Search Results (163)

Owing to their distinctive physicochemical features, their structural analogues of benzene ring bioisosteres, and their strong affinity for biomacromolecules, pyridine derivatives function both as core structural scaffolds in pharmacologically active compounds and as versatile elements for optimizing key drug-like properties, such as water solubility, membrane permeability, and metabolic stability. In this study, we synthesized five pyridine-fused heterocyclic compounds using common synthetic intermediates as precursors. Full article

The replacement of ionizable functional groups that are predominantly charged at physiological pH with neutral bioisosteres is a common strategy in medicinal chemistry; however, its impact on binding affinity is often context-dependent. Here, we investigated a series of amide derivatives of a glycomimetic E-selectin ligand, in which the carboxylate group of the lead compound is substituted with a range of amide and isosteric analogs. Despite the expected loss of the salt-bridge interaction with Arg97, several amides retained or even improved the binding affinity. Co-crystal structures revealed conserved binding poses across the series, with consistent interactions involving the carbonyl oxygen of the amide and the key residues Tyr48 and Arg97. High-level quantum chemical calculations ruled out a direct correlation between carbonyl partial charges and affinity. Instead, a moderate correlation was observed between ligand binding and the out-of-plane pyramidality of the amide nitrogen, suggesting a favorable steric adaptation within the binding site. Molecular dynamics (MD) simulations revealed that high-affinity ligands exhibit enhanced solution-phase pre-organization toward the bioactive conformation, likely reducing the entropic penalty upon binding. Further analysis of protein–ligand complexes using Molecular mechanics/Generalized born surface area (MM-GB/SA) decomposition suggested minor lipophilic contributions from amide substituents. Taken together, this work underscores the importance of geometric and conformational descriptors, beyond classical electrostatics, in driving affinity in glycomimetic ligand design and provides new insights into the nuanced role of amides as carboxylate isosteres in protein–ligand recognition. Full article

Artificial neural networks in drug discovery have shown remarkable potential in various areas, including molecular similarity assessment and virtual screening. This study presents a novel multimodal Siamese neural network architecture. The aim was to join molecular electrostatic potential (MEP) images with the texture features derived from reduced density gradient (RDG) diagrams for enhanced molecular similarity prediction. On one side, the proposed model is combined with a convolutional neural network (CNN) for processing MEP visual information. This data is added to the multilayer perceptron (MLP) that extracts texture features from gray-level co-occurrence matrices (GLCM) computed from RDG diagrams. Both representations converge through a multimodal projector into a shared embedding space, which was trained using triplet loss to learn similarity and dissimilarity patterns. Limitations associated with the use of purely structural descriptors were overcome by incorporating non-covalent interaction information through RDG profiles, which enables the identification of bioisosteric relationships needed for rational drug design. Three datasets were used to evaluate the performance of the developed model: tyrosine kinase inhibitors (TKIs) targeting the mutant T315I BCR-ABL receptor for the treatment of chronic myeloid leukemia, acetylcholinesterase inhibitors (AChEIs) for Alzheimer’s disease therapy, and heterodimeric AChEI candidates for cross-validation. The visual and texture features of the Siamese architecture help in the capture of molecular similarities based on electrostatic and non-covalent interaction profiles. Therefore, the developed protocol offers a suitable approach in computational drug discovery, being a promising framework for virtual screening, drug repositioning, and the identification of novel therapeutic candidates. Full article

Background/Objectives: To enhance the anti-glioma activity of erlotinib, we previously developed a series of carborane-based analogs exploiting the concept of three-dimensional bioisosterism. These carboranes generally exhibited improved cytotoxicity against glioma cell lines compared with the parent compound erlotinib and additionally showed varying degrees of EGFR inhibition. Given the well-described influence of lipophilicity on pharmacological properties, we aimed to determine this parameter for the new analogs and explore its correlations with biological behaviors. Methods: Lipophilicity was assessed experimentally, through chromatographic procedure, in terms of R_M⁰ and theoretically via fragment-based logP calculations (flogP) using Hansch–Fujita hydrophobic parameters π of some substituents and the experimentally determined logD_{n-octanol/buffer(7.4)} of 4-chloro-6,7-bis(2-methoxyethoxy)quinazoline. Additionally, the electronic properties of the carborane clusters were considered using the NMR chemical shifts of cluster carbon-bound protons. Results: For the series of carboranes, the R_M⁰ discretely correlated to the flogP. Neither R_M⁰ nor flogP correlated with the electronic characteristics of the carboranes. From the correlation between R_M⁰ and flogP, it was possible to estimate the π value for a nido-carboranyl substituent. Cytotoxicities, against glioma cells, exhibited a parabolic dependence on lipophilicity, finding optimal flogP for each cellular system. Some tendencies were observed between EGFR inhibition and flogP, requiring more hydrophilic compounds for optimal wild-type EGFR inhibition or a specific flogP for mutant EGFR inhibition. It was observed that the electronic features of the boron cluster also influenced both biological activities studied. Conclusions: Unlike our previous reports, which focused on the synthesis and biological evaluation of carborane-erlotinib analogs, this study establishes for the first time the correlation of lipophilicity and electronic features with cytotoxic and EGFR-inhibitory activities, providing new insights into their structure–activity relationships. Full article

Therapeutic peptides are a unique drug class due to their high-specificity binding with biological targets. However, the low bioavailability of peptides, as well as the lack of enzymatic stability, imposes a number of limitations on their biomedical application. A good strategy by which to overcome these limitations is the use of peptidomimetics, which are able to imitate the binding and activity of peptides both in vitro and in vivo. Peptidomimetics can be obtained by combining natural and synthetic amino acids in a peptide sequence. Various five-membered heterocycles are often used as structural fragments of peptide imitators to fix the chain in a certain conformation and to increase proteolytic stability. The use of 5-aminomethyl-1,2,4-triazole-3-carboxylic acid derivatives as building blocks of peptidomimetic structures may be a very attractive strategy, in which the tautomeric 1,2,4-triazole fragment is capable of flexibly forming hydrogen bonds on the protein surface of the target. In this work, a number of ethyl 5-aminomethyl-1,2,4-triazole-3-carboxylates and their derivatives were synthesized as mimetics of aliphatic amino acids. Their use as building blocks for synthesizing peptidomimetics was demonstrated. In addition, through the use of a panel of pathogenic and model strains of microorganisms and fungi, we demonstrated the lack of independent activity of the amino acid 1,2,4-triazole mimetics synthesized. This similarity of the biological properties of the obtained mimetics and their natural analogues reveals their bioisosterism. The bioisosterism and geometric similarity of 1,2,4-triazole mimetics and natural amino acid highlights the potential of their use as building blocks for therapeutic peptides. Full article

1,5-disubstituted tetrazoles (1,5-Ds-T) are heterocyclic bioisosteres of the cis-amide bond, commonly found in bioactive compounds, pharmaceuticals, and functional materials. Chromones are privileged scaffolds widely present in natural products that are well known for their diverse biological activities, including anticancer, antimicrobial, antidiabetic, anti-inflammatory, and antioxidant properties. Isocyanide-based multicomponent reactions, such as the Ugi-Azide (UA-4CR), provide a versatile strategy for synthesizing 1,5-Ds-T, which can be incorporated into other privileged heterocyclic or commercially available drugs. Herein, we describe a sonochemical one-pot synthesis of 1,5-Ds-T connected to chromone under mild conditions, highlighting their potential relevance in medicinal chemistry. Full article

We report the first green and diastereoselective synthesis of novel thiophene bioisosteres designed to mimic the privileged pyrrolo[3,2-c]quinoline core of martinelline alkaloids. The key step features an intramolecular 1,3-dipolar cycloaddition of in situ generated non-stabilized azomethine ylides from sarcosine, which proceeds with excellent yield and diastereoselectivity. This sustainable protocol, leveraging ultrasonic irradiation, recyclable hydrotalcite catalysts, and the green solvent cyclopentyl methyl ether (CPME), efficiently constructs the complex tricyclic framework. The structure and stereochemistry of the novel bioisostere were unambiguously confirmed by X-ray crystallography. This method offers a valuable, eco-friendly approach for diversifying natural product-inspired libraries in medicinal chemistry. Full article

Cyclic guanidines are valuable scaffolds for the design of compounds acting on GABAergic neurotransmission, owing to their ability to mimic the amino functionality of GABA as bioisosteres. With the aim to obtain a more potent and selective betaine/GABA transporter (BGT1) inhibitor, a basic hydrolysis of ethyl (E)-2-(acetylimino)-1-(3-phenylprop-2-yn-1-yl)hexahydropyrimidine-5-carboxylate was attempted. However, we isolated a byproduct, which was identified as the trifluoroacetate salt of 2-benzyl-5,6,7,8-tetrahydroimidazo[1,2-a]pyrimidine-6-carboxylic acid. The structure was confirmed by NMR spectroscopy and LC-MS. Herein we report the preparation, characterization, and spectral data of this fused heterocyclic compound. Full article

Candidiasis arises from the proliferation of Candida species in the human body, especially in individuals with compromised immune systems. Efficient therapeutic management of candidiasis is often hampered by the limited availability of potent antifungal drugs and the emergence of drug-resistant strains. We have previously identified the N-[(4-sulfamoylphenyl)methyl][1,1′-biphenyl]-4-carboxamide to have fungistatic and fungicidal properties, likely due to the hydrophobic biphenyl–chemical features affecting the structural organization of Candida spp. cell membrane. Here, we designed and synthesized a novel series of twelve 5-arylfuran-2-carboxamide derivatives bearing a new hydrophobic tail as bioisosteric replacement of the diphenyl fragment. Its antifungal effectiveness against C. albicans, C. glabrata, and C. parapsilosis, including ATCC and clinically isolated strains, was assessed for all compounds. The most active compound was N-benzyl-5-(3,4-dichlorophenyl)furan-2-carboxamide (6), with fungistatic and fungicidal effects against C. glabrata and C. parapsilosis strains (MIC = 0.062–0.125 and 0.125–0.250 mg/mL, respectively). No synergistic effects were observed when combined with fluconazole. Interestingly, fluorescent microscopy analysis after staining with SYTO 9 and propidium iodide revealed that compound 6 affected the cell membrane integrity in C. albicans strain 16. Finally, carboxamide 6 exhibited a dose-dependent cytotoxicity on erythrocytes, based on assessing the LDH release. Full article

Antioxidative neuroprotection is effective at preventing ischemic stroke (IS). Ferulic acid (FA) offers benefits in the treatment of many diseases, mostly due to its antioxidant activities. In this study, a glycosylated ferulic acid conjugate (FA-Glu), with 1,2,3-triazole as a linker and bioisostere between glucose at the C6 position and FA at the C4 position, was designed and synthesized. The hydrophilicity and chemical stability of FA-Glu were tested. FA-Glu’s protection against DNA oxidative cleavage was tested using pBR322 plasmid DNA under the Fenton reaction. The cytotoxicity of FA-Glu was examined via the PC12 cell and bEnd.3 cell tests. Antioxidative neuroprotection was evaluated, in vitro, via a H₂O₂-induced PC12 cell test, measuring cell viability and ROS levels. Antioxidative alleviation of cerebral ischemia–reperfusion injury (CIRI), in vivo, was evaluated using a rat middle cerebral artery occlusion (MCAO) model. The results indicated that FA-Glu was water-soluble (LogP −1.16 ± 0.01) and chemically stable. FA-Glu prevented pBR322 plasmid DNA cleavage induced via •OH radicals (SC% 88.00%). It was a non-toxic agent based on PC12 cell and bEnd.3 cell tests results. FA-Glu significantly protected against H₂O₂-induced oxidative damage in the PC12 cell (cell viability 88.12%, 100 μM) and inhibited excessive cell ROS generation (45.67% at 100 μM). FA-Glu significantly reduced the infarcted brain areas measured using TTC stain observation, quantification (FA-Glu 21.79%, FA 28.49%, I/R model 43.42%), and H&E stain histological observation. It sharply reduced the MDA level (3.26 nmol/mg protein) and significantly increased the GSH level (139.6 nmol/mg protein) and SOD level (265.19 U/mg protein). With superior performance to FA, FA-Glu is a safe agent with effective antioxidative DNA and neuronal protective actions and an ability to alleviate CIRI, which should help in the prevention of IS. Full article

Resistance of various bacterial pathogens to the activity of clinically approved drugs currently leads to serious infections, rapid spread of difficult-to-treat diseases, and even death. Taking the threats for human health in mind, researchers are focused on the isolation and characterization of novel natural products, including plant secondary metabolites. These molecules serve as inspiration and a suitable structural platform in the design and development of novel semi-synthetic and synthetic derivatives. All considered compounds have to be adequately evaluated in silico, in vitro, and in vivo using relevant approaches. The current review paper briefly focuses on the chemical and metabolic properties of resveratrol (1), as well as its oligomeric structures, viniferins, and viniferin-based molecules. The core scaffolds of these compounds contain so-called privileged structures, which are also present in many clinically approved drugs, indicating that those natural, properly substituted semi-synthetic, and synthetic molecules can provide a notably broad spectrum of beneficial pharmacological activities, including very impressive antimicrobial efficiency. Except for spectral verification of their structures, these compounds suffer from the determination or prediction of other structural and physicochemical characteristics. Therefore, the structure–activity relationships for specific dihydrodimeric and dimeric viniferins, their bioisosteres, and derivatives with notable efficacy in vitro, especially against chosen Gram-positive bacterial strains, are summarized. In addition, a set of descriptors related to their structural, physicochemical, pharmacokinetic, and toxicological properties is generated using various computational tools. The obtained values are compared to those of clinically approved drugs. The particular relationships between these in silico parameters are also explored. Full article

A group of sulfonium and selenonium salts bearing diverse benzylidene acetal substituents on their side chain moiety were designed and synthesized. Compared with our previous study, structural modifications in this study focused on multi-substitution of the phenyl ring and bioisosteric replacements at the sulfonium cation center. In vitro biological evaluation showed that selenonium replacement could significantly improve their α-glucosidase inhibitory activity. The most potent inhibitor 20c (10.0 mg/kg) reduced postprandial blood glucose by 48.6% (15 min), 52.8% (30 min), and 48.1% (60 min) in sucrose-loaded mice, outperforming acarbose (20.0 mg/kg). Docking studies of 20c with ntMGAM presented a new binding mode. In addition to conventional hydrogen bonding and electrostatic interaction, amino residue Ala-576 was first identified to contribute to binding affinity through π-alkyl and alkyl interactions with the chlorinated substituent and aromatic ring. The selected compounds exhibited a high degree of safety in cytotoxicity tests against normal cells. Kinetic characterization of α-glucosidase inhibition confirmed a fully competitive inhibitory mode of action for these sulfonium salts. Full article

Antioxidants, such as stilbenes, anthocyanidins, coumarins, tannins and flavonoids, are often based on oxygen-containing redox systems and tend to feature several hydroxyl groups in their chemical structures. From a synthetic perspective, oxygen atoms are prone to bioisosteric replacement with sulfur and, notably, selenium. The main objective of this narrative literature review is to explore if and how bioisosteric substitution of oxygen with sulfur or selenium can enhance the biological activity of natural products. This replacement boosts the biological activity of the resulting molecules considerably as they now combine the redox and antioxidant properties of the original flavonoids and other natural products with the specific redox behavior of sulfur and selenium. Besides sequestering free radicals and peroxides, they may, for instance, also catalyze the removal of oxidative stressors, capture free metal ions and even provide scope for selenium supplementation. Since these molecules resemble their natural counterparts, they also exhibit considerable selectivity inside the body and a good pharmacokinetic profile. Still, the synthesis of such hybrid molecules integrating sulfur and selenium into flavonoids and other natural products is a challenge and requires innovative synthetic strategies and approaches. Full article

N-(2-chloro-5-(3-(pyridin-4-yl)-1H-pyrazolo [3,4-b]pyridin-5-yl)pyridin-3-yl)-4-fluorobenzenesulfonamide, namely, FD274, is a promising 7-azaindazole-based PI3K inhibitor candidate with high antitumor efficacy against acute myeloid leukemia and reduced cardiotoxicity in the zebrafish model. To advance its clinical translation, in this work, we conducted comprehensive assessments of the cardiotoxicity of FD274 and preliminarily investigated its synergistic antitumor effects with an FLT3 inhibitor, Gilteritinib. The cardiotoxicity profile of FD274, as well as its bioisostere FD268 (positive control), was evaluated using the C57BL/6 mouse model and the H9C2 cell line. The cardiotoxicity of FD274 after a consecutive 20-day treatment period was further assessed in an HL-60 xenograft mouse model. The synergistic cytotoxicity of FD274 with Gilteritinib was evaluated in the HL-60 cell line and the FLT3-ITD cell line MV-4-11. FD274 demonstrated lower adverse effects associated with cardiac dysfunction, oxidative stress, and myocardial injury in the C57BL/6 mouse model and in the H9C2 cell line as compared with FD268. Its negligible adverse effect was further validated in the HL-60 xenograft mice after the 20-day treatment process. Moreover, FD274 demonstrated a synergistic pro-apoptotic effect with Gilteritinib in both HL-60 and MV-4-11 cells. Our findings confirmed the low cardiotoxicity of FD274 and its great potential for combination therapy with Gilteritinib, warranting further development. Full article

Free radicals and inflammation have pivotal role in various degenerative diseases like cancer, rheumatoid arthritis, diabetes, cardiovascular and neurodegenerative disorders. Pyrazoles possess a wide range of biological activities such as antifungal, antituberculosis, antimicrobial, antiviral, anti-inflammatory, anti-convulsant, anticancer etc. In this present study a series of dibenzalacetones and the corresponding pyrazole hybrids were designed through bioisosterism, synthesized and biologically evaluated to highlight the importance of the extended conjugated system and substitution to the anti-inflammatory and antioxidant activity. The synthesis of dibenzalacetones was achieved via Claisen-Schmidt reaction. The dihydro-pyrazoles were synthesized from the substituted dibenzacetones and phenylhydrazines, hydrazine and semicarbazide under microwave irradiation optimizing reaction conditions. The synthesized compounds were spectroscopically characterized and evaluated for their anti-lipid peroxidation (AAPH) activity, their interaction with the free radical DPPH and the inhibition of soybean LOX. The novel derivatives were studied in terms of their physicochemical properties. Many of the dihydro-pyrazoles showed potent antioxidant properties and significant inhibition of soybean lipoxygenase as a result of their physicochemical features. Compounds 4a and 4b presented the most potent anti-lipid peroxidation abilities (98% and 97%), whereas compounds 2d and 2e have proved to be the most potent lipoxygenase inhibitors with IC₅₀ values 2.5 μM and 0.35 μM. Moreover, docking studies with soybean lipoxygenase highlight the interactions of the novel derivatives with the enzyme. Full article