Strategic Incorporation of Fluorine into Taxoid Anticancer Agents for Medicinal Chemistry and Chemical Biology Studies

Regioselective Nickel-Catalyzed Hydrotrifluoroalkylation of Alkynes to Construct Trisubstituted Allylic Trifluoromethyl Alkenes

Introducing fluorine atoms or fluorine-containing groups into drug molecules has become a common approach in drug design, with the incorporation of trifluoromethyl groups as a focal point of research in the field of organic fluorochemistry. Here, we describe a nickel-catalyzed hydrotrifluoromethylation of internal alkynes with trifluoromethyl alkyl bromides to synthesize a series of highly regioselective trifluoromethyl allyl trisubstituted alkenes. This reaction is characterized by mild conditions and broad functional-group tolerance, providing an efficient and practical approach to synthesize trifluoromethyl allyl trisubstituted alkenes.

Chemistry and Pharmacology of Fluorinated Drugs Approved by the FDA (2016-2022)

Fluorine is characterized by high electronegativity and small atomic size, which provide this molecule with the unique property of augmenting the potency, selectivity, metabolic stability, and pharmacokinetics of drugs. Fluorine (F) substitution has been extensively explored in drug research as a means of improving biological activity and enhancing chemical or metabolic stability. Selective F substitution onto a therapeutic or diagnostic drug candidate can enhance several pharmacokinetic and physicochemical properties such as metabolic stability and membrane permeation. The increased binding ability of fluorinated drug target proteins has also been reported in some cases. An emerging line of research on F substitution has been addressed by using 18F as a radiolabel tracer atom in the extremely sensitive methodology of positron emission tomography (PET) imaging. This review aims to report on the fluorinated drugs approved by the US Food and Drug Administration (FDA) from 2016 to 2022. It cites selected examples from a variety of therapeutic and diagnostic drugs. FDA-approved drugs in this period have a variety of heterocyclic cores, including pyrrole, pyrazole, imidazole, triazole, pyridine, pyridone, pyridazine, pyrazine, pyrimidine, triazine, purine, indole, benzimidazole, isoquinoline, and quinoline appended with either F-18 or F-19. Some fluorinated oligonucleotides were also authorized by the FDA between 2019 and 2022.

Photoredox Microfluidic Synthesis of Trifluoromethylated Amino Acids

Fluorinated amino acids are a class of highly valuable building blocks that are widely employed in biological science and pharmaceutical industry for improved stability, activity, and folding property of proteins. However, the synthetic approach has conventionally been constrained by harsh conditions and limited substrate range. We demonstrate a general synthetic protocol for photoinduced α-CF₃ amino acids using continuous flow technology that benefits from enhanced fusion and precise control of reaction time, making it potentially useful in large-scale peptide synthesis.

Recent advances in the strategic incorporation of fluorine into new-generation taxoid anticancer agents

This account describes our recent progress on the strategic incorporation of fluorine and organofluorine moieties into new-generation taxoid anticancer agents for medicinal chemistry and chemical biology studies. In the case study 1, novel 3rd-generation fluorotaxoids bearing 3-OCF3 or 3-OCF2H group in the C2-benzoate moiety were designed, synthesized and examined for their anticancer activities. The potency of novel taxoids against drug-resistant cancer cell lines was 2-3 orders of magnitude higher than that of paclitaxel (PTX). Molecular modeling analysis indicated the favorable van der Waals interactions of OCF3 and OCHF2 groups in the binding site. Overall, taxoids bearing a OCHF2 group at the C2 benzoate position exhibited the highest potencies against multidrug-resistant (MDR) cancer cell lines and cancer stem cell (CSC)-enriched cell lines, indicating that the new 3rd-generation fluorotaxoids are promising candidates as chemotherapeutic agents. In the case study 2, novel 3rd-generation 3'-difluorovinyl (DFV)-taxoids, bearing 3-CF3O or 3-CHF2O group in the C2-benzoyl moiety, were designed, synthesized, and evaluated for their potencies and pharmacological properties. These new DFV-taxoids exhibited remarkable cytotoxicity against extremely drug-resistant cancer cell lines with subnanomolar IC50 values, indicating that these new DFV-taxoids can overcome MDR caused by the overexpression of Pgp and other ABC cassette transporters. The molecular docking analysis of new DFV-taxoids revealed that the 3'-DFV moiety and the 3-CF3O/3-CHF2O group of the C2-benzoate moiety are nicely accommodated to the deep hydrophobic pocket of the PTX/taxoid binding site in the β-tubulin, enabling an enhanced binding through unique attractive interactions between F/OCF3/OCHF2 and the protein. This enhancement in binding is reflected in the remarkable high potency of new 3rd-generation DFV-taxoids. In the case study 3.1, the therapeutic potential of new 3rd-generation DFV-taxoids in anaplastic thyroid cancer (ATC) cells was evaluated in vitro and in vivo. This study demonstrated that these new DFV-taxoids were more efficacious than PTX against ATC cell lines and tumor xenografts, as demonstrated by the efficient inhibition of cell proliferation and colony formation, induction of apoptosis via the mitotic arrest at the G2/M phase, as well as the suppression of tumorigenic potential in nude mice. Furthermore, tubulin polymerization assay and molecular docking analysis confirmed that these new DFV-taxoids promoted far more rapid polymerization of β-tubulin than PTX through stronger binding to tubulin/microtubules. Taken together, this study has indicated a promising therapeutic potential of these new DFV-taxoids against ATC. In the case study 3.2, DFV-OTX displayed potent cytotoxicity and effective induction of β-tubulin polymerization, as well as the G2/M phase arrest, leading to apoptosis in PTX-sensitive and PTX-resistant breast cancer cells. Furthermore, DFV-OTX clearly exhibited efficacy against MCF-7R and MDA-MB-231R tumor xenografts in mouse models. Thus, DFV-OTX effectively overcame PTX-resistance in MDA-MB-231R cells and tumor xenografts, wherein the drug resistance was attributed to ABCB1/ABCG2 upregulation. DFV-OTX was also effective against MCF-7R cells and tumor xenografts, which are PTX-resistant due to different MOA. Accordingly, DFV-OTX is a promising chemotherapeutic agent for the treatment of PTX-resistant cancers. Overall, these next-generation fluorotaxoids are promising candidates for highly potent chemotherapeutic agents, as well as payloads for tumor-targeting drug conjugates such as antibody-drug conjugates (ADCs).

Benchtop 19F Nuclear Magnetic Resonance (NMR) Spectroscopy Provides Mechanistic Insight into the Biginelli Condensation toward the Chemical Synthesis of Novel Trifluorinated Dihydro- and Tetrahydropyrimidinones as Antiproliferative Agents

Benchtop nuclear magnetic resonance (NMR) spectroscopy has enabled the monitoring and optimization of chemical transformations while simultaneously providing kinetic, mechanistic, and structural insight into reaction pathways with quantitative precision. Moreover, benchtop NMR proton lock capabilities further allow for rapid and convenient monitoring of various organic reactions in real time, as the use of deuterated solvents is not required. The complementary role of ¹⁹F NMR-based kinetic monitoring in the fluorination of bioactive compounds has many benefits in the drug discovery process since fluorinated motifs additionally improve drug pharmacology. In this study, ¹⁹F NMR spectroscopy was utilized to monitor the synthesis of novel trifluorinated analogs of monastrol, a small molecule dihydropyrimidinone kinesin-Eg5 inhibitor, and to probe the mechanism of the Biginelli cyclocondensation, a multicomponent reaction used to synthesize dihydropyrimidinone and tetrahydropyrimidinones through a Bronsted- or Lewis-acid catalyzed cyclocondensation between ethyl acetoacetate, thiourea, and an aryl aldehyde. In the present study, a trifluorinated ketoester serves a dual purpose as being the source of the trifluoromethyl group in our fluorinated dihydropyrimidinones and as a spectroscopic handle for real-time reaction monitoring and tracking of reactive intermediates by ¹⁹F NMR. Further, upon extending this workflow to a diverse array of 3- and 4-substituted aryl aldehydes, we were able to derive Hammett linear free energy relationships (LFER) to determine stereoelectronic effects of para- and meta-substituted aryl aldehydes to corresponding reaction rates and mechanistic routes. In addition, we used density functional theory (DFT) calculations to corroborate our experimental results through the thermodynamic values of key intermediates in each mechanism. Finally, these studies culminate in the synthesis of a novel trifluorinated analog of monastrol and its subsequent biological evaluation in vitro. More broadly, we show an application of benchtop ¹⁹F NMR spectroscopy as an analytical tool in the real-time investigation of a mechanistically and chemically complex multicomponent reaction mixture.

Friedel-Crafts Benzylation of Unprotected Anilines with Indole-3- carbinols to Access Trifluoro-methyl(indolyl)phenylmethanes

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An unprecedented protocol for the efficient and highly chemoselective alkylation of unprotected anilines with deactivated CF3-indole-3-carbinols promoted by In(OTf)3 has been developed. A series of diversified trifluoromethylated (indolyl)phenylmethanes were produced featuring the C-alkylation in moderate to high chemical yields and with high regioselectivities.

Ligand-free copper-catalyzed borylative defluorination: access to gem-difluoroallyl boronic acid derivatives

We report a ligand-free copper-catalyzed β-borylation, defluorination of β-substituted, α-trifluoromethyl-α,β-unsaturated esters. The reaction affords geminal-difluoroallyl boronic acid derivatives in moderate to good yield. The reaction was tolerant of various substrates, and the utility of products was demonstrated in the defluorinative functionalization of the difluoroalkene to afford enol ethers.

Design, synthesis and SAR study of Fluorine-containing 3rd-generation taxoids

It has been shown that the incorporation of fluorine or organofluorine groups into pharmaceutical and agricultural drugs often induces desirable pharmacological properties through unique protein-drug interactions involving fluorine. We have reported separately remarkable effects of the 2,2-difluorovinyl (DFV) group at the C3' position, as well as those of the CF₃O and CHF₂O groups at the 3-position of the C2-benzoyl moiety of the 2nd- and 3rd-generation taxoids on their potency and pharmacological properties. Thus, it was very natural for us to investigate the combination of these two modifications in the 3rd-generation taxoids and to find out whether these two modifications are cooperative at the binding site in the β-tubulin or not, as well as to see how these effects are reflected in the biological activities of the new 3rd-generation DFV-taxoids. Accordingly, we designed, synthesized and fully characterized 14 new 3rd-generation DFV-taxoids. These new DFV-taxoids exhibited remarkable cytotoxicity against human breast, lung, colon, pancreatic and prostate cancer cell lines. All of these new DFV-taxoids exhibited subnanomolar IC₅₀ values against drug-sensitive cell lines, A549, HT29, Vcap and PC3, as well as CFPAC-1. All of the novel DFV-taxoids exhibited 2-4 orders of magnitude greater potency against extremely drug-resistant cancer cell lines, LCC6-MDR and DLD-1, as compared to paclitaxel, indicating that these new DFV-taxoids can overcome MDR caused by the overexpression of Pgp and other ABC cassette transporters. Dose-response (kill) curve analysis of the new DFV-taxoids in LCC6-MDR and DLD-1 cell lines revealed highly impressive profiles of several new DFV-taxoids. The cooperative effects of the combination of the 3'-DFV group and 3-CF₃O/CHF₂O-benzoyl moiety at the C2 position were investigated in detail by molecular docking analysis. We found that both the 3'-DFV moiety and the 3-CF₃O/3-CHF₂O group of the C2-benzoate moiety are nicely accommodated to the deep hydrophobic pocket of the paclitaxel/taxoid binding site in the β-tubulin, enabling an enhanced binding mode through unique attractive interactions between fluorine/CF₃O/CHF₂O and the protein beyond those of paclitaxel and new-generation taxoids without bearing organofluorine groups, which are reflected in the remarkable potency of the new 3rd-generation DFV-taxoids.

Application of Oxidative Ring Opening/Ring Closing by Reductive Amination Protocol for the Stereocontrolled Synthesis of Functionalized Azaheterocycles

The current Account gives an insight into the synthesis of some N-heterocyclic β-amino acid derivatives and various functionalized saturated azaheterocycles accessed from substituted cycloalkenes via ring C=C bond oxidative cleavage followed by ring closing across double reductive amination. The ring-cleavage protocol has been accomplished according to two common approaches: a) Os-catalyzed dihydroxylation/NaIO4 vicinal diol oxidation and b) ozonolysis. A comparative study on these methodologies has been investigated. Due to the everincreasing relevance of organofluorine chemistry in drug research as well as of the high biological potential of β-amino acid derivatives several illustrative examples to the access of various fluorine-containing piperidine or azepane β-amino acid derivatives are also presented in the current Account.

1 Introduction

2 Olefin-Bond Transformation by Oxidative Ring Cleavage

3 Synthesis of Saturated Azaheterocycles via Oxidative Ring-Opening/Ring-Closing Double Reductive Amination

3.1 Importance of Fluorine-Containing Azaheterocycles in Pharmaceutical Research

3.2 Synthesis of Azaheterocyclic Amino Acid Derivatives with a Piperidine or Azepane Framework through Oxidative Ring Opening/Reductive Amination

3.2.1 Synthesis of Piperidine β-Amino Esters

3.2.2 Synthesis of Azepane β-Amino Esters

3.2.3 Synthesis of Fluorine-Containing Piperidine γ-Amino Esters

3.3 Synthesis of Tetrahydroisoquinoline Derivatives through Oxidative Ring Opening/Reductive Amination Protocol

3.4 Synthesis of Functionalized Benzazepines through Reductive Amination

3.4.1 Synthesis of Benzo[c]azepines

3.4.2 Synthesis of Benzo[d]azepines

3.5 Synthesis of Various N-Heterocycles via Ozonolysis/Reductive Amination

3.5.1 Synthesis of Compounds with an Azepane Ring

3.5.2 Synthesis of Piperidine β-Amino Acids and Piperidine-Fused β-Lactams

3.5.3 Synthesis of γ-Lactams with a Piperidine Ring

3.5.4 Synthesis of other N-Heterocycles

4 Summary and Outlook

5 List of Abbreviations

Hydrazones of 4-(Trifluoromethyl)benzohydrazide as New Inhibitors of Acetyl- and Butyrylcholinesterase

Based on the broad spectrum of biological activity of hydrazide–hydrazones, trifluoromethyl compounds, and clinical usage of cholinesterase inhibitors, we investigated hydrazones obtained from 4-(trifluoromethyl)benzohydrazide and various benzaldehydes or aliphatic ketones as potential inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). They were evaluated using Ellman’s spectrophotometric method. The hydrazide–hydrazones produced a dual inhibition of both cholinesterase enzymes with IC₅₀ values of 46.8–137.7 µM and 19.1–881.1 µM for AChE and BuChE, respectively. The majority of the compounds were stronger inhibitors of AChE; four of them (2-bromobenzaldehyde, 3-(trifluoromethyl)benzaldehyde, cyclohexanone, and camphor-based 2o, 2p, 3c, and 3d, respectively) produced a balanced inhibition of the enzymes and only 2-chloro/trifluoromethyl benzylidene derivatives 2d and 2q were found to be more potent inhibitors of BuChE. 4-(Trifluoromethyl)-N’-[4-(trifluoromethyl)benzylidene]benzohydrazide 2l produced the strongest inhibition of AChE via mixed-type inhibition determined experimentally. Structure–activity relationships were identified. The compounds fit physicochemical space for targeting central nervous systems with no apparent cytotoxicity for eukaryotic cell line together. The study provides new insights into this CF₃-hydrazide–hydrazone scaffold.

19F NMR as a tool in chemical biology

We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.

Fluorine NMR functional screening: from purified enzymes to human intact living cells

The substrate- or cofactor-based fluorine NMR screening, also known as n-FABS (n fluorine atoms for biochemical screening), represents a powerful method for performing a direct functional assay in the search of inhibitors or enhancers of an enzymatic reaction. Although it suffers from the intrinsic low sensitivity compared to other biophysical techniques usually applied in functional assays, it has some distinctive features that makes it appealing for tackling complex chemical and biological systems. Its strengths are represented by the easy set-up, robustness, flexibility, lack of signal interference and rich information content resulting in the identification of bona fide inhibitors and reliable determination of their inhibitory strength. The versatility of the n-FABS allows its application to either purified enzymes, cell lysates or intact living cells. The principles, along with theoretical, technical and practical aspects, of the methodology are discussed. Furthermore, several applications of the technique to pharmaceutical projects are presented.

Importance of Fluorine in Benzazole Compounds

Fluorine-containing heterocycles continue to receive considerable attention due to their unique properties. In medicinal chemistry, the incorporation of fluorine in small molecules imparts a significant enhancement their biological activities compared to non-fluorinated molecules. In this short review, we will highlight the importance of incorporating fluorine as a basic appendage in benzothiazole and benzimidazole skeletons. The chemistry and pharmacological activities of heterocycles containing fluorine during the past years are compiled and discussed.

Design, synthesis and SAR study of 3rd-generation taxoids bearing 3-CH3, 3-CF3O and 3-CHF2O groups at the C2-benzoate position

It has been shown that inclusion of CF₃O and CHF₂O groups to drug candidates often improve their pharmacological properties, especially metabolic stability, membrane permeability and PK profile. Moreover, the unique non-spherical structure of the OCHF₂ group can provide interesting and beneficial characteristics. Accordingly, new 3rd-generation taxoids, bearing 3-OCF₃ or 3-OCF₂H (and 3-CH₃ for comparison) at the C2 benzoate moiety, were synthesized and their potencies against drug-sensitive and drug-resistant cancer cell lines examined. In this study, our previous SAR studies on 3rd-generation taxoids were expanded to disclose that CH₃, CF₃O and CHF₂O groups are well tolerated at this position and enhance potency, especially against MDR-cancer cell lines so that these taxoids can virtually overcome MDR. These new taxoids exhibit up to 7 times higher cytotoxicity (IC₅₀) than paclitaxel against drug-sensitive cancer cell lines (MCF7 and LCC6-WT) and 2-3 orders of magnitude higher potency than paclitaxel against drug-resistant ovarian, breast and colon cancer cell lines with MDR-phenotype (NCI/ADR, LCC6-MDR and LDL-1), as well as pancreatic cancer cell line, CFPAC-1. Since it has been shown that a bulky group at this position reduces potency, it is noteworthy that rather bulky CF₃O and CHF₂O groups are well tolerated. Molecular modeling analysis indicated the favorable van der Waals interactions of CF₃O and CHF₂O groups in the binding site. It is also worthy of note that new taxoids, bearing a CHF₂O group at the C2 benzoate position (1-06 series), exhibited the highest potencies against MDR-cancer cell lines and cancer stem cell (CSC)-enriched cancer cell lines. These new 3rd-generation taxoids are promising candidates for highly potent chemotherapeutic agents, as well as payloads for tumor-targeting drug conjugates such as antibody-drug conjugates (ADCs).

Rational approaches of drug design for the development of selective estrogen receptor modulators (SERMs), implicated in breast cancer

Drug discovery and development have gained momentum due to the rational drug design by engaging computational tools and bioinformatics methodologies. Bioisosteric replacements and hybrid molecular approaches are the other inventive processes, used by medicinal chemists for the desired modifications of leads for clinical drug candidates. SERMs, ought to produce inhibitory activity in breast, uterus and agonist activity in other tissues, are beneficial for estrogen-like actions. ER subtypes α and β are hormone dependent modulators of intracellular signaling and gene expression, and development of ER selective ligands could be an effective approach for treatment of breast cancer. This report has critically investigated the possible designing considerations of SERMs, their in silico interactions, and potent pharmacophore generation approaches viz. indole, restricted benzothiophene [3, 2-b] indole, carborane, xanthendione, combretastatin A-4, organometallic heterocycles, OBHS-SAHA hybrids, benzopyranones, tetrahydroisoquinolines, Dig G derivatives and their specifications in drug design and development, to rationally improve the understanding in drug discovery. This also includes various strategies for the development of dual inhibitors for the management of antiestrogenic resistance.

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.

Synthesis of CF3CH2-Containing Indolines by Transition-Metal-Free Aryltrifluoromethylation of Unactivated Alkenes

With an unactivated double bond as the radical acceptor, allyl amines underwent a metal-free trifluoromethylation/cyclization cascade with CF₃SO₂Na (Langlois' reagent), affording CF₃CH₂-containing indolines and tetrahydroisoquinolines, whose practical syntheses are significant challenges. This protocol features mild conditions, low cost, and a broad substrate scope.

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.

O-Difluorodeuteromethylation of phenols using difluorocarbene precursors and deuterium oxide

A convenient synthesis of difluorodeuteromethyl aryl ethers using difluorocarbene precursors and deuterium oxide is described.