Search Results (161)

This review examines the emerging role of machine learning (ML) in pharmaceutical chemistry, with emphasis on molecular design, synthetic feasibility, and structure–property–performance (SPP) relationships. By enabling pre-synthesis prediction of physicochemical properties, reaction pathways, and pharmaceutical performance, ML can reduce empirical trial-and-error experimentation and support more efficient exploration of chemical space. A structured narrative review design with PRISMA-aligned systematic search elements was used to evaluate 101 studies, enabling transparent literature identification, eligibility screening, and thematic synthesis across heterogeneous ML applications in pharmaceutical chemistry. This review examines structure–property relationships (SPRs) and property–performance relationships (PPRs), with emphasis on key pharmaceutical endpoints such as solubility, permeability, stability, dissolution, and bioavailability. An integrated SPP framework is proposed to connect molecular structure, intermediate properties, and final performance outcomes while incorporating retrosynthetic analysis and experimental feedback and closed-loop optimization. Recent frontier developments are also discussed, including molecular foundation models, multimodal language–graph models, diffusion-based molecular generation, E(3)-equivariant models, and MolMIM-like latent-space optimization. This review also covers co-folding and joint ligand–protein modeling, Boltz-2-like affinity prediction, AlphaFold 3-related biomolecular interaction modeling, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction. Key limitations include dataset leakage, benchmark inconsistency, assay variability, conformational and protonation-state effects, reproducibility challenges, regulatory constraints, and the gap between computational prediction and prospective experimental validation. Future progress is expected to depend on hybrid physics–ML models, uncertainty-aware prospective validation, autonomous experimentation, explainable artificial intelligence, and sustainability-aware molecular design. Overall, ML is evolving from a predictive tool into a chemically informed decision-support framework for rational, synthesis-aware, and experimentally validated pharmaceutical development. Full article

The galactose/N-acetyl-D-galactosamine (Gal/GalNAc)-inhibitable lectin of Entamoeba histolytica plays essential roles in host cell adhesion and cytotoxicity. The intermediate subunit lectin-1 (Igl1) contributes to these functions, but its molecular state under different environmental conditions remains unclear. In this study, we found that Igl1 is present as multiple fragments in the culture supernatant of trophozoites, whereas a single major species corresponding to intact Igl1 was detected in cell lysates. Notably, the molecular sizes of both intact Igl1 and its extracellular fragments differed depending on culture conditions, with larger apparent sizes observed under co-culture with Caco-2 cells. These differences were not explained by changes in transcript levels, protein folding, or N-terminal truncation. Fragmentation of Igl1 was suppressed by a cysteine protease inhibitor, indicating extracellular generation. These findings demonstrate that host-cell-associated conditions alter the molecular size of Igl1 and that extracellular protease-dependent processing generates multiple Igl1 fragments, providing new insights into the regulation of this key virulence factor. The presence of extracellular fragments further suggests a potential contribution to host tissue damage during amoebiasis. Full article

Tyrosinase-related protein 1 (Tyrp1) is a melanosomal glycoprotein required for eumelanin biosynthesis through the oxidation of 5,6-dihydroxyindole-2-carboxylic acid (DHICA). Pathogenic variants in Tyrp1 cause oculocutaneous albinism type 3 (OCA3), but the molecular basis by which individual substitutions impair Tyrp1 stability and activity remains incompletely understood. Here, we examined wild-type Tyrp1 and three missense variants associated with OCA3: R356Q and R326H as OCA3-related variants, and D308N as a benign control; these were under conditions relevant to melanosome maturation. To assess stability, we developed a urea-induced unfolding assay in which His-tagged Tyrp1 variants were immobilized to Ni-NTA magnetic beads before chemical denaturation. R356Q was the most destabilized variant, with a ΔΔG of 0.695 kcal/mol at pH 5.0 (acidic conditions) and 1.998 kcal/mol at pH 7.4 (near-neutral conditions) relative to wild-type. R326H showed intermediate destabilization, whereas D308N behaved similarly to wild-type. DHICA oxidation assays in the presence of MBTH showed about 20% reduced catalytic activity for R356Q, particularly under acidic conditions. Molecular dynamics simulations and ligand docking were consistent with these findings and indicated that R356Q increases conformational flexibility and perturbs structural integrity. In contrast, glycosylation reduced conformational fluctuations and enhanced stability across Tyrp1 and mutant variants examined. Together, these results show that pH, glycosylation, and disease-associated substitutions collectively modulate Tyrp1 folding energetics and catalytic competence and identify R356Q as a strongly destabilizing OCA3 variant. By defining how disease-associated Tyrp1 substitutions affect protein stability and function, this study may provide a framework for interpreting genotype–phenotype relationships and improving molecular diagnosis of OCA3. Full article

The protein folding problem has traditionally been defined by two complementary challenges: predicting the three-dimensional structure of a protein from its amino acid sequence and understanding the mechanism by which this structure is attained. While recent advances in artificial intelligence have largely addressed the former, the latter remains unresolved. Early studies showed that many small proteins fold in a cooperative two-state manner, shifting attention toward transition states and energy landscapes. Comparative analyses of protein families further revealed that folding mechanisms are often conserved among proteins sharing the same topology, suggesting a dominant role of structure in shaping folding pathways. However, this framework does not explain when and how a protein commits to a specific topology. Metamorphic proteins, in which highly similar sequences adopt distinct native folds, provide a powerful complementary approach. Studies of these systems show that closely related sequences can follow different folding mechanisms without sharing common intermediates. These findings indicate that folding pathways are determined at very early stages and are encoded within the denatured ensemble through subtle structural and energetic biases. Here, we review the evolution of protein folding studies and propose a unified view in which folding mechanisms are selected early, with the denatured state playing a central role in defining both folding pathways and final topology. Full article

Medium-resolution cryo-electron microscopy (cryo-EM) density maps preserve substantial information about protein secondary-structure organization; however, accurately recovering the topology and connectivity of α-helices and β-strands remains challenging due to noise, structural heterogeneity, and the intrinsic resolution limitations that obscure residue-level detail. Topology determination is a key intermediate step toward building atomic protein models from medium-resolution cryo-EM density maps. It requires identifying the correct correspondence and orientation between secondary-structure elements (SSEs), i.e., α-helices and β-strands, predicted from the amino-acid sequence and those detected in the three dimensional (3D) density map. Despite significant advances in cryo-EM reconstruction and molecular modelling, this correspondence problem remains a challenging task, particularly in the presence of noisy density maps and in large, topologically complex α/β proteins. To address this issue, we propose a fully automated, classification-based framework that infers protein secondary-structure topology directly from medium-resolution cryo-EM density maps. Specifically, we cast topology determination as a supervised classification problem in three-dimensional space, leveraging geometric learning on model-derived Cα coordinate representations to establish SSE correspondences, and a Dynamic Time Warping (DTW)-based procedure to resolve density-stick directionality. Validation on a benchmark of 38 proteins spanning both simulated and experimental cryo-EM maps and covering diverse fold classes (α, β, and α/β) demonstrates strong and consistent performance. Among the evaluated predictors, the Voronoi (1-NN) classifier achieves the highest average correspondence quality, with a mean F1-score of 96.82% across the full benchmark. The framework also scales to large, topologically dense targets containing up to 65 secondary-structure elements while preserving very fast correspondence inference (<3 ms), offering a substantial improvement over prior baselines in both accuracy and computational cost. Overall, the classification-driven strategy provides reliable SSE-to-density matching and, when coupled with DTW-based direction selection, yields stronger topology constraints that directly support model building and refinement from medium-resolution cryo-EM reconstructions, while remaining easy to integrate into existing structural interpretation pipelines. Full article

This study addressed the issue of insufficient activity in CALB lipase during the catalytic synthesis of key chiral intermediates for moxifloxacin. A structure-guided protein engineering strategy was employed to systematically modify its functional domains. Through molecular dynamics simulations of CALB-I189K, multiple regions exhibiting high conformational flexibility were preliminarily identified. Subsequently, by integrating 3D structural alignment with active site pocket distance analysis, the functionally most critical region (143–146) was selected. A site-directed saturation mutation library was constructed specifically targeting this region. Building upon the previously reported CALB-I189K, a mutant I189K/L144R/A146K was ultimately obtained through high-throughput screening combined with chiral HPLC validation. This mutant maintains excellent stereoselectivity (E = 206.52) while enhancing catalytic efficiency (k_cat/Κ_m) to 273.73 min⁻¹·mM⁻¹, approximately 4.5-fold that of I189K. At a substrate concentration of 1 M, it achieves 50% conversion within 2.6 h, demonstrating kinetic resolution capabilities approaching industrial standards. Molecular simulation analysis indicates that the L144R and A146K mutations synergistically enhance catalytic performance primarily by optimizing spatial distances between catalytic residues. This study not only provides a high-performance catalyst for the efficient biosynthesis of moxifloxacin chiral intermediates but also offers new insights for enzyme rational design based on dynamic structural information. Full article

Drought severely constrains grassland stability and forage productivity. Allium mongolicum Regel, a dominant species in desert steppes, exhibits high drought tolerance, yet its multi-level adaptive responses remain incompletely understood. Here, drought stress of different intensities (15%, 30%, 45%, and 60% PEG-6000) was simulated, and root phenotypes, physiological traits, and time-series transcriptomic profiles were integrated to characterize its drought-responsive patterns. The results revealed a biphasic phenotypic response: mild to moderate drought (15–30% PEG) promoted root elongation and surface expansion, consistent with a growth-prioritized response pattern, whereas severe drought (60% PEG) suppressed elongation and induced compensatory thickening, suggesting a shift toward a more structural defense-oriented response. Physiological analyses showed progressive MDA accumulation accompanied by increased SOD and POD activities and proline content, indicating enhanced antioxidant and osmotic regulation under stress. Time-series transcriptomics suggested a three-phase transcriptional adjustment pattern, including early alarm, intermediate acclimation, and late compensation. Early-stage DEGs were mainly enriched in photosystem regulation and ROS-related pathways, while intermediate stages were associated with translational control and protein folding. At the late stage, genes involved in mitochondrial metabolism and amino acid catabolism were prominently represented, implying increased respiratory activity under prolonged drought. WGCNA further identified two key modules associated with these shifts: the steelblue module, negatively correlated with root growth traits, and the darkturquoise module, positively correlated with growth-related traits and antioxidant activities. Collectively, these results outline a multi-level adaptive framework for drought responses in A. mongolicum and provide insights into how desert plants may balance growth and defense under water-limited conditions. Full article

As synthetic biology advances, prokaryotic microorganisms have become critical platforms for heterologous biosynthesis in cell factory applications. However, conventional free enzyme systems encounter substantial challenges, including inefficient intermediate transfer, toxic intermediate accumulation, and vulnerability to temperature and pH fluctuations. Enzyme complex catalytic systems offer promising solutions to these limitations. Bacillus licheniformis, a Generally Recognized as Safe (GRAS) host with exceptional protein secretion capacity, represents an ideal chassis for enzyme complex construction. This study developed a peptide-mediated platform in B. licheniformis to enable enzyme complex self-assembly and evaluated its effects on metabolic pathway performance. Five peptide elements were screened through fusion with enhanced orange/green fluorescent proteins (eOFP/eGFP) and transglutaminase (TGase). Effective peptide pairs were identified by measuring fluorescence intensity, visualizing complex formation via laser confocal microscopy, and assessing TGase activity. Subsequently, recombinant strains expressing peptide-fused key metabolic enzymes (gadTt and KdgA) were constructed for whole-cell biotransformation using gluconate as substrate to investigate the impact of peptide-mediated enzyme complexes on pyruvate synthesis. In the fluorescent protein system, P18/D18—amphipathic peptides that drive enzyme self-assembly via intermolecular hydrophobic interactions—increased extracellular fluorescence intensity of eOFP and eGFP by 31.11% and 25.21%, respectively. The D18 peptide significantly elevated TGase activity by enhancing structural stability to over 1.3-fold that of the control. For pyruvate synthesis, the peptide-mediated enzyme complex exhibited remarkable advantages in substrate conversion rate (up to 53.08%) and thermostability, confirming the platform’s ability to enhance substrate channeling despite no optimization for absolute yield. This study established a novel peptide-mediated multienzyme self-assembly platform in B. licheniformis, providing a valuable strategy for artificial metabolic channel design in synthetic biology. Full article

Slugs are significant agricultural pests and act as vectors for zoonotic parasites. However, current molluscicide options are limited and associated with substantial environmental risks. This study investigates the role of aldehyde dehydrogenase (ALDH) in the biosynthesis of farnesoic acid (FA), a key intermediate in the sesquiterpenoid hormone pathway, in two slug species: Philomycus bilineatus and Laevicaulis alte. Transcriptomic analysis revealed that both species possess conserved sesquiterpenoid biosynthetic pathways, yet they exhibit distinct levels of ALDH gene expression and differences in FA content. RNA interference (RNAi)-mediated gene silencing was employed to validate the potential of these candidate genes as targets for molluscicide development. Structural modeling of ALDH proteins using AlphaFold2 demonstrated notable divergence in the architecture of their active sites, suggesting species-specific enzymatic properties. Citral, a known inhibitor of ALDH, significantly reduced FA production in vivo and exhibited contact toxicity against both slug species. The lethal concentration 50 (LC₅₀) values were determined to be 378.2 g/L for P. bilineatus and 85.2 g/L for L. alte, respectively. Molecular docking analyses indicated that citral binds within the conserved substrate-binding tunnel of ALDH, potentially inhibiting the oxidation of farnesal. These findings establish ALDH as a critical enzymatic target for disrupting endogenous hormone biosynthesis in slugs and support the development of novel, eco-friendly molluscicides targeting the sesquiterpenoid pathway. Full article

The RNA Recognition Motif (RRM) domain of the Ewing sarcoma (EWS) protein plays a pivotal role in RNA binding and gene regulation, being crucial for its function. However, its structural dynamics are yet to be revealed. Herein, we performed 5.5 μs cumulative molecular dynamics (MD) simulations to investigate the unfolding pathways of the EWS-RRM domain in urea and DMSO across 300–500 K. The unfolding process was characterized by using free-energy landscape (FEL) analysis, hydrogen-bond occupancy, and Gaussian Mixture Model (GMM) clustering. At lower temperatures (300–350 K), the RRM largely retained its native conformation, while extensive unfolding occurred between 400 and 450 K. Results revealed multiple conformational ensembles: native (N), native-like intermediate (I_N), intermediate (I), and unfolded (U) states, underlying the unfolding pathway of RRM. In urea at 400 K, a long-lived I-state dominated, with transient N and I_N-populations, whereas in DMSO, the I_N-state appeared more stable, that transitioned into tightly packed I-states, reflecting a stepwise unfolding via compact intermediates. At 450 K, the protein reached the U-state in both solvents, though unfolding occurred more readily in urea. This study highlights the solvent-dependent unfolding mechanisms and heterogeneous I-states of EWS-RRM, providing insight into its stability, misfolding, and potential relevance to Ewing sarcoma pathogenesis. Full article

Interest in non-canonical DNA structures continues to grow, in part fueled by the recent discovery of a new structure, G-triplex DNA. Originally proposed as folding intermediates for G-quadruplex DNA, G-triplex DNA has more recently been shown to form from truncated G-quadruplex sequence oligonucleotides and other, specifically designed sequences. In this review, we provide the first, comprehensive survey of G-triplex DNA and RNA, covering the literature up to 2024. We include reports of G-triplex DNA from bulk solution and single-molecule approaches, the structural characterization of G-triplex DNA, and the breadth of oligonucleotide sequences that have been reported to form these structures. The formation of G-triplex RNA structures is also reviewed. The evolving understanding of sequence and environmental effects on G-triplex formation are presented together with challenges due to structural polymorphism and competing formation of multimeric G-quadruplex structures. Hints of the biological relevance of G-triplexes are provided by reports of protein recognition of these structures and their effects on DNA replication in vitro. Interaction of G-triplex DNA with a variety of ligands has been reported, although the search for selective ligands that can distinguish G-triplex from G-quadruplex is on-going. The vast majority of publications in the area have focused on the utilization of G-triplex in biosensing applications, which has shown some advantages compared to G-quadruplex-based systems. These results highlight the potential utility of G-triplex structures in a variety of domains and show its promise in applications in biotechnology, medicine, and research. Full article

Methacrylyl-CoA is a key metabolic intermediate in the valine catabolic pathway. Its accumulation has been found to be cytotoxic and associated with pathological conditions. Nevertheless, detailed biological effects of methacrylyl-CoA and methacrylate in human physiology and pathology are poorly understood. We propose that the electrophilicity of the alkene bond in the methacrylyl group can react with the cysteine residues in proteins resulting in an unexplored protein post-translational modification (PTM), cysteine S-2-carboxypropylation (C2cp). To test and validate this mechanistic hypothesis, we experimentally detected and profiled S-2-carboxypropylated proteins from the complex cellular proteome with the design and application of a bioorthogonal chemical probe, N-propargyl methacrylamide. We tested the probe in different mammalian cell models and demonstrated its versatility and sensitivity to protein cysteine S-2-carboxypropylation. We established quantitative chemical proteomics for global and site-specific profiling of protein S-2-carboxypropylation, which successfully identified 403 S-2-carboxypropylated proteins and 120 cysteine modification sites from HEK293T cells. Through bioinformatic analysis, we found that C2cp-modified proteins were involved in a variety of critical cellular functions including translation, RNA splicing, and protein folding. Our chemoproteomic studies demonstrating the proteome-wide distribution of cysteine S-2-carboxypropylation provide a new biochemical mechanism for the functional investigation of methacrylyl-CoA and understanding valine-related metabolic disorders. Full article

The glial tube is a longitudinal structure predominantly composed of densely bundled, aligned astrocytes that projects from the subventricular zone (SVZ) to the olfactory bulb. Neural precursor cells (NPCs) generated in the SVZ migrate through this glial tube—referred to as the rostral migratory stream (RMS)—to replace olfactory bulb interneurons in the mammalian brain. RMS astrocytes have distinct morphological and functional characteristics. These characteristics facilitate the unique purpose of the RMS as an endogenous living scaffold directing NPC migration and maturation. However, the transcriptomic factors underlying these unique structure–function attributes versus standard stellate astrocytes have not been examined. We previously developed biofabrication techniques to create the first tissue-engineered rostral migratory stream (TE-RMS) that replicates key features of the glial tube in vivo. We have shown that TE-RMS astrocytes exhibit elongated nuclei, longitudinally aligned intermediate filaments, and enrichment of key functional proteins—cytoarchitectural and surface features characteristic of native RMS astrocytes. In the current study, we performed RNA-seq on TE-RMS astrocytes in comparison to planar astrocyte cultures to identify gene expression patterns that may underlie their profound morphological and functional differences. Remarkably, we found 4,008 differentially expressed genes in TE-RMS astrocytes, with 2076 downregulated (e.g., LOC690251 and ccn5) and 1932 upregulated (e.g., lrrc45 and cntn1) compared to planar astrocytes. Moreover, there were 256 downregulated and 91 upregulated genes with >3-fold change. We also conducted analyses of gene sets related to cytoskeleton and nuclear structure, revealing the greatest enrichment of actin-related components. Overall, the TE-RMS offers a platform to study the interplay between transcriptomic and cytoarchitectural dynamics in a unique astrocyte population. Full article

Experimental data on the folding and unfolding of small globular proteins are often well described assuming a two-state equilibrium process. It means that after careful analysis by a combination of experimental techniques, only folded and unfolded states of the protein are found to be populated under various external conditions with no detectable intermediates. One of the consequences of the two-state behavior is that the equilibrium ratio of the folded to unfolded protein states follows a simple thermodynamic relation, and the enthalpy difference between states can be obtained from the temperature dependence of the equilibrium constant. In this paper, we theoretically investigate the criteria for the two-state equilibrium behavior and discuss the thermodynamic constraint on the properties of the “hidden” folding intermediates. The literature data on the folding mechanism of lysozyme in water and glycerol, which follows a two-state equilibrium behavior but includes kinetic intermediates, is analysed in light of this constraint. Full article

Models that predict the 3D structure of proteins enable us to easily analyze the structure of unknown proteins. Though many of these models have been found to be accurate, their application in plant proteins is not always entirely accurate. Thus, we aimed to develop a versatile yet simple pipeline that can predict novel proteins with a specific function. As an example, via benchmark studies, we sought to discover novel UDP-glycosyltransferases (UGTs) potentially involved in ginsenoside biosynthesis. Since the functionality of these UGTs has been shown to be determined by a few amino acids, a 3D-structure-based pipeline was required. Our pipeline includes four sequential steps: a sequence-based homology search, AlphaFold3-based 3D structure prediction, docking simulations with ginsenoside intermediates using SwissDock and CB-Dock2, and MPEK analysis to assess interaction stability. Through the application of this benchmark, we optimized the role of each module in the pipeline and successfully identified four novel UGT candidates. These candidates are predicted to catalyze the conversion of protopanaxadiol (PPD) to compound K (CK) or protopanaxatriol (PPT) to ginsenoside F1. This pilot study demonstrates how our pipeline can be used for the functional annotation of plant proteins and the discovery of enzymes involved in specialized pathways. Full article