Recent developments in dynamic combinatorial chemistry

Generating combinatorial libraries under equilibrium conditions has the important advantage that the libraries are adaptive (i.e. they can respond to exterior influences in the form of molecular recognition events). Thus, a ligand will direct and amplify the formation of its ideal receptor and vice versa. Proof of principle of this approach has been established using small libraries showing highly efficient amplification of selected receptors. The approach has recently been extended to address folding of macromolecules, including peptides.     

Flow NMR applications in combinatorial chemistry

Flow NMR techniques are now well accepted and widely used in many areas of drug discovery. Although natural-product-, rational-drug-design-, and NMR-screening-programs have begun to use flow NMR more routinely, flow NMR has not yet gained widespread acceptance in combinatorial chemistry, even though it has been shown to be a potentially useful tool. Recent developments in DI-NMR, FIA-NMR, and LC-NMR will help flow NMR eventually gain a wider acceptance within combinatorial chemistry. These developments include LC-NMR-MS instrumentation, flow probe improvements, new pulse sequences, improved automation of NMR data analysis, and the application of flow NMR to related fields in drug discovery.     

From combinatorial chemistry to chemical microarray

Combinatorial chemistry was first applied to the generation of peptide arrays in 1984. Since then, the field of combinatorial chemistry has evolved rapidly into a new discipline. There is a great need for the development of methods to examine the proteome functionally at a global level. Using many of the techniques and instruments developed for DNA microarrays, chemical microarray methods have advanced significantly in the past three years. High-density chemical microarrays can now be synthesized in situ on glass slides or be printed through covalent linkage or non-specific adsorption to the surface of the solid-support with fully automatic arrayers. Microfabrication methods enable one to generate arrays of microsensors at the end of optical fibers or arrays of microwells on a flat surface. In conjunction with the one-bead one-compound combinatorial library method, chemical microarrays have proven to be very useful in lead identification and optimization. High-throughput protein expression systems, robust high-density protein, peptide and small-molecule microarray systems, and automatic mass spectrometers are critical tools for the field of functional proteomics.     

Recent applications of machine learning in medicinal chemistry

In recent decades, artificial intelligence and machine learning have played a significant role in increasing the efficiency of processes across a wide spectrum of industries. When it comes to the pharmaceutical and biotechnology sectors, numerous tools enabled by advancement of computer science have been developed and are now routinely utilized. However, there are many aspects of the drug discovery process, which can further benefit from refinement of computational methods and tools, as well as improvement of accessibility of these new technologies. In this review, examples of recent developments in machine learning application are described, which have the potential to impact different parts of the drug discovery and development flow scheme. Notably, new deep learning-based approaches across compound design and synthesis, prediction of binding, activity and ADMET properties, as well as applications of genetic algorithms are highlighted.     

Fragment-based drug discovery of carbonic anhydrase II inhibitors by dynamic combinatorial chemistry utilizing alkene cross metathesis

A fragment-based drug discovery approach to the synthesis and identification of small molecule inhibitors of bovine carbonic anhydrase II (bCA II) is described. The classical bCA II recognition fragment is an aromatic sulfonamide (ArSO2NH2) moiety. This fragment was incorporated into a scaffold building block, which was subsequently derivatized by dynamic combinatorial chemistry utilizing alkene cross metathesis as the reversible reaction. Screening against bCA II was then carried out and the results allowed determination of the relative bCA II binding affinities of the cross metathesis products that contained the ArSO2NH2 fragment. A bCA II competitive binding assay validated these results with a representative number of pure compounds. The results for screening, without prior isolation of the active constituent, were in full agreement with those obtained for equilibrium dissociation constants (K(i)'s) of pure compounds. Some of these compounds exhibited K(i)'s in the low nanomolar range. Heterogeneous catalysis was shown to be very effective in this drug discovery application of dynamic combinatorial chemistry.     

Microfluidic combinatorial chemistry

Microreactors are finding increasing application in the field of combinatorial chemistry. In the past few years, microreactor chemistry has shown great promise as a novel method on which to build new chemical technology and processes. It has been conclusively demonstrated that reactions performed within microreactors invariably generate relatively pure products in high yield. One of the immediate and obvious applications is therefore in combinatorial chemistry and drug discovery.     

Application of olefin metathesis in the synthesis of steroids

Over the past decade, ruthenium-mediated metathesis transformations, including cross-metathesis, ring-closing metathesis, enyne metathesis, ring-opening metathesis polymerization, and also tandem processes, belong to the most intensively studied reactions. Many applications of olefin metathesis in the synthesis of natural products have been recently described. Also in the field of steroid chemistry new methods of total synthesis and hemisynthesis based on metathesis reactions have been elaborated. Various biologically active compounds, e.g. vitamin D and hormone analogues, steroid dimers and macrocycles, etc. have been prepared using a variety of olefin-metathesis protocols.     

Nanotiterplates for combinatorial chemistry

Miniaturization has grown to be a driving force in modern chemical and biochemical laboratories. Combinatorial explosion demands for new pathways for the synthesis and screening of new substances which can act as leads in drug discovery. Highly parallelized automata that can handle the smallest amounts of substances are needed. However, the development is not always straightforward since new problems also arise in miniaturization, e.g. increasing importance of surface properties of utilized devices and evaporation of liquids. This paper reports on recent developments on the field of miniaturized reaction vessels called nanotiterplates. A survey on fabrication technologies as well as applications of nanotiterplates is given. Special emphasis is given to results of the development of an automaton for miniaturized synthesis and screening. Besides the mere fabrication of nanotiterplates with integrated microsieve bottom membranes, examples of applications in chemical synthesis and bio-assays are given. Further topics are the characterization and specific adaption of surface properties and investigations on the evaporation of solvents and measures for prevention.     

Automated synthesis and combinatorial chemistry

The advent of combinatorial chemistry for the high-throughput synthesis of compounds has driven the advancement of new and emerging technologies for synthetic chemistry laboratories. Automated methods for reaction design, information management, chemical synthesis, compound analysis, and biological testing are necessary to realize the full potential of combinatorial chemistry efforts.     

Single-bead analysis in combinatorial chemistry

Notable limitations have previously prevented the wide application of split synthesis. However, recent developments in highly condensed and miniaturized biological screening and single-bead analysis methods have argued for a revival of split combinatorial synthesis. Although there are still many challenges, we are now in a much better position to accomplish high-throughput analysis and screening of one-bead-one-compound libraries.     

Solid supports for combinatorial chemistry

Over the past year, numerous techniques have been used to study the resins commonly utilised in solid-phase synthesis to allow a greater understanding of the chemical nature and the physical properties of the supports. In addition, to overcome some of the drawbacks of existing materials, several new resins and new methods of handling solid supports have been developed. New methodologies have also been introduced to simplify the preparation of solid supports.     

Immobilized catalysts in combinatorial chemistry

As a new methodology for library synthesis in combinatorial chemistry, the use of immobilized catalysts and multi-component reactions is focused. In the past two years, many advances have been made in this emerging field, leading to the efficient library synthesis of, for example, quinolines, amino ketones and amino esters.     

Tin and iron halogenides as additives in ruthenium-catalyzed olefin metathesis

Different metal halogenides were used as additives in metathesis of 1-octene or in several cross-metathesis reactions catalysed by first and second generation Grubbs catalyst, 1 and 2, as well as by an improved first generation-type Grubbs catalyst 3. Tin(II) chloride and bromide enhance the performance of 1 and 3. The influence on 2 is rather minor under the chosen reaction conditions. The addition of iron(II) chloride and bromide results in an improvement of 1 to a lesser extent as the tin salts. The frequently observed isomerisation of olefins in metathesis reactions catalysed by 1 is suppressed in the presence of the applied tin salts.     

Synthesis of N-heterocyclic carbene ligands and derived ruthenium olefin metathesis catalysts

We describe the synthesis of commonly used free N-heterocyclic carbenes (NHCs), 1,3-bis-(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes) and 1,3-bis-(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr), and of the two corresponding ruthenium-based metathesis complexes. The complex containing IMes was found to be highly efficient in macrocyclizations involving ring-closing metatheses (RCM), whereas the complex featuring the IPr ligand shows excellent activity in both RCM and cross metathesis because of its greater stability. The free carbenes IMes and IPr are isolated in four steps, with an overall yield of ～50%. They are then used to replace a labile phosphine in precatalysts belonging to two families of ruthenium-containing complexes, benzylidene and indenylidene types, respectively. Such complexes are isolated as analytically pure compounds with 77% and 95% yield. The total time for the synthesis of the free NHCs is 56 h, and incorporation in complexes requires an additional 4-5 h.     

Synthesis of orthogonally reactive FK506 derivatives via olefin cross metathesis

Chemical inducers of dimerization (CIDs) are employed in a wide range of biological applications to control protein localization, modulate protein–protein interactions and improve drug lifetimes. These bifunctional chemical probes are assembled from two synthetic modules, which each provide affinity for a distinct protein target. FK506 and its derivatives are often employed as modules in the syntheses of these bifunctional constructs, owing to the abundance and favorable distribution of their target, FK506-binding protein (FKBP). However, the structural complexity of FK506 necessitates multi-step syntheses and/or multiple protection–deprotection schemes prior to installation into CIDs. In this work, we describe an efficient, one-step synthesis of FK506 derivatives through a selective, microwave-accelerated, cross metathesis diversification step of the C39 terminal alkene. Using this approach, FK506 is modified with an array of functional groups, including primary amines and carboxylic acids, which make the resulting derivatives suitable for the modular assembly of CIDs. To illustrate this idea, we report the synthesis of a heterobifunctional HIV protease inhibitor.     

Integrating cheminformatic analysis in combinatorial chemistry

Cheminformatic analysis of drug-related compound databases has enabled the identification of the physicochemical properties that have the greatest influence on determining the drug-like characteristics of a compound. This enables definition of the parameters and profiles used in constructing a high-quality combinatorial library. Awareness of the multi-objective nature of combinatorial library construction has also given rise to techniques designed to enhance the likelihood of including the best compounds in a given library.     

Mesofluidic devices for DNA-programmed combinatorial chemistry

Hybrid combinatorial chemistry strategies that use DNA as an information-carrying medium are proving to be powerful tools for molecular discovery. In order to extend these efforts, we present a highly parallel format for DNA-programmed chemical library synthesis. The new format uses a standard microwell plate footprint and is compatible with commercially available automation technology. It can accommodate a wide variety of combinatorial synthetic schemes with up to 384 different building blocks per chemical step. We demonstrate that fluidic routing of DNA populations in the highly parallel format occurs with excellent specificity, and that chemistry on DNA arrayed into 384 well plates proceeds robustly, two requirements for the high-fidelity translation and efficient in vitro evolution of small molecules.