Collins, W. | Search bioRxiv

bioRxiv2025

Machine Learning-Driven Prediction of TLR4 Binding Affinity: A Comprehensive Molecular Feature Analysis for Drug Discovery

Toll-like receptor 4 (TLR4) represents a promising therapeutic target for inflammatory diseases and cancer, but developing selective modulators remains challenging. We present a machine learning approach for predicting TLR4 binding affinity using comprehensive molecular descriptors. Our ensemble learning pipeline extracted 53 physicochemical features from a curated dataset of 49 unique TLR4 ligands, achieving cross-validation R2 of 0.74 {+/-} 0.10 with statistical significance confirmed by permutation testing (p < 0.01). The most predictive features were Bertz complexity (importance: 0.173), molecular shape descriptors (0.159), and molar refractivity (0.145), while traditional drug-like properties such as LogP showed lower importance (0.056). This suggests TLR4 binding follows distinct structure-activity patterns compared to conventional drug targets. Compounds with intermediate structural complexity (Bertz complexity: 400-600) demonstrated optimal binding affinity. The model successfully identified key molecular scaffolds including flavonoids and terpenoids, aligning with known natural product TLR4 modulators. This work provides the first comprehensive machine learning analysis of TLR4 binding determinants and offers a computational framework for rational design of TLR4-targeted therapeutics, with identified molecular features providing actionable insights for developing next-generation immunomodulatory drugs.

bioinformatics↗

bioRxiv2020

Homemade Bread: Repurposing an Ancient Technology for Low Cost in vitro Tissue Engineering

Numerous synthetic and naturally-occurring biomaterials have been developed to provide such architectures to support the proliferation of mammalian cells in vitro and in vivo. Our group, and others, have shown that scaffolds derived from plants can be utilized for tissue engineering applications in biomedicine and in the burgeoning cultured meat industry. Such scaffolds are ideally straightforward and inexpensive to prepare, allowing researchers to take advantage of their intrinsic 3D microarchitectures. These efforts inspired us to continue to pursue the development of novel and unconventional biomaterials that are easily produced and high performing in vitro. With this in mind, few plant-derived materials are more ubiquitous than bread. Having observed the porosity of the crumb (i.e. the internal bulk) we sought to investigate whether it might support the proliferation of mammalian cells in vitro. Here, we develop and validate a yeast-free "soda bread" that maintains its mechanical stability over several weeks in culture conditions. Importantly, we also demonstrate that control over the mechanical stability of the scaffold can also be achieved with both chemical and enzymatic means. The scaffolding is a heterogeneous and complex structure of isolated and interconnected pores which allow for the proliferation of multiple cell types. We demonstrate here that mouse fibroblasts, myoblasts and pre-osteoblasts are able to proliferate up to four weeks in culture. Immunohistochemistry demonstrates that the fibroblasts are able to deposit their own fibronectin extracellular matrix and that mouse myoblasts are able to differentiate and fuse into myotubes. Although the pre-osteoblasts proliferated over the course of four weeks their ability to differentiate was inconclusive. Metabolic analyses of proliferation, cytotoxicity and oxidative stress reveal that cells remain highly viable and functional on these novel bread scaffolds. While the results presented in this proof-of-concept study create many new questions and opportunities, the results open up novel possibilities in the development of edible scaffolds that may be utilized in future food applications. Bread derived scaffolds represent a surprising alternative to synthetic or animal-derived scaffolds for addressing a diverse variety of tissue engineering challenges in food science. Future studies will delve deeper into investigating these how possibilities might take advantage of the immense breadth of knowledge about bread making and examine their applicability in the development of lab grown foods and broader applications in cellular agriculture.

bioengineering↗