As an easy-to-handle reagent for the in situ generation of outstandingly electrophilic Tf₂C=CH₂ (Tf=CF₃SO₂), we have designed and synthesised a novel 4-substituted 2-fluoropyridinium zwitterion, in which a partially fluorinated alkyl group is attached to the pyridinium 4-position. Its zwitterionic nature has been well characterised by quantum chemical bonding analysis. By using this reagent, a wide variety of organic compounds, including commercial bioactive agents, were successfully decorated by the strongly acidic or ionic functionality. Remarkably, the 4-substituted 2-fluoropyridine derivative, which results from the zwitterion with the generation of Tf₂C=CH₂, can be rapidly separated and recovered from the reaction mixture appropriately using distillation, organic solvent extraction, or fluorous solid phase extraction techniques. Such multi-optionality for the purification methods favours in the isolation of the strongly acidic and/or ionic products.

We studied the reaction pathway of our reductive Heck hydroarylation using a palladium catalyst and a hydrosilane. A key question to verify the reaction mechanism was which active species, Ar-Pd^II-I or Si-Pd^II-H, first performs migratory insertion into the alkenes. Identifying this step is crucial to elucidate the reaction mechanism. To address this, we designed a substrate containing two trisubstituted alkenes and tested its product. The results suggest that the migratory insertion of Ar-Pd^II-I into the alkene is the initial step of the reaction. Furthermore, this reaction can construct a quaternary carbon center and give high yields with high functional group tolerance.

25-Hydroxyvitamin D₃-23,26-lactone (1) and 1α,25-dihydroxyvitamin D₃-23,26-lactone (2) have long been considered as among the end metabolites of vitamin D₃. Recently, however, we found that these lactones exhibit biological activity related to the β-oxidation of fatty acids. We hypothesized that a metabolic pathway might exist to inactivate their physiological activity. Here, by means of metabolic experiments with a variety of cytochrome P450 (CYP) enzymes, we show that CYP3A4 metabolizes the lactones. The metabolites were presumed to be hydroxylated at C4 based on the previous reports showing that metabolism of 25-hydroxyvitamin D₃ by CYP3A4 along with the current LC-MS analysis. To confirm this, we chemically synthesized 4α,25(OH)₂D₃-23,26-lactone (3), 4β,25(OH)₂D₃-23,26-lactone (4), 1α,4α,25(OH)₃D₃-23,26-lactone (5), and 1α,4β,25(OH)₃D₃-23,26-lactone (6). HPLC analysis using these authentic compounds as standards revealed that 1 was metabolized to 3 and 4, while 2 was metabolized exclusively to 6 by CYP3A4. Docking studies suggest that the hydroxyl group at C1 in 2 forms hydrogen bonds with Ser119 and Arg212 of CYP3A4, contributing to the fixation of C4β on heme iron in the CYP, thereby resulting in stereoselective hydroxylation at C4.

Recently, remarkable progress has been achieved in artificial intelligence (AI), including machine learning. Various AI models have been proposed for drug discovery, including the design of small molecules, activity prediction, and three-dimensional (3D) structure prediction of proteins. AI consists of diverse elements, including information retrieval and machine learning, and can be used in a wide range of drug discovery scenarios. In this review, we focused on AI for small-molecule drug discovery with respect to molecular design, activity prediction, and prediction of the binding poses of compounds to target molecules. We also discussed the applications of AI in academic drug discovery.

A noise filter, which is usually attached to a detector for chromatography, was applied for the improvement of a signal-to-noise ratio (S/N) on a chromatogram. The objective of this paper is to elucidate the effect of noise filtering in an UV detector of ultra HPLC (UHPLC) on the statistical reliability of chemometrically evaluated repeatability by the function of mutual information (FUMI) theory. To examine the statistical reliability of chemometrically evaluated repeatability in the UHPLC system associated with noise filtering, the standard deviation (SD) values of the area in baseline fluctuations with peak region k (s(k)) were obtained from six chromatograms with noise filtering. Further, the average of s(k) values (σ̂) was calculated from the s(k) values (n = 6) to be alternatively applied as the population SD. All s(k)/σ̂ values were within the 95% confidence intervals (CIs) at the freedom degree of 50, indicating the chemometrically estimated relative SD (RSD) of a peak area and RSD by repeated measurements of at least 50 times had equivalent reliability.

Twisted intramolecular charge transfer (TICT) is a phenomenon involving intramolecular charge transfer together with intramolecular rotation upon photoexcitation, and in general this excited state of fluorescent dyes undergoes non-radiative decay (producing no fluorescence). We recently discovered that the magnitude of TICT in rhodamine derivatives could be regulated by altering the size of the substituents on the xanthene moiety, generating differing degrees of intramolecular steric repulsion. To further illustrate the usefulness and generality of this strategy, we describe here an application of quinone methide chemistry, which is widely used as a fluorescence off/on switching reaction for fluorescence probes detecting enzymatic activity, to construct a steric repulsion-induced (sr)-TICT-based fluorescence probe targeting nitroreductase (NTR) activity. The developed probe was almost non-fluorescent in phosphate-buffered saline (PBS) due to strong induction of the TICT state. On the other hand, when the probe was incubated with NTR and nicotinamide adenine dinucleotide (NADH), a large fluorescence increase was observed over time. We confirmed that the enzymatic reaction proceeded as expected, i.e., the nitro group of the probe was reduced to the corresponding amino group, followed by spontaneous elimination of iminoquinone methide. These results suggest that our simple design strategy based on the sr-TICT mechanism, i.e., controlling intramolecular steric repulsion, would be applicable to the development of fluorescence probes for a variety of enzymes.

Surugamides are a group of non-ribosomal peptides produced by Streptomyces spp. Several derivatives possess acyl groups, which are proposed to be attached to a lysine side chain after backbone-macrocyclization during biosynthesis. To date, five different acyl groups have been identified in nature, yet their impacts on biological activity remain underexplored. Here we synthesized surugamide B derivatives with varied acyl moieties. Biological evaluations revealed that larger hydrophobic acyl groups on lysine ε-NH₂ enhance cytotoxicity.

Mid-sized cyclic peptides are a promising modality for modern drug discovery. Their larger interaction area coupled with an appropriate secondary structure is more suitable than small molecules for binding to the target protein. In this study, we conducted a structure derivatization of an immunoglobulin G (IgG)-binding peptide (15-IgBP), a β-hairpin-like cyclic peptide with a twisted β-strand and assessed the effect of the secondary structure on IgG-binding activity using circular dichroism (CD) spectra analysis. As a result, derivatization at the Ala5 and Gly9 positions affected the secondary structure of 15-IgBP, in particular the appearance of a small positive peak in the 220–240 nm region characteristic of 15-IgBP in the CD spectrum. Maintaining this peak at a moderate level may be important for the expression of IgG binding activity. We found the small methyl group at Ala5 to be crucial for retaining the preferred secondary structure; we also found Gly9 could be replaced by D-amino acids. By integrating these findings with previous results of the structure–activity relationship, we obtained four potent affinity peptides for IgG binding (K_d = 4.24–5.85 nM). Furthermore, we found the Gly9 position can be substituted for D-Lys. This is a new potential site for attaching functional units for conjugation with IgG for the preparation of homogeneous antibody–drug conjugates.

The gastric stability of eight barbiturates (BARs) (barbital, primidone, allobarbital, phenobarbital, cyclobarbital, pentobarbital, secobarbital, and thiobutabarbital (TBB)) was examined in artificial gastric juice using LC/UV detection. Among the eight BARs, only TBB was degraded at higher temperatures. Furthermore, the degradation product of TBB was isolated, structurally analyzed, and finally identified as 5-butan-2-yl-5-ethyl-1,3-diazinane-2,4,6-trione, also known as butabarbital. The study elucidated that butabarbital was formed by substituting the sulfur atom of the carbonyl group at the 2-position of TBB with an oxygen atom under acidic condition.

Gout is the second largest metabolic disease worldwide after diabetes, with acute gouty arthritis as most common symptom. Xanthine oxidase (XOD) and the NOD like receptor-3 (NLRP3) inflammasome are the key targets for acute gout treatment. Chlorogenic acid has been reported with a good anti-inflammatory activity, and Apigenin showed an excellent potential in XOD inhibition. Therefore, a series of chlorogenic acid–apigenin (CA) conjugates with varying linkers were designed and synthesized as dual XOD/NLRP3 inhibitors, and their activities both in XOD and NLRP3 inhibition were evaluated. An in vitro study of XOD inhibitory activity revealed that the majority of CA conjugates exhibited favorable XOD inhibitory activity. Particularly, the effects of compounds 10c and 10d, with an alkyl linker on the apigenin moiety, were stronger than that of allopurinol. The selected CA conjugates also demonstrated a favorable anti-inflammatory activity in RAW264.7 cells. Furthermore, compound 10d, which showed the optimal activity both in XOD inhibition and anti-inflammatory, was chosen and its inhibitory ability on NLRP3 and related proinflammatory cytokines was further tested. Compound 10d effectively reduced NLRP3 expression and the secretion of interluekin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) with an activity stronger than the positive control isoliquiritigenin (ISL). Based on these findings, compound 10d exhibits dual XOD/NLRP3 inhibitory activity and, therefore, the therapeutic effects on acute gout is worthy of further study.

The new chalcogenylation of phosphines using ⁿBu₄N‧XCN (X = S, Se) is described. The reaction in 1,2-dichloroethane at 120 °C provided the corresponding phosphine sulfides in good to high yields. The protocol could be extended to the synthesis of phosphinic acid derivatives as well as sulfurization of poly(styrene-co-4-styryldiphenylphosphine).

α-Alkoxy bridgehead radicals enable intermolecular construction of sterically congested C–C bonds due to their sterically accessible nature. We implemented these radical species into total syntheses of various densely oxygenated natural products and demonstrated their exceptional versatility. Herein, we employed different precursors to generate the same α-alkoxy bridgehead radical and compared the efficacy of the precursors for coupling reactions. Specifically, the bridgehead radical of the trioxaadamantane structure was formed from α-alkoxy carboxylic acid, selenide/telluride, and acyl selenide/acyl telluride, and reacted with 4-((tert-butyldimethylsilyl)oxy)cyclopent-2-en-1-one and 5-oxo-1-cyclopentene-1-carbonitrile. The efficiency of the bridgehead radical formation and subsequent coupling reaction significantly depended on the structures of the precursors and acceptors as well as the reaction conditions. Our findings provide new insights for selecting the appropriate substrates of key coupling reactions in the total synthesis of complex natural products.

We report chemoselective hydrogenation of α,β-unsaturated anilides catalyzed by the palladium-polymethylhydrosiloxane (hydrosilane) system. Under this condition, C–C double bonds are selectively reduced while other reducible groups such as acetyl groups, nitro groups, nitriles, benzyl ethers, and halogens are largely tolerated. This chemoselective hydrogenation is promising for the development of efficient synthetic routes for multi-functional compounds.

In recent years, there has been a growing focus on the development of medium-sized drugs based on peptides or nucleic acids owing to their potential therapeutic benefits. As some of these medium-sized drugs exert their therapeutic effects by adopting specific secondary structures, evaluating their conformational states is crucial to ensure the efficacy, quality, and safety of the drug products. It is important to assess the structural integrity of biomolecular therapeutics to guarantee their intended pharmacological activity and maintain the required standards for drug development and manufacturing. One widely utilized technique for quality evaluation is secondary structural analysis using circular dichroism (CD) spectroscopy. Given the higher production and quality control costs associated with medium-sized drugs compared with small-molecule drugs, developing analytical techniques that enable CD analysis with reduced sample volumes is highly desirable. Herein, we focused on a microsampling disk-type cell as a potential solution for reducing the required sample volume. We investigated whether CD spectral analysis using a microsampling disk could provide equivalent spectra compared with the standard cell (sample volume: approx. 300 µL). Our findings demonstrated that the microsampling disk (sample volume: 2–10 µL) could be successfully applied to CD spectral analysis of peptide and nucleic acid drugs, paving the way for more efficient and cost-effective quality evaluation processes.

The purpose of this study was to continuously monitor the pseudopolymorphic transition from anhydrate to monohydrate by measuring the NMR relaxation using time-domain NMR (TD-NMR). Taking advantage of the simplicity of the low-field NMR instrument configuration, which is an advantage of TD-NMR, the NMR instrument was connected to a humidity controller to monitor the pseudopolymorphic transition. First, ezetimibe (EZT) monohydrate was prepared from its anhydrate using a saturated salt solution method, and T₁ relaxation of EZT monohydrate and anhydrate was measured without a humidity controller. The T₁ relaxation results confirmed that EZT anhydrate and monohydrate could be distinguished using T₁ relaxation measurement. Next, continuous monitoring was conducted by TD-NMR and connected to a humidity controller. Anhydrous EZT was placed in an NMR glass tube and the T₁ relaxation measurement was repeated while maintaining the humidity on the side entering the NMR tube at 80% relative humidity. The T₁ relaxation became gradually faster from the initial to middle monitoring phases. The final T₁ relaxation was then recovered fully and these T₁ relaxation times were the same as the T₁ relaxation of EZT monohydrate. This study successfully monitored the pseudopolymorphic transition from EZT anhydrate to monohydrate via NMR relaxation.

Here, we report the first synthesis of oxyphyllin A/belchinoid A, a 7,9-seco-8,12-dinor-guaiane sesquiterpene whose isolation was reported independently by two groups in 2023. This synthesis utilizes a key sequential sulfone-mediated intermolecular alkylation/5-endo-tet cyclization reaction to establish the C1, C4, C5 stereocenters. Subsequent transformations, including regio- and stereoselective hydride addition-based desulfonylation via a π–allyl palladium complex and the Wittig reaction with a stable phosphonium ylide, facilitated the synthesis of oxyphyllin A/belchinoid A.

We report two methods for the preparation of peptide thioesters containing Tyr(SO₃H) residue(s), without use of a protecting group for the sulfate moiety. The first was based on direct thioesterification using carbodiimide on a fully protected peptide acid, prepared on a 2-chlorotrityl (Clt) resin with fluoren-9-ylmethoxycarbonyl (Fmoc)-based solid-phase peptide synthesis (Fmoc-SPPS). Subsequent deprotection of the protecting groups with trifluoroacetic acid (TFA) (0 °C, 4 h) yielded peptide thioesters containing Tyr(SO₃H) residue(s). Peptide thioesters containing one to three Tyr(SO₃H) residue(s), prepared by this method, were used as building blocks for the synthesis of the N^α-Fmoc-protected N-terminal part of P-selectin glycoprotein ligand 1 (PSGL-1) (Fmoc-PSGL-1(43–74)) via silver-ion mediated thioester segment condensation. The other method was based on the thioesterification of peptide azide, derived from a peptide hydrazide prepared on a NH₂NH-Clt-resin with Fmoc-SPPS. Peptide thioester containing two Tyr(SO₃H) residues, prepared via this alternative method, was used as a building block for the one-pot synthesis of the N-terminal extracellular portion of CC-chemokine receptor 5 (CCR5(9–26)) by native chemical ligation (NCL). The two methods for the preparation of peptide thioesters containing Tyr(SO₃H) residue(s) described herein are applicable to the synthesis of various types of sulfopeptides.

Although opioid analgesics are indispensable in treating pain, these drugs are accompanied by life-threatening side effects. While clinically relevant opioid drugs target the µ opioid receptor (MOR), a heterodimer between the MOR and the δ opioid receptor (DOR) has emerged as another target to develop safer analgesics. Although some heterodimer-preferring agonists have been reported so far, it is still difficult to activate the MOR/DOR heterodimer selectively in the presence of MOR or DOR monomers/homodimers. To gain insights to develop selective agonists for MOR/DOR, herein we prepared analogs of CYM51010, one of the reported heterodimer-preferring agonists, and collected structure–activity relationship information. We found that the ethoxycarbonyl group was needed for the activity for the heterodimer, although this group could be substituted with functional groups with similar sizes, such as an ethoxycarbonyl group. As for the acetylaminophenyl group, not a type of substituent, but rather a substituent located at a specific position (para-position) was essential for the activity. Changing the linker length between the acetylaminophenyl group and the piperidine moiety also had deleterious effects on the activity. On the other hand, the substitution of the acetylamino group with a trifluoroacetylamino group and the substitution of the phenethyl group with a benzyl group diminished the activities for the monomers/homodimers while keeping the activity for MOR/DOR, which enhanced the selectivity. Our findings herein will play an important role in developing selective agonists for MOR/DOR and for elucidating the physiological roles of this heterodimer in analgesic processes and in the establishment of side effects.

The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.

Lipid nanoparticles (LNPs), used for mRNA vaccines against severe acute respiratory syndrome coronavirus 2, protect mRNA and deliver it into cells, making them an essential delivery technology for RNA medicine. The LNPs manufacturing process consists of two steps, the upstream process of preparing LNPs and the downstream process of removing ethyl alcohol (EtOH) and exchanging buffers. Generally, a microfluidic device is used in the upstream process, and a dialysis membrane is used in the downstream process. However, there are many parameters in the upstream and downstream processes, and it is difficult to determine the effects of variations in the manufacturing parameters on the quality of the LNPs and establish a manufacturing process to obtain high-quality LNPs. This study focused on manufacturing mRNA-LNPs using a microfluidic device. Extreme gradient boosting (XGBoost), which is a machine learning technique, identified EtOH concentration (flow rate ratio), buffer pH, and total flow rate as the process parameters that significantly affected the particle size and encapsulation efficiency. Based on these results, we derived the manufacturing conditions for different particle sizes (approximately 80 and 200 nm) of LNPs using Bayesian optimization. In addition, the particle size of the LNPs significantly affected the protein expression level of mRNA in cells. The findings of this study are expected to provide useful information that will enable the rapid and efficient development of mRNA-LNPs manufacturing processes using microfluidic devices.