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Phytochemical investigation of the ethanolic extract of the aerial parts of Sisymbrium irio L. led to the isolation of four unsaturated fatty acids (1–4), including a new one (4), and four indole alkaloids (5–8). The structures of the isolated compounds were characterized with the help of spectroscopic techniques such as 1D, 2D NMR, and mass spectroscopy, and by correlation with the known compounds. In terms of their notable structural diversity, a molecular docking approach with the AutoDock 4.2 program was used to analyze the interactions of the identified fatty acids with PPAR-γ and the indole alkaloids with 5-HT1A and 5-HT2A, subtypes of serotonin receptors, respectively. Compared to the antidiabetic drug rivoglitazone, compound 3 acted as a potential PPAR-γ agonist with a binding energy of −7.4 kcal mol−1. Moreover, compound 8 displayed the strongest affinity, with binding energies of −6.9 kcal/mol to 5HT1A and −8.1 kcal/mol to 5HT2A, using serotonin and the antipsychotic drug risperidone as positive controls, respectively. The results of docked conformations represent an interesting target for developing novel antidiabetic and antipsychotic drugs and warrant further evaluation of these ligands in vitro and in vivo. On the other hand, an HPTLC method was developed to quantify α-linolenic acid in the hexane fraction of the ethanol extract of S. irio. The regression equation/correlation coefficient (r2) for linolenic acid was Y = 6.49X + 2310.8/0.9971 in the linearity range of 100–1200 ng/band. The content of α-linolenic acid in S. irio aerial parts was found to be 28.67 μg/mg of dried extract. [ABSTRACT FROM AUTHOR]

The emergence of multi-drug-resistant Mycobacterium tuberculosis (Mtb) strains has rendered many of the currently available anti-TB drugs ineffective. Hence, there is a pressing need to discover new potential drug targets/candidates. In this study, attempts have been made to identify novel inhibitors of the ribonuclease VapC2 of Mtb H37Rv using various computational techniques. Ribonuclease VapC2 Mtb H37Rv's protein structure was retrieved from the PDB databank, 22 currently used anti-TB drugs were retrieved from the PubChem database, and protein–ligand interactions were analyzed by docking studies. Out of the 22 drugs, rifampicin (RIF), being a first-line drug, showed the best binding energy (−8.8 Kcal/mol) with Mtb H37Rv VapC2; hence, it was selected as a parent molecule for the design of its derivatives. Based on shape score and radial plot criteria, out of 500 derivatives designed through SPARK (Cresset®, Royston, UK) program, the 10 best RIF derivatives were selected for further studies. All the selected derivatives followed the ADME criteria concerning drug-likeness. The docking of ribonuclease VapC2 with RIF derivatives revealed the best binding energy of −8.1 Kcal/mol with derivative 1 (i.e., RIF-155841). A quantitative structure–activity relationship study revealed that derivative 1's activity assists in the inhibition of ribonuclease VapC2. The stability of the VapC2–RIF155841 complex was evaluated using molecular dynamics simulations for 50 ns and the complex was found to be stable after 10 nsec. Further, a chemical synthesis scheme was designed for the newly identified RIF derivative (RIF-155841), which verified that its chemical synthesis is possible for future in vitro/in vivo experimental validation. Overall, this study evaluated the potential of the newly designed RIF derivatives with respect to the Mtb VapC2 protein, which is predicted to be involved in some indispensable processes of the related pathogen. Future experimental studies regarding RIF-155841, including the exploration of the remaining RIF derivatives, are warranted to verify our current findings. [ABSTRACT FROM AUTHOR]

New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases. [ABSTRACT FROM AUTHOR]

Neurodegenerative disorders involve various pathophysiological pathways, and finding a solution for these issues is still an uphill task for the scientific community. In the present study, a combination of molecular docking and dynamics approaches was applied to target different pathways leading to neurodegenerative disorders such as Alzheimer's disease. Initially, abrineurin natural inducers were screened using physicochemical properties and toxicity assessment. Out of five screened compounds, a pentacyclic triterpenoid, i.e., Soyasapogenol B appeared to be the most promising after molecular docking and simulation analysis. Soyasapogenol B showed low TPSA (60.69), high absorption (82.6%), no Lipinski rule violation, and no toxicity. Docking interaction analysis revealed that Soyasapogenol B bound effectively to all of the targeted proteins (AChE, BuChE MAO-A, MAO-B, GSK3β, and NMDA), in contrast to other screened abrineurin natural inducers and inhibitors. Importantly, Soyasapogenol B bound to active site residues of the targeted proteins in a similar pattern to the native ligand inhibitor. Further, 100 ns molecular dynamics simulations analysis showed that Soyasapogenol B formed stable complexes against all of the targeted proteins. RMSD analysis showed that the Soyasapogenol B–protein complex exhibited average RMSD values of 1.94 Å, 2.11 Å, 5.07 Å, 2.56 Å, 3.83 Å and 4.07 Å. Furthermore, the RMSF analysis and secondary structure analysis also indicated the stability of the Soyasapogenol B–protein complexes. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments. As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA). The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of −7.0 to −10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤−8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of −10.1 and −9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes. The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies. [ABSTRACT FROM AUTHOR]

[Display omitted] The escalation of many coronavirus variants accompanied by the lack of an effective cure has motivated the hunt for effective antiviral medicines. In this regard, 18 Saudi Arabian medicinal plants were evaluated for SARS CoV-2 main protease (Mpro) inhibition activity. Among them, Terminalia brownii and Acacia asak alcoholic extracts exhibited significant Mpro inhibition, with inhibition rates of 95.3 % and 95.2 %, respectively, at a concentration of 100 µg/mL. Bioassay-guided phytochemical study for the most active n -butanol fraction of T. brownii led to identification of eleven compounds, including two phenolic acids (1 , and 2), seven hydrolysable tannins (3 – 10), and one flavonoid (11) as well as four flavonoids from A. asak (12 – 15). The structures of the isolated compounds were established using various spectroscopic techniques and comparison with known compounds. To investigate the chemical interactions between the identified compounds and the target Mpro protein, molecular docking was performed using AutoDock 4.2. The findings identified compounds 4 , 5 , 10 , and 14 as the most potential inhibitors of Mpro with binding energies of −9.3, −8.5, −8.1, and −7.8 kcal mol−1, respectively. In order to assess the stability of the protein–ligand complexes, molecular dynamics simulations were conducted for a duration of 100 ns, and various parameters such as RMSD, RMSF, Rg, and SASA were evaluated. All selected compounds 4 , 5 , 10 , and 14 showed considerable Mpro inhibiting activity in vitro , with compound 4 being the most powerful with an IC 50 value of 1.2 µg/mL. MM-GBSA free energy calculations also revealed compound 4 as the most powerful Mpro inhibitor. None of the compounds (4 , 5 , 10 , and 14) display any significant cytotoxic activity against A549 and HUVEC cell lines. [ABSTRACT FROM AUTHOR]

Background: Anethum graveolens seeds have therapeutic benefits, which may be a potential approach to the treatment of different cancers. Objectives: We investigated, the antiproliferative effect of ethyl acetate fraction of dill (EAFD), on MCF-7 and PC-3 cell lines and its two most active components, anethole and carvone by molecular docking analysis. Materials and Methods: In-vitro assays, like cell viability assay and measurement of reactive oxygen species, were performed besides performing Giemsa stain and other fluorescent stains; JC-1 dye, dual mixed stain ethidium bromide/acridine orange and 4,6-diamidino-2-phenylindole stain to study morphological characteristics, including molecular docking analysis. EAFD concentrations (0.2, 0.4, 0.6, 0.8, 1.0 mg/ml) were used. Results: The EAFD prominently inhibited the proliferation of MCF-7 cells and PC-3 cells by dose-dependent and time-dependent methods. Increased exposure of EAFD to MCF-7 and PC-3 cells increases the level of intracellular oxidative stress. Similarly, EAFD exposure confirms the morphological alternations such as cell shrinkage, membrane disruption, nuclear condensation, and blebbing in phase-contrast microscopy and even fluorescent microscopy stains can lead to mitochondrial membrane degradation, chromatin condensation, nuclear fragmentation. Analyses of docking results suggest that anethole and carvone bind to the hydrophobic patches of Bcl-2 and Bcl-xL through hydrophobic interactions. Conclusion: The EAFD may be antiproliferative activity and leading to pro-apoptotic cell death. Molecular docking analysis of Bcl-2 and Bcl-xL anti-apoptotic protein indicated that the antiproliferative activity and pro-apoptotic cell deaths by EAFD are possibly due to inhibition of these proteins. [ABSTRACT FROM AUTHOR]

Introduction: Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments. Aims: As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and c-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and c-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and c-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA). Results: The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≦-8 kcal/mol against BACE-1 and c-secretase. For the selected enzyme targets, BACE-1 and c-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and c-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes. Conclusion: The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and c-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies. [ABSTRACT FROM AUTHOR]

Quinoline yellow (QY) is a synthetic yellow dye widely used as a coloring agent for various foodstuffs. In the current study, we have examined the role of QY on the aggregation propensity of hen egg-white lysozyme (HEWL) under physiological conditions. The dye induced conformational changes in HEWL leading to aggregate formation were identified by circular dichroism (CD), turbidity analysis, fluorescence measurement and microscopic (TEM) imaging. Molecular docking and molecular dynamics simulation studies were also employed to strengthen binding and aggregation results. Our results indicate that 25–100 µM of QY induces aggregation in HEWL, while lower QY concentrations (5 and 10 µM) does not have any effect on the aggregation propensity of HEWL. The kinetics of HEWL aggregation demonstrate nucleation independent aggregation of HEWL without lag phase. On the other hand, far UV-CD analysis illustrated the loss of α-helical structure with the increasing concentration of QY. TEM results also support the formation of aggregate structures in HEWL when exposed to QY. Molecular docking and simulation studies revealed that the HEWL-QY complex is stable as compared to individual entities. In silico analysis also illustrated that QY-induced aggregation of HEWL proceeds through the formation of hydrogen bonds, electrostatic (Pi-Anion) and Pi-Sulfur interactions. The above-mentioned results highlight the possible detrimental effect by food additive dyes, particularly in protein misfolding. [ABSTRACT FROM AUTHOR]

Using different chromatographic methods, four new compounds were isolated from the aerial parts of Suaeda monoica (Chenopodiaceae) along with 2-hydroxy-1-naphthoic acid (SCM-3). The structures of the new compounds were established as 6′-hydroxy-10′-geranilanyl naphtha-1-oate (SMC-1), 4,4,8β,10β-Tetramethyl-9β-isobutanyl decalin-13-ol-13-O-β-D-xylopyranoside (SCM-2), 6′-(2-hydroxynaphthalen-3-yl) hexanoic acid (SCM-4) and 1′-(2-Methoxy-3-naphthyl)-4′-(2′'-methylbenzoyl)- n -butane (SMC-5) by IR, EIMS and NMR (1 & 2D) analyses. All compounds (50 μg/mL) were tested for cell proliferative potential on cultured human liver cell HepG2 cells by MTT assay. The results revealed a marked cell proliferative potential of all compounds (1.42–1.48 fold) as compared to untreated control. The results of molecular docking and binding with specific proteins such as PTEN (Phosphatase and Tensin homolog) and p53 also justify the cell proliferative potential of the isolated compounds. Glide program with Schrodinger suit 2018 was used to evaluate the binding between SMC compounds and proteins (PTEN and p53). The binding affinity of all compounds was in order of 104–105 M−1 towards both PTEN and p53. All the SMC compounds have been found to bind at the active site of PTEN, thereby may prevent the binding of phosphatidylinositiol 3,4,5-triphosphate (PI3P). In the locked position, PTEN would not be able to hydrolyze PI3P and hence the PI3P regulated signaling pathway remains active. Similarly, SMC molecules were found to interact with the amino acid residues (Ser99, Thr170, Gly199, and Asp224) which are critically involved in the formation of tetrameric p53. The blockage of p53 to attain its active conformation thus may prevent the recruitment of p53 on DNA and hence may promote cell proliferation. [ABSTRACT FROM AUTHOR]

Myrrh is an oleo-gum-resin produced in the stem of Commiphora myrrha (Burseraceae) and used for centuries for different medicinal purposes. The present work was designed to evaluate the cytotoxic and antioxidant properties of seventeen myrrh samples (S1–S17) obtained from different retail markets of Saudi Arabia and Yemen regions, along with two furanosesquiterpenoids (CM-1 and CM-2). The cytotoxicity assay was carried out on HepG2, MCF-7 and HUVEC cell lines. S2, S5, S10, S12, CM-1, CM-2 exhibited significant cytotoxicity against HepG2/MCF-7 cell lines [IC50 (μg/mL): 13.8/10, 14/10, 14.5/11.3, 18/13.2, 9.5/12.5, 10/15.8, respectively) compare to vinblastin (IC 50 (μg/mL): 2/2.5) whereas the remaining samples were found as mild active or inactive. The antioxidant properties of the samples were tested by β-carotene-bleaching and DPPH free radical scavenging methods where the samples S8 (1000 μg/mL) exhibited the highest β-carotene bleaching (76.2%) and free radical scavenging activity (79.8%). The HPTLC analysis was performed on NP-HPTLC plate using toluene, chloroform and glacial acetic acid as mobile phase in ratio of 7:2.9:0.1 (V/V/V). The validated HPTLC method furnished sharp, intense and compact peaks of CM-1 and CM-2 at Rf = 0.39 and 0.44, respectively. The highest/lowest content of CM-1 and CM-2 were found in S12/S5 and S5/S17, respectively. The molecular docking studies of CM-1 and CM-2 with human DNA topoisomerase IIα have shown that both the compounds were bound the active sites of the respective enzymes. Molecular dynamics simulation studies further confirmed that the interactions of CM-1 and CM-2 with topoisomerase were stable in nature. This study will help us in selection of appropriate myrrh sample for the greater benefits of the population in the Middle East region. [ABSTRACT FROM AUTHOR]

Cancer and the associated secondary bacterial infections are leading cause of mortality, due to the paucity of effective drugs. Here, we have synthesized silver nanoparticles (AgNPs) from organic resource and confirmed their anti-cancer and anti-microbial potentials. Microwave irradiation method was employed to synthesize AgNPs using Pandanus odorifer leaf extract. Anti-cancer potential of AgNPs was evaluated by scratch assay on the monolayer of rat basophilic leukemia (RBL) cells, indicating that the synthesized AgNPs inhibit the migration of RBL cells. The synthesized AgNPs showed MIC value of 4–16 μg/mL against both Gram +ve and Gram -ve bacterial strains, exhibiting the anti-microbial potential. Biofilm inhibition was recorded at sub-MIC values against Gram +ve and Gram -ve bacterial strains. Violacein and alginate productions were reduced by 89.6 and 75.6%, respectively at 4 and 8 μg/mL of AgNPs, suggesting anti-quorum sensing activity. Exopolysaccharide production was decreased by 61–79 and 84% for Gram -ve and Gram +ve pathogens respectively. Flagellar driven swarming mobility was also reduced significantly. Furthermore, In vivo study confirmed their tolerability in mice, indicating their clinical perspective. Collective, we claim that the synthesized AgNPs have anti-metastasis as well as anti-microbial activities. Hence, this can be further tested for therapeutic options to treat cancer and secondary bacterial infections. [ABSTRACT FROM AUTHOR]

Polo-like kinase-1 (PLK-1) plays a key role in cell cycle progression during mitosis. Overexpression/dysfunction of PLK-1 is directly associated with cancerous transformation and has been reported in different cancer types. Here, we employed high throughput virtual screening and molecular docking to screen Selleck's natural compound library against PLK-1 kinase domain. We have identified eight bioactive compounds (Apigenin, Dihydromyricetin, Diosmetin, Hesperidin, Hesperitin, Naringenin, Phlorizi, and Quercetin) as the potential inhibitors of PLK-1. Further investigation through Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations and 15 ns molecular dynamics simulation revealed that hesperidin formed the most stable complex with PLK-1 kinase domain. Altogether, our results indicate that hesperidin interacted strongly with the key residues of the PLK-1 active site (such as Leu59, Lys61, Lys82, Cys133, Asn181, Asp194, Leu59, Cys67, Ala80, Val114, Leu130, Leu132, Cys133, Leu139, Phe183, and Phe195) through hydrogen bonding and hydrophobic interactions. The Hesperidin-PLK-1 complex was stabilized by Gibb's free energy of −13.235 kcal/mol which corresponded to the binding affinity of 5.095 × 10 9  M −1 . This is the first study wherein hesperidin has been identified as a potential inhibitor of PLK-1. Further design and optimization of the hesperidin scaffold as an inhibitor of PLK-1 kinase domain is highly recommended. [ABSTRACT FROM AUTHOR]

Acetylcholinesterase (AChE) inhibition is a key element in enhancing cholinergic transmission and subsequently relieving major symptoms of several neurological and neuromuscular disorders. Here, the inhibitory potential of geraniol and its mechanism of inhibition against AChE were elucidated in vitro and validated via an in silico study. Our in vitro enzyme inhibition kinetics results show that at increasing concentrations of geraniol and substrate, Vmax did not change significantly, but Km increased, which indicates that geraniol is a competitive inhibitor against AChE with an IC50 value 98.06 ± 3.92 µM. All the parameters of the ADME study revealed that geraniol is an acceptable drug candidate. A docking study showed that the binding energy of geraniol (−5.6 kcal mol−1) was lower than that of acetylcholine (−4.1 kcal mol−1) with AChE, which exhibited around a 12.58-fold higher binding affinity of geraniol. Furthermore, molecular dynamics simulation revealed that the RMSD of AChE alone or in complex with geraniol fluctuated within acceptable limits throughout the simulation. The mean RMSF value of the complex ensures that the overall conformation of the protein remains conserved. The average values of Rg, MolSA, SASA, and PSA of the complex were 3.16 Å, 204.78, 9.13, and 51.58 Å2, respectively. We found that the total SSE of AChE in the complex was 38.84% (α-helix: 26.57% and β-sheets: 12.27%) and remained consistent throughout the simulation. These findings suggest that geraniol remained inside the binding cavity of AChE in a stable conformation. Further in vivo investigation is required to fully characterize the pharmacokinetic properties, optimization of dose administration, and efficacy of this plant-based natural compound. [ABSTRACT FROM AUTHOR]

Psychotria malayana Jack leaf, known in Indonesia as "daun salung", is traditionally used for the treatment of diabetes and other diseases. Despite its potential, the phytochemical study related to its anti-diabetic activity is still lacking. Thus, this study aimed to identify putative inhibitors of α-glucosidase, a prominent enzyme contributing to diabetes type 2 in P. malayana leaf extract using gas chromatography-mass spectrometry (GC-MS)- and nuclear magnetic resonance (NMR)-based metabolomics, and to investigate the molecular interaction between those inhibitors and the enzyme through in silico approach. Twenty samples were extracted with different solvent ratios of methanol–water (0, 25, 50, 75, and 100% v/v). All extracts were tested on the alpha-glucosidase inhibition (AGI) assay and analyzed using GC-MS and NMR. Multivariate data analysis through a partial least square (PLS) and orthogonal partial square (OPLS) models were developed in order to correlate the metabolite profile and the bioactivity leading to the annotation of the putative bioactive compounds in the plant extracts. A total of ten putative bioactive compounds were identified and some of them reported in this plant for the first time, namely 1,3,5-benzenetriol (1); palmitic acid (2); cholesta-7,9(11)-diene-3-ol (3); 1-monopalmitin (4); β-tocopherol (5); α-tocopherol (6); 24-epicampesterol (7); stigmast-5-ene (8); 4-hydroxyphenylpyruvic acid (10); and glutamine (11). For the evaluation of the potential binding modes between the inhibitors and protein, the in silico study via molecular docking was performed where the crystal structure of Saccharomyces cerevisiae isomaltase (PDB code: 3A4A) was used. Ten amino acid residues, namely ASP352, HIE351, GLN182, ARG442, ASH215, SER311, ARG213, GLH277, GLN279, and PRO312 established hydrogen bond in the docked complex, as well as hydrophobic interaction of other amino acid residues with the putative compounds. The α-glucosidase inhibitors showed moderate to high binding affinities (−5.5 to −9.4 kcal/mol) towards the active site of the enzymatic protein, where compounds 3, 5, and 8 showed higher binding affinity compared to both quercetin and control ligand. [ABSTRACT FROM AUTHOR]

Propolis, a resin produced by honeybees, has long been used as a dietary supplement and folk remedy, and more recent preclinical investigations have demonstrated a large spectrum of potential therapeutic bioactivities, including antioxidant, antibacterial, anti-inflammatory, neuroprotective, immunomodulatory, anticancer, and antiviral properties. As an antiviral agent, propolis and various constituents have shown promising preclinical efficacy against adenoviruses, influenza viruses, respiratory tract viruses, herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Over 300 chemical components have been identified in propolis, including terpenes, flavonoids, and phenolic acids, with the specific constituent profile varying widely according to geographic origin and regional flora. Propolis and its constituents have demonstrated potential efficacy against SARS-CoV-2 by modulating multiple pathogenic and antiviral pathways. Molecular docking studies have demonstrated high binding affinities of propolis derivatives to multiple SARS-CoV-2 proteins, including 3C-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), the receptor-binding domain (RBD) of the spike protein (S-protein), and helicase (NSP13), as well as to the viral target angiotensin-converting enzyme 2 (ACE2). Among these compounds, retusapurpurin A has shown high affinity to 3CLpro (ΔG = −9.4 kcal/mol), RdRp (−7.5), RBD (−7.2), NSP13 (−9.4), and ACE2 (−10.4) and potent inhibition of viral entry by forming hydrogen bonds with amino acid residues within viral and human target proteins. In addition, propolis-derived baccharin demonstrated even higher binding affinity towards PLpro (−8.2 kcal/mol). Measures of drug-likeness parameters, including metabolism, distribution, absorption, excretion, and toxicity (ADMET) characteristics, also support the potential of propolis as an effective agent to combat COVID-19. [ABSTRACT FROM AUTHOR]

Protein aggregation and misfolding are some of the most challenging obstacles, customarily studied for their association with amyloid pathologies. The mechanism of amyloid fibrillation development is a dynamic phenomenon involving various factors such as the intrinsic properties of protein and the physical and chemical environmental conditions. The purpose of this study was to see the thermal aggregation profile of alpha-lactalbumin (α-LA) and to delineate the effect of trehalose on its aggregation profile. α-LA was subjected to thermal aggregation at high concentrations. UV-Vis spectroscopy, a turbidity assay, intrinsic fluorescence, Rayleigh scattering and a thioflavin T (ThT) assay explained the steady outcomes that 1 M trehalose repressed α-LA aggregation in the most effective way followed by 0.75 M and 0.5 M and to a significantly lesser degree by 0.25 M. Multi spectroscopic obser Sania Bashir ations were further entrenched by microscopy. Transmission electron microscopy confirmed that in the presence of its higher concentration, trehalose hinders fibril development in α-LA. In vitro studies were further validated by in silico studies. Molecular docking analysis indicated that trehalose occupied the binding pocket cavity of α-LA and offered several significant interactions, including H-bonds with important residues. This study provides a platform for trehalose in the therapeutic management of protein aggregation-related diseases. [ABSTRACT FROM AUTHOR]

Sphingosine kinase 1 (SphK1) is one of the well-studied drug targets for cancer and inflammatory diseases. Recently discovered small-molecule inhibitors of SphK1 have been recommended in cancer therapeutics; however, selectivity and potency of first-generation inhibitors are great challenge. In search of effective SphK1 inhibitors, a set of small molecules have been designed and synthesized bearing urea, sulfonylurea, sulfonamide, and sulfonyltriurea groups. The binding affinity of these inhibitors was measured by fluorescence-binding assay and isothermal titration calorimetry. Compounds 1, 5, 6, and 7 showed an admirable binding affinity to the SphK1 in the sub-micromolar range and significantly inhibited SphK1 activity with admirable IC50 values. Molecular docking studies revealed that these compounds fit well into the sphingosine binding pocket of SphK1 and formed significant number of hydrogen bonds and van der Waals interactions. These molecules may be exploited as potent and selective inhibitors of SphK1 that could be implicated in cancer therapeutics after the required in vivo validation. [ABSTRACT FROM AUTHOR]

Microtubule affinity-regulating kinase (MARK4) plays a key role in Alzheimer's disease (AD) development as its overexpression is directly linked to increased tau phosphorylation. MARK4 is a potential drug target of AD and is thus its structural features are employed in the development of new therapeutic molecules. Donepezil (DP) and rivastigmine tartrate (RT) are acetylcholinesterase (AChE) inhibitors and are used to treat symptomatic patients of mild to moderate AD. In keeping with the therapeutic implications of DP and RT in AD, we performed binding studies of these drugs with the MARK4. Both DP and RT bound to MARK4 with a binding constant (K) of 107 M−1. The temperature dependency of binding parameters revealed MARK−DP complex to be guided by static mode while MARK−RT complex to be guided by both static and dynamic quenching. Both drugs inhibited MARK4 with IC50 values of 5.3 μM (DP) and 6.74 μM (RT). The evaluation of associated enthalpy change (ΔH) and entropy change (ΔS) implied the complex formation to be driven by hydrogen bonding making it seemingly strong and specific. Isothermal titration calorimetry further advocated a spontaneous binding. In vitro observations were further complemented by the calculation of binding free energy by molecular docking and interactions with the functionally-important residues of the active site pocket of MARK4. This study signifies the implications of AChE inhibitors, RT, and DP in Alzheimer's therapy targeting MARK4. [ABSTRACT FROM AUTHOR]

Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase that works under acute transcriptional control by several stimuli, including serum and glucocorticoids. It plays a significant role in the cancer progression and metastasis, as it regulates inflammation, apoptosis, hormone release, neuro-excitability, and cell proliferation. SGK1 has recently been considered as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In the present study, we have performed structure-based virtual high-throughput screening of natural compounds from the ZINC database to find potential inhibitors of SGK1. Initially, hits were selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and other drug-like properties. Afterwards, PAINS filter, binding affinities estimation, and interaction analysis were performed to find safe and effective hits. We found four compounds bearing appreciable binding affinity and specificity towards the binding pocket of SGK1. The docking results were complemented by all-atom molecular dynamics simulation for 100 ns, followed by MM/PBSA, and principal component analysis to investigate the conformational changes, stability, and interaction mechanism of SGK1 in-complex with the selected compound ZINC00319000. Molecular dynamics simulation results suggested that the binding of ZINC00319000 stabilizes the SGK1 structure, and it leads to fewer conformational changes. In conclusion, the identified compound ZINC00319000 might be further exploited as a scaffold to develop promising inhibitors of SGK1 for the therapeutic management of associated diseases, including cancer. [ABSTRACT FROM AUTHOR]

Drug-binding and interactions with plasma proteins strongly affect their efficiency of delivery, hence considered as a key factor in determining the overall pharmacological action. Alpha-1-acid glycoprotein (AGP), a second most abundant plasma protein in blood circulation, has unique drug binding ability and involved in the transportation of various compounds. Here, we have investigated the mechanism of interaction between AGP and potential Cu/Zn metallo-drugs of benzimidazole derived organic motifs (CuL 2 and ZnL 2 , where L is Schiff base ligand) by applying integrated spectroscopic, biophysical techniques and computational molecular docking analyses. We found that both the metallo-drugs (CuL 2 and ZnL 2) were bound at the central cavity of AGP interacting with the residues of lobe I, lobe II as well as lobe III. The binding of metallo-drugs to AGP occurs in 1:1 M ratios. Hydrogen bonding, electrostatic and hydrophobic interactions played a significant role in stabilizing the AGP-metallo-drug complexes. Binding affinities of both the metallo-drugs towards AGP at 298 K were of the order of 104–105 M−1, corresponding to Gibbs free energy of stabilization of approximately −5.50 to −6.62 kcal mol−1. Furthermore, the spectroscopic investigation by circular dichroism and synchronous fluorescence analyses suggest conformational changes in AGP upon the binding of metallic compounds. Unlabelled Image • Interaction between benzimidazole moiety derived metallo-drugs and AGP was studied. • Metallo-drugs bind at the central cavity of AGP with high affinity. • Metallo-drug-AGP complex was primarily stabilized by hydrophobic interactions. • Hydrogen bonds and electrostatic also play crucial roles in the interaction. • Metallo-drugs quench AGP fluorescence by static quenching mechanism. [ABSTRACT FROM AUTHOR]

Thiazolidinedione derivatives (TZDs) have attracted attention because of their pharmacological effects. For example, certain TZDs have been reported to ameliorate type II diabetes by binding and activating PPARs (peroxisome proliferator-activated receptors). Nonetheless, no information is available on the interaction between the heterocyclic 2, 4-thiazolidinedione (2,4-TZD) moiety and serum albumin, which could affect the pharmacokinetics and pharmacodynamics of TZDs. In this study, we investigated the binding of 2,4-TZD to human serum albumin (HSA). Intrinsic fluorescence spectroscopy revealed a 1:1 binding stoichiometry between 2,4-TZD and HSA with a binding constant (Kb) of 1.69 ± 0.15 × 103 M−1 at 298 K. Isothermal titration calorimetry studies showed that 2,4-TZD/HSA binding was an exothermic and spontaneous reaction. Molecular docking analysis revealed that 2,4-TZD binds to HSA subdomain IB and that the complex formed is stabilized by van der Waal's interactions and hydrogen bonds. Molecular dynamics simulation confirmed the stability of the HSA-TZD complex. Further, circular dichroism and 3D fluorescence studies showed that the global conformation of HSA was slightly altered by 2,4-TZD binding, enhancing its stability. The results obtained herein further help in understanding the pharmacokinetic properties of thiazolidinedione. [ABSTRACT FROM AUTHOR]

A series of symmetrical salicylaldehyde-bishydrazine azo molecules, 5a–5h, have been synthesized, characterized by 1H-NMR and 13C-NMR, and evaluated for their in vitro α-glucosidase and α-amylase inhibitory activities. All the synthesized compounds efficiently inhibited both enzymes. Compound 5g was the most potent derivative in the series, and powerfully inhibited both α-glucosidase and α-amylase. The IC50 of 5g against α-glucosidase was 0.35917 ± 0.0189 µM (standard acarbose IC50 = 6.109 ± 0.329 µM), and the IC50 value of 5g against α-amylase was 0.4379 ± 0.0423 µM (standard acarbose IC50 = 33.178 ± 2.392 µM). The Lineweaver-Burk plot indicated that compound 5g is a competitive inhibitor of α-glucosidase. The binding interactions of the most active analogues were confirmed through molecular docking studies. Docking studies showed that 5g interacts with the residues Trp690, Asp548, Arg425, and Glu426, which form hydrogen bonds to 5g with distances of 2.05, 2.20, 2.10 and 2.18 Å, respectively. All compounds showed high mutagenic and tumorigenic behaviors, and only 5e showed irritant properties. In addition, all the derivatives showed good antioxidant activities. The pharmacokinetic evaluation also revealed promising results [ABSTRACT FROM AUTHOR]

A small library of new drug-1,3,4-thiazidazole hybrid compounds (3a–3i) was synthesized, characterized, and assessed for their acetyl cholinesterase enzyme (AChE) inhibitory and free radical scavenging activities. The newly synthesized derivatives showed promising activities against AChE, especially compound 3b (IC50 18.1 ± 0.9 nM), which was the most promising molecule in the series, and was substantially more active than the reference drug (neostigmine methyl sulfate; IC50 2186.5 ± 98.0 nM). Kinetic studies were performed to elucidate the mode of inhibition of the enzyme, and the compounds showed mixed-type mechanisms for inhibiting AChE. The Ki of 3b (0.0031 µM) indicates that it can be very effective, even at low concentrations. Compounds 3a–3i all complied with Lipinski's Rule of Five, and showed high drug-likeness scores. The pharmacokinetic parameters revealed notable lead-like properties with insignificant liver and skin-penetrating effects. The structure–activity relationship (SAR) analysis indicated π–π interactions with key amino acid residues related to Tyr124, Trp286, and Tyr341. [ABSTRACT FROM AUTHOR]

The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates. [ABSTRACT FROM AUTHOR]

Herein, we have synthesized and characterized a new benzimidazole-derived “BnI” ligand and its copper(II) complex, [Cu(BnI)2], 1, and zinc(II) complex, [Zn(BnI)2], 2, using elemental analysis and various spectroscopic techniques. Interaction of complexes 1 and 2 with the biomolecules viz. HSA (human serum albumin) and DNA were studied using absorption titration, fluorescence techniques, and in silico molecular docking studies. The results exhibited the significant binding propensity of both complexes 1 and 2, but complex 1 showed more avid binding to HSA and DNA. Also, the nuclease activity of 1 and 2 was analyzed for pBR322 DNA, and the results obtained confirmed the potential of the complexes to cleave DNA. Moreover, the mechanistic pathway was studied in the presence of various radical scavengers, which revealed that ROS (reactive oxygen species) are responsible for the nuclease activity in complex 1, whereas in complex 2, the possibility of hydrolytic cleavage also exists. Furthermore, the cytotoxicity of the ligand and complexes 1 and 2 were studied on a panel of five different human cancer cells, namely: HepG2, SK-MEL-1, HT018, HeLa, and MDA-MB 231, and compared with the standard drug, cisplatin. The results are quite promising against MDA-MB 231 (breast cancer cell line of 1), with an IC50 value that is nearly the same as the standard drug. Apoptosis was induced by complex 1 on MDA-MB 231 cells predominantly as studied by flow cytometry (FACS). The adhesion and migration of cancer cells were also examined upon treatment of complexes 1 and 2. Furthermore, the in vivo chronic toxicity profile of complexes 1 and 2 was also studied on all of the major organs of the mice, and found them to be less toxic. Thus, the results warrant further investigations of complex 1. [ABSTRACT FROM AUTHOR]

• A novel series of 1,2,3-triazole based 1,3,4-thiadiazole derivatives were designed, synthesized and evaluated for their cytotoxic activity. • Anti-proliferative activity was assessed against HT-1080, A-549, MCF-7 and MDA-MB-231 cells lines. • Hybrid compound 14a showed important inhibitory activity against MCF-7 and MDA-MB-231 cells lines. • Binding modes of all compounds were identified via molecular docking. • Compounds had higher affinity for Bcl-XL as compared to other compounds. One sets of 1,3,4-thiadiazole analogs 14a-c and 15a-c were synthesized by the incorporation of two heterocyclic nuclei (1,2,3-triazole & 1,3,4-thiadiazoles) in objective of developing multifunctional molecules for anticancer disease. (R)-Carvone was used as precursors for the synthesis of new heterocycles. The 1,2,3-triazole-1,3,4-thiadiazoles 14a-c and 15a-c were synthesized in good yields from the precursors using simple procedures. The chemical structures of all the newly synthesized hybrids were established using (1H and 13C) NMR and HRMS analysis. The in vitro assessment of the activity of the resultant 1,2,3-triazole-1,3,4-thiadiazoles against human cancer cells, namely fibrosarcoma (HT-1080), lung carcinoma (A-549) and breast carcinoma (MCF-7 and MDA-MB-231) was performed using viability testing (MTT). Compound 14a was the most active heterocycle, and its cytotoxic activity was three times less actives comparable to that obtained for Doxorubicin (6 µM) as a reference. The 1,3,4-thiadiazoles 15a-c showed moderate cytotoxic activities with IC 50 values ranging from 25.56 ± 1.13 to 61.81 ± 2.21 μM. Molecular docking studies were conducted against two antiapoptotic proteins namely Bcl-2, and Bcl-XL to elucidate the potential mechanisms of action. The results indicate that compounds interact favorably (binding energy = −7.6 to −9.8 kcal/mol) with the target proteins through hydrophobic, electrostatic interactions, and hydrogen bonding. The negative binding energy indicate the spontaneous nature of the interaction. Further, molecular dynamics simulation parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and solvent accessible surface area provided insights into the stability and dynamics of the protein-ligand complexes. [Display omitted] [ABSTRACT FROM AUTHOR]

• A novel series of thiazolidinone based 1,2,3-triazole derivatives were designed, synthesized, and evaluated for their cytotoxic activity. • Anti-proliferative activity was assessed against HT-1080, A-549, MCF-7 and MDA-MB-231 cells lines. • Hybrid compounds 14b and 14d showed important inhibitory activity against HT-1080 and A-549 cancer cell lines with an IC 50 value of 18 μM. • Binding modes of all compounds were identified via molecular docking. • Compounds 14b and 14d had higher affinity for Bcl-2 as compared to other compounds. A novel series of thiazolidinone based 1,2,3-triazole derivatives were designed, synthesized, and evaluated for their cytotoxic activity against four human cancer cell lines, including fibrosarcoma (HT-1080), lung carcinoma (A-549), and breast carcinoma (MCF-7 and MDA-MB-231). NMR (1H and 13C) and HRMS established the newly synthesized compounds' structural identification and molecular weight. Most synthesized compounds displayed moderate cytotoxic activity, with IC 50 values from 20 to 40 μM. Furthermore, hybrid compounds 14b and 14d showed important inhibitory activity against HT-1080 and A-549 cancer cell lines with an IC 50 value of 18 μM. Molecular docking analyses also confirmed a higher binding affinity of compounds 14a-e , as compared to Doxorubicin (control), towards Bcl-2 protein. In particular, compounds 14b and 14d had higher affinity for Bcl-2 as compared to other compounds. [Display omitted] [ABSTRACT FROM AUTHOR]

Cyclin-dependent kinase 6 (CDK6) participates in numerous signalling pathways and regulates various physiological processes. Due to its unique structural features and promising therapeutic potential, CDK6 has emerged as a drug target for designing and developing small-molecule inhibitors for anti-cancer therapeutics and other CDK6-associated diseases. The current study evaluates binding affinity and the inhibitory potential of rutin for CDK6 to develop a proof of concept for rutin as a potent CDK6 inhibitor. Molecular docking and 200 ns all-atom simulations reveal that rutin binds to the active site pocket of CDK6, forming interactions with key residues of the binding pocket. In addition, the CDK6-rutin complex remains stable throughout the simulation trajectory. A high binding constant (K a = 7.6 × 105 M−1) indicates that rutin has a strong affinity for CDK6. Isothermal titration calorimetry has further validated a strong binding of rutin with CDK6 and its spontaneous nature. The kinase activity of CDK6 is significantly inhibited by rutin with an IC 50 value of 3.10 μM. Our findings highlight the significant role of rutin in developing potential therapeutic molecules to manage cancer and CDK6-associated diseases via therapeutic targeting of CDK6. • Molecular docking suggested significant binding affinity of rutin with CDK6 protein. • MD simulation and computed free energy that suggested a stable complex formation between CDK6-rutin. • Rutin showed an appreciable binding affinity with CDK6 through fluorescence spectroscopy. • Thermodynamics parameters obtained via ITC suggested a stable CDK6-rutin complex. • Rutin showed an excellent IC 50 value for CDK6. [ABSTRACT FROM AUTHOR]

The aldose reductase (AR) enzyme is considered a potential target for the management of diabetic complications. In this study, we describe the binding and enzyme kinetics of AR by naringenin, a bioflavonoid present in many dietary sources. Naringenin showed an inhibitory effect on the activity of AR with an IC 50 value of 2.6 μM in an uncompetitive manner. Binding studies confirmed that the naringenin-AR complex has high spontaneous affinity (K a = 1.94–7.88 × 104) with negative ΔG° value (−5.78 kcal mol−1). The interaction was enthalpy driven and the microenvironment of aromatic residues of AR was also altered. Various stages of protein oxidation and glycation were also measured. Naringenin inhibited fructosamine content by approximately 31.6% at 10 μM, and at the same concentration, >93% inhibition of fluorescent advanced glycation end-products (AGEs) was achieved. There was a significant recovery in free thiol groups and carbonyl content of bovine serum albumin (BSA). Furthermore, molecular docking of naringenin with AR revealed that naringenin formed two hydrogen bonds (Asn160 and Ile260), and three Pi-Pi interactions (two with Trp20 and one with His110). This study provides molecular insight of naringenin-AR interaction and mechanism of antiglycation which may be useful in the development of inhibitors for AGEs formation. [ABSTRACT FROM AUTHOR]

The present study was aimed at investigating the binding between an important drug of Alzheimer's therapy, Rivastigmine tartrate (RT), with Bovine serum albumin (BSA). BSA is a model protein that is increasingly being used for studies related to drug-protein interaction owing to its structural similarity with human serum albumin (HSA) which is extremely abundant in the circulatory system comprising around 60% of the total plasma protein. Fluorescence spectroscopy implied that complex formation is taking place between BSA and RT; binding constant calculated was of the order of 104 M−1 implicative of the strength of this interaction. Fluorescence spectroscopy was carried out at three different temperatures in a bid to find out the operative mode of quenching; static quenching was taking place for RT-BSA interaction with a binding constant of 2.5 × 104 M−1 at 298 K. Further, changes in Far UV CD spectra clearly implied that RT induces structural transition in BSA suggestive of RT-BSA complex formation. The negative value of ∆ G 0 as obtained from fluorescence spectroscopy and isothermal titration calorimetry (ITC) suggests the reaction to be spontaneous and thermodynamically favorable. Additionally, molecular docking was employed to investigate different forces and critical residues involved in RT-BSA interaction. Furthermore, all-atom molecular dynamics simulation for 50 ns was performed on the BSA-RT complex to investigate its conformational behavior, stability and dynamics. [ABSTRACT FROM AUTHOR]

The interactions between cetyltrimethylammonium bromide (CTAB) and hen egg white lysozymes (HEWL) was carried out to investigate protein-surfactant interaction mechanisms while both exist in the overall same charged state. The interactions between CTAB and the HEWL were examined with circular dichroism (CD), dynamic light scattering (DLS), fluorescence spectroscopy, and computational docking at a pH 9.0 at room temperature. The far-UV CD and fluorescence results revealed that CTAB at concentrations from 0.15 to 10.0 mM influenced the secondary as well as the tertiary structure of HEWL. The secondary structure of the HEWL was retained, while the tertiary structure of the HEWL was disrupted in the CTAB-treated samples at pH 9.0. The hydrodynamic radii of the HEWL were also expanded in the presence of CTAB. Molecular docking studies showed that CTAB formed one electrostatic and four hydrophobic interactions, as well as one carbon hydrogen bond with HEWL. The data obtained from spectroscopic and computational studies demonstrated that the positively charged head and 18‑carbon alkyl chain of the CTAB interacted through weak electrostatic and strong hydrophobic interactions. Unlabelled Image • CTAB stabilized secondary structure of HEWL. • HEWL tertiary structure disrupted due to CTAB interaction. • Weak electrostatic and high hydrophobic interaction involved in HEWL unfolding. [ABSTRACT FROM AUTHOR]

Abstract Protein aggregation leads to vast conformational changes and plays a key role in the pathogenesis of various neurodegenerative diseases including Alzheimer's and Parkinson's. In the current piece of work, we have explored the interaction of quinoline yellow (QY) with myoglobin (Mb) at two different pH (3.5 and 7.4). Various spectroscopic techniques such as turbidity, Rayleigh light scattering (RLS), UV–Vis absorbance, fluorescence resonance energy transfer (FRET), far UV-CD along with transmission electron microscopy (TEM) and molecular docking have been utilized to characterize dye-induced aggregation in Mb. Binding results showed that interaction between QY and myoglobin is spontaneous and static in nature with high K SV value of 2.14 × 104 M−1. On the other hand, thermodynamics studies (∆H & ∆S) revealed that complex formation was driven by hydrogen and Van der Walls forces. Molecular docking analysis showed strong binding affinity (K d = 4.95 × 104 M−1) between QY and Mb at Pro100, Ile101, Lys102, Glu105, Glu136, Arg139, Lys140, and Ala143 residues. The intrinsic fluorescence and circular dichroism studies indicated that QY induced conformational changes in Mb at pH 3.5. Turbidity and RLS studies showed aggregation of Mb in the presence of QY (0.2–5 mM). Moreover, kinetics data revealed nucleation independent aggregation of myoglobin in the presence of QY. TEM analysis further established amorphous nature of Mb aggregate induced by QY. At pH (7.4), QY was unable to induce aggregation in myoglobin; it might be due to repulsive nature of negatively charged dye and myoglobin or partially altered states of protein could be pre-requisite for binding and aggregation. Graphical abstract Unlabelled Image Highlights • QY binds spontaneously to Mb with high affinity (K SV = 2.14 × 104 M−1). • Hydrogen and van der Walls forces are involved in QY-Mb interaction. • Pro, Ile, Lys, Glu, Arg, Lys and Ala residues interact with QY. • The disturbance in the Mb structure by QY leads to aggregate formation. [ABSTRACT FROM AUTHOR]

Abstract The interaction of natural polyphenolic compounds (rutin) with β-lactoglobulin (BLG) was carried out by using several optical spectroscopic (UV–visible spectroscopy, fluorescence quenching measurements, synchronous fluorescence, 3D fluorescence spectroscopy and far-UV CD measurements), molecular docking and molecular dynamics (MD) simulation methods. The fluorescence quenching results confirmed that fluorescence intensity of BLG is quenched by rutin and the quenching constant is increased with increase in temperature. The quenching mechanism between rutin-BLG was found to be dynamic in nature. The thermodynamic parameter particularly ΔH0 and ΔS0 obtained through fluorescence measurements clearly indicated that hydrophobic forces are majorly involved in the rutin-BLG interaction. The UV-absorption, synchronous and three-dimensional fluorescence results displayed that the micro-environment of BLG is changed due to rutin interaction. The secondary structure of BLG was found higher in the presence of rutin. Molecular docking results suggested that rutin binds strongly in the internal cavity of BLG at site 1 and superficially at site 2 through both hydrogen bonding and hydrophobic interactions. The binding affinity was found to be higher 5.47 × 106 M−1 for site 1 compared to site 2 (2.86 × 105 M−1). The MD simulation suggested that rutin formed a stable complex with BLG at site 1.This study will explain interacting properties of rutin with carrier BLG proteins and open a new vista for the food industry. Highlights • Dynamic quenching was found in rutin-BLG interaction. • Both hydrogen and hydrophobic interaction was found in rutin-BLG interaction. • Rutin binds inside internal cavity of BLG. • Secondary structure of BLG increases due to rutin interaction. [ABSTRACT FROM AUTHOR]

[Display omitted] Jatropha pelargoniifolia (JP) is a medicinal plant that is widely used in traditional medicine owing to its broad range of therapeutic activities. Despite its promising pharmacological activities, the use of plant extracts has several limitations which can be overcome using pharmaceutical nanotechnology. The aim of this study was to systematically investigate the effect of nanoencapsulation on the antimicrobial and anticancer activities of JP extract. JP-loaded chitosan nanoparticles (JP-CSNPs) were prepared using the ionic gelation method and characterized in terms of size, polydispersity index, zeta potential, encapsulation efficiency, and release profile. Transmission electron microscopy was used to observe the morphology of the nanoparticles. The mean particle size, zeta potential, and encapsulation efficiency of optimized JP-CSNPs were 185.5 nm, 44 mV, and 78.5%, respectively. The release profile of the JP-CSNPs was mainly dependent on the pH of the surrounding medium, and the JP extract was released in a controlled manner over time. The total phenolic and flavonoid contents in JP extract were 191.8 mg GAE/g extract and 51.4 mg of QE/g extract, respectively. The results of a 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay showed that JP-CSNPs retained the antioxidant activity of unencapsulated JP extract. JP-CSNPs also exhibited higher antimicrobial activity against gram-positive bacteria than against gram-negative bacteria, and their minimum inhibitory concentration was 1.6-fold lower than that of blank nanoparticles, indicating the synergy between JP extract and nanoparticles. In vitro cytotoxicity studies using A549 human lung adenocarcinoma cells revealed that JP-CSNPs had a 2-fold lower half-maximal inhibitory concentration than free extract. Molecular docking analyses revealed that the active phytoconstituent of JP extract, linarin, binds strongly to the active sites of bacterial DNA gyrase B and human DNA topoisomerase IIα and thus, may inhibit their activities. Computational analysis results supported the in vitro finding that JP-CSNPs act as an anticancer and antimicrobial agent. Taken together, the results of this study highlighted the advantages of using CSNPs as a nanocarrier for herbal extracts, thus providing a potential strategy for improving plant-based therapeutics. [ABSTRACT FROM AUTHOR]

Food dye quinoline yellow (Qy) induced conformational change in bovine alpha-lactalbumin (αLA), and its interaction mechanism was investigated at physiological pH. We used several biophysical techniques (circular dichroism (CD), intrinsic fluorescence, UV–Vis absorption), and computational techniques (molecular docking and simulation). Our intrinsic fluorescence results suggested that Qy dye quenched the intrinsic fluorescence of αLA via a dynamic quenching mechanism because the quenching constant increased with elevation in temperature. We also found that αLA had one equivalent binding site for Qy dye, and that the affinity of Qy dye towards αLA was of the order of 105 mol/L. Thermodynamic analysis of αLA-Qy dye interactions revealed the spontaneous nature of such interactions. The positive values of enthalpy and entropy change explained that the interactions between Qy dye and αLA were driven mainly by hydrophobic interactions. The far-UV CD and UV-absorption results revealed that the αLA conformation changes because of Qy dye interactions. Molecular docking results indicated that Qy dye binds strongly at a major binding site of αLA and that αLA-Qy dye complex is stabilized by hydrogen bonding, salt bridge, Pi-cation, and van der Waals interaction. The molecular dynamics simulation study of αLA-Qy complexes revealed the formation of a stable interaction between them. This study can provide new insights into a comprehensive understanding of food dye-induced conformational changes in biological processes. • Qy dye interacted with αLG protein through dynamic quenching. • Qy dye interacted with αLG via hydrophobic interaction. • Qy dye binds at major binding site of αLG protein. • αLG conformation was changed due to Qy dye interaction. [ABSTRACT FROM AUTHOR]

Amyloid fibril formation causes multiple neurodegenerative diseases and its possible therapy is still not available. The aim of this study was to determine the solubilizing and refolding potential of α‑cyclodextrin (α-CD) on SDS-induced amyloid fibril formation of lysozyme at pH 7.4 using turbidity, intrinsic fluorescence, dynamic light scattering (DLS), ThT binding assay, far-UV circular dichroism, and molecular docking. Spectroscopic data showed that lysozyme forms amyloid-like aggregates in the presence of 0.3 mM SDS at pH 7.4. SDS-induced lysozyme fibrils were solubilized by α-CD in a dose-dependent manner. At concentrations lower than 1.0 mM, α-CD was unable to solubilize SDS-induced lysozyme fibrils, while higher concentrations of α-CD produced complete solubilization. Far-UV CD and intrinsic fluorescence data suggest that the secondary and tertiary structures of lysozyme were restored at higher α-CD concentrations. The hydrodynamic radius was found to increase in the presence of SDS and radius is restored in the presence α-CD. Molecular docking data suggest that α-CD binds the same site on lysozyme as that occupied by SDS, albeit with higher affinity. Moreover, molecular docking between SDS and α-CD shows a direct contact via hydrogen bonding between O-atom of SDS and –OH group of α-CD. We hypothesize that the higher affinity of α-CD towards the binding site on lysozyme along with its direct interaction with SDS allows it to act as a chemical chaperone displacing SDS. The mechanisms underlying this action of α-CD may provide a foundation for the identification of drugs for the suppression of fibrillogenesis. • α-CD solubilized SDS-induced amyloid fibril. • Amyloid fibril can be reversible. • α-CD have more affinity towards lysozyme compare to the SDS. [ABSTRACT FROM AUTHOR]