Proteolysis-targeting chimeras (PROTACs) have attracted attention as an innovative drug modality that induces the selective degradation of target proteins. This technology shows higher activity than conventional inhibitors and holds great potential in the field of drug discovery. Optimization of the linker is essential for PROTACs to achieve sufficient activity, particularly with regard to cell membrane permeability. However, the correlation between membrane permeability and the activity of PROTACs has not been fully explored. To address this, we established a new molecular design approach to remove the linker and optimize PROTAC structure. These PROTAC compound groups were used to analyze the correlation between membrane permeability and activity using LC-tandem mass spectrometry (LC-MS/MS). Results revealed that the degradation activity of PROTACs fluctuates with increasing membrane permeability and changes in response to linker optimization, while sufficient proteolytic activity can be retained. These findings demonstrate the importance of considering the balance between membrane permeability and activity in PROTAC design and provide a new strategy for developing more effective PROTACs.

This study explores the synthesis of unique furanocembranoid-type marine diterpenoid, providencin. Providencin features a highly oxidized structure with two furan rings, two oxirane rings, and a bicyclo[12.2.0]hexadecane framework. Its potential as a lead compound for drug development has drawn attention to its total synthesis, particularly focusing on the challenging right-half segment involving a highly substituted cyclobutane ring. We developed a novel synthetic strategy for the fragment using a [2 + 2] cycloaddition reaction of lithium ynolates with α,β-unsaturated lactone, successfully constructing a bicyclic cyclobutene structure. Stereoselective hydrogenation of cyclobutenes was achieved by using Crabtree’s catalyst under high pressure H₂ atmosphere. After further transformation, the synthesis of the furan-substituted cyclobutanol fragment having a formyl side chain was accomplished.

Toll-like receptors (TLRs) play central roles in innate immune defense against infection by binding to microbial molecules. TLR7 and TLR8 are highly homologous sensors with an RNA ligand preference for single-stranded RNA (ssRNA). Recent works reveal that these TLR sense degradation products of RNA at two distinct binding sites, designated 1st site and 2nd site, rather than long ssRNA. The highly conserved 1st site is responsible for the binding of nucleosides and the 2nd site confers the oligonucleotide binding. Binding of the oligonucleotide at the 2nd site synergistically enhances the affinity for nucleoside to the 1st site. However, it remains unclear why these ligands synergistically activate TLR7 and TLR8. Here, we performed a molecular dynamics (MD) calculation and successive decomposition analysis to clarify what this synergistic effect is derived from. We demonstrated that the main factor of the synergistic effect during the TLR7 and TLR8 activation processes was the lowering of the LRR dimerization barrier, mainly achieved by the reduction of the electrostatic repulsion with the oligonucleotide binding at the 2nd site.

Powders used in pharmaceuticals require good flowability. The angle of repose and compressibility index are often used to measure the flowability of pharmaceutical powders. However, confirming the relationship between external forces and flowability for smooth powder handling is necessary. Therefore, we measured pharmaceutical excipient powder using a lower cell direct movable constant-volume shear tester and evaluated the powder’s physical properties. In this study, we utilized microcrystalline cellulose, widely used as a pharmaceutical excipient and developed in many grades with different physical properties such as particle shape. We measured the shear parameters that describe the characteristic friction and cohesion properties of each microcrystalline cellulose grade. We found that the relative compression ratio (RCR) correlated with the angle of repose. Differences in the shape of the powder yield locus were observed among the grades, and the ratio of the upward convex area of the powder yield locus curve (APC) was defined as the value that quantified these differences. Furthermore, to clarify the relationship between the particle shape parameters (e.g., particle size distribution and shape) and shear parameters, we analyzed these factors using partial least squares regression. RCR was correlated with linearity and was significantly influenced by particle shape. Accurate prediction formulas were also calculated for the stress transmission and relaxation ratios. There was no correlation with the individual shape parameters, and these are considered that is involved in a complex combination. In APC, in addition to the shape parameters used in this study, bulk density had a significant effect.

This study introduces a novel method for ring-closing chlorosulfenylation of alkenoic thioesters using N-chlorosuccinimide in hexafluoroisopropanol under mild conditions. This reaction efficiently forms five-membered cyclic sulfur compounds with high selectivity, representing a significant advancement in the synthesis of chlorinated S-heterocycles. Computational analysis using density functional theory demonstrates the superiority of thioester nucleophiles over traditional benzyl sulfides in this reaction, highlighting the energetic preference for thioesters.

Cell-penetrating peptides, such as arginine-rich peptides, encapsulate nucleic acid drugs and deliver them to intracellular compartments. Comprehensive tracking of drug delivery systems (DDSs) provides information about the behavior of the drug as well as the fate of the drug carrier after drug release, which is crucial for minimizing side effects. In this study, we labeled peptides designed to carry plasmid DNA with two types of dyes, traditional dye fluorescein and aggregation-induced emission (AIE) dye tetraphenylethylene, and subsequently tracked the DDS through the complementary ON and OFF fluorescence behaviors of the dyes. Traditional fluorescent dyes are susceptible to aggregation-caused quenching during bioimaging, a problem that is mitigated by using AIE dyes. However, by using both of these contrasting fluorescent labels, we were able to clearly visualize the DDS at different stages of its deployment, from drug transport and delivery to carrier dissociation and migration, demonstrating the feasibility of accurate DDS visualization by complementary fluorescence labeling.

Osteoporosis is induced by an imbalance between osteogenesis and bone resorption, and is treated with osteogenic drugs and/or resorption inhibitors. Resorption inhibitors, such as bisphosphonates, are orally used; however, orally active small molecules with osteogenic activity are not clinically available. We synthesized various types of small molecules and identified a series of diphenylamine and diphenylether derivatives that promoted osteoblast differentiation. Among them, diphenylether derivatives 13a, 13g, and 13h potently promoted osteoblast differentiation (EC₂₀₀ for increasing alkaline phosphatase activity = 11.3, 31.1, and 12.3 nM, respectively) and inhibited cyclin-dependent kinase 8 (CDK8) activity (IC₅₀ = 2.5, 7.8, and 3.9 nM, respectively), suggesting that their osteoblastgenic effects are mediated by the inhibition of CDK8. The ratio of the maximal plasma concentration after oral administration at 10 mg/kg in female rats and EC₂₀₀ for osteoblastogenesis was 148.1 for compound 13a, 53.4 for 13g, and 101.8 for 13h, indicating possible in vivo osteoblastogenic and osteogenic effects. In ovariectomized female rats, 13g and 13h at 10 mg/kg/d for 8 weeks increased plasma bone-type alkaline phosphatase activity, indicating enhanced in vivo osteoblastogenesis. Furthermore, micro-computed tomography (micro-CT) showed that both compounds increased femoral cortical bone volume and mineral contents, which were unaffected by ovariectomy, while having negligible effects on trabecular bone volume and mineral contents, which were markedly reduced by ovariectomy. In conclusion, diphenylamine and diphenylether structures are novel scaffolds for osteoblastogenesis enhancers via the inhibition of CDK8. Among them, 13g and 13h are candidates for anti-osteoporotic drugs with cortical bone-selective osteogenic effects.

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.