Fluoro Analogues Research Articles

Enhanced quantum efficiency of dicyano BODIPYs over difluoro BODIPYs: A DFT approach

The modified BODIPY (pyrromethene) dyes with cyano (-CN), substituting usual fluorine (-F), at the 4-position may give enhanced photochemical stability and quantum yield of fluorescence (QYF) when compared to the corresponding fluoro derivative. We have investigated and discussed comparatively the structural parameters of the ground (S0) and excited (S1) state geometries of a few widely used BODIPY dyes, both 4-cyano and 4-fluoro pyrromethene (PM), through DFT and TD-DFT studies and established the reasons for improved QYF of the cyano derivatives. The electrophilicity index indicates the stability of the excited geometry of the cyanated BODIPY and the calculated transition dipole moments reveal a longer lifetime of the excited state (S1) for the cyano BODIPY. The higher singlet and triplet gap in cyanated BODIPY accounts for higher QYF due to restricted transition from singlet to triplet state. This suggests that a population inversion, crucial for laser action, is easier to build up for cyano derivative than for the commonly used fluoro analogue while other gain/loss parameters of the PM dye lasers remain similar. Hence, 4-cyano derivatives of the PM dyes may be useful for more efficient lasing applications. The non-linear optical properties of the PM dyes are also investigated.

Completion of Crystallographic Data for the Series of 4-Halogenated-1H-pyrazoles: Crystal Structure Determination of 4-Iodo-1H-pyrazole and Spectroscopic Comparison

Prior to 2021, 4-bromo-1H-pyrazole (published in 1999) was the only structurally characterized 4-halogenated-1H-pyrazole in the Cambridge Crystallographic Data Center (CCDC). The structures of 4-chloro-1H-pyrazole and 4-fluoro-1H-pyrazole were published in 2021 and 2023, respectively. Herein, we report the crystal structure for 4-iodo-1H-pyrazole, completing the crystallographic data for the series of 4-halogenated-1H-pyrazoles. The bromo and chloro analogs are isostructural, forming trimeric H-bonding motifs, whereas the fluoro and iodo analogs form non-isostructural catemers. We also compare the experimental and theoretical (by DFT calculations) IR and 1H NMR spectroscopic data of the four halogenated 4-X-pzH compounds and unsubstituted pyrazole (pzH). An explanation is offered for some counterintuitive structural, infrared, and 1H-NMR spectroscopic data.

Discovery of a High-Affinity Fluoromethyl Analog of [11C]5-Cyano-N-(4-(4-methylpiperazin-1-yl)-2-(piperidin-1-yl)phenyl)furan-2-carboxamide ([11C]CPPC) and Their Comparison in Mouse and Monkey as Colony-Stimulating Factor 1 Receptor Positron Emission Tomography Radioligands.

[11C]CPPC has been advocated as a radioligand for colony-stimulating factor 1 receptor (CSF1R) with the potential for imaging neuroinflammation in human subjects with positron emission tomography (PET). This study sought to prepare fluoro analogs of CPPC with higher affinity to provide the potential for labeling with longer-lived fluorine-18 (t 1/2 = 109.8 min) and for delivery of higher CSF1R-specific PET signal in vivo. Seven fluorine-containing analogs of CPPC were prepared and four were found to have high inhibitory potency (IC50 in low to sub-nM range) and selectivity at CSF1R comparable with CPPC itself. One of these, a 4-fluoromethyl analog (Psa374), was investigated more deeply by labeling with carbon-11 (t 1/2 = 20.4 min) for PET studies in mouse and monkey. [11C]Psa374 showed high peak uptake in monkey brain but not in mouse brain. Pharmacological challenges revealed no CSF1R-specific binding in either species at baseline. [11C]CPPC also failed to show specific binding at baseline. Moreover, both [11C]Psa374 and [11C]CPPC showed brain efflux transporter substrate behavior in both species in vivo, although Psa374 did not show liability toward human efflux transporters in vitro. Further development of [11C]Psa374 in non-human primate models of neuroinflammation with demonstration of CSF1R-specific binding would be required to warrant the fluorine-18 labeling of Psa374 with a view to possible application in human subjects.

Identification and Quantitative Analysis of 2-Fluoromethamphetamine and Its Metabolites in Human Urine.

Various synthetic drugs have appeared over the past years across the world, and phenethylamine derivatives are among them; indeed, aromatic fluoro analogs of methamphetamine and amphetamine have been in the illicit drug market since the early 2000s. Although they are currently widely abused across the world, little information is available on their metabolism and toxicology. Recently, we came across an alleged 2-fluoromethamphetamine (2-FMA) drug abuse case. The urine obtained from the alleged abuser was analyzed as part of a criminal investigation. 2-FMA, 2-fluoroamphetamine (2-FAP) and some related compounds were detected by liquid chromatography-tandem mass spectrometry. In forensic science, both an "unchanged" drug and its metabolite(s) need to be detected in urine to verify the illicit drug use. Notably, the detection of 2-FAP, which is a plausible 2-FMA metabolite, is insufficient as evidence of 2-FMA use because 2-FAP is widely available and may be present as such in taken liquids. In this study, we synthesized analytical standards for N-hydroxy 2-FMA (N-OH-2-FMA) and two diastereomers of 2-fluoroephedrine, which are plausible metabolites of 2-FMA. Using these standards, the urine specimen was found to contain N-OH-2FMA and one diastereomer of 2-fluoroephedrine; moreover, the concentrations of these compounds were successfully determined. The results of our study suggest that N-hydroxylation and aliphatic hydroxylation are the characteristic metabolic pathways of 2-FMA compared with that of methamphetamine. This evidence indicates that both N-OH-2-FMA and 2-fluoroephedrine are plausible candidates as analytical targets for drug-use certification in forensic science.

Cascade Cyclization of Azadienes with Difluoroenoxysilanes: A One-Pot Formal [4 + 2] Approach to Fluorinated Polyfused Heterocycles.

A TfOH-promoted synthesis of fluorinated polyfused heterocycles via the cascade cyclization of azadienes and difluoroenoxysilanes has been developed, leading to the facile construction of fluorinated benzofuro[3,2-b]pyridines, 5H-indeno[1,2-b]pyridines, and 5,6-dihydrobenzo[h]quinolines. This one-pot formal [4 + 2] approach involves 1,4-difluoroalkylation, desulfonylation, cyclization, and dehydrated and dehydrofluorinated aromatization and represents the first application of difluoroenoxysilane in cascade transformations. Furthermore, this methodology is highlighted by the synthesis of three fluoro analogues of bioactive molecules with potent topoisomerase inhibitory activities.

Insertion of Diazo Esters into C-F Bonds toward Diastereoselective One-Carbon Elongation of Benzylic Fluorides: Unprecedented BF3 Catalysis with C-F Bond Cleavage and Re-formation.

Selective transformation of C-F bonds remains a significant goal in organic chemistry, but C-F insertion of a one-carbon-atom unit has never been established. Herein we report the BF3-catalyzed formal insertion of diazo esters as one-carbon-atom sources into C-F bonds to accomplish one-carbon elongation of benzylic fluorides. A DFT calculation study revealed that the BF3 catalyst could contribute to both C-F bond cleavage and re-formation. This elongation provided α-fluoro-α,β-diaryl esters with a high level of diastereoselectivity. Various benzylic fluorides and diazo esters were applicable. The synthetic utility of this method was demonstrated by the synthesis of a fluoro analogue of a compound that is used as a transient receptor and potential canonical channel inhibitor.

Synthesis and Screening in Mice of Fluorine-Containing PET Radioligands for TSPO: Discovery of a Promising 18F-Labeled Ligand.

Translocator protein 18 kDa (TSPO) is a biomarker of neuroinflammation. [11C]ER176 robustly quantifies TSPO in the human brain with positron emission tomography (PET), irrespective of subject genotype. We aimed to develop an ER176 analog with potential for labeling with longer-lived fluorine-18 (t1/2 = 109.8 min). New fluoro and trifluoromethyl analogs of ER176 were prepared through a concise synthetic strategy. These ligands showed high TSPO affinity and low human genotype sensitivity. Each ligand was initially labeled by a generic 11C-methylation procedure, thereby enabling speedy screening in mice. Each radioligand was rapidly taken up and well retained in the mouse brain at baseline after intravenous injection. Preblocking of TSPO showed that high proportions of brain uptake were specifically bound to TSPO at baseline. Overall, the 3-fluoro analog of [11C]ER176 ([11C]3b) displayed the most promising imaging properties. Therefore, a method was developed to label 3b with [18F]fluoride ion. [18F]3b gave similarly promising PET imaging results and deserves evaluation in higher species.

Synthesis and cytotoxicity evaluation of novel 5-fluorinated indoles

We report herein the synthesis of a small 28-membered library of novel 5-fluorinated indole phytoalexins. Target compounds were designed by a structure-based bioisosterism strategy. The newly prepared compounds were screened in vitro for cytotoxic activity against seven human cancer cell lines. The cytotoxic evaluation revealed that the 2’-(3,4-dichlorophenylamino) analogue of 5-fluorospirobrassinin was the most active against cancer cell lines without causing toxicity to HUVEC cells. Overall, 5-fluoro analogues of indole phytoalexins did not show improved anti-cancer activity compared to the lead compounds. The preliminary structure-activity relationship (SAR) study revealed that placing fluoro substituent at C-5 position of the indole ring is not crucial for inducing cytotoxicity against a cancer cell line.

Synthesis, Structure, and Bonding Properties of Hypercoordinate Triorganotin Compounds Featuring Three O→Sn Interactions

AbstractHere, heptacoordinate and hexacoordinate triorganotin compounds [o‐{(Ph2)(O)P}C6H4]3SnX (X=F (2 a), Cl (2 b), Me (2 f)) featuring three O→Sn interactions were synthesized. Chloro (2 b) and methyl (2 f) compounds were obtained from the oxygenation of the heptacoordinate triorganotin compounds {o‐(Ph2P)C6H4}3SnX (X=Cl (1 b), Me (1 f)) bearing three P donors. The fluorination of 2 b using tetrabutylammonium fluoride (TBAF) yielded the fluoro analogue 2 a. Structural studies were performed on a series of hypercoordinate triorganotin compounds, 2. The chloro analogue (2 b) exhibited a hexacoordinate geometry attributed to the Sn−Cl bond cleavage, where the highly electrophilic stannyl cation was stabilized by three O donors. In contrast, both the fluoro (2 a) and methyl (2 f) analogues exhibited heptacoordinate structures. Although 2 f adopted a tricapped tetrahedral geometry, 2 b is classified to adopt a distinctly rare bicapped trigonal pyramidal geometry featuring one strong LP(O)→σ*(Sn−F) interaction and two weak LP(O)→σ*(Sn−C) interactions (LP: lone pair electrons). The origin of the structural alternations depending on the substituent is discussed using density functional theory (DFT) calculations.

Terminal Mono- and Bis-Conjugates of Oligonucleotides with Closo-Dodecaborate: Synthesis and Physico-Chemical Properties.

Oligonucleotide conjugates with boron clusters have found applications in different fields of molecular biology, biotechnology, and biomedicine as potential agents for boron neutron capture therapy, siRNA components, and antisense agents. Particularly, the closo-dodecaborate anion represents a high-boron-containing residue with remarkable chemical stability and low toxicity, and is suitable for the engineering of different constructs for biomedicine and molecular biology. In the present work, we synthesized novel oligonucleotide conjugates of closo-dodecaborate attached to the 5′-, 3′-, or both terminal positions of DNA, RNA, 2′-O-Me RNA, and 2′-F-Py RNA oligomers. For their synthesis, we employed click reaction with the azido derivative of closo-dodecaborate. The key physicochemical characteristics of the conjugates have been investigated using high-performance liquid chromatography, gel electrophoresis, UV thermal melting, and circular dichroism spectroscopy. Incorporation of closo-dodecaborate residues at the 3′-end of all oligomers stabilized their complementary complexes, whereas analogous 5′-modification decreased duplex stability. Two boron clusters attached to the opposite ends of the oligomer only slightly influence the stability of complementary complexes of RNA oligonucleotide and its 2′-O-methyl and 2′-fluoro analogs. On the contrary, the same modification of DNA oligonucleotides significantly destabilized the DNA/DNA duplex but gave a strong stabilization of the duplex with an RNA target. According to circular dichroism spectroscopy results, two terminal closo-dodecaborate residues cause a prominent structural rearrangement of complementary complexes with a substantial shift from the B-form to the A-form of the double helix. The revealed changes of key characteristics of oligonucleotides caused by incorporation of terminal boron clusters, such as the increase of hydrophobicity, change of duplex stability, and prominent structural changes for DNA conjugates, should be taken into account for the development of antisense oligonucleotides, siRNAs, or aptamers bearing boron clusters. These features may also be used for engineering of developing NA constructs with pre-defined properties.

Unexpected Enhancement of HDACs Inhibition by MeS Substitution at C-2 Position of Fluoro Largazole.

Given our previous finding that fluorination at the C18 position of largazole showed reasonably good tolerance towards inhibitory activity and selectivity of histone deacetylases (HDACs), further modification on the valine residue in the fluoro-largazole’s macrocyclic moiety with S-Me l-Cysteine or Glycine residue was performed. While the Glycine-modified fluoro analog showed poor activity, the S-Me l-Cysteine-modified analog emerged to be a very potent HDAC inhibitor. Unlike all previously reported C2-modified compounds in the largazole family (including our recent fluoro-largazole analogs) where replacement of the Val residue has failed to provide any potency improvement, the S-Me l-Cysteine-modified analog displayed significantly enhanced (five–nine-fold) inhibition of all the tested HDACs while maintaining the selectivity of HDAC1 over HDAC6, as compared to largazole thiol. A molecular modeling study provided rational explanation and structural evidence for the enhanced inhibitory activity. This new finding will aid the design of novel potent HDAC inhibitors.

Synthesis and Preliminary Biological Evaluation of Two Fluoroolefin Analogs of Largazole Inspired by the Structural Similarity of the Side Chain Unit in Psammaplin A.

Largazole, isolated from a marine Cyanobacterium of the genus Symploca, is a potent and selective Class I HDAC (histone deacetylation enzymes) inhibitor. This natural 16-membered macrocyclic depsipeptide features an interesting side chain unit, namely 3-hydroxy-7-mercaptohept-4-enoic acid, which occurs in many other natural sulfur-containing HDAC inhibitors. Notably, one similar fragment, where the amide moiety replaces the trans alkene moiety, appears in Psammaplin A, another marine natural product with potent HDAC inhibitory activities. Inspired by such a structural similarity, we hypothesized the fluoroolefin moiety would mimic both the alkene moiety in Largazole and the amide moiety in Psammaplin A, and thus designed and synthesized two novel fluoro olefin analogs of Largazole. The preliminary biological assays showed that the fluoro analogs possessed comparable Class I HDAC inhibitory effects, indicating that this kind of modification on the side chain of Largazole was tolerable.

Designing Allele-Specific Inhibitors of Spastin, a Microtubule-Severing AAA Protein.

The bump-hole approach is a powerful chemical biology strategy to specifically probe the functions of closely related proteins. However, for many protein families, such as the ATPases associated with diverse cellular activities (AAA), we lack structural data for inhibitor-protein complexes to design allele-specific chemical probes. Here we report the X-ray structure of a pyrazolylaminoquinazoline-based inhibitor bound to spastin, a microtubule-severing AAA protein, and characterize the residues involved in inhibitor binding. We show that an inhibitor analogue with a single-atom hydrogen-to-fluorine modification can selectively target a spastin allele with an engineered cysteine mutation in its active site. We also report an X-ray structure of the fluoro analogue bound to the spastin mutant. Furthermore, analyses of other mutant alleles suggest how the stereoelectronics of the fluorine-cysteine interaction, rather than sterics alone, contribute to the inhibitor-allele selectivity. This approach could be used to design allele-specific probes for studying cellular functions of spastin isoforms. Our data also suggest how tuning stereoelectronics can lead to specific inhibitor-allele pairs for the AAA superfamily.

Examining the effect of regioisomerism on the physico-chemical properties of lysophosphatidylethanolamine-containing liposomes using fluoro probes

Lysophospholipids (LysoPLs) receive steadily increasing attention in the area of lipid chemistry and biology. However, the physico-chemical properties of individual LysoPL regioisomers have not yet been investigated. Herein, we report the synthesis of fluoro analogues of lysophosphatidylethanolamines (LPEs) and examine the physico-chemical properties of the LPE regioisomers using chemically synthesized fluoro probes.

Synthesis and properties of 4′-C-aminoalkyl-2′-fluoro-modified RNA oligomers

Synthesis and properties of double-stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs) containing 4′-C-aminoethyl-2′-deoxy-2′-fluorouridine are described. Thermal denaturation studies showed that incorporation of 4′-C-aminoethyl-2′-fluoro analog improved the thermal stabilities of dsRNAs and siRNAs compared to the corresponding 4′-C-aminoethyl-2′-O-methyl analog. siRNA incorporating eight 4′-aminoethyl-2′-fluoro analogs in the passenger strand showed sufficient RNAi activity at 1 nM concentration, which was similar to that of the unmodified siRNA. Furthermore, the siRNA containing the 4′-C-aminoethyl-2′-fluoro analog exhibited high stability in a buffer containing 20% bovine serum. Forty-eight percent of the siRNA remained intact after 48 h of incubation. Thus, modification of siRNAs by the 4′-C-aminoethyl-2′-fluoro analog would be useful for the development of therapeutic siRNA molecules.

Human Hepatocyte Metabolism of Novel Synthetic Cannabinoids MN-18 and Its 5-Fluoro Analog 5F-MN-18.

In 2014, 2 novel synthetic cannabinoids, MN-18 and its 5-fluoro analog, 5F-MN-18, were first identified in an ongoing survey of novel psychoactive substances in Japan. In vitro pharmacological assays revealed that MN-18 and 5F-MN-18 displayed high binding affinities to human CB1 and CB2 receptors, with Ki being 1.65-3.86 nmol/L. MN-18 and 5F-MN-18 were scheduled in Japan and some other countries in 2014. Despite increasing prevalence, no human metabolism data are currently available, making it challenging for forensic laboratories to confirm intake of MN-18 or 5F-MN-18. We incubated 10 μmol/L of MN-18 and 5F-MN-18 in human hepatocytes for 3 h and analyzed the samples on a TripleTOF 5600+ high-resolution mass spectrometer to identify appropriate marker metabolites. Data were acquired via full scan and information-dependent acquisition-triggered product ion scans with mass defect filter. In total, 13 MN-18 metabolites were detected, with the top 3 abundant metabolites being 1-pentyl-1H-indazole-3-carboxylic acid, pentyl-carbonylated MN-18, and naphthalene-hydroxylated MN-18. For 5F-MN-18, 20 metabolites were observed, with the top 3 abundant metabolites being 5'-OH-MN-18, MN-18 pentanoic acid, and 1-(5-fluoropentyl)-1H-indazole-3-carboxylic acid. We have characterized MN-18 and 5F-MN-18 metabolism with human hepatocytes and high-resolution mass spectrometry, and we recommend characteristic major metabolites for clinical and forensic laboratories to identify MN-18 and 5F-MN-18 intake and link observed adverse events to these novel synthetic cannabinoids.

The Synthesis and Evaluation of Fluoro-, Trifluoromethyl-, and Iodomuscimols as GABA Agonists.

Halogenated analogues of the neurotoxic alkaloid muscimol were prepared with fluorine, iodine or trifluoromethyl at the 4 position of the isoxazole ring system. These compounds were investigated as agonists for GABAA receptors. Only the C-4 fluorine-containing analogue proved to be an active compound in these assays. The fluoro analogue was less active than muscimol, however it showed differential activity between synaptic (α1 β2 γ2 ) and extrasynaptic (α4 β2 γ) GABAA receptors, having a similar potency to the neurotransmitter GABA for the extrasynaptic (α4 β2 γ) receptor.

Fluoro and pentafluorothio analogs of the antitumoral curcuminoid EF24 with superior antiangiogenic and vascular-disruptive effects

A series of 14 analogs of the curcuminoid EF24, (3E,5E)-3,5-bis[(2-fluorophenyl)methylene]-4-piperidinone, bearing fluorine or pentafluorothio substituents, were prepared and tested for antiproliferative, vascular-disruptive, and antiangiogenic activity, as well as for their influence on other cancer-relevant targets. They proved antiproliferative against eight cancer cell lines with IC50 values in the low single-digit micromolar to triple-digit nanomolar range. Like EF24, the hexafluoro 3c and 3d and bis(pentafluorothio) 4f derivatives arrested HT-29 colon carcinoma cells in G2/M phase of the cell cycle, yet inhibited angiogenesis, e.g. in zebrafish larvae, to a much greater extent. The antimigratory effects in 518A2 melanoma cells of 3c, its regioisomer 3d, and of 4f, originate from an inhibition of NF-κB translocation. Moreover, 3c and 3d showed potential as vascular-disruptive agents in chorioallantoic/vitelline membrane (CA/VM) assays.

2,4-Ditellurouracil and its 5-fluoro derivative: Theoretical investigations of structural, energetics and ADME parameters

2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6–311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.

Outsmarted by nootropics? An investigation into the thermal degradation of modafinil, modafinic acid, adrafinil, CRL-40,940 and CRL-40,941 in the GC injector: formation of 1,1,2,2-tetraphenylethane and its tetra fluoro analog.

2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil) is commonly prescribed for the treatment of narcolepsy. Increasing popularity and off-label use as a cognitive enhancer has resulted in a reputation as an intelligence boosting 'wonder drug'. Common alternatives available from online shops and other retail outlets include 2-[(diphenylmethyl)sulfinyl]-N-hydroxyacetamide (adrafinil), 2-{[bis(4-fluorophenyl)methyl]sulfinyl}acetamide (CRL-40,940), 2-{[bis(4-fluorophenyl)methyl]sulfinyl}-N-hydroxyacetamide (CRL-40,941), and N-methyl-4,4-difluoro-modafinil (modafiendz), respectively. Gas chromatography-mass spectrometry (GC-MS) is a common tool used in forensic and clinical analysis but there is a potential for inducing analysis-related ambiguities. This study reports on the thermal degradation of modafinil, modafinic acid, adrafinil, CRL-40,940, and CRL-40,941 due to exposure to the heated GC injection port dissolved in a variety of solvents. Key degradation products common to modafinil, modafinic acid, and adrafinil analysis included diphenylmethanol and 1,1,2,2-tetraphenylethane (TPE), the latter of which was verified by its synthesis and characterization by x-ray crystallography. The investigated compounds were also characterized by 1 H and 13 C NMR. Diphenylmethane and thiobenzophenone were also identified in some instances. TPE formation was suggested to involve the generation of a benzhydrylium ion and its reaction with the sulfoxide oxygen of the parent compound to give an oxysulfonium intermediate. Correspondingly, the fluorinated TPE analogue was formed during heat-induced degradation of modafiendz, CRL-40,940 and CRL-40,941, respectively. When a mixture of modafinil (non-fluorinated) and modafiendz (fluorinated) were subjected to GC analysis, 4,4'-(2,2-diphenylethane-1,1-diyl)bis(fluorobenzene) was detected as a third cross reaction product in addition to the two expected TPE analogues. These observations served as a reminder that the seemingly straightforward implementation of GC-MS analysis can lead to challenges during routine analysis.