Strategies for Exploring Functions from Dynamic Combinatorial Libraries

Kinetic Control of Complexity in Multiple Dynamic Libraries

Multiple dynamic libraries of compounds are generated when more than one reversible reaction comes into play. Commonly, two or more orthogonal reversible reactions are used, leading to non-communicating dynamic libraries which share no building blocks. Only a few examples of communicating libraries have been reported, and in all those cases, building blocks are reversibly exchanged from one library to the other, constituting an antiparallel dynamic covalent system. Herein we report that communication between two different dynamic libraries through an irreversible process is also possible. Indeed, alkyl amines cancel the dynamic regime on the nucleophilic substitution of tetrazines, generating kinetically inert compounds. Interestingly, such amine can be part of another dynamic library, an imine-amine exchange. Thus, both libraries are interconnected with each other by an irreversible process which leads to kinetically inert structures that contain parts from both libraries, causing a collapse of the complexity. Additionally, a latent irreversible intercommunication could be developed. In such a way, a stable molecular system with specific host-guest and fluorescence properties, could be irreversibly transformed when the right stimulus was applied, triggering the cancellation of the original supramolecular and luminescent properties and the emergence of new ones.

Modulating liquid-liquid phase separation of FUS: mechanisms and strategies

Liquid-liquid phase separation (LLPS) of biomolecules inspires the construction of protocells and drives the formation of cellular membraneless organelles. The resulting biomolecular condensates featuring dynamic assembly, disassembly, and phase transition play significant roles in a series of biological processes, including RNA metabolism, DNA damage response, signal transduction and neurodegenerative disease. Intensive investigations have been conducted for understanding and manipulating intracellular phase-separated disease-related proteins (e.g., FUS, tau and TDP-43). Herein, we review current studies on the regulation strategies of intracellular LLPS focusing on FUS, which are categorized into physical stimuli, biochemical modulators, and protein structural modifications, with summarized molecular mechanisms. This review is expected to provide a sketch of the modulation of FUS LLPS with its pros and cons, and an outlook for the potential clinical treatments of neurodegenerative diseases.

Graph-based Automated Macro-Molecule Assembly

We present a general molecular framework assembly algorithm that takes a largely arbitrary molecular fragment database and a user-supplied target template graph as input. Automatic assembly of molecular fragments from the database, following a prescribed, user-supplied set of connection rules, then turns the template graph into an actual, chemically reasonable molecular framework. Assembly capabilities of our algorithm are tested by producing several abstract, closed-loop shapes. To indicate a few of many possible application areas we demonstrate a host-guest complex and a road toward catalysis. Postassembly substituent exchange can be used to produce electric fields of desired values at desired points inside the framework or at its surface as a stepping stone toward rationally designed, artificial heterogeneous catalysts.

Sulfur in Dynamic Covalent Chemistry

Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

Development of "Imprint-and-Report" Dynamic Combinatorial Libraries for Differential Sensing Applications

Sensor arrays using synthetic receptors have found great utility in analyte detection, resulting from their ability to distinguish analytes based on differential signals via indicator displacement. However, synthesis and characterization of receptors for an array remain a bottleneck in the field. Receptor discovery has been streamlined using dynamic combinatorial libraries (DCLs), but the resulting receptors have primarily been utilized in isolation rather than as part of the entire library, with only a few examples that make use of the complexity of a library of receptors. Herein, we demonstrate a unique sensor array approach using "imprint-and-report" DCLs that obviates the need for receptor synthesis and isolation. This strategy leverages information stored in DCLs in the form of differential library speciation to provide a high-throughput method for both developing a sensor array and analyzing data for analyte differentiation. First, each DCL is templated with analyte to give an imprinted library, followed by in situ fluorescent indicator displacement analysis. We further demonstrate that the reverse strategy, imprinting with the fluorescent reporter followed by displacement with each analyte, provides a more sensitive method for differentiating analytes. We describe the development of this differential sensing system using the methylated Arg and Lys post-translational modifications (PTMs). Altogether, 19 combinations of 3-5 DCL data sets that discriminate all 7 PTMs were identified. Thus, a comparable sensor array workflow results in a larger payoff due to the immense information stored within multiple noncovalent networks.

Directing Transition of Synthetic Protocell Models via Physicochemical Cues-Triggered Interfacial Dynamic Covalent Chemistry

As the preliminary synthetic analogs of living cells, protocells with life-like features serve as a versatile platform to explore the origin of life. Although protocells constructed from multiple components have been developed, the transition of primitive cellular compartments toward structural complexity and advanced function remains a scientific challenge. Herein, a programmable pathway is established to exploit a simple chemistry to construct structural transition of protocell models from emulsion droplets, nanocapsules to molecularly crowded droplets. The transitional process toward distinct cell-like compartments is driven by interfacial self-assembly of simple components and regulated by physicochemical cues (e.g., mechanical force, solvent evaporation, acid/base equilibrium) triggered dynamic covalent chemistry. These protocell models are further studied by comparing their compartmentalization behavior, sequestration efficiency, and the ability to enrich biomolecules (e.g., enzyme and substrate) toward catalytic reaction or biological activity within the compartments. The results showcase physiochemical cues-driven programmable transition of life-like compartments toward functionalization, and offer a new step toward the design of living soft materials.

Design, synthesis and applications of responsive macrocycles

Inspired by the lock and key principle, the development of supramolecular macrocyclic chemistry has promoted the prosperous growth of host-guest chemistry. The updated induced-fit and conformation selection model spurred the emerging research on responsive macrocycles (RMs). This review introduces RMs, covering their design, synthesis and applications. It gives readers insight into the dynamic control of macrocyclic molecules and the exploration of materials with desired functions.

Self-Synthesizing Nanorods from Dynamic Combinatorial Libraries against Drug Resistant Cancer

Molecular self-assembly has been widely used to develop nanocarriers for drug delivery. However, most of them have unsatisfactory drug loading capacity (DLC) and the dilemma between stimuli-responsiveness and stability, stagnating their translational process. Herein, we overcame these drawbacks using dynamic combinatorial chemistry. A carrier molecule was spontaneously and quantitatively synthesized, aided by co-self-assembly with a template molecule and an anti-cancer drug doxorubicin (DOX) from a dynamic combinatorial library that was operated by disulfide exchange under thermodynamic control. The highly selective synthesis guaranteed a stable yet pH- and redox- responsive nanocarrier with a maximized DLC of 40.1 % and an enhanced drug potency to fight DOX resistance in vitro and in vivo. Our findings suggested that harnessing the interplay between synthesis and self-assembly in complex chemical systems could yield functional nanomaterials for advanced applications.