Pentafluorosulfanyl-substituted biaryl derivatives as MATE-type transporter inhibitors targeting drug-resistant bacteria

Multidrug and toxin extrusion (MATE) inhibitors improve the antimicrobial susceptibility of drug-resistant bacteria by preventing the efflux of administered antibiotics. In this study, we optimized the chemical structure of a previously identified bacterial-selective MATE inhibitor 1 (EC50 > 30 µM) to improve its activity further. Compound 1 was divided into three fragments (aromatic part, linker part, and guanidine part), and each part was individually optimized. Compound 31 (EC50 = 1.8 µM), a novel pentafluorosulfanyl-containing molecule synthesized following optimized parts, showed antimicrobial activity against MATE-expressing strains at concentrations lower than conventional inhibitor 1 when co-administrated with norfloxacin. Furthermore, 31 was not cytotoxic at effective concentrations. This suggests that compound 31 can be a promising candidate for combating bacterial infections, particularly those resistant to conventional antibiotics by MATE expression.

Rhodium-catalyzed intramolecular reductive aldol-type cyclization: Application for the synthesis of a chiral necic acid lactone

A rhodium-catalyzed intramolecular reductive aldol-type cyclization is described to give β-hydroxylactones with high diastereoselectivities. The stereoselectivity of this cyclization is highly solvent dependent and can give syn- or anti-β-hydroxylactones with high diastereoselectivity. This methodology was also applied to the synthesis of a chiral necic acid lactone which is a structural component of the pyrrolizidine alkaloid monocrotaline.

Simple synthesis of multi-halogenated alkenes from 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane)

A series of aryl fluoroalkenyl ethers that contain chlorine and bromine as well as fluorine atoms were prepared in moderate to good yields via the reactions of phenols and 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) in the presence of KOH. This simple reaction enabled the construction of highly halogenated compounds with the potential for further functionalization. The reaction involved a highly reactive difluoroethylene intermediate, which was produced by the reaction between halothane and KOH.

Synthesis of 2,2-difluoro-2-arylethylamines as fluorinated analogs of octopamine and noradrenaline

A series of 2,2-difluoro-2-arylethylamines was synthesized as fluorinated analogs of octopamine and noradrenaline with the expectation of bioisosteric OH/F exchanges. The syntheses of these compounds were performed by a Suzuki–Miyaura cross-coupling reaction of 4-(bromodifluoroacetyl)morpholine with aryl boronic acids to produce the intermediate 2,2-difluoro-2-arylacetamides, followed by transformation of difluoroacetamide to difluoroethylamine.

LCP: Simple Representation of Docking Poses for Machine Learning: A Case Study on Xanthine Oxidase Inhibitors

In this paper, we propose a simple descriptor called the ligand coordinate profile (LCP) for describing docking poses. The LCP descriptor is generated from the coordinates of the polar hydrogen and heavy atoms of the docked ligand. We hypothesize that the prediction of binding poses can be enhanced through the combination of machine learning methods with the LCP descriptor. Two docking programs were used to predict ligand docking against xanthine oxidase. Four machine learning methods-k-nearest neighbors, random forest, support vector machine, and LightGBM-were used to determine whether machine learning-based models could be used to accurately identify the correct binding poses. Regardless of the machine learning method employed, the LCP descriptor demonstrated improved performance compared to the existing descriptor. The results of the leave-one-pdb-out approach revealed that the influence of the pose descriptor was also significant, as demonstrated through cross-validation. When evaluated using top-N metrics, the machine learning models were generally more effective than the docking programs. In addition, the LCP-based models outperformed those based on the existing descriptor. The results obtained in this study suggest that our proposed binding pose descriptor is effective for improving the docking accuracy of xanthine oxidase inhibitors.

Importance of the Azole Moiety of Cimetidine Derivatives for the Inhibition of Human Multidrug and Toxin Extrusion Transporter 1 (hMATE1)

Herein, we describe the design and synthesis of cimetidine analogs, as well as their inhibitory activity toward the human multidrug and toxin extrusion transporter 1 (hMATE1), which is related to nephrotoxicity of drugs. Cimetidine is the histamine H₂-receptor antagonist, but also inhibits hMATE1, which is known to cause renal impairment. We designed and synthesized cimetidine analogs to evaluate hMATE1 inhibitory activity to reveal whether the analogs could reduce the inhibition of hMATE1. The results showed that all analogs with an unsubstituted guanidino group exhibited hMATE1 inhibitory activity. On the other hand, there was a clear difference in the hMATE1 inhibitory activity for the other compounds. That is, compounds with a methylimidazole ring exhibited hMATE1 inhibition, while compounds with a phenyl ring did not. The results suggest that the ability to form hydrogen bonds at the azole moiety is strongly involved in the hMATE1 inhibition.

Identification and Synthesis of DDI-6, a Quinolinol Analog Capable of Activating Both Caenorhabditis elegans and Mouse Spermatozoa

Sperm activation is an essential process by which the male gametes become capable of fertilization. Because the process in Caenorhabditis elegans is readily reproducible in vitro, this organism serves as an excellent model to investigate it. C. elegans sperm activation in vivo occurs during spermiogenesis. Membranous organelles (MOs) contained within spermatids fuse with the plasma membrane, resulting in extracellular release of their contents and relocation of some proteins indispensable for fertilization from the MO membrane onto the sperm surface. Intriguingly, these cytological alternations are exhibited similarly in mouse spermatozoa during the acrosome reaction, which also represents a form of sperm activation, prompting us to hypothesize that C. elegans and mice share a common mechanism for sperm activation. To explore this, we first screened a chemical library to identify compounds that activate C. elegans spermatozoa. Because a quinolinol analog named DDI-6 seemed to be a candidate sperm activator, we synthesized it to use for further analyses. This involved direct dechlorination and hydrogenolysis of commercially available 5-chloro-8-quinolinol, both of which are key steps to yield 1,2,3,4-tetrahydro-8-quinolinol, and we subsequently introduced the sulfonamide group to the compound. When C. elegans spermatids were stimulated with solvent alone or the newly synthesized DDI-6, approx. 3% and approx. 28% of spermatids became MO-fused spermatozoa, respectively. Moreover, DDI-6 triggered the acrosome reaction in approx. 20% of mouse spermatozoa, while approx. 12% became acrosome-reacted after mock stimulation. Thus, DDI-6 serves as a moderately effective activator for both C. elegans and mouse spermatozoa.

Effect of Learning Dataset for Identification of Active Molecules: A Case Study of Integrin αIIbβ3 Inhibitors

Efficient in silico approaches are needed to identify strong integrin αIIbβ3 inhibitors through a small number of measurements. To address the challenge, we investigated the effect of learning dataset on the classification performance of machine learning models focusing on weak and inactive compounds. The structure and activity information of the compounds were obtained from ChEMBL, and pCHEMBL values were used to classify them as active, inactive, or weak. Datasets with various imbalance levels from active:inactive=1 : 1 to 1 : 1000 were used for the machine learning. The prediction scores of the weak samples were found to lie between the predictive values of active and inactive compounds. In addition, another dataset that consists of 149 actives and 6.9 million inactives was screened; the results indicated that the number of positive predictions decreased for models trained with a higher number of inactives. Although there is a trade-off between false positives and false negatives, for determination of compounds with strong activity using a reduced number of measurements, it is better to use a large number of inactives for learning and identifying compounds that score higher than the weak samples.

Synthesis of aryl 2-bromo-2-chloro-1,1-difluoroethyl ethers through the base-mediated reaction between phenols and halothane

An efficient and convenient method for the synthesis of structurally unique and highly functionalized aryl 2-bromo-2-chloro-1,1-difluoroethyl ethers has been developed. This approach exhibits a broad reaction scope, a simple operation and without the need of any expensive transition-metal catalyst, highly toxic or corrosive reagents. Notably, we demonstrate the potential utility of halothane for the synthesis of aryl gem-difluoroalkyl ethers containing the bromochloromethyl group.

One-Pot Ring-Opening Peptide Synthesis Using α,α-Difluoro-β-Lactams

α,α-Difluoro-β-lactams successfully underwent ring-opening aminolysis with various amino acids in 2,2,2-trifluoroethanol to afford fluorine-containing peptides. In this aminolysis, it was found that 2,2,2-trifluoroethanol first attacked the α,α-difluoro-β-lactams with cleavage of lactam ring to form the corresponding open-chain 2,2,2-trifluoroethyl esters as reactive intermediates. The trifluoroethyl esters were more electrophilic compared with the corresponding methyl ester and thereby accelerated the aminolysis with various amino acids to form β-amino acid peptides with α,α-difluoromethylene unit.

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

Fluorescent molecules based on a fluorinated isoxazole scaffold were synthesized and investigated for their photochemical properties. The introduction of a fluorine substituent into 3,5-diarylisoxazoles led to an increase of fluorescence intensity and exhibited a redshift in the emission intensity. α-Fluorinated boron ketoiminates (F-BKIs) were also synthesized via a ring-opening reaction of 4-fluoroisoxazoles and exhibited highly fluorescent luminescence and aggregation-induced emission (AIE), showing promise as a new fluorophore.

Copper-Catalyzed Oxidative Trifluoromethylation of Terminal Alkenes Using AgCF3

A mild and convenient reaction for oxidative trifluoromethylation of terminal alkenes was developed using in situ generated AgCF₃ in the presence of a copper catalyst. The reaction proceeded under an air atmosphere to afford trifluoromethylated allylic compounds in moderate to good yield. This reaction, with no need for highly hygroscopic or corrosive reagents, features not only a simple operation but also various functional group tolerances.

Synthesis of Small Fluorescent Molecules and Evaluation of Photophysical Properties

A series of aniline-based fluorophores were newly synthesized. To increase their fluorescence quantum yields, it was particularly important to substitute 3,3,3-trifluoroprop-1-enyl (TFPE) groups next to the amino group to benefit from an extended π-electron delocalization. Among these, 5-CN-2-TFPE-aniline was found to behave as an excellent fluorophore with a reasonable fluorescence quantum yield of 0.89 even in aqueous solution. l-Alanine peptide, a nonfluorescent analogue of 5-CN-2-TFPE-aniline, was synthesized and successfully employed as an enzyme probe to detect aminopeptidase N activity.

Lewis acid promoted fluorine-alkoxy group exchange reactions for the synthesis of 5-alkoxy-4,4-difluoroisoxazoline systems

Lewis acid promoted substitution of fluorine yields novel 5-alkoxylated 4,4-difluoroisoxazolines via S_N1 type processes.

Decarboxylative aldol reaction of α,α-difluoro-β-ketocarboxylate salt: a facile method for generation of difluoroenolate

We developed a decarboxylative aldol reaction using α,α-difluoro-β-ketocarboxylate salt, carbonyl compounds, and ZnCl₂/N,N,N′,N′-tetramethylethylenediamine. The generation of difluoroenolate proceeded smoothly under mild heating to provide α,α-difluoro-β-hydroxy ketones in good to excellent yield (up to 99%). The α,α-difluoro-β-ketocarboxylate salt was bench stable and easy to handle under air, which realizes a convenient and environmentally friendly methodology for synthesis of difluoromethylene compounds.

A ZnCl₂/N,N,N′,N′-tetramethylethylenediamine complex promoted decarboxylative aldol reaction of α,α-difluoro-β-ketocarboxylate salt with carbonyl compounds has been developed.

Development of a fluorogenic small substrate for dipeptidyl peptidase-4

A series of aniline and m-phenylenediamine derivatives with electron-withdrawing 3,3,3-trifluoropropenyl substituents were synthesized as small and chemically stable fluorescent organic compounds. Their fluorescence performances were evaluated by converting 2,4-disubstituted aniline 1 to the non-fluorescent dipeptide analogue H-Gly-Pro-1 for the use as a fluorogenic substrate for dipeptidyl peptidase-4 (DPP-4). The progress of the enzymatic hydrolysis of H-Gly-Pro-1 with DPP-4 was monitored by fluorometric determination of 1 released into the reaction medium. The results suggest that 1 could be used as fluorophore in OFF–ON-type fluorogenic probes.

Rh-Catalyzed reductive Mannich-type reaction and its application towards the synthesis of (±)-ezetimibe

An effective synthesis for syn-β-lactams was achieved using a Rh-catalyzed reductive Mannich-type reaction. A rhodium–hydride complex (Rh–H) derived from diethylzinc (Et₂Zn) and a Rh catalyst was used for the 1,4-reduction of an α,β-unsaturated ester to give a Reformatsky-type reagent, which in turn, reacted with an imine to give the syn-β-lactam. Additionally, the reaction was applied to the synthesis of (±)-ezetimibe, a potent β-lactamic cholesterol absorption inhibitor.

A dramatic enhancing effect of InBr3 towards the oxidative Sonogashira cross-coupling reaction of 2-ethynylanilines

The addition of InBr3 to the oxidative Sonogashira cross-coupling reaction of 2-ethynylaniline with (E)-trimethyl(3,3,3-trifluoroprop-1-enyl)silane led to a dramatic increase in the reactivity to afford the corresponding 1,3-enynes bearing a trifluoromethyl group on their terminal sp(2) carbon. The subsequent cyclization of these 1,3-enynes under palladium catalysis provides access to the corresponding indoles bearing a 3,3,3-trifluoroprop-1-enyl group at their 2-position.

[Stereoselective Synthesis of Multi-substituted Fluoro-β-lactams and Their Conversion to Fluorinated β-Amino Acid Core]

Multi-substituted β-lactam compounds have not only attracted considerable interest as core structures of pharmaceutical compounds such as antibiotics but also have been used as building blocks for the construction of β-amino acids. Electrophilic β-lactams can be used to enhance essential biological activities. Furthermore, the ring-opening reactions of electrophilic β-lactams can be used to provide facile access to β-amino acids. The introduction of an electronegative fluorine atom to a β-lactam ring to give the corresponding fluoro-β-lactam can be used as an effective strategy for the preparation of electrophilic β-lactams. In this review, we provide a summary of our recent research towards the direct functionalization of fluoro-β-lactams. This review has been divided into four topics, including: 1) the alkylation and hydroxyalkylation of α-bromo-α-fluoro-β-lactams (1); 2) the nickel-catalyzed cross coupling reaction of 1; 3) the asymmetric synthesis of fluoro-β-lactams using chiral ligands; and 4) the utilization of fluoro-β-lactams as highly electrophilic building blocks.

Diastereoselective Synthesis of syn-β-Lactams Using Rh-Catalyzed Reductive Mannich-Type Reaction of α,β-Unsaturated Esters

The combination of Et2Zn and RhCl(PPh3)3 led to the facile generation of a rhodium-hydride complex (Rh-H) that catalyzed the 1,4-reduction of α,β-unsaturated esters. The resulting rhodium enolate performed as a Reformatsky-type reagent and reacted with various imines to give syn-β-lactams in good to excellent yields with high diastereoselectivity.

Synthesis of a fluorinated Ezetimibe analogue using radical allylation of α-bromo-α-fluoro-β-lactam

A facile and efficient synthesis of a fluorinated Ezetimibe analogue was achieved by radical allylation, Wacker oxidation, and nucleophilic arylation of α-bromo-α-fluoro-β-lactam.

One-pot synthesis of 1,3-enynes with a CF3 group on the terminal sp2 carbon by an oxidative Sonogashira cross-coupling reaction

One-pot synthesis of 1,3-enynes with a CF₃ group on the terminal sp² carbon was achieved by an oxidative Sonogashira cross-coupling reaction with (E)-trimethyl(3,3,3-trifluoroprop-1-enyl)silane.

Csp3-csp3 homocoupling reaction of benzyl halides catalyzed by rhodium

A highly reactive alkylrhodium complex was formed from Me(2)Zn and RhCl(PPh(3))(3) and effectively catalyzed a Csp(3)-Csp(3) homocoupling reaction of benzyl halides. A Csp(3)-Csp(3) coupling reaction using Rh catalyst has not been reported up to now. The reaction proceeded under very mild conditions and gave the corresponding homocoupling products even if they had reactive substituents such as an uncovered formyl or hydroxymethyl group.

Enantioselective synthesis of α,α-difluoro-β-lactams using amino alcohol ligands

A practical and highly enantioselective Reformatsky reaction of ethyl bromodifluoroacetate with imines using a cheap and commercially available amino alcohol ligand is described.

Oxidative 3,3,3-trifluoropropylation of arylaldehydes

A reaction between (E)-trimethyl(3,3,3-trifluoroprop-1-en-1-yl)silane (1) and arylaldehydes 2 was triggered by fluoride anions to afford aryl 3,3,3-trifluoropropyl ketones 3 in moderate to good yield. A mechanistic study of this reaction indicated that it occurred via an allyl alkoxide (4). A subsequent 1,3-proton shift of the benzylic proton of 4 forms 3. This reaction involves oxidative 3,3,3-trifluoropropylation of an arylaldehyde to afford 4,4,4-trifluoro-1-arylbutan-1-one.

Direct and diastereoselective alkylation and aldol reactions of α-bromo-α-fluoro-β-lactams

Herein, we describe the development of a method for the direct alkylation and aldol reaction of α-bromo-α-fluoro-β-lactams. This method provides facile access to a wide range of 3-alkyl- and 3-hydroxyalkyl-fluoro-β-lactams in good yields under mild conditions. The products were obtained with complete diastereoselectivity with regard to the relative configuration of the β-lactam ring at C3 and C4 positions. The reaction conditions were tolerant of a broad range of electrophiles, which highlights the overall scope and utility of this procedure.