Search Results (326)

Poly (ADP-ribose) polymerase 1 (PARP1) is an important enzyme that plays a central role in the DNA damage response, facilitating repair of single-stranded DNA breaks via the base excision repair (BER) pathway and thus genomic integrity. Its therapeutic relevance is compounded in breast cancer, particularly in BRCA1 or BRCA2 mutant cancers, where compromised homologous recombination repair (HRR) leaves a synthetic lethal dependency on PARP1-mediated repair. This review comprehensively discusses the recent advances in computational chemistry for the discovery of PARP1 inhibitors, focusing on their application in breast cancer therapy. Techniques such as molecular docking, molecular dynamics (MD) simulations, quantitative structure–activity relationship (QSAR) modeling, density functional theory (DFT), time-dependent DFT (TD-DFT), and machine learning (ML)-aided virtual screening have revolutionized the discovery of inhibitors. Some of the most prominent examples are Olaparib (IC₅₀ = 5 nM), Rucaparib (IC₅₀ = 7 nM), and Talazoparib (IC₅₀ = 1 nM), which were optimized with docking scores between −9.0 to −9.3 kcal/mol and validated by in vitro and in vivo assays, achieving 60–80% inhibition of tumor growth in BRCA-mutated models and achieving up to 21-month improvement in progression-free survival in clinical trials of BRCA-mutated breast and ovarian cancer patients. These strategies enable site-specific hopping into the PARP1 nicotinamide-binding pocket to enhance inhibitor affinity and specificity and reduce off-target activity. Employing computation and experimental verification in a hybrid strategy have brought next-generation inhibitors to the clinic with accelerated development, higher efficacy, and personalized treatment for breast cancer patients. Future approaches, including AI-aided generative models and multi-omics integration, have the promise to further refine inhibitor design, paving the way for precision oncology. Full article

Patchoulene, the characteristic sesquiterpene of patchouli essential oil, is highly valued in the perfume industry for its distinctive woody note and fixative properties. Beyond its olfactory applications, patchoulene has demonstrated promising biological activities, including anti-inflammatory, antimicrobial, and neuroprotective effects. Current production relies mainly on extraction from Pogostemon cablin plants, which requires long growth cycles (≥8 months), exhibits low yields, and imposes significant environmental constraints. To overcome these limitations, this study aimed to enhance the Whole-cell yield of patchoulene synthase (PcPTS) through structure-informed protein engineering. A semi-rational design approach was employed, combining homology modeling, molecular docking, evolutionary analysis, and molecular dynamics simulations to identify functional residues within the enzyme active site. Ala-scanning mutagenesis highlighted Thr532 as essential for catalytic activity, and coevolutionary analysis indicated synergistic effects between Phe456 and Thr532. Site-directed mutagenesis was conducted to generate single (F456M, T532Y) and double (F456M/T532Y, designated M2) mutants. The double mutant M2 showed a 3.62-fold increase in patchoulene production compared to the wild-type enzyme. In silico analyses suggested that the enhanced performance of M2 originates from improved substrate positioning, reduced structural flexibility, and strengthened molecular interactions, collectively contributing to a lower energy barrier for catalysis. This study provides an effective strategy for the rapid optimization of terpenoid synthases and facilitates the development of microbial cell factories for sustainable and high-yield production of plant-derived terpenoids. 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

The emergence of multidrug-resistant Pseudomonas aeruginosa strains is increasingly becoming a critical threat to global health. Among the resistance mechanisms, the MexAB–OprM efflux pump confers P. aeruginosa with an efficient method to export a broad spectrum of antibiotics. The antimicrobial peptide Esc (1-21)-1c was shown to downregulate this efflux system, though its mechanism of action has not been unveiled thus far. Here, we employed a combination of molecular modeling and experimental methods to investigate the precise peptide inhibitory mechanism. Functional proteomic experiments revealed the P. aeruginosa protein Q9I5H3, homologous to E. coli QseB, as a putative key target of Esc(1-21)-1c. Molecular docking predicted stable peptide–protein interactions, which were experimentally validated through fluorescence spectroscopy. Furthermore, electrophoretic mobility shift assays demonstrated that Q9I5H3 specifically binds the MexAB–OprM promoter and that Esc(1-21)-1c competitively inhibits this interaction in a dose-dependent manner. These findings reveal a previously uncharacterized regulatory pathway for efflux pump control and highlight Q9I5H3 as a promising therapeutic target against multidrug-resistant P. aeruginosa. Full article

Background: Cytochrome P450 (CYP450) enzymes play a central role in the metabolism of xenobiotics, including plant-derived compounds such as terpenoids. Objectives: This study aimed to predict the molecular interactions of linalool (LIN) and linalyl acetate (LINAct), major constituents of lavender essential oil, with the canine CYP2B11, CYP2C21, and CYP2D15 isoforms, using in silico approaches. Methods: Three-dimensional (3D) models of the target enzymes were generated through homology modeling using SWISS-MODEL and validated based on global model quality estimate (GMQE) and QMEAN Z-score metrics. Ligand structures were optimized in the Molecular Operating Environment (MOE), and pharmacophoric features were analyzed. Molecular docking simulations were performed using AutoDock Vina, followed by visualization of interactions in MOE. Results: LIN and LINAct exhibit favorable binding affinities with all three isoforms, suggesting their potential as substrates or modulators. Hydrogen bonding and hydrophobic interactions were the predominant forces stabilizing the ligand–enzyme complexes. Conclusions: These findings provide a computational basis for understanding the hepatic metabolism of LIN and LINAct in dogs, offering preliminary insights into the role of specific CYP isoforms in their biotransformation. Full article

Control strategies for leishmaniasis increasingly target sand fly vectors through sugar feeding approaches containing bioactive compounds. This study investigated the behavioral and toxicological effects of the iridoids plumericin and isoplumericin, isolated from Himatanthus sucuuba, on Lutzomyia longipalpis by integrating computational and experimental approaches focused on gustatory system interactions. The iridoids were purified by column chromatography and characterized by GC-MS. The gustatory receptor A0A1B0CHD5 was structurally characterized through homology modeling, followed by molecular docking and 100 ns molecular dynamics simulations. Behavioral assays evaluated survival, repellency, and feeding preferences using sugar solutions supplemented with an iridoid mixture. Toxicity was assessed in Drosophila melanogaster as a non-target organism model. Molecular docking results revealed comparable binding affinities between sucrose (ChemPLP score 57.96) and the iridoids plumericin (49.08) and isoplumericin (47.75). Molecular dynamics simulations confirmed the stability of the ligand–receptor complexes and revealed distinct conformational changes. The iridoids did not affect L. longipalpis survival, showed no repellency, and did not reduce sugar feeding acceptance. Preference for the control diet was observed only after continuous exposure (48 h), suggesting involvement of post-ingestive sensory processing. No acute toxicity was observed in D. melanogaster (96% survival). These findings demonstrate that iridoids preserve vector feeding behavior and survival while exhibiting low toxicity to non-target organisms, supporting their potential use in gustatory modulation strategies in leishmaniasis vector control without compromising ecological safety. Full article

Dopamine D2-like receptors, including D2, D3, and D4, are members of the aminergic G protein-coupled receptor (GPCR) family and are targets for neurological disorders. The development of subtype selective ligands is important for enhanced therapeutics and reduced side effects; however, it is challenging to design and develop selective ligands owing to the high degree of sequence homology among D2-like subtypes. To gain insight into the structural basis of subtype selectivity of piperazinylalkyl pyrazole/isoxazole analogs for D2-like dopamine receptors, we carried out 3D quantitative structure–activity relationship (3D-QSAR) and molecular docking studies. The 3D-QSAR models for the D2, D3, and D4 subtypes showed robust correlation coefficients (r²) of 0.960, 0.912, and 0.946, as well as reliable predictive values (Q²) of 0.511, 0.808, and 0.560, respectively. Contour map analysis revealed key structural determinants for ligand activity, highlighting the distinct steric and electrostatic requirements for each subtype. These findings were further rationalized by molecular docking studies, which confirmed that interactions with non-conserved residues modulate binding affinity. Crucially, our analysis identified a critical structural basis for D4 subtype selectivity. This selectivity is attributed to a spatial constraint within the hydrophobic pocket formed by TMs 3, 5, and 6. This constraint restricts the orientation of bulky substituents on the 4-phenylpiperazine moiety. These findings provide actionable structural insights for the rational design of next-generation subtype-selective antagonists for D2-like dopamine receptors. Full article

Transketolase-like protein 1 (TKTL-1) has been implicated in altered cancer metabolism, yet its structure and molecular function remain poorly understood. In this study, we established a homology model of TKTL-1 using multiple templates and validated it through sequence alignment and structural comparison with the canonical transketolase (TKT). Binding-site identification was performed using CASTp, receptor cavity mapping, and blind docking, all of which consistently pointed to a conserved region involving interactive residues shared between TKT and TKTL-1. Comparative docking revealed the reduced affinity of TKTL-1 for TDP, supporting functional divergence between TKTL-1 and TKT. We further analyzed conserved residues and receptor surfaces, which enabled us to propose predictive scaffolds as potential modulators of TKTL-1. While these scaffolds remain theoretical, they provide a computational framework to guide future pharmacophore modeling, molecular dynamics simulations, and experimental validation. Together, our study highlights the structural features of TKTL-1, establishes its key differences from TKT, and lays the groundwork for future drug discovery efforts targeting cancer metabolism. Full article

The secondary contamination of nodularin disinfection by-products (NOD-DBPs) is a problem worthy of attention. In this study, prototypical NOD-R-DBPs were prepared, and their toxicity was assessed using conventional protein phosphatase (PPs) inhibition assay, confirming that structural changes in “Adda³” during chlorination are key factors leading to a significant reduction in NOD-R toxicity. However, some NOD-R-DBPs still exhibit certain levels of toxicity (2.8–81% of NOD-R). To elucidate the mechanism underlying the potential inhibitory effect of NOD-R-DBPs on protein phosphatase 2A (PP2A), molecular simulations were employed to establish interaction models between prototypical NOD-R-DBPs and PP2A using homology modeling strategies, and molecular docking was used to obtain candidate interaction parameters between prototypical NOD-R-DBPs and PP2A. Structural changes in “Adda³” weakened the hydrogen bonds “Adda³”Asn₁₁₇ and “Adda³”His₁₁₈. Subsequently, the disruption of “Adda³” altered key interactions between NOD-R-DBPs and PP2A (hydrogen bond Mdhb⁵ ← Arg₈₉, ionic bond Glu⁴-Arg₈₉, metal bond His₂₄₁-Mn₁²⁺, etc.). The changes in these interactions further altered the interactions between conserved amino acids and the catalytic center Mn²⁺ (ionic bond Asp₅₇-Mn₂²⁺), thereby increasing Mn²⁺ exposure. Meanwhile, the retained interactions promoted the binding of -PO₄ with the conserved amino acids His₁₁₈ and Arg₈₉. Prototypical NOD-R-DBPs retained the aforementioned key interactions and thus exhibit potential inhibitory effects on PP2A. The varying degrees of damage to the Adda³ structure led to significant differences in the inhibitory effects of different NOD-R-DBPs on PP2A. Full article

H5N1 Influenza A virus continues to pose a significant zoonotic threat, with increasing evidence of interspecies transmission and genetic adaptation. Previous studies primarily focused on avian or human isolates, with limited comprehensive analysis of H5N1 evolution across multiple mammalian hosts. Existing molecular surveillance often lags behind viral evolution; this study underscores the necessity for real-time monitoring of ongoing mutations affecting pathogenicity and transmissibility. Our goals are (1) to retrieve and analyze HA, NP and NA gene sequences of H5N1 Influenza A virus from diverse hosts, including humans, poultry and multiple mammalian species, to assess genetic diversity and evolutionary patterns and (2) to evaluate positive selection sites across the three major genes (HA, NP and NA) to determine adaptive mutations linked to host adaptation and viral survival. To achieve these goals, in this study, we considered (78 HA), (62 NP) and (61 NA) gene sequences from diverse hosts, including humans, poultry and multiple mammalian species, retrieved from the NCBI database. Phylogenetic analysis revealed distinct clade formations, indicating regional spread and cross-species transmission events, particularly from avian sources to mammals and humans. Selection pressure analysis identified positive selection across all three genes, suggesting adaptive mutations contributing to host adaptation and viral survival. Homology modeling and molecular dynamics simulations were performed to generate high-quality structural models of HA, NP and NA proteins, which were subsequently validated using multiple stereochemical parameters. Domain analysis confirmed conserved functional motifs, while protein–ligand docking demonstrated stable interactions at conserved binding sites, despite observed residue substitutions in recent isolates. Earlier research concentrated on HA alone; this study integrates HA, NP and NA genes for a broader understanding of viral evolution and adaptation. These findings highlight ongoing evolutionary changes in H5N1 genes that may enhance viral adaptability and pathogenicity, underscoring the need for continuous molecular surveillance and updated antiviral strategies. Full article

Background: Hydroxycarboxylic acid receptor 3 (HCAR3) is a receptor that is mainly expressed in human adipose tissue. It can inhibit lipolysis through the inhibition of adenylyl cyclase; thus, it is closely related to the regulation of lipids in the human body. This makes HCAR3 a compelling target for developing drugs against dyslipidemia. Notably, the reported active compounds for HCAR3 are all carboxylic acids. This observation is in line with the fact that ARG111 has been reported as the key residue to anchor the active compound in a closely related homologous protein—HCAR2. Methods: In this study, we aim to discover new chemicals, through virtual screening, that may bind with HCAR3. As there are several choices for the receptor conformation, cross-docking was conducted and the root-mean-square deviation of the docking pose from the conformation of the crystal ligand was employed to determine the best receptor conformation for screening. Ligands from the ZINC20 database were screened through molecular docking, and 30 candidates were subjected to 100 ns MD simulations. Six stable complexes were further assessed by umbrella sampling to estimate binding affinity. Results: The homology model (HCAR3_homology) was selected as the receptor. Following the protocol determined by the retrospective docking process, prospective docking was conducted to screen the ligands from the ZINC20 database. Subsequently, the top 30 compounds with a good docking score and a good interaction with ARG111 were subjected to 100 ns molecular dynamics (MD) simulations, and their binding stability was analyzed based on the resulting trajectories. Finally, six compounds were chosen for binding free energy calculation using umbrella sampling; all showed negative binding affinities. Conclusions: All six compounds selected for umbrella sampling showed negative binding affinities, suggesting their potential as novel HCAR3 ligands for the development of drugs against dyslipidemia. Full article

As benthic filter feeders, bivalve mollusks serve as ideal biological indicators. Bisphenol A (BPA) and its substitutes (BPS, BPF, and BPAF) are endocrine disruptors with reproductive toxicity, targeting estrogen receptors (ERs). However, their binding sites and affinity for shellfish ERs remain unclear. This study aims to identify ER binding sites of BPA and its substitutes, compare toxicity via molecular docking, and validate results through exposure experiments. The full-length cDNA of Corbicula fluminea ER was cloned using the RACE technique for the first time, the sequence length is 2138bp. Homologous models of LBD sequences from Danio rerio, C. fluminea, Azumapecten farreri, and Ruditapes philippinarum ERs were constructed via homology modeling and screened for optimal fit. Hydrogen bonds were observed during the docking process, with interaction sites including Glu-66, Arg-177, and other amino acid residues. Exposure experiments (1, 10, and 100 μg/L) showed an enhancement in ER mRNA expression. Based on the docking energies and results of the exposure experiments, it was concluded that the toxicity of BPA and BPS is similar and greater than that of BPF and BPAF. This study provides data for a reproductive risk assessment and aquatic toxicological monitoring of bisphenols. Full article

Clear cell renal cell carcinoma (ccRCC), the most common RCC subtype, displays significant intratumoral heterogeneity driven by metabolic reprogramming, which complicates our understanding of disease progression and limits treatment efficacy. This study aimed to construct a comprehensive cellular and transcriptional landscape of ccRCC, with emphasis on gene expression dynamics during malignant progression. An integrated analysis of 90 scRNA-seq samples comprising 534,227 cells revealed a progressive downregulation of sodium ion transport-related genes, particularly CHP1 (calcineurin B homologous protein isoform 1), which is predominantly expressed in epithelial cells. Reduced CHP1 expression was confirmed at both mRNA and protein levels using bulk RNA-seq, CPTAC proteomics, immunohistochemistry, and ccRCC cell lines. Survival analysis showed that high CHP1 expression correlated with improved prognosis. Functional analyses, including pseudotime trajectory, Mfuzz clustering, and cell–cell communication modeling, indicated that CHP1⁺ epithelial cells engage in immune interaction via PPIA–BSG signaling. Transcriptomic profiling and molecular docking suggested that CHP1 modulates amino acid transport through SLC38A1. ZNF460 was identified as a potential transcription factor of CHP1. Virtual screening identified arbutin and imatinib mesylate as candidate CHP1-targeting compounds. These findings establish CHP1 downregulation as a novel molecular feature of ccRCC progression and support its utility as a prognostic biomarker. Full article

Early embryonic loss is a major cause of reproductive inefficiency in cattle, primarily due to premature luteolysis. Interferon tau (IFN-τ), secreted by the trophoblast, plays a critical role in maternal recognition of pregnancy by maintaining corpus luteum function. However, its practical application has been limited by its rapid degradation and short half-life in vivo. Here, we developed a novel formulation of recombinant bovine IFN-τ, combining chitosan-based microencapsulation with starch–chitosan hydrogel delivery, enabling sustained intrauterine release. This dual-delivery strategy offers a significant improvement over conventional IFN-τ administration methods that rely on repeated intrauterine infusions of soluble protein. The rbIFN-τ was expressed in Pichia pastoris, purified to 90.1% homogeneity, and structurally validated via homology modeling and molecular docking, confirming its interaction with type I interferon receptors. The encapsulated formulation retained antiviral activity, stimulated transcription of interferon-stimulated genes (PKR, OAS1, OAS2), and showed sustained release in vitro for up to 26 days. In vivo evaluation demonstrated safety and biological efficacy, with treated cattle showing inhibited luteolysis, sustained serum progesterone levels, and preserved corpus luteum integrity. This formulation represents a promising biotechnological approach to improve reproductive efficiency through a long-acting, species-specific IFN-τ delivery system. Full article

(1) Background: The highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b is an emerging threat that poses a great risk to the poultry industry. A few human cases have been linked to the infection with this clade in many parts of the world, including the USA. Unfortunately, there are no specific vaccines or antiviral drugs that could help prevent and treat the infection caused by this virus in birds. Our major objective is to identify/repurpose some (novel/known) antiviral compounds that may inhibit viral replication by targeting some key viral proteins. (2) Methods: We used state-of-the-art machine learning tools such as molecular docking and MD-simulation methods from Biovia Discovery Studio (v24.1.0.321712). The key target proteins such as hemagglutinin (HA), neuraminidase (NA), Matrix-2 protein (M2), and the cap-binding domain of PB2 (PB2/CBD) homology models were validated through structural assessment via DOPE scores, Ramachandran plots, and Verify-3D metrics, ensuring reliable structural representations, confirming their reliability for subsequent in silico approaches. These approaches include molecular docking followed by molecular dynamics simulation for 50 nanoseconds (ns), highlighting the structural stability and compactness of the docked complexes. (3) Results: Molecular docking revealed strong binding affinities for both sofosbuvir and GS441524, particularly with the NA and PB2/CBD protein targets. Among them, GS441524 exhibited superior interaction scores and a greater number of hydrogen bonds with key functional residues of NA and PB2/CBD. The MM-GBSA binding free energy calculations further supported these findings, as GS441524 displayed more favorable binding energies compared to several known standard inhibitors, including F0045S for HA, Zanamivir for NA, Rimantadine and Amantadine for M2, and PB2-39 for PB2/CBD. Additionally, 50 ns molecular dynamics simulations highlighted the structural stability and compactness of the GS441524-PB2/CBD complex, further supporting its potential as a promising antiviral candidate. Furthermore, hydrogen bond monitor analysis over the 50 ns simulation confirmed persistent and specific interactions between the ligand and proteins, suggesting that GS441524 may effectively inhibit the NA, and PB2/CBD might potentially disrupt PB2-mediated RNA synthesis. (4) Conclusions: Our findings are consistent with previous evidence supporting the antiviral activity of certain nucleoside analog inhibitors, including GS441524, against various coronaviruses. These results further support the potential repurposing of GS441524 as a promising therapeutic candidate against H5N1 avian influenza clade 2.3.4.4b. However, further functional studies are required to validate these in silico predictions and support the inhibitory action of GS441524 against the targeted proteins of H5N1, specifically clade 2.3.4.4b. Full article