Soluble decoy receptors for broad neutralization of viruses and their variants

Glycoproteins on the surface of enveloped viruses are often the targets of both inhibitors and neutralizing antibodies due to their critical role in mediating attachment and fusion to host cells. However, the high tolerance of glycoproteins for sequence diversity of the viral genome can lead to escape mutations. In principle, soluble receptors based on the cell entry receptors could potentially limit the mutational possibilities for evasion. These soluble receptors resemble their membrane-bound counterparts but possess mutations to enhance their recognition by viral glycoproteins and to act as decoys for virus neutralization. Here, I show how deep mutational scanning informs the functional sequence space of viral glycoproteins for escape mutations and of their host receptors as decoys. First, mutations are screened in the receptor binding domain of spike S of SARS-CoV-2 for high specificity for wild-type ACE2 over an engineered ACE2 decoy, determining that such single-site substitutions are rare and do not escape the soluble decoy. Then, it is demonstrated that the engineered ACE2 decoy tightly binds and neutralizes multiple omicron lineages of SARS-CoV-2. From these two studies, I conclude that soluble decoys are broadly effective across diverse strains and variants. Next, I explore the sequence basis of selectivity in ephrin-B2 (EFNB2) for binding the attachment glycoprotein G of Nipah virus over native Eph receptors. I develop a soluble EFNB2 decoy with orthogonality to (i.e. no longer participates in) binding Eph receptors and pan-specificity for potent neutralization of closely-related, EFNB2-utilizing henipaviruses. Together, these chapters illustrate the potential of soluble decoy receptors for therapeutic and diagnostic use. In the last chapter, I interrogate the mutational landscape of a plant sugar and hormone transporter to expand the scope of deep mutational scanning as a generalizable methodology. This study introduces deep mutagenesis to the plant sciences as well as reveals novel mutations for enhanced cellular influx of sugars, which have potential biotechnological applications.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2023

Author dc:creator

• Narayanan, Krishna K.

Contributors dc:contributor

• Procko, Erik
• Stadtmueller, Beth M
• Jin, Hong
• Wu, Nicholas C

• Deep Mutational Scanning
• Soluble Decoy Receptor

Statement dc:rights

• Copyright 2023 Krishna Kumar Narayanan

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/121237

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F121237