# Multiscale Modeling of B. Anthracis Surface Layer Assembly and Depolymerization by Nanobodies

> **NIH NIH R21** · COLORADO SCHOOL OF MINES · 2023 · $215,360

## Abstract

Project Summary
Alternative strategies to conventional antibiotics are needed to combat rising antibiotic
resistance in bacteria. Therapeutics that target virulence factors would instead disarm bacteria
and mitigate the risk of developing antibiotic resistance. In this proposal, we investigate the
disruption of bacterial surface layer proteins (SLPs), which self-assemble into a para-crystalline
surface layer (S-layer), a virulence factor that mediates bacterial aggregation, adhesion, and
protection. Nanobodies, which exhibit low immunogenicity in humans, and are easier to purify
and deliver compared to monoclonal antibodies, were recently demonstrated to depolymerize S-
layers in the case of Bacillus anthracis, which led to complete survival in mice models under
sustained treatment. Our scientific premise is that nanobody-based inhibition of S-layers is a
viable antivirulence strategy once tuned for each bacterial pathogen. We propose to leverage
our multiscale computer simulation expertise to identify the as-yet unknown mechanism of
action and to determine sequence motifs that enhance nanobody-induced S-layer
depolymerization in Bacillus anthracis. Our aims include (1) verification that depolymerization is
induced by S-layer rigidification through the use of coarse-grained modeling and simulation and
(2) determination of nanobodies with improved antivirulence by computationally tailoring existing
nanobodies. The computational protocols developed herein are systematic and generalizable
beyond Bacillus anthracis. We expect our findings and computational tools to extend to other
SLP-expressing bacteria, including urgent antibiotic-resistant threats such as Clostridioides
difficile, and aid the global fight against antibiotic-resistant bacteria.

## Key facts

- **NIH application ID:** 10615187
- **Project number:** 5R21AI168838-02
- **Recipient organization:** COLORADO SCHOOL OF MINES
- **Principal Investigator:** Alexander Pak
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $215,360
- **Award type:** 5
- **Project period:** 2022-05-01 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10615187

## Citation

> US National Institutes of Health, RePORTER application 10615187, Multiscale Modeling of B. Anthracis Surface Layer Assembly and Depolymerization by Nanobodies (5R21AI168838-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10615187. Licensed CC0.

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