Search Results (153)

Background/Objectives: Poly (ADP-ribose) polymerase (PARP1) has emerged as a promising therapeutic target in human breast cancer particularly in BRCA1/2 mutation carriers where a synthetic lethal interaction leads to massive tumor cell death upon specific inhibitors’ administration. Current clinically approved PARP inhibitors (Talazoparib and Olaparib) show outstanding therapeutic capabilities but suffer from severe side effects. Most importantly, some of them can cause life-threatening cardiotoxicity through hERG off-target effects. Here, we performed an extensive study to identify lead compounds with improved binding modes and favorable predicted pharmacokinetics using an integrated computational strategy. Methods: An artificial intelligence-driven drug design (AIDDISON™ v2023) workflow was employed to search ultra-large chemical space libraries for active compounds, which were then optimized via computer-aided methods to form a PARP-Tailored Database (PTD). This database was then analyzed through a virtual screening workflow, molecular docking studies, molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, DFT analysis and ADME/Tox predictions using the Schrödinger suite (v2023-2), MobaXterm v25.2, Gaussian 16.0, ProTox-3 and Pred-hERG v5.0 respectively. Results: Three compounds (1a–1c) were identified as promising candidates. Among them 1a appeared to be the most active compound with a favorable docking score (−9.488 kcal/mol) that is not only higher than 1b and 1c but also higher than that of Talazoparib (−6.778 kcal/mol). MD simulations of 1a–1c in the active site revealed an average RMSD of ~2.5–3.6 Å which is better compared to the parent Talazoparib (5.6 Å). Interestingly, on the 250 ns extended MD study, 1a exhibited a slightly reduced RMSD between 2.4 and 3.2 Å, whereas Talazoparib retained higher fluctuations of ~5 Å to 6 Å. MM/GBSA binding energy analysis indicated 1a to have better predicted binding affinity (−67.820 kcal/mol), which is also better than Talazoparib (−63.734 kcal/mol). DFT calculations showed good electronic properties and in silico ADMET studies also indicated 1a to have good drug-likeness and lower predicted hepatotoxicity and cardiotoxicity risk. Conclusions: These findings identify compound 1a as a promising lead, while compounds 1b and 1c remain viable candidates for further optimization. However, experimental validation is critical to confirm the predicted biological activity and safety profiles. Full article

Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder characterized by the accumulation of the toxic protein amyloid-β, formation of tau-containing neurofibrillary tangles, neuroinflammation, and synaptic dysfunction, highlighting the need for new therapeutic strategies capable of modulating multiple pathological pathways simultaneously. In this study, a structure-based in silico approach was applied to evaluate the multi-target potential of two previously reported pyrrole-based compounds (pyrrole 1 and pyrrole 2) with known monoamine oxidase-B (MAO-B) inhibitory activity and low neurotoxicity. Molecular docking studies were performed against a panel of key AD-related targets, including GSK-3β, APP, MAO-B, BACE1, AChE, BChE, COX-2, GABA-B receptor, NMDA receptor, and E3 ubiquitin ligase CHIP, using Glide XP docking. The results revealed that compound pyrrole 1 may have favorable predicted binding affinities across several targets, with relatively strong docking scores for GSK-3β and COX-2. The binding mode analysis indicated that pyrrole 1 adopts poses consistent with interaction patterns commonly observed for ATP-competitive GSK-3β inhibitors and COX-2 ligands. In silico ADMET profiling using the software SwissADME and ProTox 3.0 indicated distinct pharmacokinetic and safety profiles for the two compounds, with pyrrole 2 showing superior drug-likeness and predicted blood–brain barrier penetration, while pyrrole 1 displayed a more favorable overall toxicity profile. Collectively, these findings identify pyrrole 1 as a theoretically promising multi-target candidate for AD requiring experimental validation, while providing a strong structural basis for further optimizations and subsequent experimental confirmation. Full article

Quantitative structure–activity relationship (QSAR) modeling has conventionally relied on expert-designed molecular descriptors to encode chemical structures. DeepSnap is a descriptor-free QSAR approach that converts prepared three-dimensional molecular conformers into image representations and feeds them directly into convolutional neural networks for activity prediction. This focused narrative review traces DeepSnap from its introduction in 2018 to its current state and places it within the broader landscape of descriptor-based QSAR, topology-based and 3D-aware graph neural networks, and related image-based or semi-image-based molecular representation approaches. Previous studies applied DeepSnap to Tox21 nuclear receptor and molecular initiating event endpoints, rat hepatic clearance, blood–brain barrier penetration, acute oral toxicity, and cosmetics–pharmaceutical compound classification. Across the DeepSnap series, image-based and descriptor-based predictions have provided complementary information, particularly in ensemble or consensus models. However, high or near-ceiling ROC–AUC values reported for selected endpoints should not be interpreted as indicating deterministic or universally generalizable predictions; rather, they should be considered in the context of endpoint-specific model development, image-rendering parameter optimization, possible class imbalance, split dependence, limited matched external replication, and incomplete benchmarking against modern molecular representation models. Limitations include a dependence on nonphysical rendering parameters, single- or representative-conformer input, incomplete matched benchmarking against 2D and 3D molecular representation models, and an interpretability gap addressed in part by CAM-family visualization in the AI-based Substance Hazard Integrated Prediction System (AI-SHIPS) and S-COPHY (a model developed by Shiseido for cosmetics–pharmaceutical compound classification). Future directions include standardized image-generation protocols, conformer-ensemble extensions, systematic interpretability analysis, matched benchmarking, and potential integration with graph-based and 3D-aware molecular learning approaches. Full article

Hypertension remains a leading cause of global morbidity and mortality, and angiotensin-converting enzyme (ACE) represents a central therapeutic target within the renin–angiotensin–aldosterone system. Marine microalgae, particularly Phaeodactylum tricornutum, provide an underexplored reservoir of structurally diverse metabolites with potential cardiovascular relevance. In this in silico study, we characterized metabolites putatively annotated by UPLC-ESI-HRMS and evaluated their predicted ACE inhibitory potential. We performed molecular docking with AutoDock 4 and assessed pharmacokinetic and toxicological properties using the SwissADME, PASS, and ProTox platforms. Several metabolites showed favorable binding orientations within the ACE catalytic pocket, including interactions with key residues and proximity to the zinc-binding motif. Lehualide G, Val–Asn–Pro, tanariflavanone B, hydroxyterbinafine, and anhydro-vitamin A exhibited the most favorable docking profiles. PASS predictions indicated vascular-related bioactivity signals for selected compounds, whereas ADMET modeling revealed heterogeneous but classifiable pharmacokinetic and safety characteristics. The convergence of predicted binding compatibility, bioactivity signals, and stratified safety margins supports P. tricornutum as a promising source of candidate molecules for further experimental validation in antihypertensive research. Full article

A series of coumarin–amino acid hybrids of glycine, γ-aminobutyric acid, and L-glutamic acid was developed. These compounds were evaluated for their antioxidant and anti-inflammatory activities in vitro and for their drug-likeness in silico. Antioxidant activity was assessed in vitro using the AAPH-induced linoleic acid peroxidation assay. Soybean lipoxygenase and ovine cyclooxygenase 2 were used in vitro to test the inhibitory activity of the adducts. An in silico evaluation was performed using the open-access platforms Molinspiration, SwissADME, PreADMET, Molsoft, GLORYx, CypRules, and LiverTox Workspace. The synthesis of the compounds proceeded via a facile procedure through the corresponding acid in very good yields. The antioxidant activity of the compounds is shown to be highly dependent on the linkage used, with compound 15 presenting the highest activity (93% inhibition). The most active LOX inhibitor is compound 4 (IC₅₀ = 58 μM), while compounds 4 and 5 are the most potent COX-2 inhibitors (IC₅₀ = 55 μM for both). Compounds 4, 9, and 15 are depicted as pleiotropic molecules (compound 4: IC₅₀ for SLOX-1 = 58 μM and IC₅₀ for COX-2 = 55 μM; compound 9: IC₅₀ for COX-2 = 60 μM, and 59% antilipid peroxidation; compound 15: IC₅₀ for COX-2 = 70.5 μM, 93% antilipid peroxidation). An in silico evaluation showed favorable properties of the designed agents, which were quantified, with all the compounds showing a QED score higher than 0.5. The overall results highlight that compound 4 can be used as a lead molecule for the design of more potent agents with a pleiotropic profile. Full article

Background/Objectives: The purpose of this study was the chemical design, synthesis, and evaluation of the antimicrobial and antibiofilm potentials of 20 novel thiazolyl-methylthio-thiadiazole hybrid compounds (6a–j and 8a–j). Methods: The compounds were designed as structural analogues of halicin with two points of variation and were synthesized through a process with multiple condensation steps. The compounds were evaluated in vitro through MIC determinations for the antimicrobial activity and percentage of biofilm inhibition, and in silico, respectively, through molecular docking, druggability, and ADMETox prediction. A 2D-QSAR study was conducted for antimicrobial activity using the Free-Wilson model. Results: In terms of antibacterial activity, all compounds displayed important activity on the tested strains (MICs = 15.62–250 μg/mL), except against Staphylococcus aureus. Regarding the antifungal activity, the effect against Candida albicans was similar to fluconazole in most cases (MIC = 15.62 μg/mL). With respect to the antibiofilm activity, the most effective activity was registered against the Pseudomonas aeruginosa biofilm. The in vitro results for the antibacterial activity against Escherichia coli were correlated with the observations drawn in the molecular docking study on the ATPase domain of the GyrB subunit of E. coli. The in silico predictions of the molecular properties concluded that all compounds have good druggability properties, while the ADMETox predictions concluded that the compounds could have low gastrointestinal absorption and blood–brain barrier permeation capacity, but raised safety flags (e.g., hepatotoxicity and high acute oral toxicity). The 2D-QSAR study concluded that the thiazolyl-methylthio-thiadiazole scaffold had the highest contribution to antimicrobial activity in almost all cases. Conclusions: The two series of compounds highlight the impact of structural modulations of the scaffold and its substituents on the investigated biological activities. Full article

Multicomponent reactions with isocyanides (IMCRs) enable the one-step assembly of complex molecules and remain a powerful strategy for accessing bioactive scaffolds. Here, we report the first synthesis of an abietane diterpene isocyanide derived from aminoimide methyl maleopimarate 1, a levopimaric acid-maleic anhydride adduct. This isocyanide was further engaged in Passerini, Ugi, and azido-Ugi reactions to provide a series of α-acyloxy- and α-acylaminocarboxamides, as well as tetrazoles, in high yields under optimized conditions. The structures of all products were confirmed by comprehensive physicochemical analysis. In silico ADME, drug-likeness, target prediction, and toxicity studies (SwissADME, ProTox-III) revealed moderate lipophilicity with favorable membrane permeability and solubility, high gastrointestinal absorption, and selective CYP3A4 inhibition with no significant effects on other CYP450 isoforms. The compounds fulfill major drug-likeness criteria, lacking undesirable reactive fragments, with only acceptable deviations in molecular weight and flexibility typical for MCR-derived products. The modifications broaden the spectrum of predicted biological targets while maintaining low overall toxicity and absence of predicted hepato- or carcinogenicity. These results demonstrate that diterpene isocyanide is a valuable building block for chemical libraries of structurally diverse abietane derivatives with peptide-like termini and highlight its potential as a source of cytotoxic, antiviral, and anti-inflammatory candidates. Full article

Antibiotic resistance among several bacteria is a warning sign that reinforces the need for research to identify new compounds that are effective against resistant strains. In this sense, bioinformatics stands out as an excellent tool for identifying drug candidates by using computational methodologies to detect compounds with potential biological activity. Two pivot compounds (QNZ and 0Y5) with biological activity against Staphylococcus aureus were selected. A virtual screening was performed in the MolPort database with a Tanimoto index of 0.5, resulting in 20,000 compounds, 10,000 compounds for each template. Then, methodologies were applied to calculate pharmacokinetic and toxicological parameters using Discovery Studio software; molecular docking via DockThor; lethal dose via ProTOX; lipophilicity, solubility, and Lipinski parameters via SwissADME; in silico prediction of bacterial activity via Way2Drug; theoretical synthetic accessibility via SwissADME and AMBIT-SA; and, finally, molecular dynamics simulations via AMBER 18. After the entire methodological process, 10 compounds were identified with potential results according to the criteria adopted in this study and with possible antimicrobial activity against resistant bacterial strains of S. aureus. Our theoretical findings suggest 10 potential candidates with possible antimicrobial activity against S. aureus and other genera and species of bacteria as these compounds presented excellent results using the proposed methodology. Certainly, more in vitro and in vivo study steps are necessary. Full article

Background: Numerous plant-derived products have shown notable potential in preclinical studies and traditional use for the management of periodontitis, although clinical studies validating their efficacy remain scarce. The present study investigated the efficacy of a polyherbal phytopreparation as an adjunctive therapy to scaling and root planing (SRP) in patients with periodontitis, and further examined its underlying mechanisms of action, pharmacokinetic behavior, and toxicological profile using in silico approaches. Methods: Eighty patients with moderate periodontitis (stage II, grade A) were randomly assigned to two groups: a control group (n = 40) treated with SRP alone, and an experimental group (n = 40) receiving SRP followed by topical phytotherapeutic treatment with the polyherbal Tinctura paradentoica^®. Efficacy was evaluated using the gingival index, periodontal pocket depth, and cytomorphometric analysis of gingival cells before treatment and one month after. The in silico analysis, guided by HPLC profiling, included MolDock-based docking to assess interactions of bioactive compounds with cyclooxygenase isoforms COX-1 and COX-2 as anti-inflammatory targets, and evaluation of their pharmacokinetic and toxicity properties (ADME/Tox) using SwissADME, ProTox-3.0, and pkCSM. Results: Compared with SRP treatment, the experimental treatment significantly reduced the gingival index and periodontal pocket depth (p < 0.05), as well as the assessed cytomorphometric parameters (nuclear area, perimeter, and Feret’s diameter values) (p < 0.001). Rerank analysis revealed van der Waals-driven isoform selectivity: compact phenolic acids and aglycones favored COX-1, whereas bulky glycosides (e.g., rutin, narcissoside) were optimized for COX-2, with luteolin-7-O-glucoside showing near-balanced engagement. The ADME/Tox analysis indicated generally favorable pharmacokinetic and safety characteristics of phenolic compounds from the phytopreparation, including low systemic absorption and no predicted mutagenicity or skin sensitization potential. Conclusions: The topical application of the polyherbal phytopreparation demonstrated significant potential to enhance the efficacy of conventional SRP therapy by promoting the regression of gingival inflammation in patients with moderate periodontitis, further supported by in silico findings. Full article

Malaria is a major global health concern caused by Plasmodium parasites, among which Plasmodium falciparum is responsible for the most severe and fatal cases. The emergence of drug resistance to existing antimalarial therapies necessitates the discovery of novel molecular targets and chemically distinct inhibitors. Current study employed an integrated in silico drug discovery pipeline combining high-throughput structure-based virtual screening of 1549 deep-sea marine microbial metabolites with MM-GBSA binding free-energy estimation, QikProp-based ADME/Tox profiling, and 100 ns molecular dynamics (MD) simulations to link rapid screening with dynamic verification of binding stability. Molecular docking against Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH; PDB ID: 7KZ4) yielded five top-ranked compounds with Glide scores ranging from −12.02 to −10.61 kcal·mol⁻¹, which is higher than the Primaquine (−6.920 kcal·mol⁻¹; a clinically approved antimalarial reference compound). MM-GBSA analysis further refined hit selection, producing binding free energies (ΔG_bind) between −63.28 and −31.37 kcal·mol⁻¹. The selected lead compounds included (±)-puniceusine P, aspergilol F, tersaphilone C, 4-carbglyceryl-3,3′-dihydroxy-5,5′-dimethyldiphenyl ether, and 15-O-methyl ML-236A. The top hits were subjected to 100 ns MD simulations in Desmond, demonstrating stable protein–ligand complexes, particularly for (±)-puniceusine P and 15-O-methyl ML-236A (protein backbone root mean square deviation (RMSD; ~0.8–1.0 Å). ADME profiling indicated acceptable predicted physicochemical and pharmacokinetic properties. Overall, these in silico findings highlight deep-sea marine microbial metabolites as promising PfDHODH inhibitor candidates requiring experimental validation. Full article

Background: The growing interest in developing new bioactive agents from natural sources led to medicinal and aromatic plants. These plants provide valuable phytochemicals that can serve as natural preservatives, food additives, and flavorings, with various applications. The aim of this study is to evaluate the potential of Juniperus oxycedrus berries’ supercritical extract through preliminary screenings related to in vitro antibacterial activity, as well as bioinformatics assessments of absorption and toxicity. Methods: Supercritical carbon dioxide (CO₂) was used to extract the bioactive phytochemical compounds from the berries. The extract was characterized using spectrophotometric methods and reverse-phase high-performance liquid chromatography (RP-HPLC). The antibacterial potential was tested against Staphylococcus aureus ATCC 25923, where the Minimal Inhibitory Concentration and the Minimal Bactericidal Concentration were determined. Additionally, the influence of the extract on the growth curve kinetics of S. aureus was assessed. For the bioinformatics analyses, SwissADME and ProTox-3.0 prediction software were utilized, focusing on the identified phenolic compounds as fingerprint molecules. Results: The results demonstrated that exposure to the juniper extract inhibited bacterial growth, resulting in a prolonged lag phase of 6 to 8 h, depending on the concentration of the extract. The software predictions revealed that the investigated phenolic compounds might exhibit high gastrointestinal absorption, along with potential interactions with metabolic mediators and pathways. Conclusions: The in vitro and in silico findings support the application of J. oxycedrus berries extract as an alternative or complementary strategy for pharmacological treatment and food applications aimed at targeting S. aureus. Full article

Background/Objectives: Pyrazole carboxamides are widely used as adaptable medicinal-chemistry scaffolds and have been explored as cholinesterase (ChE) inhibitor chemotypes. In this work, we prepared a new series of 4-arylazo-3,5-diamino-N-tosyl-1H-pyrazole-1-carboxamides 5(a–m) and evaluated their inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), supported by structure-based computational analyses. Methods: Thirteen derivatives 5(a–m) were synthesized, fully characterized with analytical techniques (FT-IR, H NMR, and C NMR), and tested in vitro against AChE and BChE, with tacrine (THA) used as the reference inhibitor. Docking calculations were used to examine plausible binding modes. The top-ranked complexes (7XN1–5e and 4BDS–5i) were further examined by 100 ns explicit-solvent molecular dynamics (MD) simulations in Cresset Flare, followed by RMSD/RMSF analysis and contact-persistence profiling. Predicted ADME/Tox. properties were also assessed to identify potential developability issues. Results: The series showed strong ChE inhibition, and several compounds were more potent than THA. Compound 5e (4-nitro) was the most active AChE inhibitor (K_I = 20.86 ± 1.61 nM) compared with THA (K_I = 164.40 ± 20.84 nM). For BChE, the K_I values ranged from 31.21 to 87.07 nM and exceeded the reference compound’s activity. MD trajectories supported stable binding in both systems (10–100 ns mean backbone RMSD: 2.21 ± 0.17 Å for 7XN1–5e; 1.89 ± 0.11 Å for 4BDS–5i). Most fluctuations were confined to flexible regions, while key contacts remained in place, consistent with the docking models. ADME/Tox. predictions suggested moderate lipophilicity but generally low aqueous solubility; all compounds were predicted as non-BBB permeant, and selected liabilities were flagged (e.g., carcinogenicity for 5e/5g/5h/5i; nephrotoxicity for 5f/5g). Conclusions: The 4-arylazo-3,5-diamino-N-tosyl-1H-pyrazole-1-carboxamide scaffold delivers low-nanomolar ChE inhibition, with docking and MD supporting stable binding modes. Future optimization should prioritize solubility improvement and mitigation of predicted toxicities and metabolic liabilities, especially given the predicted lack of BBB permeability for CNS-directed applications. Full article

Type 2 diabetes mellitus (T2DM) involves chronic hyperglycemia, insulin resistance, low-grade inflammation, and oxidative stress that drive cardiometabolic and renal damage despite current therapies. Sodium–glucose cotransporter (SGLT) inhibitors have reshaped the treatment landscape, but residual risk and safety concerns highlight the need for new agents that combine glucose-lowering efficacy with redox–inflammatory modulation. LASSBio-1986 is a synthetic N-acylhydrazone (NAH) derivative designed as a gliflozin-like scaffold with the potential to interact with SGLT1/2 while also influencing oxidative and inflammatory pathways. Here, we integrated in silico and in vivo approaches to characterize LASSBio-1986 as a multifunctional antidiabetic lead in murine models of glucose dysregulation. PASS and target class prediction suggested a broad activity spectrum and highlighted transporter- and stress-related pathways. Molecular docking indicated high-affinity binding to both SGLT1 and SGLT2, with a modest energetic preference for SGLT2, and ADME/Tox predictions supported favorable oral drug-likeness. In vivo, intraperitoneal LASSBio-1986 improved oral glucose tolerance and reduced glycemic excursions in an acute glucose challenge model in C57BL/6 mice, while enhancing hepatic and skeletal muscle glycogen stores. In a dexamethasone-induced insulin-resistance model, LASSBio-1986 improved insulin sensitivity, favorably modulated serum lipids, attenuated thiobarbituric acid-reactive substances (TBARS), restored reduced glutathione (GSH) levels, and rebalanced pro- and anti-inflammatory cytokines in metabolic tissues, with efficacy broadly comparable to dapagliflozin. These convergent findings support LASSBio-1986 as a preclinical, multimodal lead that targets SGLT-dependent glucose handling while mitigating oxidative and inflammatory stress in models relevant to T2DM. Chronic disease models, formal toxicology, and pharmacokinetic studies, particularly with oral dosing, will be essential to define its translational potential. Full article

Background: Melanin protects skin and hair from the effects of ultraviolet (UV) radiation damage, which contributes to all forms of skin cancer, including melanoma. Human melanocytes produce two main types of melanin: eumelanin provides effective photoprotection, and pheomelanin offers less protection against UV-induced skin damage. The agouti signaling protein (ASIP) antagonizes the melanocortin-1 receptor (MC1R), hinders melanocyte signaling, and shifts pigmentation toward pheomelanin, promoting UV vulnerability. In this study, we aim to discover compounds that inhibit ASIP–MC1R interaction and effectively preserve eumelanogenic signaling. Methods: The ASIP–MC1R interface-based pharmacophore model from ASIP is implicated in MC1R receptor protein engagement. We performed virtual screening with a validated pharmacophore model for ~4000 compounds curated from ZINCPharmer and applied drug-likeness filters, viz. ADMET and toxicity profiling tests. Further, the screened candidates were targeted for docking to the ASIP C-terminal domain corresponding to the MC1R-binding moiety. Top compounds underwent a 100-nanosecond (ns) run of molecular dynamics (MD) simulations to assess complex stability and persistence of key contacted residues. Results: Sequential triage, including pharmacophore, ADME–toxicity (ADMET), and docking/ΔG, yielded a focused group of candidates against ASIP antagonists with a favorable fit value. The MD run for 100 ns supported pose stability at the targeted pocket. Based on these predictions and analyses, compound ZINC14539068 was screened as a new potent inhibitor of ASIP to preserve α-MSH-mediated signaling of MC1R. Conclusions: Our in silico pipeline identifies ZINC14539068 as a potent inhibitor of ASIP at its C-terminal interface. This compound is predicted to disrupt ASIP–MC1R binding, thereby maintaining eumelanin-biased signaling. These findings motivate experimental validation in melanocytic models and in vivo studies to confirm pathway modulation and anti-melanoma potential. Full article

Hybrid molecules, integrating multiple pharmacophores within a single scaffold, represent a modern strategy in drug discovery, offering improved selectivity and safety. Anthranilic acid is a versatile building block with diverse biological activities. In this work, we designed and synthesized novel anthranilic acid-based hybrids with enhanced pharmacokinetic potential. The methods used include cheminformatics- guided library design, followed by amide bond formation between anthranilic acid derivatives and substituted 2-phenylethylamines. Purification and structural characterization were achieved via NMR, IR, and HRMS. The compounds exhibited favorable, predicted ADME/Tox profiles and synthetic accessibility. These results provide a foundation for further biological evaluation toward therapies for smooth muscle dysfunction and inflammation. Full article