Stereoselectively fluorinated N-heterocycles: a brief survey

Origami with small molecules: exploiting the C-F bond as a conformational tool

When present within an organic molecule, the C-F bond tends to align in predictable ways with neighbouring functional groups, due to stereoelectronic effects such as hyperconjugation and electrostatic attraction/repulsion. These fluorine-derived conformational effects have been exploited to control the shapes, and thereby enhance the properties, of a wide variety of functional molecules including pharmaceutical agents, liquid crystals, fragrance chemicals, organocatalysts, and peptides. This comprehensive review summarises developments in this field during the period 2010-2024.

Recent progress in therapeutic applications of fluorinated five-membered heterocycles and their benzo-fused systems

Heterocyclic derivatives grafted with fluorine atom(s) have attracted the attention of scientists due to the unique physicochemical properties of the C-F bond. The inclusion of fluorine atom(s) into organic compounds often increases their lipophilicity and metabolic stability, enhancing their bioavailability and affinity for target proteins. Therefore, it is not surprising to find that more than 20% of the medications on the market contain fluorine, and nearly 300 fluorine-containing drugs have been officially approved for use as medicines. In this review article, we are interested in classifying and describing the reports comprising varied therapeutic activities of the directly fluorinated five-membered heterocycles and their fused systems during the last two decades. These therapeutic activities included antiviral, anti-inflammatory, enzymatic inhibitory, antimalarial, anticoagulant, antipsychotic, antioxidant, antiprotozoal, histamine-H3 receptor, serotonin receptor, chemokine receptor, prostaglandin-D2 receptor, and PBR inhibition activities. In many cases, the activities of fluorinated azoles were almost equal to or exceeded the potency of reference drugs.

Amodiaquine Analogs Are Potent Inhibitors of Interleukin-6 Production Induced by Activation of Toll-Like Receptors Recognizing Pathogen Nucleic Acids

Excessive inflammatory responses to viral infections, known as cytokine storms, are caused by overactivation of endolysosomal Toll-like receptors (TLRs) (TLR3, TLR7, TLR8, and TLR9) and can be lethal, but no specific treatment is available. Some quinoline derivatives with antiviral activity were tried during the recent coronavirus disease 2019 (COVID-19) pandemic, but showed serious toxicity, and their efficacy for treating viral cytokine storms was not established. Here, in order to discover a low-toxicity quinoline derivative as a candidate for controlling virally induced inflammation, we synthesized a series of derivatives of amodiaquine (ADQ), a quinoline approved as an antimalarial, and tested their effects on TLRs-mediated production of inflammatory cytokines and cell viability in vitro. In J774.1 murine macrophages, ADQ inhibited interleukin-6 (IL-6) production induced by TLR3 agonist poly(I:C), TLR7 agonist imiquimod, and TLR9 agonist cytosine-phosphate-guanosine oligodeoxynucleotide (CpG ODN) with IC50 values of 2.43, 3.48, and 0.0359 µM, respectively, indicating that ADQ has a high inhibitory selectivity for TLR9 signaling. A structure-activity relationship study revealed that an appropriately substituted amino group on the phenol moiety and a halogen substituent on quinoline are important for potent anti-inflammatory activity and low cytotoxicity. ADQ analogs bearing N-butylethyl, N-3-fluoropiperidinyl, and N-4-fluoropiperidinyl groups in place of the N-diethyl group exhibited more potent activity and lower cytotoxicity than ADQ. ADQ and its analogs appear to inhibit the activity of TLRs recognizing pathogen nucleic acids via alkalinization of endolysosomes. Our results suggest that ADQ analogs are promising candidates as therapeutic agents for cytokine storms mediated by TLRs recognizing pathogen nucleic acid with reduced side effects.

Chiral Anthranyl Trifluoromethyl Alcohols: Structures, Oxidative Dearomatization and Chiroptical Properties

Chiral trifluoromethyl alcohol groups were introduced at the hindered ortho positions of 9,10-diphenylanthracenes to investigate their effects on the physical properties and reactivity towards oxidative dearomatization. In such compact structures, the position in different quadrants and the preferred orientation of the -CH(OH)CF₃ groups were determined by the relative and absolute configurations of each stereoisomer, respectively. As a consequence, the stereochemistry governs the organization of the H-bonded molecules in single crystals (homochiral dimers vs ribbon), whereas in chlorinated solvents, they all behave as discrete compounds. Concerning their reactivity, the stereospecific dearomative oxidation of these molecules leads to 9,10-bis-spiro-isobenzofuran-anthracenes, when using organic single-electron transfer oxidants. The chiroptical properties of the alcohols and the corresponding dearomatized products were compared and showed an important modulation of the intensity.

Diastereoselective Synthesis, Glycosidase Inhibition, and Docking Study of C-7-Fluorinated Casuarine and Australine Derivatives

C-7-fluorinated derivatives of two important polyhydroxylated pyrrolizidines, casuarine and australine, were synthesized with organocatalytic stereoselective α-fluorination of aldehydes as the key step. The strategy is extensively applicable to some synthetically challenging fluorinated iminosugars and carbohydrates. The docking studies indicated that the potent inhibitions of trehalase and amyloglucosidase by the fluorinated polyhydroxylated pyrrolizidines are due to the interaction modes dominated by fluorine atoms in these iminosugars with the amino acids' residues of the corresponding enzymes. Steady interactions were established between the C-7 fluoride and a hydrophobic pocket in amyloglucosidase by untypical anion-π interactions. These unexpected docking modes and related structure-activity relationship studies emphasize the value of fluorination in the design of polyhydroxylated pyrrolizidine glycosidase inhibitors.

Enantioenriched γ-Aminoalcohols, β-Amino Acids, β-Lactams, and Azetidines Featuring Tetrasubstituted Fluorinated Stereocenters via Palladacycle-Catalyzed Asymmetric Fluorination of Isoxazolinones

Enantiopure fluorine containing β-amino acids are of large biological and pharmaceutical interest. Strategies to prepare β-amino acid derivatives possessing a F-containing tetrasubstituted stereocenter at the α-C atom in a catalytic asymmetric sense are rare, in particular using an enantioselective electrophilic C-F bond formation. In the present study, a highly enantioselective palladacycle-catalyzed fluorination of isoxazolinones was developed. It is demonstrated that isoxazolinones are useful precursors toward enantiopure β-amino acid derivatives by diastereo- and chemoselective reduction. The formed γ-aminoalcohols served as valuable precursors toward β-amino acids, β-amino acid esters, and β-lactams, all featuring tetrasubstituted fluorinated stereocenters. In addition, by this work, enantioenriched fluorinated azetidines were accessible for the first time.

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

A straightforward conversion of 1,4-quinones into polycyclic pyrazoles via [3 + 2]-cycloaddition with fluorinated nitrile imines

In-situ-generated N-aryl nitrile imines derived from trifluoroacetonitrile efficiently react with polycyclic 1,4-quinones, yielding fused pyrazole derivatives as the exclusive products. The reactions proceed via the initially formed [3 + 2]-cycloadducts, which undergo spontaneous aerial oxidation to give aromatized heterocyclic products. Only for 2,3,5,6-tetramethyl-1,4-benzoquinone, the expected [3 + 2]-cycloadduct exhibited fair stability and could be isolated in moderate yield (53%). The presented method offers a straightforward access to hitherto little known trifluoromethylated polycyclic pyrazoles. All products were isolated as pale colored solids with medium-intensity absorption maxima in the range of 310-340 nm for naphthoquinone-derived products and low-intensity bands in the visible region (≈400 nm) for the anthraquinone series.

Recent advances in the synthesis and reactivity of quinoxaline

Quinoxalines are observed in several bioactive molecules and have been widely employed in designing molecules for DSSC's, optoelectronics, and sensing applications. Therefore, developing newer synthetic routes as well as novel ways for their functionalization is apparent.

The role of allyl ammonium salts in palladium-catalyzed cascade reactions towards the synthesis of spiro-fused heterocycles

There is a continuous need for designing new and improved synthetic methods aiming at minimizing reaction steps while increasing molecular complexity. In this respect, catalytic, one-pot cascade methodologies constitute an ideal tool for the construction of complex molecules with high chemo-, regio-, and stereoselectivity. Herein, we describe two general and efficient cascade procedures for the synthesis of spiro-fused heterocylces. This transformation combines selective nucleophilic substitution (S_N2′), palladium-catalyzed Heck and C–H activation reactions in a cascade manner. The use of allylic ammonium salts and specific Pd catalysts are key to the success of the transformations. The synthetic utility of these methodologies is showcased by the preparation of 48 spiro-fused dihydrobenzofuranes and indolines including a variety of fluorinated derivatives.

Synthetic methods aiming at minimizing reaction steps while increasing molecular complexity are highly sought after by organic chemists. Here, the authors report two cascade procedures combining nucleophilic substitution, palladium-catalyzed Heck and C–H activation reactions for the synthesis of spiro-fused heterocycles.

Diastereoselective synthesis and conformational analysis of 4,5-difluoropipecolic acids

Stereoselectively-fluorinated analogs of pipecolic acid have been investigated through a combined theoretical and experimental approach. Three of the four possible diastereoisomers of 4,5-difluoropipecolic acid were successfully synthesized via deoxyfluorination chemistry, navigating a complex reaction network that included neighboring group participation, rearrangement, and elimination pathways. A DFT-based conformational study, supported by NMR J-based analysis, revealed that the different diastereoisomers of 4,5-difluoropipecolic acid preferentially adopt different puckers of the six-membered ring. These findings could have future relevance for the conformational control of biologically active peptides.

Stereocontrolled Synthesis of Functionalized Azaheterocycles from Carbocycles through Oxidative Ring Opening/Reductive Ring Closing Protocols

Fluorine-containing organic scaffolds are of significant interest in medicinal chemistry. The incorporation of fluorine into biomolecules can lead to remarkable changes in their physical, chemical, and biological properties. There are already many drugs on the market, which contain at least one fluorine atom. Saturated functionalized azaheterocycles as bioactive substances have gained increasing attention in pharmaceutical chemistry. Due to the high biorelevance of organofluorine molecules and the importance of N-heterocyclic compounds, selective stereocontrolled procedures to the access of new fluorine-containing saturated N-heterocycles are considered to be a hot research topic. This account summarizes the synthesis of functionalized and fluorine-containing saturated azaheterocycles starting from functionalized cycloalkenes and based on oxidative ring cleavage of diol intermediates followed by ring expansion with reductive amination.

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε

Background

(−)-Balanol is an ATP-mimicking inhibitor that non-selectively targets protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA). While PKA constantly shows tumor promoting activities, PKC isozymes can ambiguously be tumor promoters or suppressors. In particular, PKCε is frequently implicated in tumorigenesis and a potential target for anticancer drugs. We recently reported that the C5(S)-fluorinated balanol analogue (balanoid 1c) had improved binding affinity and selectivity for PKCε but not to the other novel PKC isozymes, which share a highly similar ATP site. The underlying basis for this fluorine-based selectivity is not entirely comprehended and needs to be investigated further for the development of ATP mimic inhibitors specific for PKCε.

Results

Using molecular dynamics (MD) simulations assisted by homology modelling and sequence analysis, we have studied the fluorine-based selectivity in the highly similar ATP sites of novel PKC (nPKC) isozymes. The study suggests that every nPKC isozyme has different dynamics behaviour in both apo and 1c-bound forms. Interestingly, the apo form of PKCε, where 1c binds strongly, shows the highest degree of flexibility which dramatically decreases after binding 1c.

Conclusions

For the first time to the best of our knowledge, we found that the origin of 1c selectivity for PKCε comes from the unique dynamics feature of each PKC isozyme. Fluorine conformational control in 1c can synergize with and lock down the dynamics of PKCε, which optimize binding interactions with the ATP site residues of the enzyme, particularly the invariant Lys437. This finding has implications for further rational design of balanol-based PKCε inhibitors for cancer drug development.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2373-1) contains supplementary material, which is available to authorized users.

Bifidenone: Structure-Activity Relationship and Advanced Preclinical Candidate

Bifidenone is a novel natural tubulin polymerization inhibitor that exhibits antiproliferative activity against a range of human cancer cell lines, making it an attractive candidate for development. A synthetic route was previously developed to alleviate supply constraints arising from its isolation in microgram quantities from a Gabonese tree. Using that previously published route, we present here 42 analogues that were synthesized to examine the structure-activity relationship of bifidenone derivatives. In addition to in vitro cytotoxicity data, data from murine xenograft and pharmacokinetic studies were used to evaluate the analogues. Compounds 45b and 46b were found to demonstrate promising efficacy in murine xenograft experiments, and 46b had significantly more potent in vitro antiproliferative activity against taxane-resistant cell lines compared to that of paclitaxel.

Memory of Chirality as a Prominent Pathway for the Synthesis of Natural Products through Chiral Intermediates

The ability of a chiral molecule to be able to transform from one structure to another, whilst remembering its original molecular information by means of an appropriate transition state is an abstract notion that may very well play a key role in important synthetic processes, and has thus attracted a considerable amount of attention among the chemistry community. Here, we have highlighted this concept of "memory of chirality" (MOC) and extended it beyond the case of a simple molecule to larger and more complex natural products. Updated approaches that have recently been elucidated to obtain these asymmetric natural products are described, some of which may, until now, have been overcomplicated or overlooked.

Organocatalytic Asymmetric Synthesis of α-Oxetanyl and α-Azetidinyl Tertiary Alkyl Fluorides and Chlorides

Asymmetric thiourea and squaramide catalysis provides access to synthetically versatile α-oxetanyl and α-azetidinyl alkyl halides exhibiting a tetrasubstituted chiral carbon center with high yields and enantioselectivities. The products are readily transformed with negligible erosion of enantiopurity and excellent diastereoselectivity to a diverse group of multifunctional compounds including fluorooxindoles with two contiguous chirality centers, fluorinated heterocyclic spiranes, and polyspiro compounds.

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA

(-)-Balanol is an adenosine triphosphate mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is known as a tumor promoter, PKC isozymes can be tumor promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood. Interestingly, in contrast to PKA, PKCε is more sensitive to this fluorine effect. Here we investigate the global fluorine effect on the different binding responses of PKCε and PKA to balanoids using molecular dynamics (MD) simulations. For the first time to the best of our knowledge, we found that a structurally equivalent residue in each kinase, Thr184 in PKA and Ala549 in PKCε, is essential for the different binding responses. Furthermore, the study revealed that the invariant Lys, Lys73 in PKA and Lys437 in PKCε, already known to have a crucial role in the catalytic activity of kinases, serves as the main anchor for balanol binding. Overall, while Thr184 in PKA attenuates the effect of fluorination, Ala549 permits remote response of PKCε to fluorine substitution, with implications for rational design of future balanol-based PKCε inhibitors.

Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions

Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive natural product structural framework (reasonable chaos), can be directed to confer dynamically new protein–ligand interactions beyond the basic lock–key model (imaginative order). Here we summarise our work on exploring conformational diversity from fluorinated natural product fragments, and how this approach of conformation-coupled diversity-oriented synthesis can be used to iteratively derive ligands with enhanced specificity against highly homologous protein domains. Our results demonstrate that the conformation entropic states of highly conserved protein domains differ significantly, and this conformational diversity, beyond primary sequence analysis, can be duly captured and exploited by natural-product derived ligands with complementary conformational dynamics for enhancing recognition specificity in drug lead discovery.

Divergent synthesis from reactions of 2-trifluoromethyl-1,3-conjugated enynes with N-acetylated 2-aminomalonates

Divergent synthesis of fluorinated heterocycles from the reactions of 2-trifluoromethyl-1,3-conjugated enynes with N-acetylated 2-aminomalonates and subsequent gold-catalysed cyclization were developed.

Diastereoselective Trifluoroacetylation of Highly Substituted Pyrrolidines by a Dakin-West Process

A robust approach allowing for the efficient trifluoroacetylation of a series of highly substituted pyrrolidines in a diastereoselective manner is reported. The transformation is based on a Dakin-West reaction of advanced pyrrolidine 2-carboxylic acid derivatives that can be assembled stereoselectively in four synthetic steps. Importantly, this work demonstrates how the introduction of lateral substituents on the pyrrolidine scaffold enables the generation of the desired trifluoroacetylation products, which was not possible previously due to the exclusive formation of trifluoromethylated oxazoles (vide infra). In the course of this work we succeeded for the first time in isolating and characterizing (HRMS, IR, ¹H, ¹³C and ¹⁹F NMR, X-ray) different intermediates of the Dakin-West reaction allowing us to probe its mechanism.

Stereoselective Synthesis of α-Fluoro-γ-nitro Thioesters under Organocatalytic Conditions

Fluorinated monothiomalonates (F-MTMs) were used as building blocks for the stereoselective synthesis of organofluorine compounds. We present conjugate addition reactions between F-MTMs with nitroolefins that proceed under mild organocatalytic conditions and provide access to α-fluoro-γ-nitro thioesters with adjacent tetrasubstituted and tertiary stereogenic centers. Only 1 mol % of a cinchona alkaloid-urea catalyst is necessary to obtain the addition products in excellent yields and stereoselectivities. The methodology allowed for the straightforward synthesis of a fluorinated analogue of the PAR-2 agonist AC-264613.

Fluorination methods in drug discovery

Fluorination reactions of medicinal and biologically-active compounds will be discussed. Late stage fluorination strategies of medicinal targets have recently attracted considerable attention on account of the influence that a fluorine atom can impart to targets of medicinal importance, such as modulation of lipophilicity, electronegativity, basicity and bioavailability, the latter as a consequence of membrane permeability. Therefore, the recourse to late-stage fluorine substitution on compounds with already known and relevant biological activity can provide the pharmaceutical industry with new leads with improved medicinal properties. The fluorination strategies will take into account different fluorinating reagents, either of nucleophilic or electrophilic, and of radical nature. Diverse families of organic compounds such as (hetero)aromatic rings, and aliphatic substrates (sp(3), sp(2), and sp carbon atoms) will be studied in late-stage fluorination reaction strategies.

Enantioselective Organocatalyzed Transformations of β-Ketoesters

The β-ketoester structural motif continues to intrigue chemists with its electrophilic and nucleophilic sites. Proven to be a valuable tool within organic synthesis, natural product, and medicinal chemistry, reports on chiral β-ketoester molecular skeletons display a steady increase. With the reignition of organocatalysis in the past decade, asymmetric methods available for the synthesis of this structural unit has significantly expanded, making it one of the most exploited substrates for organocatalytic transformations. This review provides comprehensive information on the plethora of organocatalysts used in stereoselective organocatalyzed construction of β-ketoester-containing compounds.

Conformation-induced regioselective and divergent opening of epoxides by fluoride: facile access to hydroxylated fluoro-piperidines

Utilizing molecular conformation as a controlling factor, epoxide-containing 2-aryl-piperidines can be ring-opened with the reagent combination of tetrabutylammonium fluoride (TBAF) and potassium bifluoride (KHF2) in a regioselective and divergent fashion. Four different types of hydroxylated fluoro-piperidines, valuable building blocks in drug development, were readily synthesized using this method. The basic nature of the reagent combination allowed a one-pot deprotection/ring opening process, which increased the efficacy of this transformation.

Diastereoselective Synthesis and Conformational Analysis of (2R)- and (2S)-Fluorostatines: An Approach Based on Organocatalytic Fluorination of a Chiral Aldehyde

Stereoselectively fluorinated analogues of the amino acid statine have been efficiently synthesized. The key step is an organocatalytic electrophilic fluorination of a chiral β-oxygenated aldehyde, which provided a test of both diastereoselectivity and chemoselectivity. The target statine analogues were found to adopt unique conformations influenced by the fluorine gauche effect, rendering them potentially valuable building blocks for incorporation into bioactive peptides.

Gem-difluoromethylated and trifluoromethylated derivatives of DMDP-related iminosugars: synthesis and glycosidase inhibition

Gem-difluoromethylated and trifluoromethylated derivatives of DMDP-related iminosugars have been synthesized from cyclic nitrones and assayed against various glycosidases.

Novel stereocontrolled syntheses of tashiromine and epitashiromine

A novel stereocontrolled approach has been developed for the syntheses of tashiromine and epitashiromine alkaloids from cyclooctene β-amino acids. The synthetic concept is based on the azetidinone opening of a bicyclic β-lactam, followed by oxidative ring opening through ring C-C double bond and reductive ring-closure reactions of the cis- or trans-cyclooctene β-amino acids.