A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein

The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used mRNA display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor binding domain, N-terminal domain and S2 region, distal to the ACE2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target

A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein

The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used messenger RNA (mRNA) display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor-binding domain, N-terminal domain, and S2 region, distal to the angiotensin-converting enzyme 2 receptor-interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target

Clotho: Decoupling Memory Page Layout from Storage Organization

As database application performance depends on the utilization of the memory hierarchy, smart data placement plays a central role in increasing locality and in improving memory utilization. Existing techniques, however, do not optimize accesses to all levels of the memory hierarchy and for all the different workloads, because each storage level uses different technology (cache, memory, disks) and each application accesses data using different patterns. Clotho is a new buffer pool and storage management architecture that decouples inmemory page layout from data organization on non-volatile storage devices to enable independent data layout design at each level of the storage hierarchy. Clotho can maximize cache and memory utilization by (a) transparently using appropriate data layouts in memory and non-volatile storage, and (b) dynamically synthesizing data pages to follow application access patterns at each level as needed. Clotho creates in-memory pages individually tailored for compound and dynamically changing workloads, and enables efficient use of different storage technologies (e.g., disk arrays or MEMS-based storage devices). This paper describes the Clotho design and prototype implementation and evaluates its performance under a variety of workloads using both disk arrays and simulated MEMS-based storage devices

The Infectious Bronchitis Virus Nucleocapsid Protein Binds RNA Sequences in the 3′ Terminus of the Genome

AbstractThe infectious bronchitis virus (IBV) nucleocapsid protein was expressed as a bacterial fusion protein which differed from the native protein only in the addition of six amino terminus histidine residues. Using RNA overlay protein blot assays, the recombinant protein was shown to bind to RNA fragments specific for the positive sense 3′ noncoding end of the IBV genome. At greater concentrations of sodium chloride, the native and fusion nucleocapsid proteins similarly bound to G RNA, representing the terminal 1805 3′ nt of the genome, whereas bovine serum albumin and allantoic fluid protein did not bind to labeled G RNA. Competitive gel shift assays with labeled G RNA indicated that the protein interacted with several unlabeled RNA representing sequences at the 3′ noncoding end of the IBV genome. Cache Valley virus (a bunyavirus) mRNA transcribed from the small segment cDNA also inhibited the interaction with IBV G RNA to approximately the same extent as homologous unlabeled G RNA, whereas reactions with bovine liver RNA and yeast tRNA were considerably weaker. Whereas yeast tRNA did not inhibit the interaction with the labeled large G RNA, interactions of the fusion protein with EF, a region from 78 to 217 nt from the 3′ terminus of the IBV genome, were also apparently weaker than interactions with fragment CD which consisted of the 3′ terminal 155 nt. On a molar basis, the latter interacted in an identical nature to a RNA consisting of CD and an additional 1053 nt of plasmid sequences. Compared to bovine liver RNA, unlabeled G specifically inhibited binding to the two smaller labeled IBV fragments in gel shift assays. The binding of IBV nucleocapsid protein with RNA probably requires specific sequences and/or structures that are present on the genome, and may represent a common mechanism used by similar viral nucleoproteins whose functions depend on binding to RNA

Clotho: Decoupling page layout from storage organization

Appliance, Oracle, Panasas, Seagate, Sun, and Veritas) for their interest, insights, feedback, and support. This work is funded in part by NSF grants CCR-0113660, IIS-0133686, and CCR-0205544, as well as by an IBM faculty partnership award