COVID-19 Literature Review

Please help with writing of a manuscript by doing literature review

Introduction

COVID-19 caused by the positive-sense single-stranded RNA virus, SARS-CoV-2 is a pandemic. During a viral outbreak, antibodies against the virus are often effective therapies, as exemplified by mAB114 and REGN-EB3, which reduced the mortality rate against the Zaire species of Ebola virus (Mulangu et al, 2019). These antibodies are typically discovered in the blood of survivors of the disease. During the beginning phase of an outbreak, it is imperative to start clinical trials with promising therapies such as monoclonal antibodies as soon as possible to minimize the number of deaths. Time is of the essence. However, it takes time to find promising neutralizing antibodies. A designed antibody mimic could be developed faster and effective in the current COVID-19 outbreak and also in a future outbreak due to a similar coronavirus. Natural antibodies are often ineffective against a different viral species even when their sequences are similar like SARS-CoV and SARS-CoV-2 (Tian et al., 2020). One promising approach at the beginning phase of an outbreak is to use the soluble portion of a human receptor that binds to the virus. Such therapies are referred to as decoy receptors. These decoy receptors could be combined with the Fc portion of IgG to stimulate the immune system. In the case of COVID-19, the RNA sequence of SARS-CoV-2 was sequenced quickly (reference). Because of its similarity to the sequence of SARS-CoV, another coronavirus that caused an outbreak in 2003, people suspected SARS-CoV-2 uses human angiotensin converting enzyme 2 (hACE2) as a site of attachment for entry into the human cell like SARS-CoV. This suspicion has been confirmed (reference). Even before the confirmation, a clinical trial could have started with soluble hACE2 since it was safe and well tolerated in previous phase I and II clinical trials (reference). Soluble hACE2 binds to the receptor binding domain of the SARS-CoV-2 Spike Protein and blocks viral cell entry (references). The effectiveness of a decoy receptor therapy depends on its binding affinity to the virus and its availability at the site of action, which is the epithelial surface of the lungs in the case of COVID-19 (reference). In this study, using the available Cryo-EM and X-ray crystal structures (references) and molecular dynamics simulations, we designed mutations to improve the binding affinity of hACE2 to SARS-CoV-2 Spike Protein. We also designed a smaller protein that could bind to SARS-CoV-2 with a high binding affinity.

Interaction between COVID-19 Spike Protein and Human ACE2

Thus far three membrane ectopeptidases, dipeptidyl peptidase 4 (DPP4), angiotensin-converting enzyme 2 (ACE2) and aminopeptidase N (APN), have been identified as entry receptors for human-infecting coronaviruses.

The Kd of SARS-CoV-2 spike protein-2 to soluble ACE2 (residue 1-615) was reported to be ~15 nM while that of SARS-CoV spike protein was ~326 nM.

https://www.cdc.gov/coronavirus/types.html

Fusion of Viral Envelope with Host Membrane

Virus Endocytosis

Which cells are infected by coronaviruses? https://www.ncbi.nlm.nih.gov/pubmed/24737708

Modern mRNA Vaccine

Moderna and NIH have started a mRNA vaccine clinical trial (https://www.nytimes.com/2020/03/16/health/coronavirus-vaccine.html), which uses the nanoparticle technology that our collaborator at OHSU uses to express CFTR in mice. In this approach, mRNA will be expressed in the human body to make the viral spike protein. Our lab will study an alternative decoy receptor therapy.

Proteases that Cleave COVID-19 Spike Protein

Interaction between COVID-19 and B0AT1

How biologics travel to target tissues

Many biologics are monoclonal antibodies, which can cross the capillary endothelium through transcytosis.

https://www.ncbi.nlm.nih.gov/pubmed/31112823

Structural basis of receptor recognition by SARS-CoV-2

https://www.nature.com/articles/s41586-020-2179-y_reference.pdf

The coronavirus spike protein mediates coronavirus entry into the host, SARS-CoV-2 RBD recognizes hACE2. The study aimed to crystallize the SARS-CoV-2 RBD/hACE2 complex. A previously crystallized SARS-CoV RBD/hACE2 complex was used for this study. Using this previously crystallized complex and the RBM from SARS-CoV-2 a chimeric RBD was designed. The chimeric RBD design is highly similar to the determined structure of SARS-CoV-2, confirming a successful design. When designing the chimeric RBD a short loop from SARS-CoV RBM was kept, this maintains a strong salt bridge between Arg426 from the RBD and Glu329 from hACE2. The chimeric RBD had the highest affinity for hACE2 consistent with the introduced N-O bridge between the chimeric RBD and hACE2. The paper then discusses the structures of SARS-CoV and SARS-CoV-2 RBMs and why these differences lead to different binding affinities. I suggest looking at Figures 1 and 2 to help understand the comparison.

Compared with SARS-CoV, SARS-CoV-2 RBM contains structural changes in the hACE2-binding ridge, largely caused by a four-residue motif (residues 482-485: Gly-Val-Glu-Gly). This structural change allows the ridge of the RBM to become more compact and form better contact with the N-terminal helix of hACE2. In addition, Phe486 from SARS-CoV-2 RBM inserts into a hydrophobic pocket. The corresponding residue in SARS-CoV RBM is a leucine, which likely forms weaker contact with hACE2 due to its smaller side chain. Finally, both virus-binding hotspots have become more stabilized at the RBM/hACE2 interface through interactions with SARS-CoV-2 RBM. These hotspots on hACE2 are critical for coronavirus binding because they involve two lysine residues that need to be accommodated properly in hydrophobic environments. Neutralizing the charges of the lysines is key to the binding of coronavirus RBDs to hACE2. SARS-CoV-2 RBM has evolved strategies to stabilize the two hotspots: Gln493 and Leu455 stabilize hotspot-31, whereas Asn501 stabilizes hotspot-353. Hotspot-31 is a salt bridge between Lys31 and Glu35. Hotspot-353 is a salt bridge between Lys353 and Asp38.

Previous structural work identified 14 positions that are key for binding of SARS-CoV SB to hACE2: T402, R426, Y436, Y440, Y442, L472, N473, Y475, N479, Y484, T486, T487, G488, and Y491 (Li et al., 2005a). Analysis of the 144 SARS-CoV-2 genome sequences available from the Global Initiative on Sharing All Influenza Data (GISAID) (Elbe and Buckland-Merrett, 2017) shows that 8 out of these 14 positions are strictly conserved in SARS-CoV-2 SB, whereas the other 6 positions are (semi)conservatively substituted: R426SARS-CoVN439SARS-CoV-2, Y442SARS-CoVL455SARS-CoV-2, L472SARS-CoVF486SARS-CoV-2, N479SARS-CoVQ493SARS-CoV-2, Y484SARS-CoVQ498SARS-CoV-2, and T487SARS-CoVN501SARS-CoV-2.