@article {2375, title = {Biophysical properties of the isolated spike protein binding helix of human ACE2.}, journal = {Biophys J}, volume = {120}, year = {2021}, month = {2021 07 20}, pages = {2785-2792}, abstract = {

The entry of the severe acute respiratory syndrome coronavirus 2 virus in human cells is mediated by the binding of its surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. A 23-residue long helical segment (SBP1) at the binding interface of human ACE2 interacts with viral spike protein and therefore has generated considerable interest as a recognition element for virus detection. Unfortunately, emerging reports indicate that the affinity of SBP1 to the receptor-binding domain of the spike protein is much lower than that of the ACE2 receptor itself. Here, we examine the biophysical properties of SBP1 to reveal factors leading to its low affinity for the spike protein. Whereas SBP1 shows good solubility (solubility \> 0.8\ mM), circular dichroism spectroscopy shows that it is mostly disordered with some antiparallel β-sheet content and no helicity. The helicity is substantial (\>20\%) only upon adding high concentrations (>=20\% v/v) of 2,2,2-trifluoroethanol, a helix promoter. Fluorescence correlation spectroscopy and single-molecule photobleaching studies show that the peptide oligomerizes at concentrations \>50\ nM. We hypothesized that mutating the hydrophobic residues (F28, F32, and F40) of SBP1, which do not directly interact with the spike protein, to alanine would reduce peptide oligomerization without affecting its spike binding affinity. Whereas the mutant peptide (SBP1) shows substantially reduced oligomerization propensity, it does not show improved helicity. Our study shows that the failure of efforts, so far, to produce a short SBP1 mimic with a high affinity for the spike protein is not only due to the lack of helicity but is also due to the heretofore unrecognized problem of oligomerization.

}, keywords = {Angiotensin-Converting Enzyme 2, COVID-19, Humans, Peptidyl-Dipeptidase A, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus}, issn = {1542-0086}, doi = {10.1016/j.bpj.2021.06.017}, author = {Das, Anirban and Vishvakarma, Vicky and Dey, Arpan and Dey, Simli and Gupta, Ankur and Das, Mitradip and Vishwakarma, Krishna Kant and Roy, Debsankar Saha and Yadav, Swati and Kesarwani, Shubham and Venkatramani, Ravindra and Maiti, Sudipta} } @article {2363, title = {SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 11}, pages = {114-119}, abstract = {

The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha). In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

}, keywords = {Antibodies, Neutralizing, Cell Fusion, Cell Line, COVID-19 Vaccines, Female, Health Personnel, Humans, Immune Evasion, India, Kinetics, Male, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vaccination, Virus Replication}, issn = {1476-4687}, doi = {10.1038/s41586-021-03944-y}, author = {Mlcochova, Petra and Kemp, Steven A and Dhar, Mahesh Shanker and Papa, Guido and Meng, Bo and Ferreira, Isabella A T M and Datir, Rawlings and Collier, Dami A and Albecka, Anna and Singh, Sujeet and Pandey, Rajesh and Brown, Jonathan and Zhou, Jie and Goonawardane, Niluka and Mishra, Swapnil and Whittaker, Charles and Mellan, Thomas and Marwal, Robin and Datta, Meena and Sengupta, Shantanu and Ponnusamy, Kalaiarasan and Radhakrishnan, Venkatraman Srinivasan and Abdullahi, Adam and Charles, Oscar and Chattopadhyay, Partha and Devi, Priti and Caputo, Daniela and Peacock, Tom and Wattal, Chand and Goel, Neeraj and Satwik, Ambrish and Vaishya, Raju and Agarwal, Meenakshi and Mavousian, Antranik and Lee, Joo Hyeon and Bassi, Jessica and Silacci-Fegni, Chiara and Saliba, Christian and Pinto, Dora and Irie, Takashi and Yoshida, Isao and Hamilton, William L and Sato, Kei and Bhatt, Samir and Flaxman, Seth and James, Leo C and Corti, Davide and Piccoli, Luca and Barclay, Wendy S and Rakshit, Partha and Agrawal, Anurag and Gupta, Ravindra K} } @article {2290, title = {Strategies to target SARS-CoV-2 entry and infection using dual mechanisms of inhibition by acidification inhibitors.}, journal = {PLoS Pathog}, volume = {17}, year = {2021}, month = {2021 07}, pages = {e1009706}, abstract = {

Many viruses utilize the host endo-lysosomal network for infection. Tracing the endocytic itinerary of SARS-CoV-2 can provide insights into viral trafficking and aid in designing new therapeutic strategies. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV-2 spike protein is internalized via the pH-dependent CLIC/GEEC (CG) endocytic pathway in human gastric-adenocarcinoma (AGS) cells expressing undetectable levels of ACE2. Ectopic expression of ACE2 (AGS-ACE2) results in RBD traffic via both CG and clathrin-mediated endocytosis. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, reduce the uptake of RBD and impede Spike-pseudoviral infection in both AGS and AGS-ACE2 cells. The inhibition by BafilomycinA1 was found to be distinct from Chloroquine which neither affects RBD uptake nor alters endosomal pH, yet attenuates Spike-pseudovirus entry. By screening a subset of FDA-approved inhibitors for functionality similar to BafilomycinA1, we identified Niclosamide as a SARS-CoV-2 entry inhibitor. Further validation using a clinical isolate of SARS-CoV-2 in AGS-ACE2 and Vero cells confirmed its antiviral effect. We propose that Niclosamide, and other drugs which neutralize endosomal pH as well as inhibit the endocytic uptake, could provide broader applicability in subverting infection of viruses entering host cells via a pH-dependent endocytic pathway.

}, keywords = {Ammonium Chloride, Angiotensin-Converting Enzyme 2, Animals, Antiviral Agents, Cell Line, Chlorocebus aethiops, Chloroquine, Clathrin, COVID-19, Drug Synergism, Endocytosis, Endosomes, Humans, Hydrogen-Ion Concentration, Hydroxychloroquine, Macrolides, Niclosamide, Protein Binding, Protein Domains, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, Virus Internalization}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1009706}, author = {Prabhakara, Chaitra and Godbole, Rashmi and Sil, Parijat and Jahnavi, Sowmya and Gulzar, Shah-E-Jahan and van Zanten, Thomas S and Sheth, Dhruv and Subhash, Neeraja and Chandra, Anchal and Shivaraj, Akshatha and Panikulam, Patricia and U, Ibrahim and Nuthakki, Vijay Kumar and Puthiyapurayil, Theja Parassini and Ahmed, Riyaz and Najar, Ashaq Hussain and Lingamallu, Sai Manoz and Das, Snigdhadev and Mahajan, Bhagyashri and Vemula, Praveen and Bharate, Sandip B and Singh, Parvinder Pal and Vishwakarma, Ram and Guha, Arjun and Sundaramurthy, Varadharajan and Mayor, Satyajit} }