Search Results (27)

The rapid emergence of multidrug-resistant (MDR) bacterial pathogens poses a critical threat to global health, creating an urgent need for novel antimicrobial agents. In this study, we evaluated a small library of natural and semisynthetic phytocannabinoids against a broad panel of MDR Gram-positive bacterial strains, evidencing very good activity in the low µM range. We provide evidence of the antibacterial activity of the two separated enantiomers of cannabidiol, offering novel insights into the stereochemical aspects of their bioactivity. To investigate the possible molecular targets and clarify the mechanism of action, we employed Inverse Virtual Screening (IVS), a computational approach optimized for predicting potential protein–ligand interactions, on three selected MDR bacterial species. Interestingly, key targets belonging to important bacterial metabolic pathways and defense mechanisms were retrieved, and the results were used to rationalize the observed biological activities. To the best of our knowledge, this study marks the first application of IVS to microorganisms, offering a novel strategy for identifying bacterial protein targets. The results pave the way for future experimental validation, structure-based drug design, and the development of novel antibacterial agents. Full article

Recent bioassay studies have unexpectedly supported the high (computationally predicted) binding affinities of angiotensin receptor blockers (ARBs) at α-adrenergic receptors (αARs) in isolated smooth muscle. Computational predictions from ligand docking studies are consistent with very low concentrations of ARBs (e.g., sartans or bisartans) that partially reduce (20–50%) the contractile response to phenylephrine, suggesting that some ARBs may function as partial inverse agonists at αARs. Virtual ligand screening (docking) and molecular dynamics (MD) simulations were carried out to explore the binding affinities and stabilities of selected non-peptide ligands (e.g., ARBs and small-molecule opioids) for several G-protein coupled receptor (GPCR) types, including angiotensin II (AngII) type 1 receptor (AT₁R), α1AR, α2AR, and μ-(µOR) and ժ-opioid receptors (ժOR). Results: All ligands docked preferentially to the binding pocket on the cell surface domain of the GPCR types investigated. Drug binding was characterized by weak interactions (hydrophobic, hydrogen bonding, pi-pi) and stronger ionic and salt-bridge interactions (cation-pi and cation-anion interactions). Ligands specific to each GPCR category showed considerable cross-binding with alternative GPCRs, with small-molecule medications appearing less selective than their peptide or ARB functional equivalents. ARBs that exhibit higher affinities for AT₁R also demonstrate higher affinities for µORs and ժORs than opiate ligands, such as fentanyl and naltrexone. Moreover, ARBs had a higher affinity for αARs than either alpha agonists (epinephrine and phenylephrine) or inhibitors (prazosin and doxazosin). MD simulations of membrane-embedded ARB-GPCR complexes proved stable over nanosecond time scales and suggested that some ARBs may behave as agonists or antagonists depending on the GPCR type. Based on the results presented in this and related investigations, we propose that agonists bind to the resting A-site of GPCRs, while inverse agonists occupy the desensitizing D-site, which partial agonists like morphine and fentanyl share, contributing to addiction. ARBs block both AngII and alpha receptors, suggesting that they are more potent antihypertensive drugs than ACE inhibitors. ARBs have the potential to inhibit morphine tolerance and appear to disrupt receptor desensitization processes, potentially by competing at the D-site. Our results suggest the possible therapeutic potential of ARBs in treating methamphetamine and opiate addictions. Full article

Background/Objectives: The purpose of this study was to evaluate the association between risk-taking behaviors, vestibular symptoms/impairment and perception–action coupling behavior in recently concussed adolescents. Methods: This study utilized a cross-sectional design to evaluate the early effects of concussion on 12–18-year-old adolescents (n = 47) recruited from a concussion specialty clinic at their presenting clinical appointment. The Perception–Action Coupling Task (PACT) was used to assess action boundary perception by evaluating the participant’s ability to quickly and accurately determine whether a virtual “ball” fits in a virtual “hole”. Accuracy, response time and inverse efficiency were evaluated at the 0.8 and 1.2 ratios of ball–hole pairings, where 0.8 indicates the ball was slightly smaller than the hole and 1.2 indicates the ball was slightly larger than the hole. The Balloon Analog Risk Task (BART) is a computerized test which measures risk-taking behavior by “pumping” up a balloon. Each pump provides a small amount of virtual money into their bank; the goal is to make as much money as possible without popping the virtual balloon. The Vestibular Ocular Motor Screening (VOMS) tool is a brief screening tool designed to identify ocular or vestibular dysfunction following sport-related concussion, where horizontal/vertical vestibular ocular reflex (VOR) and visual motion sensitivity (VMS) are the primary vestibular outcomes. Pearson correlation matrices were developed to evaluate the association between BART, VOMS and PACT outcomes within the study cohort of concussed adolescents. Results: PACT inverse efficiency at the 1.2 ball–hole ratio was significantly correlated with all three VOMS outcomes (r = 0.33–0.37). The standard deviation of pump reaction time during BART was significantly correlated with accuracy (r = −0.47) and inverse efficiency (r = 0.42) at the 1.2 ratio. The standard deviation of the total number of pumps during BART was significantly correlated with PACT response time at the 1.2 ratio (r = 0.34). Horizontal VOR correlated with balloons collected (r = −0.30) and balloons popped (r = −0.30). Conclusions: The results of this study suggest that risk-taking behaviors and vestibular symptoms/impairment are associated with worse action boundary perception in adolescents following concussion. This relationship is more pronounced in male adolescents than females. Full article

Bacterial keratitis caused by Pseudomonas aeruginosa is indeed a serious concern due to its potential to cause blindness and its resistance to antibiotics, partly attributed to biofilm formation and cytotoxicity to the cornea. The present study uses a meta-analysis of a transcriptomics dataset to identify important genes and pathways in biofilm formation of P. aeruginosa induced keratitis. By combining data from several studies, meta-analysis can enhance statistical power and robustness, enabling the identification of 83 differentially expressed candidate genes, including fis that could serve as therapeutic targets. The approach of combining meta-analysis with virtual screening and in vitro methods provides a comprehensive strategy for identifying potential target genes and pathways crucial for bacterial biofilm formation and development anti-biofilm medications against P. aeruginosa infections. The study identified 83 candidate genes that exhibited differential expression in the biofilm state, with fis proposed as an ideal target for therapy for P. aeruginosa biofilm formation. These techniques, meta-analysis, virtual screening, and invitro methods were used in combination to diagnostically identify these genes, which play a significant role in biofilms. This finding has highlighted a hallmark target list for P. aeruginosa anti-biofilm potential treatments. Full article

Autism spectrum disorder is a complex neurodevelopmental disorder. The available medical treatment options for autism spectrum disorder are very limited. While the etiology and pathophysiology of autism spectrum disorder are still not fully understood, recent studies have suggested that wide alterations in the GABAergic, glutamatergic, cholinergic, and serotonergic systems play a key role in its development and progression. Histamine neurotransmission is known to have complex interactions with other neurotransmitters that fit perfectly into the complex etiology of this disease. Multitarget-directed compounds with an affinity for the histamine H₃ receptor indicate an interesting profile of activity against autism spectrum disorder in animal models. Here, we present the results of our research on the properties of (4-piperazin-1-ylbutyl)guanidine derivatives acting on histamine H₃ receptors as potential multitarget ligands. Through the virtual screening approach, we identified promising ligands among 32 non-imidazole histamine H₃ receptor antagonists/inverse agonists with potential additional activity against the dopamine D₂ receptor and/or cholinesterases. The virtual screening protocol integrated predictions from SwissTargetPrediction, SEA, and PPB2 tools, along with molecular docking simulations conducted using GOLD 5.3 and Glide 7.5 software. Among the selected ligands, compounds 25 and 30 blocked radioligand binding to the D₂ receptor at over 50% at a screening concentration of 1 µM. Further experiments allowed us to determine the pK_i value at the D₂ receptor of 6.22 and 6.12 for compounds 25 and 30, respectively. Our findings suggest that some of the tested compounds could be promising multitarget-directed ligands for the further research and development of more effective treatments for autism spectrum disorder. Full article

G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand–receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives. Full article

Image inversion is a powerful tool for investigating cognitive mechanisms of visual perception. However, studies have mainly used inversion in paradigms presented on twodimensional computer screens. It remains open whether disruptive effects of inversion also hold true in more naturalistic scenarios. In our study, we used scene inversion in virtual reality in combination with eye tracking to investigate the mechanisms of repeated visual search through three-dimensional immersive indoor scenes. Scene inversion affected all gaze and head measures except fixation durations and saccade amplitudes. Our behavioral results, surprisingly, did not entirely follow as hypothesized: While search efficiency dropped significantly in inverted scenes, participants did not utilize more memory as measured by search time slopes. This indicates that despite the disruption, participants did not try to compensate the increased difficulty by using more memory. Our study highlights the importance of investigating classical experimental paradigms in more naturalistic scenarios to advance research on daily human behavior. Full article

Mammography is considered the gold standard for breast cancer screening and diagnostic imaging; however, there is an unmet clinical need for complementary methods to detect lesions not characterized by mammography. Far-infrared ‘thermogram’ breast imaging can map the skin temperature, and signal inversion with components analysis can be used to identify the mechanisms of thermal image generation of the vasculature using dynamic thermal data. This work focuses on using dynamic infrared breast imaging to identify the thermal response of the stationary vascular system and the physiologic vascular response to a temperature stimulus affected by vasomodulation. The recorded data are analyzed by converting the diffusive heat propagation into a virtual wave and identifying the reflection using component analysis. Clear images of passive thermal reflection and thermal response to vasomodulation were obtained. In our limited data, the magnitude of vasoconstriction appears to depend on the presence of cancer. The authors propose future studies with supporting diagnostic and clinical data that may provide validation of the proposed paradigm. Full article

Natural products bear a multivariate biochemical profile with antioxidant, anti-inflammatory, antibacterial, and antitumoral properties. Along with their natural sources, they have been widely used both as anti-aging and anti-melanogenic agents due to their effective contribution in the elimination of reactive oxygen species (ROS) caused by oxidative stress. Their anti-aging activity is mainly related to their capacity of inhibiting enzymes like Human Neutrophil Elastase (HNE), Hyaluronidase (Hyal) and Tyrosinase (Tyr). Herein, we accumulated literature information (covering the period 1965–2020) on the inhibitory activity of natural products and their natural sources towards these enzymes. To navigate this information, we developed a database and server termed ANTIAGE-DB that allows the prediction of the anti-aging potential of target compounds. The server operates in two axes. First a comparison of compounds by shape similarity can be performed against our curated database of natural products whose inhibitory potential has been established in the literature. In addition, inverse virtual screening can be performed for a chosen molecule against the three targeted enzymes. The server is open access, and a detailed report with the prediction results is emailed to the user. ANTIAGE-DB could enable researchers to explore the chemical space of natural based products, but is not limited to, as anti-aging compounds and can predict their anti-aging potential. ANTIAGE-DB is accessed online. Full article

Cannabis sativa L. is a plant belonging to the Cannabaceae family, cultivated for its psychoactive cannabinoid (Δ⁹-THC) concentration or for its fiber and nutrient content in industrial use. Industrial hemp shows a low Δ⁹-THC level and is a valuable source of phytochemicals, mainly represented by cannabinoids, flavones, terpenes, and alkaloids, with health-promoting effects. In the present study, we investigated the phytochemical composition of leaves of the industrial hemp cultivar Futura 75, a monoecious cultivar commercially used for food preparations or cosmetic purposes. Leaves are generally discarded, and represent waste products. We analyzed the methanol extract of Futura 75 leaves by HPLC and NMR spectroscopy and the essential oil by GC-MS. In addition, in order to compare the chemical constituents, we prepared the water infusion. One new cannabinoid derivative (1) and seven known components, namely, cannabidiol (2), cannabidiolic acid (3), β-cannabispirol (4), β-cannabispirol (5), canniprene (6), cannabiripsol (7), and cannflavin B (8) were identified. The content of CBD was highest in all preparations. In addition, we present the outcomes of a computational study focused on elucidating the role of 2α-hydroxy-Δ^3,7-cannabitriol (1), CBD (2), and CBDA (3) in inflammation and thrombogenesis. Full article

Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1. Full article

Diabetes mellitus is a metabolic disease and one of the leading causes of deaths worldwide. Numerous studies support that the Mediterranean diet has preventive and treatment effects on diabetes. These effects have been attributed to the special bioactive composition of Mediterranean foods. The objective of this work was to decipher the antidiabetic activity of Mediterranean edible plant materials using the DIA-DB inverse virtual screening web server. A literature review on the antidiabetic potential of Mediterranean plants was performed and twenty plants were selected for further examination. Subsequently, the most abundant flavonoids, phenolic acids, and terpenes in plant materials were studied to predict their antidiabetic activity. Results showed that flavonoids are the most active phytochemicals as they modulate the function of 17 protein-targets and present high structural similarity with antidiabetic drugs. Their antidiabetic effects are linked with three mechanisms of action, namely (i) regulation of insulin secretion/sensitivity, (ii) regulation of glucose metabolism, and (iii) regulation of lipid metabolism. Overall, the findings can be utilized to understand the antidiabetic activity of edible Mediterranean plants pinpointing the most active phytoconstituents. Full article

Phytochemical investigation of Egyptian mandarin orange (Citrus reticulata Blanco, F. Rutaceae) seeds afforded thirteen known compounds, 1–13. The structures of isolated compounds were assigned using 1D and 2D NMR and HRESIMS analyses. To characterize the pharmacological activity of these compounds, several integrated virtual screening-based and molecular dynamics simulation-based experiments were applied. As a result, compounds 2, 3 and 5 were putatively identified as hyaluronidase, xanthine oxidase and tyrosinase inhibitors. The subsequent in vitro testing was done to validate the in silico-based experiments to highlight the potential of these flavonoids as promising hyaluronidase, xanthine oxidase and tyrosinase inhibitors with IC₅₀ values ranging from 6.39 ± 0.36 to 73.7 ± 2.33 µM. The present study shed light on the potential of Egyptian mandarin orange’s waste product (i.e., its seeds) as a skin health-promoting natural agent. Additionally, it revealed the applicability of integrated inverse docking-based virtual screening and MDS-based experiments in efficiently predicting the biological potential of natural products. Full article

To ensure efficiency in discovery and development, the application of computational technology is essential. Although virtual screening techniques are widely applied in the early stages of drug discovery research, the computational methods used in lead optimization to improve activity and reduce the toxicity of compounds are still evolving. In this study, we propose a method to construct the residue interaction profile of the chemical structure used in the lead optimization by performing “inverse” mixed-solvent molecular dynamics (MSMD) simulation. Contrary to constructing a protein-based, atom interaction profile, we constructed a probe-based, protein residue interaction profile using MSMD trajectories. It provides us the profile of the preferred protein environments of probes without co-crystallized structures. We assessed the method using three probes: benzamidine, catechol, and benzene. As a result, the residue interaction profile of each probe obtained by MSMD was a reasonable physicochemical description of the general non-covalent interaction. Moreover, comparison with the X-ray structure containing each probe as a ligand shows that the map of the interaction profile matches the arrangement of amino acid residues in the X-ray structure. Full article

Withaferin-A (Wi-A), a secondary metabolite extracted from Ashwagandha (Withania somnifera), has been shown to possess anticancer activity. However, the molecular mechanism of its action and the signaling pathways have not yet been fully explored. We performed an inverse virtual screening to investigate its binding potential to the catalytic site of protein kinases and identified ABL as a strong candidate. Molecular docking and molecular dynamics simulations were undertaken to investigate the effects on BCR-ABL oncogenic signaling that is constitutively activated yielding uncontrolled proliferation and inhibition of apoptosis in Chronic Myeloid Leukemia (CML). We found that Wi-A and its closely related withanolide, Withanone (Wi-N), interact at both catalytic and allosteric sites of the ABL. The calculated binding energies were higher in the case of Wi-A at catalytic site (−82.19 ± 5.48) and allosteric site (−67.00 ± 4.96) as compared to the clinically used drugs Imatinib (−78.11 ± 5.21) and Asciminib (−54.00 ± 6.45) respectively. Wi-N had a lesser binding energy (−42.11 ± 10.57) compared to Asciminib at the allosteric site. The interaction and conformational changes, subjected to ligand interaction, were found to be similar to the drugs Imatinib and Asciminib. The data suggested that Ashwagandha extracts containing withanolides, Wi-A and Wi-N may serve as natural drugs for the treatment of CML. Inhibition of ABL is suggested as one of the contributing factors of anti-cancer activity of Wi-A and Wi-N, warranting further in vitro and in vivo experiments. Full article