Late-Stage Functionalization of Drug-Like Molecules Using Diversinates

Reaction strategies for the meta-selective functionalization of pyridine through dearomatization

The pyridine moiety is a crucial structural component in various pharmaceuticals. While the direct ortho- and para-functionalization of pyridines is relatively straightforward, the meta-selective C-H functionalization remains a significant challenge. This review highlights dearomatization strategies as a key area of interest in expanding the application of meta-C-H functionalization of pyridines. Dearomatization enables the meta-functionalization through various catalytic methods that directly generate dearomatization products, and some products can be rearomatized back to pyridine derivatives. Furthermore, this article also covers the dearomatization of multiple positions of pyridine in the synthesis of polycyclic compounds. It offers a comprehensive overview of the latest advancements in dearomatization at different positions of pyridine, aiming to provide a valuable resource for researchers in this field. It also highlights the advantages and limitations of existing technologies, aiming to inform a broader audience about this important field and foster its future development.

Organophotoredox Catalysis: Switchable Radical Generation from Alkyl Sodium Sulfinates for Sulfonylation and Alkylative Activation of C-C Bonds of Cyclopropenes

Generating alkyl radicals from the sulfonyl radicals remains challenging in synthetic chemistry. Here, we report an efficient photocatalyzed strategy using alkyl sodium sulfinates as both sulfonylating and alkylating reagents by controlling the reaction temperature. This methodology provides a versatile protocol for synthesizing diastereoselective sulfonylated cyclopropanes and poly-substituted styrene derivatives. This methodology is successfully demonstrated with a wide variety of cyclopropenes and alkyl sulfinates, showcasing its broad substrate scope, high diastereo- and E/Z selectivity, and yielding good to excellent yields.

Predictive Minisci late stage functionalization with transfer learning

Structural diversification of lead molecules is a key component of drug discovery to explore chemical space. Late-stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity of LSF is still an open challenge in the field. Numerous efforts from chemoinformatics and machine learning (ML) groups have made strides in this area. However, it is arduous to isolate and characterize the multitude of LSF products generated, limiting available data and hindering pure ML approaches. We report the development of an approach that combines a message passing neural network and 13C NMR-based transfer learning to predict the atom-wise probabilities of functionalization for Minisci and P450-based functionalizations. We validated our model both retrospectively and with a series of prospective experiments, showing that it accurately predicts the outcomes of Minisci-type and P450 transformations and outperforms the well-established Fukui-based reactivity indices and other machine learning reactivity-based algorithms.

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.

Alkyl sulfinates as cross-coupling partners for programmable and stereospecific installation of C(sp3) bioisosteres

In recent years, a variety of cycloalkyl groups with quaternary carbons, in particular cyclopropyl and cyclobutyl trifluoromethyl groups, have emerged as promising bioisosteres in drug-like molecules. The modular installation of such bioisosteres remains challenging to synthetic chemists. Alkyl sulfinate reagents have been developed as radical precursors to prepare functionalized heterocycles with the desired alkyl bioisosteres. However, the innate (radical) reactivity of this transformation poses reactivity and regioselectivity challenges for the functionalization of any aromatic or heteroaromatic scaffold. Here we showcase the ability of alkyl sulfinates to engage in sulfurane-mediated C(sp3)-C(sp2) cross-coupling, thereby allowing for programmable and stereospecific installation of these alkyl bioisosteres. The ability of this method to simplify retrosynthetic analysis is exemplified by the improved synthesis of multiple medicinally relevant scaffolds. Experimental studies and theoretical calculations for the mechanism of this sulfur chemistry reveal a ligand-coupling trend under alkyl Grignard activation via the sulfurane intermediate, stabilized by solvation of tetrahydrofuran.

Late-stage functionalization of 5-nitrofurans derivatives and their antibacterial activities

Structure modification of drugs is a reliable way to optimize lead compounds, among which the most striking and direct method is late-stage functionalization (LSF). Here, we employed the Cu-catalyzed C-H LSF to modify 5-nitrofuran drugs. A series of modifications have been carried out including hydroxylation, methylation, azidination, cyanation, arylation, etc. Antibacterial activities of all compounds in vitro were measured. The results showed that compound 1 and compound 18 were the most active among all compounds. Meanwhile, the cell cytotoxicity assays of potent compounds 1, 3, 4, 5 & 18 and the parent drug FZD were conducted.

Metal-Free C-H Difluoromethylation of Imidazoles with the Ruppert-Prakash Reagent

The reaction of trimethyl(trifluoromethyl)silane-tetrabutylammonium difluorotriphenylsilicate (CF₃SiMe₃-TBAT) with a series of imidazoles gives products of the formal difluorocarbene insertion into the C-H bond at the C-2 position (i.e., C-difluoromethylation). According to NMR spectra, the corresponding 2-(trimethylsilyl)difluoromethyl-substituted derivatives are likely formed as the intermediates in the reaction, and then, they slowly convert to 2-difluoromethyl-substituted imidazoles. Quantum chemical calculations of two plausible reaction mechanisms indicate that it proceeds through the intermediate imidazolide anion stabilized through the interaction with solvent molecules and counterions. In the first proposed mechanism, the anion reacts with difluorocarbene without an activation barrier, and then, the CF₂ moiety of the adduct attacks the CF₃SiMe₃ molecule. After the elimination of the CF₃ anion, 2-(trimethylsilyl)difluromethyl-substituted imidazole is formed. Another possible reaction pathway includes silylation of imidazolide anion at the N-3 atom, followed by the barrierless addition of difluorocarbene at the C-2 atom and then by 1,3-shift of the SiMe₃ group from N-3 to the carbon atom of the CF₂ moiety. Both proposed mechanisms do not include steps with high activation barriers.

Fluorinated Sulfinates as Source of Alkyl Radicals in the Photo-Enantiocontrolled β-Functionalization of Enals

The generation of sulfonyl radicals has long been known as a flexible strategy in a wide range of different sulfonylative transformations. Meanwhile their use in alkylation processes has been somehow limited due to their inherent difficulty in evolving to less-stable radicals after sulfur dioxide extrusion. Herein we report a convenient strategy that involves gem-difluorinated sulfinates as an "upgrading-mask", allowing these precursors to decompose into their corresponding alkyl radicals. The electron-donor character of sulfinates in the formation of an electron donor-acceptor (EDA) complex with transient iminium ions is displayed, achieving the first example of a stereocontrolled light-driven insertion of gem-difluoro derivatives into unsaturated aldehydes. This methodology is compatible with flow conditions, maintaining identical levels of enantiocontrol.

SynthI: A New Open-Source Tool for Synthon-Based Library Design

Most of the existing computational tools for de novo library design are focused on the generation, rational selection, and combination of promising structural motifs to form members of the new library. However, the absence of a direct link between the chemical space of the retrosynthetically generated fragments and the pool of available reagents makes such approaches appear as rather theoretical and reality-disconnected. In this context, here we present Synthons Interpreter (SynthI), a new open-source toolkit for de novo library design that allows merging those two chemical spaces into a single synthons space. Here synthons are defined as actual fragments with valid valences and special labels, specifying the position and the nature of reactive centers. They can be issued from either the "breakup" of reference compounds according to 38 retrosynthetic rules or real reagents, after leaving group withdrawal or transformation. Such an approach not only enables the design of synthetically accessible libraries and analog generation but also facilitates reagents (building blocks) analysis in the medicinal chemistry context. SynthI code is publicly available at https://github.com/Laboratoire-de-Chemoinformatique/SynthI.

Recent Advances in Transition-Metal-Free Late-Stage C-H and N-H Arylation of Heteroarenes Using Diaryliodonium Salts

Transition-metal-free direct arylation of C-H or N-H bonds is one of the key emerging methodologies that is currently attracting tremendous attention. Diaryliodonium salts serve as a stepping stone on the way to alternative environmentally friendly and straightforward pathways for the construction of C-C and C-heteroatom bonds. In this review, we emphasize the recent synthetic advances of late-stage C(sp2)-N and C(sp2)-C(sp2) bond-forming reactions under metal-free conditions using diaryliodonium salts as arylating reagent and its applications to the synthesis of new arylated bioactive heterocyclic compounds.

Synthesis of New Triazolopyrazine Antimalarial Compounds

A radical approach to late-stage functionalization using photoredox and Diversinate^™ chemistry on the Open Source Malaria (OSM) triazolopyrazine scaffold (Series 4) resulted in the synthesis of 12 new analogues, which were characterized by NMR, UV, and MS data analysis. The structures of four triazolopyrazines were confirmed by X-ray crystal structure analysis. Several minor and unexpected side products were generated during these studies, including two resulting from a possible disproportionation reaction. All compounds were tested for their ability to inhibit the growth of the malaria parasite Plasmodium falciparum (3D7 and Dd2 strains) and for cytotoxicity against a human embryonic kidney (HEK293) cell line. Moderate antimalarial activity was observed for some of the compounds, with IC₅₀ values ranging from 0.3 to >20 µM; none of the compounds displayed any toxicity against HEK293 at 80 µM.

Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?

Joint academic-industrial projects supporting drug discovery are frequently pursued to deploy and benchmark cutting-edge methodical developments from academia in a real-world industrial environment at different scales. The dimensionality of tasks ranges from small molecule physicochemical property assessment over protein-ligand interaction up to statistical analyses of biological data. This way, method development and usability both benefit from insights gained at both ends, when predictiveness and readiness of novel approaches are confirmed, but the pharmaceutical drug makers get early access to novel tools for the quality of drug products and benefit of patients. Quantum-mechanical and simulation methods particularly fall into this group of methods, as they require skills and expense in their development but also significant resources in their application, thus are comparatively slowly dripping into the realm of industrial use. Nevertheless, these physics-based methods are becoming more and more useful. Starting with a general overview of these and in particular quantum-mechanical methods for drug discovery we review a decade-long and ongoing collaboration between Sanofi and the Kast group focused on the application of the embedded cluster reference interaction site model (EC-RISM), a solvation model for quantum chemistry, to study small molecule chemistry in the context of joint participation in several SAMPL (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenges. Starting with early application to tautomer equilibria in water (SAMPL2) the methodology was further developed to allow for challenge contributions related to predictions of distribution coefficients (SAMPL5) and acidity constants (SAMPL6) over the years. Particular emphasis is put on a frequently overlooked aspect of measuring the quality of models, namely the retrospective analysis of earlier datasets and predictions in light of more recent and advanced developments. We therefore demonstrate the performance of the current methodical state of the art as developed and optimized for the SAMPL6 pKa and octanol-water log P challenges when re-applied to the earlier SAMPL5 cyclohexane-water log D and SAMPL2 tautomer equilibria datasets. Systematic improvement is not consistently found throughout despite the similarity of the problem class, i.e. protonation reactions and phase distribution. Hence, it is possible to learn about hidden bias in model assessment, as results derived from more elaborate methods do not necessarily improve quantitative agreement. This indicates the role of chance or coincidence for model development on the one hand which allows for the identification of systematic error and opportunities toward improvement and reveals possible sources of experimental uncertainty on the other. These insights are particularly useful for further academia-industry collaborations, as both partners are then enabled to optimize both the computational and experimental settings for data generation.

Preparation of Tertiary Amines from Tris(2-cyanoethyl)amine Using Three Successive Cobalt-Catalyzed Electrophilic Aminations with Organozinc Halides

We report a stepwise preparation of triple alkylated or arylated tertiary amines, starting from commercially available tris(2-cyanoethyl)amine using three successive reaction sequences involving a selective oxidation (formation of an N-oxide followed by a Cope elimination) leading to an intermediate hydroxylamine, a benzoylation, and a cobalt-catalyzed electrophilic amination with organozinc halides.

18F-Trifluoromethanesulfinate Enables Direct C-H 18F-Trifluoromethylation of Native Aromatic Residues in Peptides

18F labeling strategies for unmodified peptides with [18F]fluoride require 18F-labeled prosthetics for bioconjugation more often with cysteine thiols or lysine amines. Here we explore selective radical chemistry to target aromatic residues applying C-H 18F-trifluoromethylation. We report a one-step route to [18F]CF3SO2NH4 from [18F]fluoride and its application to direct [18F]CF3 incorporation at tryptophan or tyrosine residues using unmodified peptides as complex as recombinant human insulin. The fully automated radiosynthesis of octreotide[Trp(2-CF218F)] enables in vivo positron emission tomography imaging.

Reaction of Papaverine with Baran DiversinatesTM

The reaction of papaverine with a series of Baran Diversinates^TM is reported. Although the yields were low, it was possible to synthesize a small biodiscovery library using this plant alkaloid as a scaffold for late-stage C–H functionalization. Ten papaverine analogues (2–11), including seven new compounds, were synthesized. An unexpected radical-induced exchange reaction is reported where the dimethoxybenzyl group of papaverine was replaced by an alkyl group. This side reaction enabled the synthesis of additional novel fragments based on the isoquinoline scaffold, which is present in numerous natural products. Possible reasons for the poor yields in the Diversinate^TM reactions with this particular scaffold are discussed.

The importance of synthetic chemistry in the pharmaceutical industry

Innovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matter. We identify some of the most important recent advances in synthetic chemistry as well as opportunities at the interface with partner disciplines that are poised to transform the practice of drug discovery and development.

Overview of Recent Strategic Advances in Medicinal Chemistry

Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.

Late Stage Functionalization of Secondary Amines via a Cobalt-Catalyzed Electrophilic Amination of Organozinc Reagents

A general preparation of polyfunctional hydroxylamine benzoates from the corresponding secondary amines is reported. This convenient synthesis allows the setup of a late-stage functionalization of various secondary amines, including pharmaceuticals and peptidic derivatives. Thus, a cross-coupling of hydroxylamine benzoates with various alkyl-, aryl-, and heteroaryl-zinc chlorides in the presence of 5 mol % CoCl₂ (25 °C, 2 h) provides a range of polyfunctional tertiary amines. This method was used to prepare penfluridol and gepirone.