A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry

Photocatalytic functionalization of white phosphorus with aryl bromides and chlorides

We report the implementation of a consecutive photoinduced electron transfer (conPET) strategy for the functionalization of white phosphorus (P4) with inexpensive and widely available aryl bromides and chlorides. By employing a well-known acridinium-based photocatalyst under near-UV irradiation, this protocol gives direct access to valuable triarylphosphines and tetraarylphosphonium salts. The reaction mechanism is elucidated by NMR spectroscopic studies and model reactions.

Trityl isocyanide as a general reagent for visible light mediated photoredox-catalyzed cyanations

A photoredox catalytic strategy has been developed to enable the functionalization of a variety of commercially available, structurally different radical precursors by the use of a bench-stable isonitrile as an efficient cyanating reagent. Specifically, a radical-based reaction has provided a mild and convenient procedure for the cyanation of primary, secondary and tertiary radicals derived from widely accessible sp3-hybridized carboxylic acids, alcohols and halides under visible light irradiation. The reaction tolerates a variety of functional groups and it represents a complementary method for the cyanation of structurally different scaffolds that show diverse native functionalities, expanding the scope of previously reported methodologies.

Iron-Catalyzed, Light-Driven Decarboxylative Alkoxyamination

An iron-catalyzed visible-light driven decarboxylative alkoxyamination is disclosed. In the presence of FeBr2 and TEMPO, a large array of carboxylic acids including marketed drugs and biobased molecules is turned into the corresponding alkoxyamine derivatives. The versatility of the latter offers an entry towards molecular diversity generation from abundant starting materials and catalyst. Overall, this method proposes a unified and general approach for LMCT-based iron-catalyzed decarboxylative functionalization.

Building Block-Centric Approach to DNA-Encoded Library Design

DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.

Transition metal-free decarboxylative olefination of carboxylic acid salts

The cost-effective and efficient synthesis of alkenes is highly significant due to their extensive applications in both synthetic and polymer industries. A transition metal-free approach has been devised for the chemoselective olefination of carboxylic acid salts. This modular approach provides direct access to valuable electron-deficient styrenes in moderate to good yields. Detailed mechanistic studies suggest anionic decarboxylation is followed by halogen ion transfer. This halogen transfer leads to an umpolung of reactant electronics, allowing for a rate-limiting rebound elimination.

Toward a Chemical Constructor: A Lego-Like Approach for Formal α-Alkylation of Cyclic Ketones

A conceptual strategy for a formal α-alkylation of α-methylene ketones was developed. Diverse 1° and 2° alkyl substituents were generated in the α-position of various ketones via synthesis of enaminone (step 1) and treatment with organomagnesium (step 2) with subsequent catalytic hydrogenation (step 3, 1° alkyl) or organocopper reagents (step 4, 2° alkyl). Tolerance toward ester, Boc-protected amine, and α-fluoro-substituted ketone moieties was demonstrated. The suitability of the method for late-stage natural product modification was shown.

Hydroamination of Triisopropylsilyl Acetylene Sulfur Pentafluoride - a Bench-top Route to Pentafluorosulfanylated Enamines

Synthetic access to a variety of aliphatic and vinylic pentafluorosulfanylated building blocks remains a major challenge in contemporary organofluorine chemistry hampering its investigation in the context of medicinal chemistry, agrochemistry and functional materials. Herein, we report a bench-top protocol to access the virtually unknown class of α-SF5 -enamines under mild reaction conditions in good to excellent yields (up to 95 %). This reaction combines the protodesilylation of the commercially available precursor TASP with the in situ hydroamination of HC≡C-SF5 . The on-site use of highly toxic gases or corrosive reagents is avoided, making access to this motif applicable to a wide chemical audience. The excellent E-diastereoselectivity of this two-step cascade reaction is suggested to be the result of the convergence of the fast Z-/E- isomerization of a vinyl anion as well as the isomerization of the iminium ion. The remarkable thermal stability of these SF5 -enamines encourages further studies of their synthetic utility.

SNAr or Sulfonylation? Chemoselective Amination of Halo(het)arene Sulfonyl Halides for Synthetic Applications and Ultralarge Compound Library Design

The chemoselectivity of halo(het)arene sulfonyl halide aminations is studied thoroughly under parallel synthesis conditions, and the scope and limitations of the method are established. It is shown that SNAr-reactive sulfonyl halides typically undergo sulfonamide synthesis during the first step; the second amination is also possible provided that the SNAr-active center is sufficiently reactive. On the contrary, sulfonyl fluorides bearing an arylating moiety undergo selective transformation at the latter reactive center under proper control. Further sulfur-fluoride exchange (SuFEx) is also possible, which can be especially valuable for some sulfonyl halide classes. The developed two-step parallel double amination protocol provides access to a 6.67-billion compound synthetically tractable REAL-type chemical space (76% expected synthesis success rate).

Organocatalytic Decarboxylative Borylation of Cyclopropane N-Hydroxyphthalimide Esters

A convenient protocol for the two-step organocatalytic decarboxylative borylation of 1,1-disubstituted, 1,2-disubstituted, and bicyclic cyclopropane carboxylic acids via the corresponding N-hydroxyphthalimide esters is described, using tert-butyl or ethyl isonicotinate as an inexpensive and readily available catalyst. The scope of the method was demonstrated, being limited mainly by electron-poor substrates. The reaction sequence showed good scalability (up to 51.5 g) and excellent trans diastereoselectivity (for the case of 1,2-disubstituted substrates). Therefore, the proposed approach is a very promising alternative to other existing (i.e., metal-catalyzed) methods for borodecarboxylation.

Photoredox-Catalyzed Generation of Tertiary Anions from Primary Amines via a Radical Polar Crossover

A method for the generation of tertiary carbanions via a deaminative radical-polar crossover is reported using redox active imines from α-tertiary primary amines. A variety of benzylic amines and amino esters can be used in this approach, with the latter engaging in a novel "aza-Reformatsky" reaction. Electronic trends correlate the stability of the resulting carbanion with reaction efficiency. The anions can be trapped with different electrophiles including aldehydes, ketones, imines, Michael acceptors, and H2 O/D2 O. Selective anion formation can be achieved in the presence of another equivalent or more acidic C-H bond in both an inter- and intramolecular fashion. Mechanistic studies suggest the intermediacy of a discrete carbanion intermediate.

Aza-Heterocyclic Building Blocks with In-Ring CF2 -Fragment

Modern organic chemistry is a titan supporting and reinforcing pharmaceutical, agricultural, food and material science products. Over the past decades, the organic compounds market has been evolving to meet all the research demands. In this regard, medicinal chemistry is especially dependent on available chemical space as subtle tuning of the molecule structure is required to create a drug with relevant physicochemical properties and a remarkable activity profile. The recent rapid evolution of synthetic methodology to deploy fluorine has brought fluorinated compounds to the spotlight of MedChem community. And now unique properties of fluorine still keep fascinating more and more as its justified installation into a molecular framework has a beneficial impact on membrane permeability, lipophilicity, metabolic stability, pharmacokinetic properties, conformation, pKa , etc. The backward influence of medicinal chemistry on organic synthesis has also changed the landscape of the latter towards new fluorinated topologies as well. Such complex relationships create a flexible and ever-changing ecosystem. Given that MedChem investigations strongly lean on the ability to reach suitable building blocks and the existence of reliable synthetic methods in this review we collected advances in the chemistry of respectful, but still enigmatic gem-difluorinated aza-heterocyclic building blocks.

Decarboxylative Cross-Electrophile Coupling of (Hetero)Aromatic Bromides and NHP Esters

Aryl bromides are known to be challenging substrates in the decarboxylative cross-electrophile coupling with redox-active NHP esters-the majority of such processes utilize aryl iodides. Herein, we describe the development of conditions that are suitable for the decarboxylative cross-electrophile coupling of NHP esters and a wide range of (hetero)aryl bromides. The key advances that allowed for the use of aryl bromides in this reaction are (1) the identification of ligand L3 as an optimal ligand for the use of electron-neutral and deficient aryl bromides and (2) the significant improvement in yield that iodide salts and excess heterogenous zinc impart to this reaction. A wide variety of NHP esters perform well under the optimized conditions, including methyl, primary, secondary, and several strained tertiary systems. Likewise, a variety of aromatic and heteroaromatic bromides relevant to medicinal chemistry perform well in this transformation, including an aryl bromide precursor to the known drug dapagliflozin.

Evaluation of the Topology Space of DNA-Encoded Libraries

DNA-encoded libraries (DELs) are widely used in the discovery of drug candidates, and understanding their design principles is critical for accessing better libraries. Most DELs are combinatorial in nature and are synthesized by assembling sets of building blocks in specific topologies. In this study, different aspects of library topology were explored and their effect on DEL properties and chemical diversity was analyzed. We introduce a descriptor for DEL topological assignment (DELTA) and use it to examine the landscape of possible DEL topologies and their coverage in the literature. A generative topographic mapping analysis revealed that the impact of library topology on chemical space coverage is secondary to building block selection. Furthermore, it became apparent that the descriptor used to analyze chemical space dictates how structures cluster, with the effects of topology being apparent when using three-dimensional descriptors but not with common two-dimensional descriptors. This outcome points to potential challenges of attempts to predict DEL productivity based on chemical space analyses alone. While topology is rather inconsequential for defining the chemical space of encoded compounds, it greatly affects possible interactions with target proteins as illustrated in docking studies using NAD/NADP binding proteins as model receptors.

Which boronic acids are used most frequently for synthesis of bioactive molecules?

Boronic acids are essential building blocks used for the synthesis of bioactive molecules, the generation of chemical libraries and the exploration of structure-activity relationships. As a result, more than ten thousand boronic acids are commercially available. Medicinal chemists are therefore facing a challenge; which of them should they select to maximize information obtained by the synthesis of new target molecules. The present article aims to help them to make the right choices. The boronic acids used frequently in the synthesis of bioactive molecules were identified by mining several large molecular and reaction databases and their properties were analyzed. Based on the results a diverse set of boronic acids covering well the bioactive chemical space was selected and is suggested as a basis for library design for the efficient exploration of structure-activity relationships. A Boronic Acid Navigator web tool which helps chemists to make their own selection is also made available at https://bit.ly/boronics.

Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case

The development of DNA-encoded library (DEL) technology introduced new challenges for the analysis of chemical libraries. It is often useful to consider a chemical library as a stand-alone chemoinformatic object─represented both as a collection of independent molecules, and yet an individual entity─in particular, when they are inseparable mixtures, like DELs. Herein, we introduce the concept of chemical library space (CLS), in which resident items are individual chemical libraries. We define and compare four vectorial library representations obtained using generative topographic mapping. These allow for an effective comparison of libraries, with the ability to tune and chemically interpret the similarity relationships. In particular, property-tuned CLS encodings enable to simultaneously compare libraries with respect to both property and chemotype distributions. We apply the various CLS encodings for the selection problem of DELs that optimally "match" a reference collection (here ChEMBL28), showing how the choice of the CLS descriptors may help to fine-tune the "matching" (overlap) criteria. Hence, the proposed CLS may represent a new efficient way for polyvalent analysis of thousands of chemical libraries. Selection of an easily accessible compound collection for drug discovery, as a substitute for a difficult to produce reference library, can be tuned for either primary or target-focused screening, also considering property distributions of compounds. Alternatively, selection of libraries covering novel regions of the chemical space with respect to a reference compound subspace may serve for library portfolio enrichment.

Enabling Deoxygenative C(sp2)-C(sp3) Cross-Coupling for Parallel Medicinal Chemistry

Herein we report the development of an automated deoxygenative C(sp2)-C(sp3) coupling of aryl bromide with alcohols to enable parallel medicinal chemistry. Alcohols are among the most diverse and abundant building blocks, but their usage as alkyl precursors has been limited. Although metallaphotoredox deoxygenative coupling is becoming a promising strategy to form C(sp2)-C(sp3) bond, the reaction setup limits its widespread application in library synthesis. To achieve high throughput and consistency, an automated workflow involving solid-dosing and liquid-handling robots has been developed. We have successfully demonstrated this high-throughput protocol is robust and consistent across three automation platforms. Furthermore, guided by cheminformatic analysis, we examined alcohols with comprehensive chemical space coverage and established a meaningful scope for medicinal chemistry applications. By accessing the rich diversity of alcohols, this automated protocol has the potential to substantially increase the impact of C(sp2)-C(sp3) cross-coupling in drug discovery.

Late-stage Functionalization for Improving Drug-like Molecular Properties

The development of late-stage functionalization (LSF) methodologies, particularly C-H functionalization, has revolutionized the field of organic synthesis. Over the past decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, allowing for the drug discovery process to become more efficient. Most reported applications of late-stage C-H functionalization of drugs and drug-like molecules have been to rapidly diversify screening libraries to explore structure-activity relationships. However, there has been a growing trend toward the use of LSF methodologies as an efficient tool for improving drug-like molecular properties of promising drug candidates. In this review, we have comprehensively reviewed recent progress in this emerging area. Particular emphasis is placed on case studies where multiple LSF techniques were implemented to generate a library of novel analogues with improved drug-like properties. We have critically analyzed the current scope of LSF strategies to improve drug-like properties and commented on how we believe LSF can transform drug discovery in the future. Overall, we aim to provide a comprehensive survey of LSF techniques as tools for efficiently improving drug-like molecular properties, anticipating its continued uptake in drug discovery programs.

Synthesis of 2-Fluorobenzofuran by Photocatalytic Defluorinative Coupling and 5-endo-trig Cyclization

An alkyl radical-triggered dual C-F bond cleavage of α-CF₃-ortho-hydroxystyrenes for the synthesis of 2-fluorobenzofurans was developed. The visible-light-induced defluorinative cross-coupling reactions of α-CF₃-ortho-hydroxystyrenes with a variety of carboxylic acids produced gem-difluoroalkenes, which underwent S_NV-type 5-endo-trig cyclization to give 2-fluorobenzofurans. Mechanistic studies indicated that the electron transfer between phenoxyl radicals and carboxylates was the major pathway for the generation of alkyl radicals.

An update on late-stage functionalization in today's drug discovery

INTRODUCTION

Late-stage functionalization (LSF) allows for the introduction of new chemical groups toward the end of a synthetic sequence, which means new molecules can be rapidly accessed without laborious de novo chemical synthesis. Over the last decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, affording benefits such as efficient access to diverse libraries to explore structure-activity relationships and the improvement of physicochemical and pharmacokinetic properties.

AREAS COVERED

An overview of the key advancements in LSF methodology development from 2019 to 2022 and their applicability to drug discovery is provided. In addition, several examples from both academia and industry where LSF methodologies have been applied by medicinal chemists to their drug discovery programs are presented.

EXPERT OPINION

Utilization of LSF by medicinal chemists is on the rise, both in academia and in industry. The maturation of the LSF field to produce methodologies bearing increased regioselectivity, scope, and functional group tolerance is envisaged to narrow the gap between methodology development and medicinal chemistry research. The authors predict that the sheer versatility of these techniques in facilitating challenging chemical transformations of bioactive molecules will continue to increase the efficiency of the drug discovery process.

Computational approaches streamlining drug discovery

Computer-aided drug discovery has been around for decades, although the past few years have seen a tectonic shift towards embracing computational technologies in both academia and pharma. This shift is largely defined by the flood of data on ligand properties and binding to therapeutic targets and their 3D structures, abundant computing capacities and the advent of on-demand virtual libraries of drug-like small molecules in their billions. Taking full advantage of these resources requires fast computational methods for effective ligand screening. This includes structure-based virtual screening of gigascale chemical spaces, further facilitated by fast iterative screening approaches. Highly synergistic are developments in deep learning predictions of ligand properties and target activities in lieu of receptor structure. Here we review recent advances in ligand discovery technologies, their potential for reshaping the whole process of drug discovery and development, as well as the challenges they encounter. We also discuss how the rapid identification of highly diverse, potent, target-selective and drug-like ligands to protein targets can democratize the drug discovery process, presenting new opportunities for the cost-effective development of safer and more effective small-molecule treatments.

Aryl diazonium intermediates enable mild DNA-compatible C-C bond formation for medicinally relevant combinatorial library synthesis

Forging carbon-carbon (C-C) linkage in DNA-encoded combinatorial library synthesis represents a fundamental task for drug discovery, especially with broad substrate scope and exquisite functional group tolerance. Here we reported the palladium-catalyzed Suzuki-Miyaura, Heck and Hiyama type cross-coupling via DNA-conjugated aryl diazonium intermediates for DNA-encoded chemical library (DEL) synthesis. Starting from commodity arylamines, this synthetic route facilely delivers vast chemical diversity at a mild temperature and pH, thus circumventing damage to fragile functional groups. Given its orthogonality with traditional aryl halide-based cross-coupling, the aryl diazonium-centered strategy expands the compatible synthesis of complex C-C bond-connected scaffolds. In addition, DNA-tethered pharmaceutical compounds (e.g., HDAC inhibitor) are constructed without decomposition of susceptible bioactive warheads (e.g., hydroxamic acid), emphasizing the superiority of the aryl diazonium-based approach. Together with the convenient transformation into an aryl azide photo-crosslinker, aryl diazonium's DNA-compatible diversification synergistically demonstrated its competence to create medicinally relevant combinatorial libraries and investigate protein-ligand interactions in pharmaceutical research.

Chemical Multiverse: An Expanded View of Chemical Space

Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, and other research areas have attracted the scientific community's attention. The large- and ultra-large chemical spaces are associated with the significant increase in the number of compounds that can potentially be made and exist and the increasing number of experimental and calculated descriptors, that are emerging that encode the molecular structure and/or property aspects of the molecules. Due to the importance and continued evolution of compound libraries, herein, we discuss definitions proposed in the literature for chemical space and emphasize the convenience, discussed in the literature to use complementary descriptors to obtain a comprehensive view of the chemical space of compound data sets. In this regard, we introduce the term chemical multiverse to refer to the comprehensive analysis of compound data sets through several chemical spaces, each defined by a different set of chemical representations. The chemical multiverse is contrasted with a related idea: consensus chemical space.

Approaches for enhancing the analysis of chemical space for drug discovery

INTRODUCTION

Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemical compounds in databases, generators of chemical structures, and tools to calculate molecular descriptors, novel approaches to generate visual representations of chemical space in low dimensions are emerging and evolving. Such approaches include a wide range of commercial and free applications, software, and open-source methods.

AREAS COVERED

The current state of chemical space in drug design and discovery is reviewed. The topics discussed herein include advances for efficient navigation in chemical space, the use of this concept in assessing the diversity of different data sets, exploring structure-property/activity relationships for one or multiple endpoints, and compound library design. Recent advances in methodologies for generating visual representations of chemical space have been highlighted, thereby emphasizing open-source methods.

EXPERT OPINION

Quantitative and qualitative generation and analysis of chemical space require novel approaches for handling the increasing number of molecules and their information available in chemical databases (including emerging ultra-large libraries). In addition, it is of utmost importance to note that chemical space is a conceptual framework that goes beyond visual representation in low dimensions. However, the graphical representation of chemical space has several practical applications in drug discovery and beyond.

Synthesis of α-C-Stereochemically Pure Secondary Sulfonamides

A convenient "green" stereoretentive approach to sp³-enriched secondary sulfonamides bearing an asymmetric center at the α position to the sulfur atom is described. The method relies on the electrophilic amination of the corresponding stereochemically pure sulfinates with N-alkylhydroxylamine sulfonic acids (in turn easily prepared from N-alkylhydroxylamine and HSO₃Cl). It is shown that the efficiency of the approach is governed mainly by steric factors; its tolerance to several functional groups (e.g., ether, phthalimide, or N-Boc carbamate) is also demonstrated.

Exploration of Ultralarge Compound Collections for Drug Discovery

Designing new medicines more cheaply and quickly is tightly linked to the quest of exploring chemical space more widely and efficiently. Chemical space is monumentally large, but recent advances in computer software and hardware have enabled researchers to navigate virtual chemical spaces containing billions of chemical structures. This review specifically concerns collections of many millions or even billions of enumerated chemical structures as well as even larger chemical spaces that are not fully enumerated. We present examples of chemical libraries and spaces and the means used to construct them, and we discuss new technologies for searching huge libraries and for searching combinatorially in chemical space. We also cover space navigation techniques and consider new approaches to de novo drug design and the impact of the "autonomous laboratory" on synthesis of designed compounds. Finally, we summarize some other challenges and opportunities for the future.

Palladium-Mediated Hydroamination of DNA-Conjugated Aryl Alkenes

C-N bond formation is one of the most commonly used reactions in medicinal chemistry. Herein, we report an efficient Pd-promoted hydroamination reaction between DNA-conjugated aryl alkenes and a wide scope of aliphatic amines. The described reactions are demonstrated in good to excellent conversions to furnish C (sp3)–N bonds on DNA. This DNA-compatible transformation has strong potentials for the application into DNA-encoded library synthesis.