Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor

Visible Light-Induced Radical Cascade Difluoromethylation/Cyclization of Unactivated Alkenes: Access to CF2H-Substituted Polycyclic Imidazoles

An efficient and mild protocol for the visible light-induced radical cascade difluoromethylation/cyclization of imidazoles with unactivated alkenes using easily accessible and bench-stable difluoromethyltriphenylphosphonium bromide as the precursor of the -CF2H group has been developed to afford CF2H-substituted polycyclic imidazoles in moderate to good yields. This strategy, along with the construction of Csp3-CF2H/C-C bonds, is distinguished by mild conditions, no requirement of additives, simple operation, and wide substrate scope. In addition, the mechanistic experiments have indicated that the difluoromethyl radical pathway is essential for the methodology.

Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn?

Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.

Applications of Bioisosteres in the Design of Biologically Active Compounds

The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.

Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains

Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.

Controlled Synthesis of α-CF2H or α-CF2Cl Styrenes from the Same Precursors: Dehydrazinative Hydrogenation or Chlorination of 3,3-Difluoroallyl Hydrazines

By carefully choosing the reaction conditions, we have developed the controllable FeCl₃- or CuCl₂-mediated dehydrazinative hydrogenation or chlorination of 3,3-difluoroallyl hydrazines to access α-CF₂H or α-CF₂Cl styrenes. The current reaction provides for the first time a facile method for the direct and selective synthesis of α-CF₂H and α-CF₂Cl styrenes starting from the same precursors, which is easy to scale up and displays a broad substrate scope and good functional group tolerance. Moreover, product derivatization experiments demonstrated that the resulting α-CF₂Cl styrenes are practical and versatile building blocks for the diversified synthesis of fluorinated molecules.

Electronically Ambivalent Hydrodefluorination of Aryl‐CF3 groups enabled by Electrochemical Deep‐Reduction on a Ni Cathode

We report a general procedure for the direct mono- and di-hydrodefluorination of ArCF3 compounds. Exploiting the tunability of electrochemistry and the selectivity enabled by a Ni cathode, the deep reduction garners high selectivity with good to excellent yields up to gram scale. The late-stage peripheral editing of CF3 feedstocks to construct fluoromethyl moieties will aid the rapid diversification of lead-compounds and compound libraries.

Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes

The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational n_o → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.

Synthesis of Difluoromethylated Pyrazoles by the [3 + 2] Cycloaddition Reaction of Difluoroacetohydrazonoyl Bromides

As novel and efficient difluoromethyl building blocks, difluoroacetohydrazonoyl bromides have been synthesized for the first time. The synthetic utility of this reagent for the construction of difluoromethyl organic compounds is demonstrated by their effective regioselective [3 + 2] cycloaddition reactions with ynones, alkynoates, and ynamides. The reactions provide a novel and efficient protocol to access difluoromethyl-substituted pyrazoles in good to excellent yields.

Direct electrochemical hydrodefluorination of trifluoromethylketones enabled by non-protic conditions

CF₂H groups are unique due to the combination of their lipophilic and hydrogen bonding properties. The strength of H-bonding is determined by the group to which it is appended. Several functional groups have been explored in this context including O, S, SO and SO₂ to tune the intermolecular interaction. Difluoromethyl ketones are under-studied in this context, without a broadly accessible method for their preparation. Herein, we describe the development of an electrochemical hydrodefluorination of readily accessible trifluoromethylketones. The single-step reaction at deeply reductive potentials is uniquely amenable to challenging electron-rich substrates and reductively sensitive functionality. Key to this success is the use of non-protic conditions enabled by an ammonium salt that serves as a reductively stable, masked proton source. Analysis of their H-bonding has revealed difluoromethyl ketones to be potentially highly useful dual H-bond donor/acceptor moieties.

The electrochemical hydrodefluorination of trifluoromethylketones under non-protic conditions make this single-step reaction at deeply reductive potentials uniquely amenable to challenging electron-rich substrates and reductively sensitive functionalities.

Copper-catalyzed carbo-difluoromethylation of alkenes via radical relay

Organic molecules that contain alkyl-difluoromethyl moieties have received increased attention in medicinal chemistry, but their synthesis in a modular and late-stage fashion remains challenging. We report herein an efficient copper-catalyzed radical relay approach for the carbo-difluoromethylation of alkenes. This approach simultaneously introduces CF2H groups along with complex alkyl or aryl groups into alkenes with regioselectivity opposite to traditional CF2H radical addition. We demonstrate a broad substrate scope and a wide functional group compatibility. This scalable protocol is applied to the late-stage functionalization of complex molecules and the synthesis of CF2H analogues of bioactive molecules. Mechanistic studies and density functional theory calculations suggest a unique ligand effect on the reactivity of the Cu-CF2H species.

Modulation of the H-Bond Basicity of Functional Groups by α-Fluorine-Containing Functions and its Implications for Lipophilicity and Bioisosterism

Modulation of the H-bond basicity (pK_HB) of various functional groups (FGs) by attaching fluorine functions and its impact on lipophilicity and bioisosterism considerations are described. In general, H/F replacement at the α-position to H-bond acceptors leads to a decrease of the pK_HB value, resulting, in many cases, in a dramatic increase in the compounds' lipophilicity (log P_o/w). In the case of α-CF₂H, we found that these properties may also be affected by intramolecular H-bonds between CF₂H and the FG. A computational study of ketone and sulfone series revealed that α-fluorination can significantly affect overall polarity, charge distribution, and conformational preference. The unique case of α-di- and trifluoromethyl ketones, which exist in octanol/water phases as ketone, hemiketal, and gem-diol forms, in equilibrium, prevents direct log P_o/w determination by conventional methods, and therefore, the specific log P_o/w values of these species were determined directly, for the first time, using Linclau's ¹⁹F NMR-based method.

Deprotonative Functionalization of the Difluoromethyl Group

The functionalization of 3-(difluoromethyl)pyridine has been developed via direct deprotonation of -CHF₂ with a lithiated base and subsequent trapping with various electrophiles in THF. In situ quenching gives access to 3-pyridyl-CF₂-SiMe₂Ph as a new silylated compound, which can be postfunctionalized with a fluoride source to obtain a larger library of 3-(difluoroalkyl)pyridines that could not be accessed via direct deprotonation.

Fluoroalkyl-Substituted Cyclopropane Derivatives: Synthesis and Physicochemical Properties

A series of all 12 cis- and trans-cyclopropanecarboxylic acids and cyclopropylamines bearing CH₂F, CHF₂, and CF₃ substituents were synthesized by different methods on a multigram scale. Dissociation constants (pK_a) and log P values were measured for the obtained compounds or their derivatives to evaluate the influence of the type and relative position of fluoroalkyl substituents on the acidity and lipophilicity of monofunctionalized cyclopropanes. An analysis of the selected products by X-ray crystallography was carried out to obtain a better insight into the observed differences in physicochemical properties.

Quantifying how step-wise fluorination tunes local solute hydrophobicity, hydration shell thermodynamics and the quantum mechanical contributions of solute–water interactions

Locally tuning solute–water interactions with fluorination.

Applications of fluorine-containing amino acids for drug design

Fluorine-containing amino acids are becoming increasingly prominent in new drugs due to two general trends in the modern pharmaceutical industry. Firstly, the growing acceptance of peptides and modified peptides as drugs; and secondly, fluorine editing has become a prevalent protocol in drug-candidate optimization. Accordingly, fluorine-containing amino acids represent one of the more promising and rapidly developing areas of research in organic, bio-organic and medicinal chemistry. The goal of this Review article is to highlight the current state-of-the-art in this area by profiling 42 selected compounds that combine fluorine and amino acid structural elements. The compounds under discussion represent pharmaceutical drugs currently on the market, or in clinical trials as well as examples of drug-candidates that although withdrawn from development had a significant impact on the progress of medicinal chemistry and/or provided a deeper understanding of the nature and mechanism of biological action. For each compound, we present features of biological activity, a brief history of the design principles and the development of the synthetic approach, focusing on the source of tailor-made amino acid structures and fluorination methods. General aspects of the medicinal chemistry of fluorine-containing amino acids and synthetic methodology are briefly discussed.

CF2H as a hydrogen bond donor group for the fine tuning of peptide bond geometry with difluoromethylated pseudoprolines

CF₂H-Pseudoprolines obtained from difluoroacetaldehyde hemiacetal and serine are stable proline surrogates. The consequence of the incorporation of the CF₂H group is an important decrease of the trans to cis amide bond isomerization energy and a remarkable stabilisation of the cis conformer by an hydrogen bond.

Access to Unprotected β-Fluoroalkyl β-Amino Acids and Their α-Hydroxy Derivatives

Unprotected β-(het)aryl-β-fluoroalkyl β-amino acids and their α-hydroxy derivatives can be readily obtained using a decarboxylative Mannich-type reaction without protection/deprotection steps. This protocol utilizes lithium hexamethyldisilazide and (het)arylfluoroalkyl ketones to generate NH-ketimine intermediates. The mild reaction conditions allow the preparation of original fluorinated β-amino acids as useful building blocks in a practical and scalable manner.

Aromatic fluorocopolymers based on α-(difluoromethyl)styrene and styrene: synthesis, characterization, and thermal and surface properties

A study on the α-(difluoromethyl)styrene (DFMST) reactivity under conventional radical copolymerization conditions is presented. Although the homopolymerization of DFMST failed, its radical bulk copolymerization with styrene (ST) led to the synthesis of fluorinated aromatic polymers (FAPs). The resulting novel poly(DFMST-co-ST) copolymers were characterized by 1H, 19F and 13C NMR spectroscopies that evidenced the successful incorporation of DFMST units into copolymers and enabled the assessment of their respective molar percentages (10.4-48.2 mol%). The molar masses were in the range of 1900-17 200 g mol-1. The bulkier CF2H group in the α-position induced the lower reactivity of the DFMST comonomer. ST and DFMST monomer reactivity ratios (r DFMST = 0.0 and r ST = 0.70 ± 0.05 at 70 °C) were determined based on linear least-square methods. These values indicate that DFMST monomer is less reactive than ST, retards the polymerization rate, and thus reduces the molar masses. Moreover, the thermal properties (T g, T d) of the resulting copolymers indicate that the presence of DFMST units incorporated into poly(ST) structure promotes an increase of the T g values up to 109 °C and a slightly better thermal stability than that of poly(ST). Additionally, the thermal decomposition of poly(DFMST-co-ST) copolymer (10.4/89.6) was assessed by simultaneous thermal analysis coupled with Fourier-transform infrared spectroscopy and thermogravimetric analysis coupled with mass spectrometry showing that H2O, CO2, CO and styrene were released. The surface analysis was focused on the effects of the -CF2H group at the α-position of styrene comonomers on surface free energy of the copolymer films. Water and diiodomethane contact angle (CA) measurements confirmed that these copolymers (M n = 2300-17 200 g mol-1) are not exactly the same as polystyrenes (M n = 2100-21 600 g mol-1) in the solid state. The CA hysteresis for poly(ST) (6-8°) and poly(DFMST-co-ST) copolymers (3-5°) reflected these differences even more accurately.

Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design

The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.