Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.

The synthesis of poly(arylthiols) and their utilization in the preparation of cross-linked dynamic covalent polymer nanoparticles and hydrogels

Poly(arylthiols) can reversibly cross-link to form nanoparticles and hydrogels.

Enhancing the kinetics of hydrazone exchange processes: an experimental and computational study

Hydrogen-bond acceptors (A) stabilize the transition state, lowering the energy barrier to rapid hydrazone exchange, without need for exogenous catalyst.

Label-Free Detection of Tear Biomarkers Using Hydrogel-Coated Gold Nanoshells in a Localized Surface Plasmon Resonance-Based Biosensor

The dependence of the localized surface plasmon resonance (LSPR) of noble-metal nanomaterials on refractive index makes LSPR a useful, label-free signal transduction strategy for biosensing. In particular, by decorating gold nanomaterials with molecular recognition agents, analytes of interest can be trapped near the surface, resulting in an increased refractive index surrounding the nanomaterial, and, consequently, a red shift in the LSPR wavelength. Ionic poly( N-isopropylacrylamide- co-methacrylic acid) (PNM) hydrogels were used as protein receptors because PNM nanogels exhibit a large increase in refractive index upon protein binding. Specifically, PNM hydrogels were synthesized on the surface of silica gold nanoshells (AuNSs). This composite material (AuNS@PNM) was used to detect changes in the concentration of two protein biomarkers of chronic dry eye: lysozyme and lactoferrin. Both of these proteins have high isoelectric points, resulting in electrostatic attraction between the negatively charged PNM hydrogels and positively charged proteins. Upon binding lysozyme or lactoferrin, AuNS@PNM exhibits large, concentration-dependent red shifts in LSPR wavelength, which enabled the detection of clinically relevant concentration changes of both biomarkers in human tears. The LSPR-based biosensor described herein has potential utility as an affordable screening tool for chronic dry eye and associated conditions.

Probing the Surfaces of Biomacromolecules with Polymer-Scaffolded Dynamic Combinatorial Libraries

Methods to analyze and compare biomacromolecular surfaces are still in their relative infancy on account of the challenges involved in comparing surfaces computationally. We describe a systems chemistry approach that utilizes polymer-scaffolded dynamic combinatorial libraries to experimentally probe biomacromolecular surfaces in aqueous solution which provides feedback as to the nature of the surfaces, allowing the comparison of three globular proteins and a nucleic acid.

Templated Self-Assembly of Dynamic Peptide Nucleic Acids

Template-directed macromolecule synthesis is a hallmark of living systems. Inspired by this natural process, several fundamentally novel mechanisms for template-directed assembly of nucleic acid analogues have been developed. Although these approaches have broad significance, including potential applications in biotechnology and implications for the origins of life, there are unresolved challenges in how to characterize in detail the complex assembly equilibria associated with dynamic templated reactions. Here we describe mechanistic studies of template-directed dynamic assembly for thioester peptide nucleic acid (tPNA), an informational polymer that responds to selection pressures under enzyme-free conditions. To overcome some of the inherent challenges of mechanistic studies of dynamic oligomers, we designed, synthesized, and implemented tPNA-DNA conjugates. The DNA primer region affords a high level of control over the location and register of the tPNA backbone in relation to the template strand. We characterized the degree and kinetics of dynamic nucleobase mismatch correction at defined backbone positions. Furthermore, we report the fidelity of dynamic assembly in tPNA as a function of position along the peptide backbone. Finally, we present theoretical studies that explore the level of fidelity that can be expected for an oligomer having a given hybridization affinity in dynamic templated reactions and provide guidance for the future development of sequence self-editing polymers and materials. As our results demonstrate, the use of molecular conjugates of constitutionally static and dynamic polymers establishes a new methodology for expediting the characterization of the complex chemical equilibria that underlie the assembly of dynamic informational polymers.

A Closer Look at the Impact of Molecular Imprinting on Adsorption Capacity and Selectivity for Protein Templates

Molecularly imprinted polymers (MIPs) are often investigated as lower cost, more environmentally robust alternatives to natural recognitive biomolecules, such as antibodies. When synthesized on the surface of nanomaterial supports, MIPs are capable of quick and effective binding of macromolecular templates when compared to traditional bulk-imprinted polymers. We have developed a method for imprinting proteins on biodegradable nanoparticle supports and have used these materials to investigate the impact of molecular imprinting on adsorption capacity and selectivity for lysozyme, the template protein. The imprinting process increased the adsorption capacity of the polymer for the template, lysozyme, with the MIPs being able to bind up to 83.5% of their dry weight as compared to 55.7% for nonimprinted polymers (NIPs). In noncompetitive binding experiments, where proteins were independently incubated with MIPs, the difference between adsorption capacity for lysozyme and proteins with much lower isoelectric points (pI < 8.0) was statistically significant. However, there was no statistical difference between adsorption capacity for lysozyme and other high-isoelectric point proteins, suggesting that MIPs are semiselective for this class of proteins. In competitive binding experiments, both MIPs and NIPs preferentially bound lysozyme over other high-isoelectric point proteins. This result demonstrated that imprinting alone could not account for the observed selectivity for lysozyme. Analysis of the solvent accessible surface area of lysozyme and its high-isoelectric point competitors revealed why lysozyme is an exceptional binder to the polymer system used in this work, with or without imprinting.

Switching biological functionalities of biointerfaces via dynamic covalent bonds

We construct a stimuli responsive biointerface via a dynamic covalent bond that could switch its surface biofunctionalities on demand. The switchability is achieved via reversible attaching/detaching of aldehyde end-functionalized biomacromolecules.

Templating carbohydrate-functionalised polymer-scaffolded dynamic combinatorial libraries with lectins

The templation of carbohydrate-functionalised Polymer-Scaffolded Dynamic Combinatorial Libraries affords polymers possessing significantly enhanced affinities for the template, with enhancements in free energy of binding in the range of 5.2–8.8 kJ mol⁻¹ observed.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

Mimicking nature with synthetic macromolecules capable of recognition

Nature has, through billions of years of evolution, assembled a multitude of polymeric macromolecules capable of exquisite molecular recognition. This functionality arises from the precise control exerted over their biosynthesis that results in key residues being anchored in the appropriate positions to interact with target substrates. Developing 'wholly synthetic' macromolecular analogues that can mimic this behaviour presents a considerable challenge to chemists, who lack the 'biological machinery' used in nature to assemble polymers with such precision. In addressing this challenge, familiar chemical concepts, such as combinatorial methods and supramolecular interactions, have been adapted for application in the macromolecular arena. Working from a limited set of residues, synthetic macromolecules have been produced that display surprisingly high binding affinities towards target proteins, even possessing useful in vivo activities. These observations are all the more surprising when one considers the heterogeneity inherent within these synthetic macromolecular receptors, and provoke intriguing questions regarding our assumptions about the design of receptors.