9 Oct 2020

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication (Nat. Commun.)

The main protease, Mpro (or 3CLpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor. Here, M. J. Lemieux show the prodrug and its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals. The work here lays the framework for their use in human trials for the treatment of COVID-19.

9 Oct 2020

Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex (Cell)

SARS-CoV-2 is the causative agent of the 2019–2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here E.A.Campbell et. al. present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template product in complex with two molecules of the nsp13 helicase. The Nidovirales order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12 thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-trancribing holo-RdRp, constraining models for nsp13 function. They also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapy development.

24 Sep 2020

Growth, detection, quantification, and inactivation of SARS-CoV-2 (Virology)

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is the agent responsible for the coronavirus disease 2019 (COVID-19) global pandemic. SARS-CoV-2 is closely related to SARS-CoV, which caused the 2003 SARS outbreak. Although numerous reagents were developed to study SARS-CoV infections, few have been applicable to evaluating SARS-CoV-2 infection and immunity. Current limitations in studying SARS-CoV-2 include few validated assays with fully replication-competent wild-type virus. M.S. Diamond et. al.  have developed protocols to propagate, quantify, and work with infectious SARS-CoV-2. Here, we describe: (1) virus stock generation, (2) RT-qPCR quantification of SARS-CoV-2 RNA; (3) detection of SARS-CoV-2 antigen by flow cytometry, (4) quantification of infectious SARS-CoV-2 by focus-forming and plaque assays; and (5) validated protocols for virus inactivation. Collectively, these methods can be adapted to a variety of experimental designs, which should accelerate our understanding of SARS-CoV-2 biology and the development of effective countermeasures against COVID-19.

12 Aug 2019

Quo Vadis Biomolecular NMR Spectroscopy?

In Quo Vadis Biomolecular NMR Spectroscopy? Phil Selenko reviews recent methodological spin-off applications whose developments were stimulated by cellular NMR approaches.

8 Aug 2019

Essay on Biomembrane Structure

Christoph Gerle provides historical outline of how we arrived at our current understanding of biomembranes and the models we use to describe them in Essay on Biomembrane Structure. A selection of direct experimental findings on the nano-scale structure of biomembranes is taken up to discuss their physical nature, and special emphasis is put on the surprising insights that arise from atomic scale descriptions.

5 Aug 2019

Role of integrative structural biology in understanding transcriptional initiation

Role of integrative structural biology in understanding transcriptional initiation is discussed by Philip Robinson et. al. in a review, which presents a general background to integrative structural biology, describes of how it should be practically implemented, and shows how it has furthered our understanding of the biology of large transcriptional assemblies. 

5 Aug 2019

Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies

In this publication Sriram Subramaniam et. al. report on structural studies of G protein–coupled receptors, spliceosomes, and fibrillar specimens and illustrate the progress made by advanced cryo-EM methods.

1 Aug 2019

The evolution of solution state NMR pulse sequences through the ‘eyes’ of triple-resonance spectroscopy

Lewis Kay in The evolution of solution state NMR pulse sequences through the ‘eyes’ of triple-resonance spectroscopy highlights how pulse sequence ‘engineering’ has evolved during past decades with the focus on liquid state NMR applications.

Principles for Integrative Structural Biology Studies

Guru of integrative structural biology computation Andrej Sali and Michale P. Rout summarize in the recent Cell Primer Principles for Integrative Structural Biology Studies.

Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age

The topical review by Alok K. Mitra recapitulates developments and transformational advances of cryo-EM technology.

16 Jul 2019

The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryo-EM

Samar Hasnain et. al. describe the steadily-expanding methodologies for atomic resolution studies in The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryo-EM. Of note is the following statistics: Despite the wealth of structures in the Protein Data Bank, a closer examination reveals that 89% of the structures, i.e. 126 994, are of proteins or complexes with a molecular weight of less than 160 kDa. Furthermore, only 4% of the deposited structures have a molecular weight in excess of 300 kDa.