Immobilization of proteins in silica gel: Biochemical and biophysical properties

The development of silica-based sol-gel techniques compatible with the retention of protein structure and function started more than 20 years ago, mainly for the design of biotechnological devices or biomedical applications. Silica gels are optically transparent, exhibit good mechanical stability, are manufactured with different geometries, and are easily separated from the reaction media. Biomolecules encapsulated in silica gel normally retain their structural and functional properties, are stabilized with respect to chemical and physical insults, and can sometimes exhibit enhanced activity in comparison to the soluble form. This review briefly describes the chemistry of protein encapsulation within the pores of a silica gel three-dimensional network, the mechanism of interaction between the protein and the gel matrix, and its effects on protein structure, function, stability and dynamics. The main applications in the field of biosensor design are described. Special emphasis is devoted to silica gel encapsulation as a tool to selectively stabilize subsets of protein conformations for biochemical and biophysical studies, an application where silica-based encapsulation demonstrated superior performance with respect to other immobilization techniques

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{https://github.com/QizhiPei/BioT5}{Github}$.Comment: Accepted by Empirical Methods in Natural Language Processing 2023 (EMNLP 2023

Synthesis of Novel Fluorescent Benzothiazole Cyanine Dyes as Potential Imaging Agents

Near-infrared (NIR) fluorescence imaging has emerged as an attractive non-invasive approach for direct visualization of diseases which depends on the development of stable, highly specific and sensitive optical probes. The NIR region of the electronic spectrum offers a reduction in the background autofluorescence and an increase in the tissue penetration depth. Cyanine dyes have often been considered promising contrast optic agents owing to their photophysical properties. Herein the synthesis of various penta- and heptamethine benzothiazole cyanine dyes has been described and their in vivo imaging efficacy was determined. Varying functionalities on the benzothiazole aromatic ring and changing substituents on the benzothiazolium nitrogen atom reflected subsequent changes in the imaging pattern and have resulted in the development of promising brain targeting agents

A fragment based approach to the development of novel antibacterial agents inspired by the natural product simocyclinone D8

The novel mechanism of simocyclinone D8 (SD8) against DNA gyrase has inspired medicinal chemists for over a decade. The search for antibiotics with new mechanisms of action has never been more important with ever increasing prevalence of resistance. This project had three objectives. Firstly to contribute towards the total synthesis of SD8, by exploring chlorination reactions of dihydroxycoumarins and their corresponding starting reagents. Additionally, there was a need to establish a viable route towards the complex polyketide scaffold. Secondly, to generate a library of coumarins and screen for a low molecular weight fragment that could be taken forward as a lead compound. Thirdly, inspired by the bi-functional mode of action of SD8, the project sought to design and synthesise a coumarin-quinolone hybrid via a fragment-based approach. Herein we exploit ortho and para directing effects of phenolic OH groups to selectively chlorinate starting materials. However, we show chlorination of reagents prior to forming a coumarin is not a viable synthetic strategy. This is due to the reduced nucleophilicity imparted by the halogen on adjacent atoms. Consequently, this abrogates any ring closure reaction. We illustrate that a previously established Diels-Alder route can furnish a novel isomerised pericyclic adduct. This provides a good starting point for reaction optimisation and the onward enantioselective synthesis of the complex polyketide scaffold. Lastly, 27 different coumarin fragments were synthesised and assessed for biological activity. We illustrate that simple coumarins lack inhibition in supercoiling assays against DNA gyrase. Furthermore, when ciprofloxacin is attached to a linker there is an attenuation of activity. Strikingly, when a simple coumarin is joined to ciprofloxacin, via a linker there is a restoration of activity. We show DNA gyrase inhibition is via cleavage stabilisation. Moreover, we demonstrate activity is related to the coumarin structure and not the presence of an aromatic ring

A Balanced Secondary Structure Predictor

Secondary structure (SS) refers to the local spatial organization of the polypeptide backbone atoms of a protein. Accurate prediction of SS is a vital clue to resolve the 3D structure of protein. SS has three different components- helix (H), beta (E) and coil (C). Most SS predictors are imbalanced as their accuracy in predicting helix and coil are high, however significantly low in the beta. The objective of this thesis is to develop a balanced SS predictor which achieves good accuracies in all three SS components. We proposed a novel approach to solve this problem by combining a genetic algorithm (GA) with a support vector machine. We prepared two test datasets (CB471 and N295) to compare the performance of our predictors with SPINE X. Overall accuracy of our predictor was 76.4% and 77.2% respectively on CB471 and N295 datasets, while SPINE X gave 76.5% overall accuracy on both test datasets

A Balanced Secondary Structure Predictor

Secondary structure (SS) refers to the local spatial organization of the polypeptide backbone atoms of a protein. Accurate prediction of SS is a vital clue to resolve the 3D structure of protein. SS has three different components- helix (H), beta (E) and coil (C). Most SS predictors are imbalanced as their accuracy in predicting helix and coil are high, however significantly low in the beta. The objective of this thesis is to develop a balanced SS predictor which achieves good accuracies in all three SS components. We proposed a novel approach to solve this problem by combining a genetic algorithm (GA) with a support vector machine. We prepared two test datasets (CB471 and N295) to compare the performance of our predictors with SPINE X. Overall accuracy of our predictor was 76.4% and 77.2% respectively on CB471 and N295 datasets, while SPINE X gave 76.5% overall accuracy on both test datasets

Stable Fluorinated Antimicrobial Coatings

Contact antimicrobials for use in the medical device industry are being studied extensively to minimize the risk of hospital acquired infections, which are among the top ten leading causes of death in the US. Surfaces modified with quaternary ammonium containing side chains have been known to demonstrate excellent antimicrobial properties. Prior work has indicated that polyurethane surfaces with copolyoxetane soft blocks consisting of fluorinated and quaternary ammonium side chains can act as good antimicrobials. However, stabilizing the positive charge on the surface has been a challenge. The dissertation is aimed at creating a surface modifier that would confer a stable contact kill antimicrobial surface at very low modifier content, that is, less than 2 wt%. To achieve this objective, the study explored the introduction of a different fluorous group in the soft block to enhance stability. In particular, prior studies by other groups and early work by Kurt have shown that replacement of one of the terminal “chaperone” C-F bonds by C-H decreased surface tension. This led to the hypothesis that a –CF2H terminated “chaperone” group would be “amphiphilic” resulting in surface stability under both dry and wet conditions. Keeping this hypothesis in mind, a –CF2-CF2H (4F) terminal “chaperone” group was created in a modifier having two different 4F to quaternerary C12 ratios. It was found that polyurethanes prepared with a 66:34 ratio of 4F:C12 as the diol, performed as a very good surface modifier with high zeta potentials over a long period of time compared to the –CF3 based modifier. Antimicrobial tests performed within one week and four weeks after coating preparation have provided promising results that demonstrate improved biocidal stability. Guided by improved antimicrobial properties obtained with surface modifier polyurethanes made from P[(4F)(C12)-66:34-Mn], a new concept was explored by end-capping the same diol with isocyanatopropyltriethoxysilane and blending the end-capped diol with base polyurethane along with a 10 wt % cross linker. These modifiers show excellent antimicrobial properties (100% kill of bacteria) over one month with no observable changes in the zeta potential or surface morphologies. XPS analysis confirms the presence of quaternary ammonium on the surface. Preliminary kinetic studies show excellent antimicrobial properties for a 2 wt% modifier and 100% kill within 1 hr