Biology subjects

Weidenbacher, P. A.

Publications and source records attributed to Weidenbacher, P. A..

4 recordsLinked to original sources

bioRxiv2023

Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern

With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered form of the SARS-CoV-2 spike protein. In non-human primates, DCFHP-alum elicits neutralizing antibodies against all known VOCs that have emerged to date and SARS-CoV-1. During development of the DCFHP antigen, we investigated the incorporation of strain-specific mutations from the major VOCs that had emerged to date: D614G, Epsilon, Alpha, Beta, and Gamma. Here, we report the biochemical and immunological characterizations that led us to choose the ancestral Wuhan-1 sequence as the basis for the final DCFHP antigen design. Specifically, we show by size exclusion chromatography and differential scanning fluorimetry that mutations in the VOCs adversely alter the antigens structure and stability. More importantly, we determined that DCFHP without strain-specific mutations elicits the most robust, cross-reactive response in both pseudovirus and live virus neutralization assays. Our data suggest potential limitations to the variant-chasing approach in the development of protein nanoparticle vaccines, but also have implications for other approaches including mRNA-based vaccines.

biochemistry↗

bioRxiv2022

Efficient evolution of human antibodies from general protein language models and sequence information alone

Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could accelerate artificial evolution. Here, we report that deep learning algorithms known as protein language models can evolve human antibodies with high efficiency, despite providing the models with no information about the target antigen, binding specificity, or protein structure, and also requiring no additional task-specific finetuning or supervision. We performed language-model-guided affinity maturation of seven diverse antibodies, screening 20 or fewer variants of each antibody across only two rounds of evolution. Our evolutionary campaigns improved the binding affinities of four clinically relevant antibodies up to 7-fold and three unmatured antibodies up to 160-fold across diverse viral antigens, with many designs also demonstrating improved thermostability and viral neutralization activity. Notably, our algorithm requires only a single wildtype sequence and computes recommended amino acid changes in less than a second. Moreover, the same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, indicating that these results generalize to many natural settings. Contrary to prevailing notions of evolution as difficult and resource-intensive, our results suggest that when constrained to a narrow manifold of evolutionary plausibility, evolution can become much easier, which we refer to as the "efficient manifold hypothesis."

synthetic biology↗

bioRxiv2020

A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice

Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (S{Delta}C-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of S{Delta}C-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with S{Delta}C-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.

immunology↗

bioRxiv2018

Protect, Modify, Deprotect (PMD): A strategy for creating vaccines to elicit antibodies targeting a specific epitope

In creating vaccines against infectious agents, there is often a desire to direct an immune response toward a particular conformational epitope on an antigen. We present a method, called Protect, Modify, Deprotect (PMD), to generate immunogenic proteins aimed to direct a vaccine-induced antibody response toward an epitope defined by a specific monoclonal antibody (mAb). The mAb is used to protect the target epitope on the protein. Then, the remaining exposed surfaces of the protein are modified to render them non-immunogenic. Finally, the epitope is deprotected by removal of the mAb. The resultant protein is modified at surfaces other than the target epitope. We validate PMD using the well-characterized antigen, hen egg white lysozyme (HEWL). Then, we demonstrate the utility of PMD using influenza virus hemagglutinin (HA). Specifically, we use a mAb to protect a highly conserved epitope on the stem domain of HA. Exposed surface amines are then modified by introducing short polyethylene glycol (PEG) chains. The resultant antigen shows markedly reduced binding to mAbs that target the variable head region of HA, while maintaining binding to mAbs at the epitope of interest in the stem region. This antigenic preference is also observed with yeast cells displaying antibody fragments. Antisera from guinea pigs immunized with the PMD-modified HA show increased cross-reactivity with HAs from other influenza strains, as compared to antisera obtained with unmodified HA trimers. PMD has the potential to direct an antibody response at high-resolution and could be used in combination with other such strategies. There are many attractive targets for the application of PMD.

immunology↗