Docking Analysis Research Articles

Structure-guided mutations in CDRs for enhancing the affinity of neutralizing SARS-CoV-2 nanobody

The optimization of antibodies to attain the desired levels of affinity and specificity holds great promise for the development of next generation therapeutics. This study delves into the refinement and engineering of complementarity-determining regions (CDRs) through in silico affinity maturation followed by binding validation using isothermal titration calorimetry (ITC) and pseudovirus-based neutralization assays. Specifically, it focuses on engineering CDRs targeting the epitopes of receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. A structure-guided virtual library of 112 single mutations in CDRs was generated and screened against RBD to select the potential affinity-enhancing mutations. Protein-protein docking analysis identified 32 single mutants of which nine mutants were selected for molecular dynamics (MD) simulations. Subsequently, biophysical ITC studies provided insights into binding affinity, and consistent with in silico findings, six mutations that demonstrated better binding affinity than native nanobody were further tested in vitro for neutralization activity against SARS-CoV-2 pseudovirus. Leu106Thr mutant was found to be most effective in virus-neutralization with IC50 values of ∼0.03 μM, as compared to the native nanobody (IC50 ∼0.77 μM). Thus, in this study, the developed computational pipeline guided by structure-aided interface profiles and thermodynamic analysis holds promise for the streamlined development of antibody-based therapeutic interventions against emerging variants of SARS-CoV-2 and other infectious pathogens.

Synthesis and Antifungal Activities of Glucosamine Aromatic Derivatives Against Four Phytopathogenic Fungi of Crops.

A series of diversified glucosamine derivatives (3a-3y) was synthesized and their antifungal activity was examined against four kinds of phytopathogens, Fusarium graminearum (F. graminearum), Fusarium moniliforme (F. moniliforme), Curvularia. lunata (C. lunata), and Rhizoctonia solani (R. solani) which cause seriously economic losses worldwide by affecting crops. The compound 3o showed remarkable antifungal activity against F. graminearum with EC50 value of 3.96 μg/mL, compared to the standard drug triadimefon (10.1 μg/mL). 3D-QSAR model with the statistically recommended values (r2=0.915, q2=0.872) showed that positive charge group or bulky group in the benzyl ring was favorable for the antifungal activity. Enzyme activity assays confirmed that 3o had a moderate inhibition of trehalase with inhibition rate of 51.4 % at 5 μg/mL, which is comparable to those of commercial inhibitor validamycin A with inhibition rate of 83.3 %. Molecular docking analysis revealed that 3o also had a hydrogen bond interaction with key amino acid residue compared to validoxylamine.

Novel sulfonylamido benzoxazole derivatives: synthesis, characterisation, molecular docking, DFT, and antimicrobial activity investigations.

In this work, numerous novel 2-(p-substitutedphenyl)-5-[(p-substitutedphenyl)sulfonylamido]benzoxazole derivatives were designed, synthesized, and structurally characterized using mass spectroscopy, 1H-NMR, 13C-NMR, and elemental analysis approaches. The antimicrobial activity against several Gram (+), Gram (-), and fungal species was determined using the in vitro microdilution technique. A molecular docking analysis was performed on all produced compounds utilizing the S. aureus Gyrase complex with Ciprofloxacin and DNA. Two of the most effective compounds against S. aureus, N4 and N9, have binding energies of -8.7 kcal/mol and -8.6 kcal/mol, respectively, and their interactions have been demonstrated in 2D and 3D. Furthermore, utilizing the 6-311G(d,p) base set and DFT/B3LYP theory, MEP analysis, geometric optimization, and molecular reactivity analysis (HOMO-LUMO) of N4 and N9 were performed, and the results were presented. All compounds' theoretical ADMET profiles were computed as well, and they met Lipinski and other strict criteria. With all of this knowledge, this study could be a pioneer in the development of novel anti-S. aureus compounds.

Network pharmacology combined with molecular docking revealed the potential targets of Coridius chinensis in prostate cancer treatment.

Prostate cancer (PCa) has high morbidity and mortality rates in elderly men. With a history of thousands of years, traditional Chinese medicine derived from insects could be an important source for developing cancer-targeted drugs to prevent tumorigenesis, enhance therapeutic effects, and reduce the risk of recurrence and metastasis. Multiple studies have shown that Coridius chinensis (Cc) has anticancer effects. To elucidate the mechanism of action of Cc against PCa via network pharmacology and molecular docking. Potential targets for Cc and PCa were predicted using ChemDraw 19.0 software, the PharmMapper database and the GeneCards database. Then, the STRING database was used to construct the protein-protein interaction network. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and molecular docking analyses were subsequently conducted to identify the key targets, active ingredients and pathways involved. GO and KEGG analyses indicated that the PI3K-Akt signalling pathway was the critical pathway (P value < 1.0 × 10-8). Multiple targeting ingredients that can affect multiple pathways in PCa have been identified in Cc. Seven active compounds (asponguanosines A, asponguanine B, asponguanine C, aspongpyrazine A, N-acetyldopamine, aspongadenine B and aspongpyrazine B) were selected for molecular docking with 9 potential targets, and the results revealed that aspongpyrazine A and asponguanosine A are the main components by which Cc affects PCa (affinity<-5 kcal/mol, hydrogen bonding), but more studies are needed. We used network pharmacology to predict the bioactive components and important targets of Cc for the treatment of PCa, supporting the development of Cc as a natural anticancer agent.

Network Pharmacology, Molecular Dynamics and In Vitro Assessments of Indigenous Herbal Formulations for Alzheimer’s Therapy

Alzheimer’s disease (AD) is an age-associated neurodegenerative condition marked by amyloid plaques, synaptic dysfunction, and neuronal loss. Besides conventional medical care, herbal therapies, both raw and refined, have attracted researchers for their potential therapeutic effects. As a proof-of-concept, our study combined HPLC-DAD analysis of bioactive constituents, network pharmacology, molecular dynamics (MD), molecular docking, post-MD analysis, and experimental verification to investigate the mechanisms of crude drug formulations as a therapeutic strategy for AD. We identified nine bioactive compounds targeting 188 proteins and 1171 AD-associated genes. Using a Venn diagram, we found 47 overlapping targets, forming “herb-compound-target (HCT)” interaction networks and a protein‒protein interaction (PPI) network. Simulations analyzed binding interactions among the three core targets and their compounds. MD assessed the stability of the best-ranked poses and beneficial compounds for each protein. Among the top 22 hub genes, AChE, BChE, and MAO, ranked 10, 14, and 34, respectively, were selected for further analysis. Two tetraherbal formulations, Form A and Form B, showed notable activity against AChE. Form A exhibited significant (p &lt; 0.0001) inhibitory activity (IC50 = 114.842 ± 2.084 µg/mL) compared to Form B (IC50 = 142.829 ± 4.258 µg/mL), though weaker than galantamine (IC50 = 27.950 ± 0.122 µg/mL). Form B had significant inhibitory effects on BChE (IC50 = 655.860 ± 32.812 µg/mL) compared to Form A (IC50 = 679.718 ± 20.656 µg/mL), but lower than galantamine (IC50 = 23.126 ± 0.683 µg/mL). Both forms protected against Fe2+-mediated brain injury by inhibiting MAO. Docking identified quercetin (−10.2 kcal/mol) and myricetin (−10.1 kcal/mol) for AChE; rutin (−10.6 kcal/mol) and quercetin (−9.7 kcal/mol) for BChE; and kaempferol (−9.1 kcal/mol) and quercetin (−8.9 kcal/mol) for MAO. These compounds were thermodynamically stable based on MD analysis. Collectively, the results offer a scientific rationale for the use of these specifically selected medicinal herbs as AD medications.

Fungicidal Activity of Novel 6-Isothiazol-5-ylpyrimidin-4-amine-Containing Compounds Targeting Complex I Reduced Nicotinamide Adenine Dinucleotide Oxidoreductase.

To discover novel inhibitors of the complex I reduced nicotinamide adenine dinucleotide (NADH) oxidoreductase as fungicides, a series of 6-isothiazol-5-ylpyrimidin-4-amine-containing compounds were designed using a computer-aided pesticide design method and splicing of substructures from diflumetorim and isotianil. In vitro fungicidal bioassays indicated that compounds T17-T24 showed high inhibitory activity against Rhizoctonia solani with an effective concentration (EC50) value falling between 2.20 and 23.85 μg/mL, which were more active than or equivalent to the lead diflumetorim with its EC50 of 19.80 μg/mL. In vivo antifungal bioassays demonstrated that, at a concentration of 200 μg/mL, T7 and T21 showed higher inhibition against Pseudoperonospora cubensis than all other compounds, while T23 exhibited the highest inhibition against Sphaerotheca fuliginea. T23 showed an approximately twofold lower inhibition potency against R. solani complex I NADH oxidoreductase than diflumetorim. Molecular docking and transcriptomic analyses indicated that T23 and diflumetorim both might share the same mode of action, targeting NADH oxidoreductase. T23 as a good fungicidal candidate against R. solani is worthy of further investigation.

Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach.

This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.

Examination of Triazolinedione-Derived Dihydropyrrole Hybrid Compounds: ER Stress-Related Apoptosis in Breast Cancer Cells, Molecular Docking, and ADMET Analysis

Examination of Triazolinedione-Derived Dihydropyrrole Hybrid Compounds: ER Stress-Related Apoptosis in Breast Cancer Cells, Molecular Docking, and ADMET Analysis

Elucidating the protective mechanism of ganoderic acid DM on breast cancer based on network pharmacology and in vitro experimental validation.

Ganoderma lucidum, a popular medicinal fungus, has been utilized to treat a variety of diseases. It possesses a unique therapeutic and pharmacological reputation in suppressing cancer/tumor progression, especially breast cancer, due to its embedded rich bioactive chemical constituents, mainly triterpenoids (ganoderic acids). The most prevalent malignant tumor in women with a high mortality and morbidity rate is breast cancer. Ganoderic acids A, D, DM, F, and H are evidenced in previous research to have breast cancer-preventive properties by exhibiting autophagic and apoptosis, anti-proliferative, and anti-angiogenesis effects. However, the anti-breast cancer mechanism remains unclear. The putative targets of the ganoderic acids were further determined using bioinformatics techniques and molecular docking calculation. Finally, the key targets were verified in vitro. A total of 53 potential target proteins associated with 202 pathways were predicted to be related to breast cancer. The potential targets were narrowed down to six key targets (AKT1, PIK3CA, epidermal growth factor receptor [EGFR], STAT1, ESR1, and CTNNB1), using different algorithms of the CytoHubba plugin, which were further validated using molecular docking analysis. The ganoderic acid DM (GADM) and the targets (PIK3CA and EGFR) with the strongest interactions were validated via MDA-MB-231 and MCF7 cells. The expression level of PIK3CA in both MDA-MB-231 and MCF7 cells was dose-dependently suppressed by GADM, whereas EGFR expression was unexpectedly increased, which warrants further investigation. These data indicated that the network pharmacology-based prediction of GADM targets for treating human breast cancer could be reliable.

Inhibition mechanism of buckwheat hulls polyphenols on α-amylase and α-glucosidase using kinetics, spectroscopics and molecular docking approaches

The work investigated the activity inhibition of phenolic compounds in buckwheat (Fagopyrum esculentum Moench) hulls (BH) on α-amylase and α-glucosidase, and clarified their possible mechanisms based on kinetics, spectroscopics and molecular docking analysis. The total polyphenols (BHP) from BH using an ultrasound-assisted alcohol extraction method was 210.50 mg GAE/g DW. The study identified a total of 33 polyphenolic compounds in the extracts of BH using UPLC-Q-Exactive Orbitrap/MS, revealing that sixteen of these were novel polyphenolic substances not previously documented in this plant. BHP demonstrated significant inhibitory effects on both α-amylase and α-glucosidase enzymes, with IC50 values recorded at 27.16 μg/mL and 7.00 μg/mL, respectively, suggesting noncompetitive and mixed-type inhibition mechanisms. The fluorescence intensity of the enzymes was effectively quenched by BHP through a combination of dynamic and static quenching mechanisms, driven predominantly by hydrophobic interactions. BHP's interaction with the enzymes resulted in conformational changes that reduced their enzymatic activities. Molecular docking further revealed that six polyphenolic components of BHP had a strong affinity for binding with the active sites nestled in the enzymes' hydrophobic cavities, inhibiting their activity and potentially contributing to a reduction in blood glucose levels. The results could provide perspective for using BHP in the functional components of sugar-controlling foods.

In silico Discovery of Leptukalins, The New Potassium Channel Blockers from the Iranian Scorpion, Hemiscorpius Lepturus.

Blocking Kv 1.2 and Kv 1.3 potassium channels using scorpion venom- derived toxins holds potential therapeutic value. These channels are implicated in autoimmune diseases such as neurodegenerative diseases, multiple sclerosis, rheumatoid arthritis, and type 1 diabetes. The present work aims at the discovery and in silico activity analysis of potassium channel blockers (KTxs) from the cDNA library derived from the venom gland of Iranian scorpion Hemiscorpius lepturus (H. lepturus). The sequence regarding potassium channel blockers were extracted based on Gene Ontology for H. lepturus venom gland. Homology analyses, superfamily, family, and evolutionary signatures of H. lepturus KTxs (H.L KTxs) were determined by using BLASTP, COBALT, PROSITE, and InterPro servers. The predicted 3D structures of H.L KTxs were superimposed against their homologs to predict structure activity relationship. Molecular docking analysis was also performed to predict the binding affinity of H.L KTxs to Kv 1.2 and Kv 1.3 channels. Finally, the toxicity was predicted. Seven H.L KTxs, designated as Leptukalin, were extracted from the cDNA library of H. lepturus venom gland. Homology analyses proved that they can act as potassium channel blockers and they belong to the superfamily and family of Scorpion Toxin-like and Short-chain scorpion toxins, respectively. Structural alignment results confirmed the activity of H.L KTxs. Binding affinity of all H.L KTxs to Kv 1.2 and Kv 1.3 channels ranged from -4.4 to -5.5 and -4 to -5.7 Kcal/mol, respectively. In silico toxicity assay showed that Leptukalin 3, Leptukalin 5, and Leptukalin 7 were non-toxic. Three non-toxic KTxs, Leptukalin 3, 5, and 7, were successfully discovered from the cDNA library of H. lepturus venom gland. Gathering all data together, the discovered peptides are promising potassium channel blockers. Accordingly, Leptukalin 3, 5, and 7 could be suggested for complementary in vitro studies and mouse model of autoimmune diseases.

Effects of L-Proline on the Stability of Mulberry Anthocyanins and the Mechanism of Interaction between L-Proline and Cyanidin-3-O-Glycoside.

The protective effects of L-aspartic acid, L-valine, and L-proline on the stability of mulberry anthocyanins were investigated. Results showed that L-aspartic acid, L-valine, and L-proline significantly enhanced (p < 0.05) the stability of mulberry anthocyanins under constant light or ascorbic acid (AA). L-Proline had the best protective effect against anthocyanin degradation. The interaction between L-proline and cyanidin-3-O-glucoside (C3G) through hydrogen bonding and van der Waals forces, which improved the stability of C3G, was confirmed using FT-IR, 1H NMR, XRD, and molecular docking analyses, as well as molecular dynamics modes. In vitro digestion experiments yielded that both 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radical scavenging capacities of the C3G/Pro group were increased in the intestinal fluid (p < 0.05). The above findings suggest that L-proline effectively slowed down the degradation of mulberry anthocyanins, and that it could be used as an auxiliary pigment and food additive to extend the optimal flavor period of products containing mulberry anthocyanins, and can improve the bioavailability of mulberry anthocyanins.

In vitro and in silico assessment of cytotoxicity of dinitramine via calcium dysregulation and mitochondrial dysfunction in bovine mammary glands

The herbicide market is expanding rapidly due to the global increase in herbicide usage. Dairy cows are susceptible to herbicide exposure through the ingestion of contaminated plants, which can adversely affect the mammary gland health and reduce milk production. Dinitramine, a synthetic herbicide in the dinitroaniline family, is typically used to control weeds by inhibiting their sprouting and root development. While previous studies have demonstrated the cytotoxicity of dinitramine in aquatic organisms, research on its toxicity in cattle is limited. In this study, bovine mammary epithelial cells (MAC-T) were used to verify the detrimental effects on dairy cows, especially on the mammary glands. First, we evaluated the cytotoxic effects of dinitramine on MAC-T cells and examined various cellular responses to dinitramine treatment, including alterations in apoptotic cells, mitochondrial dysfunction, and calcium dysregulation. Moreover, the expression levels of AKT and MAPK signaling proteins were confirmed in response to dinitramine treatment. Alterations in the mRNA levels of genes related to milk production and inflammatory response following dinitramine exposure were evaluated using quantitative PCR. Finally, we assessed the binding affinity between dinitramine and the target proteins using in silico molecular docking analysis. Overall, the cumulative evidence of the various toxic effects of dinitramine on MAC-T cells suggests its potential to reduce both milk yield and quality.

Discovery of Cinnamic Acid Derivatives as Potent Anti-H. pylori Agents

Antibiotics are currently used for the treatment of Helicobacter pylori (H. pylori), which is confirmed to be the major cause of gastric disorders. However, the long-term consumption of antibiotics has already caused antibiotic resistance and side effects in vivo. Therefore, there is an emerging need for searching for safe and effective anti-H. pylori agents. Inspired by the excellent bioactivities of cinnamic acid, a series of cinnamic acid derivatives (compounds 1–30) were synthesized and determined for H. pylori inhibition. The initial screening revealed that compound 23, a 2,4-dinitro cinnamic acid derivative containing 4-methoxyphenol, showed excellent H. pylori inhibition with an MIC value of 4 μM. Further studies indicated that compound 23 showed anti-bacterial activity and had a bactericidal effect on H. pylori due to the destruction of the bacterial structure. Molecular docking analysis revealed that the 2,4-dinitro groups in cinnamic acid moiety formed hydrogen bonding with amino acid residues in an active pocket of H. pylori protein. Interestingly, the ester moiety fitted into the hydrophobic pocket, attaining additional stability to compound 23. Above all, the present study reveals that compound 23 could be considered a promising anti-H. pylori agent to treat H. pylori causing gastritis.

Ultrasound-assisted extraction of polyphenols from Phyllanthi Fructus: Comprehensive insights from extraction optimization and antioxidant activity

Phyllanthi Fructus (PF) is a valuable botanical resource with a long history of traditional use, known for potent antioxidant and anti-inflammatory effects attributed to its rich contents of bioactive compounds, particularly polyphenols. However, current extraction techniques limit the utilization of polyphenols from PF. This study aimed to achieve the maximum polyphenol yield and improve the antioxidant activity of PF extracts to promise PF’s prospects for modern healthcare.Firstly, ultrasonic-assisted extraction (UAE) was employed to extract the polyphenols in PF and a combination of Plackett-Burman designs (PBD) and response surface methodology (RSM) was applied to optimize UAE’s conditions. Next, cellular superoxide dismutase (SOD) and malondialdehyde (MDA) were used to assess the antioxidant activity of extracted polyphenols. Ultra-Performance Liquid Chromatography coupled with Quadrupole Time-of-Flight Mass Spectrometry (UPLC-Q-TOF MS) was utilized to characterize polyphenol components in the PF extracts. Finally, network pharmacology and molecular docking analysis were performed to screen the potential target proteins of polyphenols from PF.As a result, the optimized polyphenol yield was 213.49 mg/g, and the antioxidant activities, measured by ability of DPPH scavenging, ABTS+ scavenging, and FRAP were 76.95 %, 2.24 mmol/g, 2.34 mmol/g, respectively. PF extracts also showed good antioxidant capabilities at cellular level. 26 polyphenol components were identified in the PF extracts. Among these, ellagic acid, myricetin, and eriodictyol may exert antioxidant effects by interacting with AKT serine/threonine kinase 1 (AKT1).In conclusion, our study provides valuable insights into the optimizing PF extraction and underscores its potential applications in enhancing natural polyphenols extraction using UAE with a combination of PBD and RSM. These findings offer a promising avenue for the development and utilization of PF, and could serve as a reference for similar extraction processes in the future.

Identification of Aurora A kinase allosteric inhibitors: A comprehensive virtual screening through fingerprint-based similarity search, molecular docking, machine learning and molecular dynamics simulation

The Aurora A kinase (AAK) protein controls spindle assembly and promotes cell divisions in various diseases including cancer. In the present study, allosteric inhibition of AAK protein through different advanced computational screening approaches is employed to target AAK’s allosteric inhibition-modulation. Precisely, extensive computational techniques including allosteric binding sites recognition of AAK protein, fingerprint-based similarity search, multi-step molecular docking through AutoDock Vina and PLANTS, and a 100 ns molecular dynamics (MD) simulations studies were carried out followed by the calculation of binding free energy with MM-GBSA based approaches, has been employed for identification of potential allosteric inhibitors-modulators of AAK protein. The study outcome highlighted that all three identified small molecular chemical entities exhibit strong binding interaction affinity in both the docking analyses at the allosteric domain of AAK protein and also greater interaction stability in comparison to the considered standard compound. In addition, all identified three screened hits also show acceptable pharmacokinetics and medicinal chemistry properties, which certainly dictates their potentiality for becoming good drug-like compounds for inhibiting-modulating the activity of AAK protein binds with similar amino acids of the allosteric domain of AAK protein with selected three compounds. All the selected molecules were found to show an acceptable ADMET profile. Moreover, the MM-GBSA-based binding energy was found to be in the range of −8 to −35 Kcal/mol, which showed a strong association between proposed molecules and AAK protein. Comprehensive computational approach shows that the selected proposed three inhibitors of AAK protein are the best candidates as potential inhibitors.

Genetic and in-silico approaches for investigating the mechanisms of ciprofloxacin resistance in Salmonella typhi: Mutations, extrusion, and antimicrobial resistance

Salmonella enterica serovar Typhi spreads typhoid infection in humans through the consumption of contaminated food and water. Poor sanitation plays a pivotal role in its dissemination. Over time, the bacterium has acquired resistance to many promising antibiotics, posing a growing global health concern and hindering the achievement of sustainable development goals. This study aims to elucidate the molecular complexity of fluoroquinolone resistance, a first-line treatment for typhoid infection. To achieve this aim, 80 clinical isolates were collected from various diagnostic laboratories. These isolates were confirmed based on morphological characteristics and biochemical tests. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates were identified using the Kirby-Bauer disc diffusion method. The mechanism of ciprofloxacin resistance was investigated by sequencing the quinolone resistance-determining region (QRDR) genes and identifying the presence of the qnrS1 gene. As a result of this study, 60 % of isolates showed resistance to ciprofloxacin. At the same time, the qnrS1 gene was present in all the selected strains while mutation analysis identified significant mutation in QRDR of DNA gyrase subunit A (gyrA) and Topoisomerase IV (parC) gene. The combinatorial effect was further investigated by downloading 286 draft genomes. The Mutation analysis reveals significant mutations at gyrA S83F, gyrA D87N, gyrA S83Y, gyrB S464F, parC S80I, and parE L416F. Additionally, docking analysis indicates reduced binding affinity and altered solvent accessibility, which show the structural changes at mutation sites. This study provides crucial insights that mutation reduces the binding affinity while qnrS1 acts as a transport channel to extrude the ciprofloxacin. In the future, further validation through experimental mutagenesis is recommended, for targeted therapeutic interventions against the mounting threat of antibiotic-resistant S. Typhi.

Antioxidant Activity and Hypoallergenicity of Egg Protein Matrices Containing Polyphenols from Citrus Waste.

This study reports on the interactions of egg proteins, which represent a major health concern in food allergy, with polyphenols obtained from orange and lemon peels. The antioxidant properties of such citrus peel extracts prior to protein binding were evaluated. The resulting edible, and therefore inherently safe, matrices exhibit reduced IgE binding compared to pure proteins in indirect immunological assays (ELISA) using individual sera from patients allergic to ovalbumin and lysozyme. The reduced allergenicity could arise from the interactions with polyphenols, which alter the structure and functionality of the native proteins. It is hypothesized that the anti-inflammatory and antioxidant properties of the polyphenols, described as inhibitors of the allergic response, could add immunomodulatory features to the hypoallergenic complexes. A docking analysis using lysozyme was conducted to scrutinize the nature of the protein-polyphenol interactions. An in silico study unravelled the complexity of binding modes depending on the isoforms considered. Altogether, the presented results validate the antioxidant properties and reduced allergenicity of polyphenol-fortified proteins. Lastly, this study highlights the upgrading of vegetable wastes as a source of natural antioxidants, thus showing the benefits of a circular economy in agri-food science.

Molecular Docking and Dynamic Simulation Approach to Target Penicillin-Binding Protein 1B (LpoB) of Salmonella typhimurium with Flavonoids

Background and Objective: Lipopolysaccharide (LPS) is an essential constituent of the outer membrane of gram-negative bacteria, such as Salmonella typhimurium, and it plays a crucial role by inducing disease in the host. Penicillin-binding protein 1B (LpoB) is a key enzyme in the production of peptidoglycans, making it a potential target for the development of new antimicrobials. Flavonoids are naturally occurring plant-derived chemicals with a wide range of pharmacological properties, including antibacterial capabilities. The goal of this study was to identify the potential flavonoid that inhibits the protein LpoB using computational approaches and compare it with the standard antibiotic ciprofloxacin. Methods: The study was carried out by selecting fifty flavonoids based on Lipinski’s rule of five. Molecular docking was carried out for selected flavonoids and ciprofloxacin against the LpoB protein using AutoDock 4. A 100 nanosecond molecular dynamic simulation was performed for apoprotein, LopB-fisetin, and LpoB-ciprofloxacin complexes, followed by free energy calculation by Molecular Mechanics Generalized Born Surface Area (MMGBSA) solvation analysis. Results: The docking results revealed that fisetin displayed five hydrogen bonds with a binding affinity of -4.67 kcal/mol, and ciprofloxacin exhibited a binding affinity of -4.36 kcal/mol with two hydrogen bonds. The apoprotein and fisetin complex remained stable throughout the 100 ns molecular dynamic simulation, while the ciprofloxacin complex lost its stability. The MMGBSA analysis with fisetin showed better binding free energy compared to ciprofloxacin. Conclusion: The present study has emphasized the potential of flavonoids as probable candidates that can inhibit the protein LpoB. The integration of molecular docking, dynamic simulations, and MMGBSA analysis has provided significant insight into the thermodynamics and binding interactions of the LpoB- fisetin complex, and it has enabled further experimental validations.

Novel benzothiazole/benzothiazole thiazolidine-2,4-dione derivatives as potential FOXM1 inhibitors: In silico, synthesis, and in vitro studies.

The oncogenic transcription factor FOXM1 overexpressed in breast and other solid cancers, is a key driver of tumor growth and progression through complex interactions, making it an attractive molecular target for the development of targeted therapies. Despite the availability of small-molecule inhibitors, their limited specificity, potency, and efficacy hinder clinical translation. To identify effective FOXM1 inhibitors, we synthesized novel benzothiazole derivatives (KC10-KC13) and benzothiazole hybrids with thiazolidine-2,4-dione (KC21-KC36). These compounds were evaluated for FOXM1 inhibition. Molecular docking and molecular dynamics simulation analysis revealed their binding patterns and affinities for the FOXM1-DNA binding domain. The interactions with key amino acids such as Asn283, His287, and Arg286, crucial for FOXM1 inhibition, have been determined with the synthesized compounds. Additionally, the molecular modeling study indicated that KC12, KC21, and KC30 aligned structurally and interacted similarly to the reference compound FDI-6. In vitro studies with the MDA-MB-231 breast cancer cell line demonstrated that KC12, KC21, and KC30 significantly inhibited FOXM1, showing greater potency than FDI-6, with IC50 values of 6.13, 10.77, and 12.86 µM, respectively, versus 20.79 µM for FDI-6. Our findings suggest that KC12, KC21, and KC30 exhibit strong activity as FOXM1 inhibitors and may be suitable for in vivo animal studies.