Forty years of combinatorial technology

Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.

Toward in Silico Modeling of Dynamic Combinatorial Libraries

Dynamic combinatorial libraries (DCLs) display adaptive behavior, enabled by the reversible generation of their molecular constituents from building blocks, in response to external effectors, e.g., protein receptors. So far, chemoinformatics has not yet been used for the design of DCLs-which comprise a radically different set of challenges compared to classical library design. Here, we propose a chemoinformatic model for theoretically assessing the composition of DCLs in the presence and the absence of an effector. An imine-based DCL in interaction with the effector human carbonic anhydrase II (CA II) served as a case study. Support vector regression models for the imine formation constants and imine-CA II binding were derived from, respectively, a set of 276 imines synthesized and experimentally studied in this work and 4350 inhibitors of CA II from ChEMBL. These models predict constants for all DCL constituents, to feed software assessing equilibrium concentrations. They are publicly available on the dedicated website. Models rationally selected two amines and two aldehydes predicted to yield stable imines with high affinity for CA II and provided a virtual illustration on how effector affinity regulates DCL members.

Design of Stimuli-Responsive Dynamic Covalent Delivery Systems for Volatile Compounds (Part 1): Controlled Hydrolysis of Micellar Amphiphilic Imines in Water

Despite their intrinsic hydrolysable character, imine bonds can become remarkably stable in water when self-assembled in amphiphilic micellar structures. In this work, we systematically studied some of these structures and the influence of various parameters that can be used to take control of their hydrolysis, including pH, concentration, the position of the imine function in the amphiphilic structure, relative lengths of the linked hydrophilic and hydrophobic moieties. Thermodynamic and kinetic data led us to the rational design of stable imines in water, partly based on the location of the imine function within the hydrophobic part of the amphiphile and on a predictable quantitative term that we define as the total hydrophilic-lipophilic balance (HLB). In addition, we show that such stable systems are also stimuli-responsive and therefore, of potential interest in trapping and releasing micellar components on demand.

Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry

Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.

Configurational and Constitutional Dynamics of Enamine Molecular Switches

Dual configurational and constitutional dynamics in systems based on enamine molecular switches has been systematically studied. pH-responsive moieties, such as 2-pyridyl and 2-quinolinyl units, were required on the "stator" part, also providing enamine stability through intramolecular hydrogen-bonding (IMHB) effects. Upon protonation or deprotonation, forward and backward switching could be rapidly achieved. Extension of the stator π-system in the 2-quinolinyl derivative provided a higher E-isomeric equilibrium ratio under neutral conditions, pointing to a means to achieve quantitative forward/backward isomerization processes. The "rotor" part of the enamine switches exhibited constitutional exchange ability with primary amines. Interestingly, considerably higher exchange rates were observed with amines containing ester groups, indicating potential stabilization of the transition state through IMHB. Acids, particularly BiIII , were found to efficiently catalyze the constitutional dynamic processes. In contrast, the enamine and the formed dynamic enamine system showed excellent stability under basic conditions. This coupled configurational and constitutional dynamics expands the scope of dynamic C-C and C-N bonds and potentiates further studies and applications in the fields of molecular machinery and systems chemistry.

Engineering multilayer chemical networks

Dynamic multilevel systems emerged in the last few years as new platforms to study thermodynamic systems. In this work, unprecedented fully communicated three-level systems are studied. First, different conditions were screened to selectively activate thiol/dithioacetal, thiol/thioester, and thiol/disulfide exchanges, individually or in pairs. Some of those conditions were applied, sequentially, to build multilayer dynamic systems wherein information, in the form of relative amounts of building blocks, can be directionally transmitted between different exchange pools. As far as we know, this is the first report of one synthetic dynamic chemical system where relationships between layers can be changed through network operations.

QCM sensing of multivalent interactions between lectins and well-defined glycosylated nanoplatforms

Quartz crystal microbalance (QCM) methodology has been adopted to unravel important factors contributing to the "cluster glycoside effect" observed in carbohydrate-lectin interactions. Well-defined, glycosylated nanostructures of precise sizes, geometries and functionalization patterns were designed and synthesized, and applied to analysis of the interaction kinetics and thermodynamics with immobilized lectins. The nanostructures were based on Borromean rings, dodecaamine cages, and fullerenes, each of which carrying a defined number of carbohydrate ligands at precise locations. The synthesis of the Borromeates and dodecaamine cages was easily adjustable due to the modular assembly of the structures, resulting in variations in presentation mode. The binding properties of the glycosylated nanoplatforms were evaluated using flow-through QCM technology, as well as hemagglutination inhibition assays, and compared with dodecaglycosylated fullerenes and a monovalent reference. With the QCM setup, the association and dissociation rate constants and the associated equilibrium constants of the interactions could be estimated, and the results used to delineate the multivalency effects of the lectin-nanostructure interactions.

Autopoietic Behavior of Dynamic Covalent Amphiphiles

The condensation of aldehydes and amines in water to give amphiphilic imines can lead to a particular autocatalytic behavior known as autopoiesis, in which the closed micellar structure made by the amphiphile at the mesoscale can accelerate the condensation of its constituents. Herein, through a combination of analytical tools, including diffusion ordered spectroscopy (DOSY) as well as light, neutron, and X-ray scattering techniques, the thermodynamic and kinetic parameters were probed at both the level of dynamic covalent imine bond formation and the level of the resulting micellar self-assemblies. It was found that the autopoietic behavior was the result of a combination of several parameters, including solubilization of hydrophobic building blocks, template effect at the core-shell interface, and growth/division cycles of the micellar objects.

Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3

Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC₅₀ =2.6 μm) and ALKBH3 (8; IC₅₀ =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.

Resolving a Reactive Organometallic Intermediate from Dynamic Directing Group Systems by Selective C-H Activation

Catalyst discovery from systems of potential precursors is a challenging endeavor. Herein, a new strategy applying dynamic chemistry to the identification of catalyst precursors from C-H activation of imines is proposed and evaluated. Using hydroacylation of imines as a model reaction, the selection of an organometallic reactive intermediate from a dynamic imine system, involving many potential directing group/metal entities, is demonstrated. The identity of the amplified reaction intermediate with the best directing group could be resolved in situ by ESI-MS, and coupling of the procedure to an iterative deconvolution protocol generated a system with high screening efficiency.

Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library

Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.

Dynamic Covalent Chemistry of Aldehyde Enamines: BiIII - and ScIII -Catalysis of Amine-Enamine Exchange

The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry.

Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins

We report a functional synthetic model for studying the noncovalent networks (NCNs) required for complex protein functions. The model [2]-catenane is self-assembled from dipeptide building blocks and contains an extensive network of hydrogen bonds and aromatic interactions. Perturbations to the catenane cause compensating changes in the NCNs structure and dynamics, resulting in long-distance changes reminiscent of a protein. Key findings include the notion that NCNs require regions of negative cooperativity, or "frustrated" noncovalent interactions, as a source of potential energy for driving the response. We refer to this potential energy as latent free energy and describe a mechanistic and energetic model for responsive systems.

Dynamic Covalent Nanoparticle Building Blocks

Rational and generalisable methods for engineering surface functionality will be crucial to realising the technological potential of nanomaterials. Nanoparticle-bound dynamic covalent exchange combines the error-correcting and environment-responsive features of equilibrium processes with the stability, structural precision, and vast diversity of covalent chemistry, defining a new and powerful approach for manipulating structure, function and properties at nanomaterial surfaces. Dynamic covalent nanoparticle (DCNP) building blocks thus present a whole host of possibilities for constructing adaptive systems, devices and materials that incorporate both nanoscale and molecular functional components. At the same time, DCNPs have the potential to reveal fundamental insights regarding dynamic and complex chemical systems confined to nanoscale interfaces.

Enzyme classification using complex dynamic hemithioacetal systems

A complex dynamic hemithioacetal system was used in combination with pattern recognition methodology to classify lipases into distinct groups.

A complex dynamic hemithioacetal system was generated for the evaluation of lipase reactivities in organic media. In combination with pattern recognition methodology, twelve different lipases were successfully classified into four distinct groups following their reaction selectivities and reactivities. A probe lipase was further categorized using the training matrix with predicted reactivity.

Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library

Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.

Light Scattering Strategy for the Investigation of Time-Evolving Heterogeneous Supramolecular Self-Assemblies

Supramolecular self-assembly is a multiple length-scale and time-dependent process involving many coexisting components. Such complexity requires suitable strategies to extract quantitative dynamical and structural information on all involved species. Here, we detail an original light scattering method to study the kinetics of tailored triarylamine molecules capable of self-assembling in supramolecular highly conductive nanowires upon light exposure. These micrometric assemblies cause the emergence of intermittences in the scattered intensity and the construction of a predominant slow mode in the correlation function making separation between small-and large-size species impossible using conventional treatments. Our strategy is based on the time monitoring of intermittences and allows us to determine the fraction of nanowires as well as those of small critical nuclei and triarylamine building blocks as a function of time and light exposure, in good agreement with recent theoretical predictions.

trans-Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions

The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3-proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two-dimensional dynamic systems with a high degree of complexity evolution. The transamination-transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate-limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity-generating element.

A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies

DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.