentioning

confidence: 99%

“…For a period of time bioinformatics studies show the penetrance of IDPs in viruses and all domain of life from bacteria to eukaryotes (10)(11)(12)(13)(14). Recently, bioinformatics based study by our group showed that NSP1 of SARS-CoV-2 regions (amino acids 137-145 and 172-179) are identified as a molecular recognition feature (MoRFs) region (2). Generally, most of IDPs are unfolded in solution and switch to a conformation when bind with particular ligands and undergo coupled folding and binding (15)(16)(17)(18).…”

Section: Introductionmentioning

confidence: 99%

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SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region

Kumar¹,

Kumar²,

Kumar³

et al. 2020

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Nonstructural protein 1 (NSP1) of SARS-CoV-2 plays a key role in downregulation of RIG-I pathways and interacts with 40 S ribosome. Recently, the cryo-EM structure in complex with 40S ribosome is deciphered. However, the structure of full length NSP1 without any partner has not been studies. Also, the conformation of NSP1-C terminal region in isolation is not been studied. In this study, we have investigated the conformational dynamics of NSP1C-terminal region (NSP1-CTR; amino acids 130-180) in isolation and under different solvent environments. The NSP1-CTR is found to be intrinsically disordered in aqueous solution. Further, we used alpha helix inducer, trifluoroethanol, and found induction of alpha helical conformation using CD spectroscopy. Additionally, in the presence of SDS, NSP1-CTR is showing a conformational change from disordered to ordered, possibly gaining alpha helix in part. But in presence of neutral lipid DOPC, a slight change in conformation is observed. This implies the possible role of hydrophobic interaction and electrostatic interaction on the conformational changes of NSP1. The changes in structural conformation were further studied by fluorescence-based studies, which showed significant blue shift and fluorescence quenching in the presence of SDS and TFE. Lipid vesicles also showed fluorescence-based quenching. In agreement to these result, fluorescence lifetime and fluorescence anisotropy decay suggests a change in conformational dynamics. The zeta potential studies further validated that the conformational dynamics is mostly because of hydrophobic interaction. In last, these experimental studies were complemented through Molecular Dynamics (MD) simulation which have also shown a good correlation and testify our experiments. We believe that the intrinsically disordered nature of the NSP1-CTR will have implications in disorder based binding promiscuity with its interacting proteins.

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“…In our recent study, we analysed the propensity of intrinsic disorder in SARS-CoV-2 proteins and correlated it with its evolutionary closer human SARS and Bat SARS-like coronaviruses [9]. The multiple sequence alignment of SARS-CoV-2 nsp11 with SARS-CoV and Bat SARS-like coronavirus represents difference in protein sequence at 5 th and 6 th positions where glutamine and serine are observed to substitute serine and threonine residues, respectively [9]. As an uncharacterised protein of potential function, published literature on nsp11 protein of murine hepatitis virus shows cleavage mutants nsp10/nsp11 are not replication viable [10].…”

Section: Introductionmentioning

confidence: 99%

Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

Gadhave

Kumar

et al. 2020

Preprint

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The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of disordered proteome is also proven and are related with its conformational dynamics inside the host. The SARS-CoV-2 virus has a large proteome, in which, structure and functions of many proteins are not known as of yet. Previously, we have investigated the dark proteome of SARS-CoV-2. However, the disorder status of non-structural protein 11 (nsp11) was not possible because of very small in size, just 13 amino acid long, and for most of the IDP predictors, the protein size should be at least 30 amino acid long. Also, the structural dynamics and function status of nsp11 was not known. Hence, we have performed extensive experimentation on nsp11. Our results, based on the Circular dichroism spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behaviour of nsp11 in the presence of membrane mimetic environment, alpha helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. At the end, we again confirmed the IDP behaviour of nsp11 using molecular dynamics simulations.

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Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses

Cited by 109 publications

References 157 publications

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically disordered region

Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions

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