Engineering Immunological Solutions for Pandemic-Level Threats

Author: Caldera, Luis Fernando

Year: 2026

Degree: Dissertation (Ph.D.)

Advisors: Bjorkman, Pamela J.; Mayo, Stephen L.

Committee Members: Rothenberg, Ellen V.; Bjorkman, Pamela J.; Mayo, Stephen L.; Bois, Justin S.

Option: Bioengineering

Abstract

Pandemics remain among the most serious threats to global public health, especially when viruses can efficiently spread and persist in human populations. Two major examples are the AIDS pandemic caused by HIV-1, which emerged in the early 1980s, and the COVID-19 pandemic caused by SARS-CoV-2, which began in late 2019. Despite their differences in timescale and transmission, HIV-1 and SARS-CoV-2 exhibit high antigenic diversity that drives an ongoing arms race between viral escape and the development of vaccines and therapeutics. This thesis presents three molecular engineering strategies to confront that problem. For SARS-CoV-2, we utilized computational tools to generate mosaic nanoparticle vaccines displaying engineered SARS-CoV-2 or selected sarbecovirus receptor-binding domains (RBDs) sharing conserved antigenic features to drive immunity toward eliciting cross-reactive responses. In naïve and pre-vaccinated mice, our lead candidate, mosaic-7COM, elicited broader and more potent cross-reactive antibody responses compared to our prior mosaic-8b candidate. For HIV-1, we engineered a stabilized CD4-Ig reagent specific to HIV-1 envelope (Env) glycoprotein with greatly reduced off-target recognition of MHC class II. The final CD4 design had markedly increased thermostability (>20°C) and a nearly 50-fold improvement in mammalian expression compared to the wild-type construct, highlighting its potential as a therapeutic biologic. Additionally, we developed a yeast-display screening platform to isolate nanobody (VHH) domains against the caldera, a conserved, glycan-free epitope exposed on Env upon engagement with CD4. This campaign yielded five VHH-Fc candidates that bind receptor-bound Env and established a foundation for future biologic development targeting a previously inaccessible site on the virus.