Search Results (3,725)

Molecular simulation is central to modern drug discovery but is often limited by high computational cost and the complexity of molecular interactions. Deep-learning drug–target interaction (DTI) prediction can accelerate screening; however, many models underuse the local functional structure features—binding motifs, reactive groups, and residue-level fragments—that drive recognition. We present LoF-DTI, a framework that explicitly represents and couples such local features. Drugs are converted from SMILES into molecular graphs and targets from sequences into feature representations. On the drug side, a Jumping Knowledge (JK) enhanced Graph Isomorphism Network (GIN) extracts atom- and neighborhood-level patterns; on the target side, residual CNN blocks with progressively enlarged receptive fields, augmented by N-mer substructural statistics, capture multi-scale local motifs. A Gated Cross-Attention (GCA) module then performs atom-to-residue interaction learning, highlighting decisive local pairs and providing token-level interpretability through attention scores. By prioritizing locality during both encoding and interaction, LoF-DTI delivers competitive results across multiple benchmarks and improves early retrieval relevant to virtual screening. Case analyses show that the model recovers known functional binding sites, suggesting strong potential to provide mechanism-aware guidance for molecular simulation and to streamline the drug design pipeline. Full article

Chemosensory systems are essential in insect behavior, with several key genes associated with these systems emerging as potential targets for pest control. Porphyrophora sophorae (Archangelskaya, 1935), a destructive pest of Chinese licorice (Glycyrrhiza uralensis, Fabaceae), poses a significant threat to the healthy cultivation of licorice. However, the molecular mechanisms underlying its host detection and olfactory recognition remain poorly understood. In this study, we present the first identification of odorant-binding proteins (OBPs) and olfactory receptors (ORs) from the transcriptome of P. sophorae. The identified OBPs contain six conserved cysteine residues, while predictive analysis suggests that PsopOrco may contain six transmembrane domains. Phylogenetic analysis demonstrated that the majority of these olfactory proteins are closely related to OBPs and ORs found in other scale insects. Using RT-qPCR, we assessed the anatomical structures expression of these genes and found that PsopOBP3, PsopOBP6, and PsopOrco were predominantly expressed in the antennae. Additionally, expression levels of OBPs and ORs varied across different tissues, suggesting anatomical structure regulation. These findings expand the gene repertoire of P. sophorae and provide valuable resources for further functional analysis of these key olfactory genes. Full article

Background: Antibody-dependent cellular cytotoxicity (ADCC) is an immune response where antibodies bind to target cells and activate effector cells through Fcγ receptors, ultimately leading to the destruction of the target cells. Methods: This study examined the ADCC activities of charge variants of a therapeutic IgG₁, MAB1, using an internally developed reporter gene assay. In this assay, the proprietary target was expressed on DiFi cells, while FcγRIIIa was expressed on Jurkat effector cells. Results: The results revealed that different charge variants had varying levels of ADCC activity, with variants containing C-terminal lysine residues showing enhanced activity. The charge variants arose from modifications such as the presence of sialic acid at the glycan moiety, deamidation, and C-terminal lysine truncation, including K2 (two C-terminal lysine residues), K1 (one C-terminal lysine residue), and K0 (no C-terminal lysine residues) variants. Notably, the K1 and K2 variants demonstrated higher ADCC activity compared to the K0 and acidic variants. However, the observed increase was attributed not to the lysine residue itself, but rather to the MAN5 glycan associated with the lysine-containing variants. Conclusion: These findings challenge previous assumptions about the role of C-terminal lysine in ADCC, suggesting a shift in understanding the functional significance of charge variants and emphasizing the critical influence of glycan composition in therapeutic antibody efficacy. Full article

Stress granules (SGs) are dynamic membrane-less structures assembled in response to stress. The formation of stress granules in plants is poorly understood, especially the mechanism of mRNA recruitment. The problem of the specificity of mRNA interaction with stress granule proteins is unexplored. Oligouridylate binding protein 1B (UBP1B) is considered as the core element of plant SGs. In this study, we expressed the AtUBP1b protein from Arabidopsis thaliana in E. coli cells. Mass spectroscopic analysis showed that the AtUBP1b protein expressed in E. coli cells is phosphorylated at serine, threonine, and tyrosine residues. We also performed a de novo phosphorylation reaction in wheat germ extracts with the addition of radioactively labeled phosphorus and showed AtUBP1b phosphorylation in plant extracts. We hypothesized that phosphorylation or dephosphorylation of AtUBP1b in plant cells is a signal for protein binding to RNA. The purified protein was tested for its ability to bind to mRNA in vitro. In gel-shifting assays we demonstrated that AtUBP1b protein binds specifically to 5′-untranslated regions (5′UTR) of mRNA. When AtUBP1b was added to a cell-free wheat germ translation system, it exerted different effects on protein synthesis. We showed that AtUBP1b had a significant inhibitory effect on the expression of mRNAs containing 5′UTRs that were shown to bind to the protein in the gel-shifting reaction. Full article

In the present study, seven previously undescribed resin glycosides, designated cusponins I-VII (1–7), together with one known analog (8), were isolated from the seeds of Cuscuta japonica, a traditional medicine used in China. Structural elucidation revealed them to be glycosidic acid methyl esters, generated through on-column methyl esterification of naturally occurring resin glycosides catalyzed by NH₂-functionalized silica gel. All isolates were characterized as either pentasaccharides or tetrasaccharides, incorporating D-glucose, L-rhamnose, or D-fucose units as the sugar residues. Notably, compounds 1 and 3–7 contained the uncommon aglycone, 11S-hydroxypentadecanoic acid. Bioactivity assessments demonstrated that compounds 1–4, 6 and 8 suppressed α-glucosidase activity, with IC₅₀ values between 8.02 and 71.39 μM. In addition, compounds 3 and 5 exhibited inhibitory effects on protein tyrosine phosphatase 1B (PTP1B), with IC₅₀ values of 14.19 ± 1.29 μM and 62.31 ± 8.61 μM, respectively, marking the first report of PTP1B inhibitory activity among resin glycosides. Enzyme kinetic analyses indicated that compound 2 acted as an uncompetitive α-glucosidase inhibitor (K_is = 3.02 μM), whereas compound 3 inhibited PTP1B via a mixed-type mechanism (Kᵢ = 24.82 μM; K_is = 64.24 μM). Molecular docking combined with molecular dynamics simulations suggested that compounds 2 and 3 interacted with α-glucosidase-pNPG and PTP1B, respectively, forming stable complexes with favorable binding free energies. Collectively, this study reported eight resin glycosides from C. japonica, seven of them newly identified, with compounds 2 and 3 highlighted as promising scaffolds for antidiabetic drug discovery. Full article

Vitamin D deficiency is highly prevalent in Pakistan, but there is limited data on its genetic aspects. This case–control pilot study aimed to determine the association of rs782153744, rs200183599, rs118204011, and rs28934604 with vitamin D deficiency along rs7041 which has been studied in our population. The DNA of a total of 600 subjects (300 cases and 300 controls) was extracted and genotyped by tetra ARMS PCR, followed by Sanger DNA sequencing of exon 4 of the CYP2R1 and CYP27B1 genes and exon 8 of the GC gene. SNP Stat was employed to analyze the data, while logistic regression was used to calculate the p-values and odds ratios (ORs). The R package version R studio (2025.05.1) Build 513 was used to statistically analyze rs782153744. In silico modeling of wild and mutant CYP2R1 and GC proteins was performed in Swiss-Model, Swiss-Dock, Discovery Studio, and PyMol using 3c6g and IJ78 as templates to perform binding pocket analysis of vitamin D3. The rs782153744 showed a protective association in the additive (OR: 0.15, 95% CI: 0.08–0.27, p-value < 0.001), recessive (OR: 0.19, 95% CI: 0.10–0.33, p-value < 0.001), and dominant (OR: 0.19, CI = 0.10–0.33, p-value < 0.001) models, while GC rs7041 (T > A, T > G) displayed a p-value < 0.0001 across all genetic models. Sanger sequencing yielded insignificant results, and the SNPs rs200183599, rs118204011, and rs28934604 had no significant association with vitamin D deficiency. The molecular pocket analysis of wild and mutant CYP2R1 proteins carrying rs782153744 polymorphisms revealed no changes. GC proteins carrying the rs7041 polymorphism revealed a shift in their 3D and 2D configuration, as well as a change in the amino acid residue of the binding pocket of VD3. The risk-associated rs7041 and protective rs782153744 variants back genetic screening for vitamin D deficiency risk stratification, allowing targeted supplementation in predisposed subjects and assisting in formulating a genotype-specific therapeutic approach. Full article

Lysine methylation is a critical post-translational modification catalyzed by lysine methyltransferases (KMTs), originally characterized in the regulation of histones. However, the breadth of non-histone targets remains largely unexplored. Here, we used a systematic peptide array-based approach to define a substrate preference motif for the SET-domain-containing KMT MLL4 (KMT2D), a member of the COMPASS complex and a known H3K4 methyltransferase. Using this motif, we identified CXXC finger protein 1 (CFP1), a core component of Setd1A/B complexes, as a putative MLL4 substrate. In vitro methyltransferase assays confirmed robust methylation of CFP1 by an MLL4-WRAD complex. Surprisingly, while initial predictions implicated K328, array-based methylation profiling revealed multiple lysine residues within CFP1’s lysine-rich basic domain as methylation targets, including K331, K335, K339, and K340. We further demonstrated that CFP1 methylation likely modulates its interaction with MLL4’s PHD cassettes and facilitates binding to Setd1A. Binding preferences of MLL4’s PHD1–3 and PHD4–6 domains varied with methylation state and site, suggesting non-histone methyl mark recognition by these cassettes. Pulldown assays confirmed that methylated, but not unmethylated, CFP1 binds Setd1A, supporting a potential methyl-switch mechanism. Together, our findings propose CFP1 as a potential non-histone substrate of MLL4 and suggest that MLL4 may regulate Setd1A/B function indirectly via CFP1 methylation. This study expands the substrate landscape of MLL4 and lays the groundwork for future investigations into non-histone methylation signaling in chromatin regulation. Full article

Background/Objectives: Ginsenosides, one of the most pharmaceutically valuable chemical compounds in Panax ginseng, are synthesized with several enzymes, including UGTs. UGTs determine absorbability and physiological function upon consumption. Thus, understanding the functional residues of ginsenoside biosynthesis-associated UGTs is crucial for enhancing the production of valuable ginsenoside varieties. Methods: We collected the UGT homologs of high sequence similarity from two rate-limiting steps of the biosynthetic pathway. The 3D structures of these proteins were predicted using the AlphaFold3 model. The ligand-binding interactions of these UGTs were examined using SwissDock and CB-Dock2. Enzyme kinetics were analyzed with MPEK. Using these tools, we performed in silico mutagenic analyses to identify the functional residues of UGTs in detail. Results: We elucidated the molecular mechanisms of experimentally verified functional residues in UGTs, many of which were associated with optimal ligand interaction angles that expose target carbons. We also identified putatively important amino acid residues that mediate ligand interactions and modulate reaction kinetics by more than 25%. In this study, residues at positions 62, 224, 397, and 398 were shown to significantly influence enzyme kinetics. Conclusions: Our study provides the first structural analysis of the functional residues of ginsenoside biosynthetic UGTs based on their 3D structures. We identified several key amino acid residues essential for proper ginsenoside biosynthesis: (1) residues determining ligand interactions, (2) residues modulating ligand binding angles, and (3) residues affecting reaction kinetics. Our findings demonstrate an effective approach to identifying functional residues in plant enzymes and present valuable UGT candidates for future experimental validation. Full article

In response to the pressing environmental challenges posed by electrolytic manganese residue (EMR) and red mud (RM), this study proposes an innovative cementitious material technology for the synergistic co-utilization of these industrial wastes. By employing steel slag (SS) as a calcium-rich skeleton, the system effectively immobilizes sulfates from EMR and alkalinity from RM, converting hazardous wastes into value-added construction materials. Through orthogonal experimentation, an optimal mix proportion was established—30% RM, 20% EMR, and 50% SS at a water-to-binder ratio of 0.28—which achieved a 28-day compressive strength of 20.40 MPa, meeting relevant industry standards for auxiliary cementitious materials. Microstructural analysis unveiled a multi-stage alkali-sulfate synergistic activation mechanism: (1) the high alkalinity derived from RM rapidly activates the dissolution of aluminosilicate phases in both SS and EMR; (2) sulfate ions released from EMR promote extensive formation of ettringite (AFt), enhancing early-age structural integrity; and (3) calcium ions from SS facilitate the development of a dense C-S-H gel matrix, which serves as the primary binding phase. More profoundly, this process exemplifies a self-stabilizing waste-to-resource conversion mechanism, whereby harmful constituents (sulfates and free alkalis) are constructively incorporated into stable hydration products. This work not only elucidates a coherent scientific framework for the safe and efficient reclamation of multi-source solid wastes, but also demonstrates a scalable and ecologically viable pathway for million-ton-scale valorization of EMR and RM. Furthermore, it presents feasibility insights for the application of high-dosage steel slag-based material systems, thereby unifying significant environmental and economic advantages. Full article

Traditional sample preparation for terpene analysis includes distillation, solvent extraction, and solid phase extraction and is followed by using gas chromatography with a mass spectrometer (GC-MS) to complete identification and quantification. The preparations rely on the volatility and low polarity of terpenes which exist in free form. However, terpenes in bound form are still largely retained in the extracted residues because, by binding with sugar moiety, they have high polarity and water solubility and low volatility. In this study, distributions and profiles of free and bound form terpenes in different fruit and crop byproducts were evaluated by using different extraction media followed by acid hydrolysis. The acid hydrolysis significantly broke down the binding between terpene and sugar moiety and freed the bound terpene. The concentration of bound terpenes in fruit peel or corn silk was much higher than that of originally existing free terpenes. For example, the terpene concentration in watermelon peel increased from 47.0 to 101 μg/g after hydrolysis. The profile of bound terpenes was also more diverse than that of free terpenes. Among the three extraction media, water, ethanol, and acetone, acetone was the best media to extract bound terpenes with over one and a half times higher total bound terpene extraction yield than ethanol or water extract. The findings of this study explored the bound form terpenes in agricultural products which are usually underexplored in current terpene research. It also demonstrated an effective sample preparation and approach for determining bound terpenes in plants. This study could be an initiating effort and work to assist in exploring rarely mindful bound terpenes in foods and plants. The odorless nature and high stability and water solubility of bound terpenes could provide them a great advantage over free terpenes in various applications requiring neutral scent. Full article

This study investigated the interaction between cannabidiol (CBD) derivatives and the GPR55 receptor using a bioinformatics-driven molecular docking approach. GPR55, implicated in central nervous system (CNS) pathologies, represents a promising target for novel therapeutics. Drug-likeness evaluation via SwissADME confirmed that all selected derivatives complied with Lipinski′s Rule of Five, exhibiting favorable physicochemical properties with molecular weights below 500 Da and acceptable logP values. Molecular docking simulations, performed using AutoDock Vina through PyRx, revealed strong binding affinities, with docking scores ranging from −9.2 to −7.2 kcal/mol, indicating thermodynamically feasible interactions. Visualization and interaction analysis identified a conserved binding pocket involving key residues, including TYR101, PHE102, TYR106, ILE156, PHE169, MET172, TRP177, PRO184, LEU185, LEU270 and MET274. Ligand clustering in this region further supports the presence of a structurally defined binding site. Molecular dynamics simulations of GPR55 in complex with the three top-scoring ligands (3″-HOCBD, THC, and CBL) revealed that all ligands remained stably bound within the cavity over 100 ns, with ligand-specific rearrangements. Predicted oral bioavailability was moderate (0.55), consistent with the need for optimized formulations to enhance systemic absorption. These findings suggest that CBD derivatives may act as potential modulators of GPR55, offering a basis for the development of novel CNS-targeted therapeutics. Full article

Neopestalotiopsis zimbabwana is an emerging phytopathogen with multiple hosts. Considering the environmental, toxicological, and resistance issues linked to synthetic fungicides, Origanum vulgare L. essential oil (OEO) was evaluated through in vitro, in vivo, and in silico approaches. The pathogen, isolated from Watsonia borbonica L., was molecularly identified. Gas chromatography–mass spectrometry (GC–MS) analysis showed hexadecanoic acid (15.98%), dodecanoic acid (15.74%), terpinen-4-ol (11.61%), and thymol (7.65%) as the main components. In vitro assays determined a minimum inhibitory concentration (MIC) of 30% OEO and a minimal fungicidal concentration (MFC) of 60% OEO. Growth chamber trials demonstrated that preventive sprays maintained 0% foliar damage—similar to Captan^®—while controls reached ≈98%; suspending applications after week 4 resulted in ≈45% damage by week 8. These results confirm that OEO lacks systemic residual activity, acting only as a protectant within preventive integrated pest management (IPM) schemes. Docking to cytochrome b (protein data bank, PDB: 5TL8) indicated strong binding of α-farnesene (−7.638 kcal·mol⁻¹), isoterpinolene (−6.944), and α-terpineol (−6.918), suggesting disruption of mitochondrial respiration via Complex III. OEO represents a promising eco-friendly alternative for managing N. zimbabwana under controlled conditions and reducing reliance on synthetic fungicides. Full article

Corbicula fluminea protein (CFP) and cyanidin-3-O-glucoside (C3G) are natural nutrient fortifiers. During consumption or processing, they may interact with each other, inducing alternations in their structural and functional properties. However, nothing was known about the mechanism of their interaction and their synergistic antioxidant effect. In this research, C3G was physically mixed with CFP to simulate practical scenarios. The impact of the presence of C3G on the multispectral characteristics, antioxidant activity, and particle properties of CFP was examined and compared to chemically fabricated C3G-CFP covalent conjugates. The results indicate that C3G tended to spontaneously bind to CFP and formed compact non-covalent complex, with hydrophobic forces predominantly governing the interaction. This binding resulted in the statically quenched intrinsic fluorescence of CFP, accompanied by a dynamic model. Moreover, C3G preferentially induced Trp residue in CFP exposed to a more polar microenvironment, yet it exerted nearly no effects on CFP when analyzed using ultraviolet–visible (UV-Vis) spectroscopy and synchronous fluorescence spectroscopy (SFS). Additionally, although the formed non-covalent complex demonstrated strengthened antioxidant capacity, C3G displayed an antagonistic effect with CFP, whereas lower C3G concentrations led to synergistic effects in covalent conjugates. These findings provide new insights into the effective application of C3G and CFP as nutritional antioxidants. Full article

Metallocarboxypeptidase (MCP) is a crucial protein enzyme involved in food digestion and absorption in animals, which has a potential influence on the differentiation of the trophic niche. Considering that stomatopods have raptorial appendage-specific trophic niches, the present study screened and compared the MCP M14 gene family of three stomatopods (Lysiosquillina maculata, Odontodactylus scyllarus, and Oratosquilla oratoria) with different raptorial appendage morphologies based on full-length transcriptome information. There are 13 and 17 MCP M14 gene family members identified in L. maculata and O. scyllarus, respectively, which are classified as M14A, M14B, and M14D subfamilies. However, 15 MCP M14 family members have been identified in O. oratoria, all belonging to the M14A subfamily. The physicochemical properties, phylogenetic relationships, conserved motifs, and secondary and tertiary structures of the MCP M14 amino acid sequences were also analyzed in the present study. The results revealed that each amino acid sequence had unique physicochemical properties. Ten conserved motifs were further characterized across the MCP M14 amino acid sequences, and the type and number of motifs from the same subfamily remained highly conserved. Meanwhile, we found that most of the MCP M14 gene family members have critical residues (including Zn²⁺ binding sites [His69, Glu72, and His196], substrate-binding residues [Arg124, Arg127, and Arg145], and disulfide bond-forming residues [Cys138 and Cys161]) involved in disulfide bond formation and enzyme activity stabilization. Furthermore, the random coil is the predominant structural feature of the MCP M14 amino acid sequence. In conclusion, these results are undoubtedly valuable for exploring the evolution and regulation mechanisms of the trophic niche in stomatopods. Full article

Chiral amines are vital structural motifs in pharmaceuticals and agrochemicals, where enantiomeric purity governs bioactivity and environmental behavior. We identified a novel (R)-selective amine transaminase (MwoAT) from Mycobacterium sp. via genome mining, which exhibits activity toward the synthesis of the chiral amine (R)-1-methyl-3-phenylpropylamine. The enzyme displayed optimal activity at pH 7.0 and 40 °C, with high thermostability and solvent tolerance. Using an AlphaFold3-guided semi-rational engineering strategy integrating molecular docking, alanine scanning, and saturation mutagenesis, residue L175 was pinpointed as critical for substrate binding. The resulting L175G variant exhibited a 2.1-fold increase in catalytic efficiency (k_cat/K_m) and improved thermal stability. Applied to the asymmetric synthesis of (R)-1-methyl-3-phenylpropylamine—a precursor for the antihypertensive drug dilevalol and potential scaffold for crop protection agents—the mutant achieved 26.4% conversion with ≥99.9% ee. The enzyme also accepted several ketones relevant to agrochemical synthesis, underscoring its versatility. This work delivers an engineered biocatalyst for sustainable chiral amine production and demonstrates an AI-assisted protein engineering framework applicable to both medicinal and agricultural chemistry. Full article