Search Results (287)

Tramadol acts via μ-opioid receptor agonism and monoamine reuptake inhibition but is clinically limited by metabolic dependence, interindividual variability, and addiction risks. Structural modification aims to resolve these limitations. This review systematically summarizes tramadol’s structure–activity relationships and mechanisms, focusing on key strategies for structural optimization. Major advances include: (i) synergistic strategies, such as tramadol–celecoxib cocrystals (tramadol and celecoxib coexist in the supramolecular crystal network at a 1:1 molar ratio), achieving multimodal analgesia at lower doses; (ii) mechanism-balancing strategies such as tapentadol (derivatives of tramadol with a dual mechanism of action), which enhance μ-opioid agonism and norepinephrine reuptake inhibition while attenuating serotonergic effects to improve efficacy; (iii) metabolic optimization utilizing M1 analogues to circumvent CYP2D6 polymorphisms (tramadol is metabolized by this enzyme into the active metabolite M1 to exert analgesic effects); and (iv) pharmacophore optimization leveraging tramadol–morphine homology and “message–address” concepts to design selective ligands. Novel derivatives demonstrate improved potency and metabolic stability but continue to face challenges regarding opioid risks and clinical translation. Future research should integrate rational drug design, delivery systems, and personalized medicine to facilitate the development of safer next-generation analgesics. Full article

The berberine derivative 13-(2-methylbenzyl)-berberine (BED) has been shown to inhibit the MexXY-OprM efflux system of Pseudomonas aeruginosa (PA), a key contributor to aminoglycoside resistance, by interacting with the inner membrane protein MexY at an allosteric pocket (ALP). To enhance binding efficacy, this study aims to identify novel chemical scaffolds that target the MexY allosteric pocket through an integrated computational strategy. In this work, a ligand-based virtual screening (LBVS) approach was employed using a 2D/3D pharmacophore model derived from BED to perform in silico screening of an Enamine compound library, which encompasses a broad and diverse chemical space. A key objective was to compare the predictive performance of this pharmacophore-based workflow with a structure-based (SB) strategy incorporating molecular docking and molecular dynamics (MD) simulations. Notably, the top-ranked LBVS hits were consistently validated by docking and MD analyses, showing stable binding and interaction patterns comparable or superior to those of BED. This convergence between ligand-based (LB) and SB methods highlights the internal coherence of the workflow and supports the robustness of the pharmacophore hypothesis. The identified scaffolds generally displayed high hydrophobicity, consistent with the physicochemical nature of the binding site, but resulting in limited aqueous solubility and complicating their experimental evaluation. While these features confirm the importance of hydrophobic interactions in MexY recognition, with a particular focus on some few residues, such as Phe560, it also underscores the need for formulation strategies or rational scaffold modifications introducing moderate polarity without weakening key contacts. Overall, the integrated computational strategy not only yields promising lead chemical structures but also provides a solid basis for their future optimization, ultimately supporting the design of new efflux pump inhibitors (EPIs) capable of contributing to improved antibiotic susceptibility in multidrug-resistant PA strains. Full article

Antimicrobial resistance (AMR) remains a major threat to modern medicine, fueled by the excessive use of antibiotics and the spread of multidrug-resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA). In this study, we designed and synthesized a series of 2-aryl-4-aminoquinazoline derivatives bearing an aminoalkylimidazole linker, combining two pharmacophoric motifs associated with antimicrobial activity. Starting from anthranilamide, the compounds were prepared in three straightforward steps, affording good yields and high purity. Their structures were confirmed by FT-IR spectroscopy, ¹H and ¹³C nuclear magnetic resonance (NMR), and high-resolution mass spectrometry (HRMS). Biological evaluation showed that series 5 exhibited strong selectivity toward S. aureus, with compounds 5c and 5d displaying minimum inhibitory concentrations (MICs) between 2.2 and 4.4 µM. No significant activity was observed against other tested strains. Cytotoxicity assays in HepG2 cells revealed moderate to low inhibition. Molecular docking indicated preferential binding to dihydrofolate reductase (DHFR) and relevant interactions with topoisomerase IV, resembling reference inhibitors. ADME analysis predicted favourable absorption, blood–brain barrier permeability, and compliance with Lipinski’s rules. Full article

The rapid spread of antibiotic resistance through plasmid-mediated conjugation remains a primary global health concern. Despite its critical role in horizontal gene transfer, no approved drugs currently target this process, leaving a critical therapeutic gap. Integration Host Factor (IHF), a DNA-binding protein essential for plasmid replication and mobilization, emerges as a promising yet underexplored target for anti-conjugation strategies. This work aimed to develop a predictive computational model and identify small molecules that disrupt IHF function, thereby reducing plasmid transfer and limiting resistance gene dissemination. A curated dataset of 65 compounds with reported anti-plasmid activity was analyzed using a 3D-QSAR model based on algebraic descriptors computed with QuBiLS-MIDAS. The model was validated through leave-one-out cross-validation (Q² = 0.82), Tropsha’s criteria, and Y-scrambling. Representative compounds were selected via pharmacophore clustering and evaluated through molecular docking at both the DNA-binding site and a predicted allosteric pocket of IHF. The most promising complexes underwent 200 ns molecular dynamics simulations to assess stability and interaction patterns. The QSAR model demonstrated strong predictive performance (R² = 0.90). Docking simulations revealed more favorable binding energies at the allosteric site (up to −12.15 kcal/mol) compared to the DNA-binding site. Molecular dynamics confirmed the stability of these interactions, with allosteric complexes showing lower RMSD fluctuations and consistent binding energy profiles. Dynamic cross-correlation analysis revealed that allosteric ligand binding induces conformational changes in key catalytic residues, including Pro65, Pro61, and Leu66. These alterations may compromise DNA recognition and disrupt the initiation of replication. To our knowledge, this is the first computational study proposing allosteric inhibition of IHF as an anti-conjugation strategy. These findings provide a foundation for experimental validation and the development of novel agents to prevent horizontal gene transfer, offering a promising approach to restoring antibiotic efficacy against multidrug-resistant pathogens. Full article

Background: There is currently increasing interest in atypical opioid compounds capable of expanding their clinical applications beyond pain management, including the treatment of psychiatric disorders and substance abuse. In this context, the cyclotetrapeptide c[Trp-Phe-D-Pro-Phe] (CJ-15,208, 1) and its derivatives represent an unusual class of opioid peptides. This compound was found to be a mixed KOR/MOR antagonist in vitro, but it acted as an agonist in vivo. For its diverse analogues, it appeared that receptors’ affinity, selectivity, and agonist/antagonist activity greatly varied upon modifications to backbone geometry and the 3D display of pharmacophores. Methods: We utilized NMR, molecular dynamics, and molecular docking to analyze 3D structures and pharmacodynamic properties of selected representative cyclopeptide analogues of 1. Results: The simulations support that, despite its contradictory functional activity in vitro and in vivo, 1 can bind to the active conformation of receptors in an agonist-like fashion. In general, Trp appeared to be the fundamental pharmacophore in the ligand–receptor complexes. In particular, agonists showed a direct interaction between the indole ring and the carboxylate of the conserved Asp(3:32). Conclusions: These studies support a distinctive pharmacodynamic model for this class of compounds, potentially useful for the design of opioid compounds with novel binding/activity profiles and improved therapeutic effects. Full article

The emergence of multidrug-resistant (MDR) bacterial pathogens has heightened the urgency for novel antibacterial agents. The bacterial cell wall usually comprises peptidoglycan, which presents a prime target for antibacterial drug development due to its indispensable role in maintaining cellular integrity. Conventional antibiotics such as β-lactams and glycopeptides hinder peptidoglycan synthesis through competitive binding of penicillin-binding proteins (PBPs) and sequestration of lipid-linked precursor molecules. Nevertheless, prevalent resistance mechanisms including target modification, β-lactamase hydrolysis, and multi-drug efflux pumps have limited their clinical utility. This comprehensive analysis explicates the molecular machinery underlying bacterial cell wall assembly, evaluates both explored and unexplored enzymatic nodes within this pathway, and highlights the transformative impact of high-resolution structural elucidation in accelerating structure-guided drug discovery. Novel targets such as GlmS, GlmM, GlmU, Mur ligases, D,L-transpeptidases are assessed for their inclusiveness for the discovery of next-generation antibiotics. Additionally, cell wall inhibitors are also examined for their mechanisms of action and evolutionary constraints on MDR development. High-resolution crystallographic data provide valuable insights into molecular blueprints for structure-guided optimization of pharmacophores, enhancing binding affinity and circumventing resistance determinants. This review proposes a roadmap for future innovation, advocating for the convergence of computational biology platforms, machine learning-driven compound screening, and nanoscale delivery systems to improve therapeutic efficacy and pharmacokinetics. The synergy of structural insights and cutting-edge technologies offers a multidisciplinary framework for revitalizing the antibacterial arsenal and combating MDR infections efficiently. Full article

Objectives: Combining two pharmacophores into one molecule with multiple applications presents interest in the field of medicinal chemistry. Quinazolinones are among privileged scaffolds due to their wide biological activities, whereas hydrazones are versatile linkers with pharmacological potential. Thus, this article focused on a green method for the synthesis of new N-acyl-hydrazones of 2-(2-methyl-4-oxoquinazolin-3(4H)-yl)acetohydrazide and the exploration of their biological potential. Methods: The novel N-acyl-hydrazones (1a–1f) were synthesized under microwave irradiation, using various substituted salicylaldehydes and benzaldehydes. The products were characterized by FT-IR, ¹H-NMR, ¹³C-NMR, and HRMS. Their pharmacological profile was assessed by in silico methods and docking simulations. Biological evaluation included antioxidant, antimicrobial, and cytotoxic activities, as well as preliminary toxicity on Artemia franciscana. Results: Spectroscopic data indicated syn-E and anti-E isomers. Compound 1c showed the highest antioxidant activity. Antimicrobial assays indicated narrow-spectrum activity, with compounds 1a and 1b being most effective against C. albicans and S. aureus. Biofilm inhibition assays revealed that 1a and 1c interfered with microbial adhesion, highlighting their potential in combating biofilm-associated infections. Cytotoxicity tests on HT-29 and A431 cancer cell lines showed selective anticancer effects for compounds 1a–1d, with minimal toxicity on normal Vero cells, especially for 1b and 1d. Toxicity against Artemia franciscana correlated with in vitro cytotoxicity data, revealing low lethality for all N-acyl-hydrazones. Docking studies indicate that the antibacterial activity may involve inhibition of S. aureus DNA gyrase B, whereas the cytotoxic effects could be mediated by interaction with the EGFR kinase. Conclusions: These findings may increase the chances of identifying a lead compound in this class, supporting the further development of selected N-acyl-hydrazones and their pharmacological exploration. Full article

Pestasulfamides A and B are phenylbenzene-sulfonamides with an eight-membered dilactam, produced by mangrove endophytic fungus Pestalotiopsis sp. HNY36-1D. In bioassay, pestasulfamide A (1) exhibited potent anti-acetylcholine esterase (AChE) activities with an IC50 value of 11.94 μM, offering new pharmacophores with relevance to anti-Alzheimer’s disease drug discovery. Although the dimerization reaction of anthranilic acid derivatives forges an dibenzodiazocin-2,6-dione framework, the application of the dimerization to total synthesis of pestasulfamides A (1) and B (2) has not yet been realized. Herein, the first total synthesis of pestasulfamides A and B was achieved through one-pot protocol. The key step features a sulfonylation-induced iminoketene dimerization of anthranilic acid in a pyridine/THF system. Full article

Τhe synthesis of a novel series of mono-substituted 4H-1,2,6-thiadiazine derivatives was reported, aiming at enhancing antioxidant and lipoxygenase inhibitory activities via pharmacophore combination. The compounds were prepared from 3,5-dichloro-4H-1,2,6-thiadiazin-4-one and 2-(3,5-dichloro-4H-1,2,6-thiadiazin-4-ylidene)malononitrile. All the derivatives were evaluated for radical scavenging activity towards 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azobis(2-methylpropionamidine) dihydrochloride (AAPH)-induced lipid peroxidation inhibition, and soybean lipoxygenase (sLOX) inhibition. The compounds exhibited moderate to good antioxidant activity and variable sLOX inhibition. Notably, 2-[3-(benzo[d]oxazol-2-ylthio)-5-chloro-4H-1,2,6-thiadiazin-4-ylidene]malononitrile showed the strongest antioxidant effect (92% DPPH scavenging at 60 min and 70% inhibition of AAPH-induced lipid peroxidation) but low sLOX inhibition, whereas 3-chloro-5-(4-phenylpiperazin-1-yl)-4H-1,2,6-thiadiazin-4-one displayed the most potent sLOX inhibition (IC₅₀: 7.5 μM), with a docking score of −8.3 kcal/mol developing hydrophobic interactions with Phe134 and Val520. Full article

Heterocyclic systems such as 1,2,4-triazoles and piperazines play an important role in modern medicinal chemistry due to their structural diversity and broad spectrum of biological activities. In this Short Note, we report the synthesis and spectroscopic characterization of a new hybrid molecule combining both pharmacophoric fragments: 1-[4-(4-chlorophenyl)piperazin-1-yl]-2-[(4-phenyl-4H-1,2,4-triazol-3-yl)sulfanyl]ethan-1-one (compound 3). The compound was obtained in 70% yield via S-alkylation of 4-phenyl-1,2,4-triazole-3-thione with a chloroacetyl derivative of 4-chlorophenylpiperazine under alkaline conditions. The structure of 3 was confirmed by ¹H and ¹³C NMR spectroscopy, DEPT-135, 2D NMR (COSY, NOESY, HSQC, HMBC), FT-IR, and elemental analysis. These results support the utility of combining triazole and piperazine fragments in the design of new heterocyclic frameworks with potential biological relevance. Full article

Bile acids provide a versatile platform for the design of biologically active compounds due to their amphiphilic structure, biocompatibility, and capacity for diverse chemical modifications. Among them, lithocholic acid is a promising scaffold for designing and revealing new antiviral agents. A novel lithocholic acid-based 3-spiro-1,2,4-trioxolane was synthesized by Griesbaum co-ozonolysis of methyl 3-O-methyl-oximino-lithocholate and 4-(trifluoromethyl)-cyclohexanone, and its structure was confirmed by 2D NMR and X-ray crystallographic analysis. Lithocholic acid derivatives were evaluated for cytotoxicity and anti-influenza activity against A/Puerto Rico/8/34 (H1N1), showing that steroid 1,2,4-trioxolane 3 exhibited the highest potency (IC₅₀ 4.3 µM, SI 11) compared to the parent methyl-3-oxo-lithocholate 1 (IC₅₀ > 84 µM, SI 1). In silico ADME predictions revealed several favorable drug-like properties, including a highly three-dimensional structure (Fsp³ = 0.97), significant lipophilicity (LogP = 7.54), and the presence of key pharmacophores such as a peroxide moiety and a trifluoromethyl group. Taken together, a stereospecific synthesis of a lithocholic acid 3-spiro-1,2,4-trioxolane by Griesbaum co-ozonolysis was realized and the first evidence of anti-influenza activity in the steroid-1,2,4-trioxolane series was found. Full article

Helicobacter pylori urease (HpU) plays a central role in bacterial survival and virulence by hydrolyzing urea into ammonia and carbon dioxide, neutralizing gastric acidity, and facilitating host colonization. The increasing prevalence of antibiotic resistance underscores the need for alternative strategies targeting essential bacterial enzymes such as urease. In this study, a multistage computational pipeline integrating pharmacophore modeling, machine learning (ML), ensemble docking, and enhanced molecular dynamics simulations were applied to identify novel triazole-based HpU inhibitors. Starting from over seven million compounds in the ZINC15 database, pharmacophore- and ML-based filters progressively reduced the chemical space to 7062 candidates. Ensemble docking across 25 conformational frames of HpU, followed by quantum-polarized ligand docking (QPLD), identified seven promising ligands exhibiting strong binding energies and stable metal coordination. Molecular dynamics (MD) simulations under progressively relaxed restraints revealed three highly stable complexes (CA1, CA3, and CA6). Subsequent well-tempered metadynamics (WT-MetaD) simulations reconstructed free-energy landscapes showing deep, localized basins for CA3 and CA6, comparable to the potent reference inhibitor DJM, supporting their potential as strong urease binders. Finally, unsupervised chemical space mapping using the UMAP algorithm positioned these candidates within molecular regions associated with potent urease inhibitors, further validating their structural coherence and pharmacophoric relevance. An ADMET assessment confirmed that the selected candidates exhibit physicochemical and early safety properties compatible with subsequent in vitro evaluation. This multilevel screening strategy demonstrates the power of combining ML-driven classification, ensemble docking, and enhanced sampling simulations to discover non-hydroxamic urease inhibitors. Although the current findings are computational, they provide a rational foundation for future in vitro validation and for expanding the discovery of triazole-based scaffolds targeting ureolytic enzymes. Full article

Background: The synthesis and biological investigation of pyrrolidine (L-gulo) iminosugars bearing an organic boron pharmacophore in ortho and meta positions of an N-benzyl group is reported. This paper completes the structure–activity relationship data for this novel family of boron-bearing iminosugars. These can establish reversible intramolecular interactions via dative bonding from nucleophilic amino acid side chains to the empty p-orbital of the boron atom. Methods: Inhibitory activities against two panels of glycosidases and cancer cell lines were investigated to ascertain structure–activity relationship profiles for these novel iminosugar drug leads. Results: These iminosugars display selective, moderate-to-weak inhibitions (IC₅₀s = 116–617 μM) of β-D-galactosidase (bovine liver), and indications of inhibition of β-D-glucosidases (almond, bovine liver) (IC₅₀s = 633 and 710 μM) and α-D-glucosidases (rice, yeast, rat intestinal maltase) (IC₅₀s = 106–784 μM). The boronic acid group emerges as a useful pharmacophore for management of lysosomal storage disorders via the chaperone-mediated therapy approach. The cancer assays revealed that the A2780 ovarian carcinoma cell line is selectively inhibited by all compounds screened and the MIA-Pa-Ca2 pancreatic carcinoma cell line is selectively inhibited by most compounds. Growth inhibition and GI₅₀ values were most potent for the meta 7 side-product. Conclusions: Beyond the cancer cell line inhibition and dose-response capabilities, the real therapeutic potential of these borylated drugs lies in their switch on/switch off activation under boron neutron capture therapy (BNCT) radiotherapeutic conditions, thus providing an important area of application for borylated monosaccharides. Full article

Background/Objectives: The development of effective oncologic therapies with fewer adverse effects is often limited by the intrinsic and acquired resistance of tumor cells. Hybrid molecules, rationally designed to combine different pharmacophores, represent a promising strategy by providing synergistic effects, dose reduction, and a lower risk of resistance. In this study, the antitumor potential and mechanisms of action of 22 novel hybrid compounds derived from xanthene and pyran scaffolds (SJ022–SJ103) were investigated. The hybrids were initially evaluated through in vitro screening in four breast, three ovarian, and two prostate cancer cell lines, followed by the selection of T-47D, OVCAR-3, and LNCaP cells for detailed assays assessing cytotoxicity, apoptosis, cell cycle distribution, DNA damage, caspase-3/7 activity, morphology, and PI3K/AKT/mTOR pathway modulation. Methods: Cytotoxicity assays were performed in the selected cell lines, while mechanistic studies included apoptosis and cell cycle analysis by flow cytometry, γH2AX detection, Western blotting for PI3K/AKT/mTOR pathway proteins, and 3D spheroid assays. Combinatorial effects with hormone therapies (tamoxifen, fulvestrant, and letrozole) and the AKT inhibitor MK2206 were evaluated. AKT silencing by esiRNA and molecular docking was performed to confirm target engagement. Results: SJ028 demonstrated broad activity across all tested cell lines, whereas SJ064 and SJ078 exhibited higher selectivity. Treatments induced apoptosis, S/G2-M arrest, and DNA damage, accompanied by decreased phospho-AKT levels and stable PI3K and mTOR expression. In 3D models, the hybrids increased caspase-3/7 activity and necrotic core expansion. Co-administration with hormone therapies resulted in synergistic effects in breast and ovarian cancer cells, reducing IC₅₀ values by more than 50% in both parental and resistant models, while combinations with MK2206 were antagonistic across all tumor subtypes. AKT silencing abrogated cytotoxicity, and docking confirmed SJ028 binding to AKT. Conclusions: Xanthene- and pyran-based hybrids—particularly SJ028, SJ064, and SJ078—showed strong antitumor activity through apoptosis induction, cell cycle arrest, and PI3K/AKT pathway modulation. Their preserved efficacy in resistant models and synergistic interactions with hormone therapies contrasted with the antagonism observed with AKT inhibition, highlighting their potential as promising candidates for the treatment of hormone-responsive and -resistant cancers. Full article

Background/Objectives: In this work, a series of six new indazole-benzimidazole hybrids (M1–M6) were designed, synthesized, and fully characterized. The design of these compounds was based on the combination of two pharmacophoric units, indazole and benzimidazole, both known for their broad spectrum of biological activities. Methods: The molecular hybridization strategy was planned to combine these scaffolds through an effective synthetic pathway, using 6-nitroindazole, two 2-mercaptobenzimidazoles, and 1,3- or 1,5-dihaloalkanes as key precursors, affording the desired hybrids in good yields and with enhanced biological activity. Quantum chemical calculations were performed to investigate the structural, electronic, and electrostatic properties of M1–M6 molecules using Density Functional Theory (DFT) at the B3LYP/6-311++G(d,p) level. The antimicrobial activity efficacy of these compounds was assessed in vitro against four Gram-positive bacteria (Staphylococcus aureus, Enterococcus faecalis, Bacillus cereus, and Lactobacillus plantarum), four Gram-negative bacteria (Salmonella enteritidis, Escherichia coli, Campylobacter coli, Campylobacter jejuni), and four fungal strains (Saccharomyces cerevisiae, Candida albicans, Candida tropicalis, and Candida glabrata) using ampicillin and tetracycline as reference standard drugs. Results: Among the series, compound M6 exhibited remarkable antimicrobial activity, with minimum inhibitory concentrations (MIC) of 1.95 µg/mL against S. cerevisiae and C. tropicalis, and 3.90 µg/mL against S. aureus, B. cereus, and S. enteritidis, while the standards Ampicillin (AmB) (MIC ≥ 15.62 µg/mL) and Tetracycline (TET) (MIC ≥ 7.81 µg/mL) exhibited higher MIC values. To gain molecular insights into the compounds, an in silico docking study was performed to determine the interactions of M1–M6 ligands against the antimicrobial target beta-ketoacyl-acyl carrier protein (ACP) synthase III complexed with malonyl-COA (PDB ID: 1HNJ). Molecular modeling data provided valuable information on the structure-activity relationship (SAR) and the binding modes influencing the candidate ligand-protein recognition. Amino acid residues, such as Arg249, located in the solvent-exposed region, were essential for hydrogen bonding with the nitro group of the 6-nitroindazole moiety. Furthermore, polar side chains such as Asn274, Asn247, and His244 participated in interactions mediated by hydrogen bonding with the 5-nitrobenzimidazole moiety of these compound series. Conclusions: The hybridization of indazole and benzimidazole scaffolds produced compounds with promising antimicrobial activity, particularly M6, which demonstrated superior potency compared to standard antibiotics. Computational and docking analyses provided insights into the structure–activity relationships, highlighting these hybrids as potential candidates for antimicrobial drug development. Full article