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Multidrug-resistant (MDR) Salmonella remains a significant global health threat. This study aimed to explore the potential of essential oil components as novel inhibitors of the Salmonella MDR efflux pumps AcrAB and AcrD. Salmonella isolates were characterized for serotype, antibiotic resistance, and efflux pump activity. Essential oil components were screened for inhibitory effects using phenotypic and genotypic methods. In silico docking and molecular dynamics simulations were conducted to investigate binding interactions and stability. Salmonella Typhimurium was the predominant serotype with high MDR rates. Efflux pump activity was prevalent. Cumin and cinnamon oils demonstrated promising inhibitory effects on these pumps. Molecular docking simulations revealed strong binding affinities of analyzed compounds to the AcrAB and AcrD binding pocket. The 2-methyl-1-(p-tolyl)propan-2-ol exhibited higher stability within the AcrAB binding pocket compared to (1S,3R,5R)-1-isopropyl-4-methylenebicyclo[3.1.0]hexan-3-ol within the AcrD binding pocket. Treatment with these oils significantly downregulated efflux pump genes (robA, acrB, mdtB, acrF, acrD, soxS, mdsB, marA). The novel approach of combining in silico and molecular dynamics simulations with precise gene expression analysis provides a valuable framework for future studies aimed at combating MDR Salmonella efflux pumps. [ABSTRACT FROM AUTHOR]

Synthesis, crystallization, and in silico docking studies and third-order nonlinear optical (NLO) properties of (E)-1-(thiophen-2-yl)-3-(p-tolyl)prop-2-en-1-one (TPT) are outlined in the article. The molecular structure of TPT was established by a single-crystal X-ray diffraction study. The intermolecular interactions in the solid state were analyzed through Hirshfeld surface analysis (HSA). The third-order nonlinear optical properties were explored using open- and closed-aperture Z-scan techniques. The nonlinear co-efficient η2, third-order nonlinear susceptibility χ, and nonlinear absorption co-efficient β for the crystals are found to be 3.76E−10 cm2/W, 4.60E−08 esu, and 2.92E−06 cm/W, respectively. Density functional theory (DFT) calculations were used to optimize the molecular structure and band gap. Frontier orbital calculations showed a band gap of 4.18 eV for TPT and its value is in excellent agreement with the experimental value of 4.12 eV which is calculated by Tauc's plot. To study the substance's effectiveness as an anti-COVID target, in silico docking studies were performed with suitable receptors, and TPT is found to be a promising bioactive drug. [ABSTRACT FROM AUTHOR]

Widespread usage of antifungals has led to the development of antifungal resistance, causing a change in the epidemiology of the responsible agents from albicans to non-Candida albicans species. Pharmaceutical repurposing is an alternate strategy that has provided a cost-effective method to address the increasing resistance to antifungal medications. The objective of this work was to examine the antifungal properties of Alexidine dihydrochloride (AXD) and Hexachlorophene (HCP) against a non-Albicans Candida model, C. glabrata. The lowest inhibitory doses of AXD and HCP against C. glabrata were determined by in vitro methods to be 0.69-1.03 µM and 14.75-19.66 µM, respectively. The minimum doses of AXD and HCP that caused fungicidal effects were defined as 1.375 µM and 61.44 µM, respectively. Three proteins involved in crucial physiological pathways, namely cell wall production (Kre1p, Kre2p, Ecm33p), membrane calcium channel (Mid1p, Ecm7p), and ergosterol biosynthesis (Erg5p), were chosen as potential targets for the medications due to their functions in survival and disease development. SWISS MODEL was used to create the 3D structures of predicted targets of C. glabrata. The quality of these structures was assessed using Ramachandran plot statistics. AXD and HCP were analyzed by docking software AutoDock Vina against these targets. The findings of computational investigations have shown that both medicines exhibit interaction affinities with all the selected protein types. The binding energy profiles of AXD and HCP showed that Mid1p had the lowest binding energies at -10.1 kcal/mol and -9.2 kcal/mol, respectively. Kre2p had binding energies of -7.9 kcal/mol and -7.1 kcal/mol, respectively. Erg5p had binding energies of -6.6 kcal/mol and -6.2 kcal/mol, respectively. Ecm7p had binding energies of -6.6 kcal/mol and -6.1 kcal/mol, respectively. Recm7p had binding energies of -4.8 kcal/mol and -7.7 kcal/mol, respectively. These results suggest that these genes are likely targets of the two drugs in C. glabrata. [ABSTRACT FROM AUTHOR]

Herein, the constructing synthon pyrazolyl-pyrimidine derivatives were synthesized and utilized for building a wide variety of 1,2,3-triazole and tetrazole compounds that can be used as antimicrobial and antitubercular medications. The structures of all synthesized compounds were characterized using different spectroscopic techniques (1H, 13C NMR, IR and MS). The novel o,p-dihydroxyphenyl and isopropyl substituted tetrazoles have a remarkable antimicrobial activity against K. pneumoniae (MICs = 4.93±0.02, 4.13±0.01 µg/mL) and S. aureus (MICs = 7.72±0.02, 17.34±0.01 µg/mL). Antifungal activity of pyrazolyl-pyrimidine containing with p-hydroxybenzyl, o-hydroxy, and m-nitrophenyltriazoles displayed potent antifungal activity against A. niger, and its MIC was found to be, 5.45±0.02, 4.12±0.03, and 6.31±0.01 µg/mL. All the prepared tetrazoles exposed excellent antitubercular activity comparison with the standard drug against H37RV strain. From docking investigations, the p-hydroxybenzyl-linked triazole revealed the strongest H-bonds among the residues Ile14(A), Arg45(A), Gln68(A), Gln98(A) × 2, Thr46(A), and Gly96(A) against 1DF7 protein. Finally, the in silico pharmacokinetic profile of all the derivatives was estimated using SwissADME and some of the compounds have Lipinski rule of five without deviation. [ABSTRACT FROM AUTHOR]

The inhibition of HDAC activity is presently one of the main targets for anticancer drug development. This study aimed to investigate the anticancer effect of cowanol via inhibition of HDAC and apoptosis induction in leukemic Jurkat cells. Computational analysis and HDAC inhibitor screening assays were used to determine the properties of cowanol as an HDAC inhibitor in Jurkat cells. MTT assays and Hoechst staining were performed to observe the cytotoxicity and apoptotic induction effect of cowanol. In silico docking analysis revealed that cowanol could tightly bind to the active sites of both HDAC class I (HDAC 2 and 8) and HDAC class II (HDAC 4 and 7) with a similar mode of binding to the reference inhibitors. Importantly, cowanol obviously interacts with the zinc ion at the catalytic center as well as with other amino acid residues in the active region, indicating its possible function as an HDAC inhibitor. The ADME results showed that cowanol possessed acceptable pharmacokinetics and drug-likeness properties, which suggested oral bioavailability. In addition, the screening assay demonstrated that cowanol could inhibit HDAC at 20 - 60 % compared to the standard HDAC inhibitor, SAHA. Moreover, the cytotoxic effect of cowanol against Jurkat cells with the IC50 was 18.19 ± 0.44 µM. For the mode of cell death, nuclear condensation and apoptotic bodies were characterized, supporting the role of the apoptosis inducer cowanol. Hence, our results indicated a potential new role of cowanol as an HDAC inhibitor. The cytotoxic mode of cowanol was illustrated as apoptotic inducer, which is a well-known target for anticancer drug development. [ABSTRACT FROM AUTHOR]

PMM2-CDG, a disease caused by mutations in phosphomannomutase-2, is the most common congenital disorder of glycosylation. Yet, it still lacks a cure. Targeting phosphomannomutase-2 with pharmacological chaperones or inhibiting the phosphatase activity of phosphomannomutase-1 to enhance intracellular glucose-1,6-bisphosphate have been proposed as therapeutical approaches. We used Recombinant Bacterial Thermal Shift Assay to assess the binding of a substrate analog to phosphomannomutase-2 and the specific binding to phosphomannomutase-1 of an FDA-approved drug - clodronate. We also deepened the clodronate binding by enzyme activity assays and in silico docking. Our results confirmed the selective binding of clodronate to phosphomannomutase-1 and shed light on such binding. • PMM2-CDG is a congenital disorder of glycosylation caused by mutations in phosphomannomutase-2 (PMM2). It has no cure. • Alpha- glucose-1,6-bisphosphate is a PMM2 stabilizer and activator, hydrolysed by a phosphatase in vivo. • We evaluated two approaches to develop therapies: pharmacological chaperones to stabilize PMM2 or specific phosphatase inhibitors. • We deepened the effect of Clodronate. Clodronate is a selective inhibitor for the main phosphatase acting on glucose-1,6-bisphosphate. • Recombinant Bacterial Cellular Thermal Shift Assay can be helpful in fast and preliminary drug screening. [ABSTRACT FROM AUTHOR]

In order to address the drastic demand for novel broad-spectrum antibacterial and anticancer medicines with enhanced activity, computer modelling was utilized to rationally develop newer anticancer triazole based drugs. A unique series of benzo[d][1,3]oxazin-4-one linked 1,2,3-triazoles was synthesised in five steps, with good yields and an assessment of their antibacterial and anticancer activities. IR spectroscopy, 1H NMR, 13C NMR, and mass spectrometry were used to characterize the synthesis of triazole compounds. From antibacterial screening, the prepared derivatives namely, 8a, 8e, 8h and 8k showed excellent inhibitory potential against S. aureus with ZI of 28 ± 0.48, 30 ± 0.42, 30 ± 0.11, 35 ± 0.23 mm respectively, compared to moxifloxacin (33 ± 0.15 mm). Compared to doxorubicin (IC50 = 2.45 ± 0.14 μM), compounds 8h and 8k demonstrated superior and exceptional cytotoxicity against the A549 cell line (IC50 = 2.30 ± 0.26 and 1.90 ± 0.30 μM, respectively). Latter All the derivatives were further subjected to in silico docking studies against human lung (PDB: 2P85), VEGFR2 kinase domain (PDB: 3CP9) and could serve as ideal leads for additional modification in the field of anticancer research. Based on docking results, 8e showed that the amino acids Arg373(A), Gly113(A), Glu103(A), Asp108(A), Ser119(A), Asn375(A), Val374(A), Lys387(A), and Asn120(A) exhibited highly stable binding to cytochrome P4502A13 receptor of lung cancer. Furthermore, Density Functional Theory (DFT) calculations are performed to support the molecular docking studies. Compounds 8e, 8h, and 8k were discovered to have estimated energy gaps (eV) of 3.181, 4.034, and 3.539 eV, respectively. Triazole 8h exhibited the lowest chemical hardness (1.962 eV) and the highest chemical softness (0.252 eV), which also suggests that it is more reactive than all the other compounds under study. Moreover, these scaffolds physicochemical characteristics, filtration molecular properties, assessment of toxicity, and bioactivity scores were assessed in relation to ADME (absorption, distribution, metabolism, and excretion). In conclusion, we discovered a novel benzoxazinone linked 1,2,3-triazoles with promising antimicrobial and anticancer activity and a favorable pharmacokinetic profile.

Abstract Alzheimer’s disease (AD) is associated with cognitive deficits and epigenetic deacetylation that can be modulated by natural products. The role of natural oxyresveratrol-β-cyclodextrin (ORV) on cognition and histone deacetylase activity in AD is unclear. Herein, in-silico docking and molecular dynamics simulation analysis determined that oxyresveratrol potentially targets histone deacetylase-2 (HDAC2). We therefore evaluated the in vivo ameliorative effect of ORV against cognitive deficit, cerebral and hippocampal expression of HDAC in experimental AD rats. Intracerebroventricular injection of STZ (3 mg/kg) induced experimental AD and the rats were treated with low dose (200 mg/kg), high dose (400 mg/kg) of ORV and donepezil (10 mg/kg) for 21 days. The STZ-induced AD caused cognitive and behavioural deficits demonstrated by considerable increases in acetylcholinesterase activity and escape latency compared to sham control. The levels of malondialdehyde (MDA) and HDAC activity were significantly increased in AD disease group comparison to the sham. Interestingly, the ORV reversed the cognitive-behavioural deficit and prominently reduced the MDA and HDAC levels comparable to the effect of the standard drug, donepezil. The findings suggest anti-AD role of ORV via antioxidant effect and inhibition of HDAC in the hippocampal and frontal cortical area of rats for AD.

Quinoxaline-based compounds show promising inhibition of protoporphyrinogen oxidase (PPO), a key enzyme in chlorophyll production and a prime target for herbicide development. However, their precise molecular interactions remain largely unexplored. This study investigates 1-propyl-3-phenylquinoxalin-2(1H)-one (Qnz), a novel quinoxaline derivative designed and synthesized as a representative system. We examined its interaction, at the atomic level, with the active site of Nicotiana tabacum PPO (NtPPO) using an integrated molecular docking and DFT-based quantum mechanics cluster approach. The nature and strength of observed noncovalent interactions were theoretically evaluated using quantum theory of atoms-in-molecules (QTAIM), independent gradient model (IGM), and natural bond orbital (NBO) methods. Our analysis revealed a fascinating set of unconventional interactions that contribute to the stability of the Qnz–NtPPO complex, namely weak hydrogen bonding, homopolar dihydrogen interactions, π–stacking, and carbonyl–carbonyl interactions. Interestingly, the study uncovered the unexpected role of several less common amino acids—including Gly178, Ser235, and nonpolar aliphatic leucines—in facilitating molecular recognition. Moreover, the employed computational approaches have proven to be a powerful tool for analyzing interactions within the binding pocket. [ABSTRACT FROM AUTHOR]

Background: The identification of novel therapeutic strategies for ovarian cancer (OC), the most lethal gynecological neoplasm, is of utmost urgency. Here, we have tested the effectiveness of the compound 2c (4-hydroxy-2,6-bis(4-nitrobenzylidene)cyclohexanone 2). 2c interferes with the cysteine-dependent deubiquitinating enzyme (DUB) UCHL5, thus affecting the ubiquitin-proteasome-dependent degradation of proteins. Methods: 2c phenotypic/molecular effects were studied in two OC 2D/3D culture models and in a mouse xenograft model. Furthermore, we propose an in silico model of 2c interaction with DUB-UCHL5. Finally, we have tested the effect of 2c conjugated to several linkers to generate 2c/derivatives usable for improved drug delivery. Results: 2c effectively impairs the OC cell line and primary tumor cell viability in both 2D and 3D conditions. The effectiveness is confirmed in a xenograft mouse model of OC. We show that 2c impairs proteasome activity and triggers apoptosis, most likely by interacting with DUB-UCHL5. We also propose a mechanism for the interaction with DUB-UCHL5 via an in silico evaluation of the enzyme-inhibitor complex. 2c also reduces cell growth by down-regulating the level of the transcription factor E2F1. Eventually, 2c activity is often retained after the conjugation with linkers. Conclusion: Our data strongly support the potential therapeutic value of 2c/derivatives in OC. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is associated with cognitive deficits and epigenetic deacetylation that can be modulated by natural products. The role of natural oxyresveratrol-β-cyclodextrin (ORV) on cognition and histone deacetylase activity in AD is unclear. Herein, in-silico docking and molecular dynamics simulation analysis determined that oxyresveratrol potentially targets histone deacetylase-2 (HDAC2). We therefore evaluated the in vivo ameliorative effect of ORV against cognitive deficit, cerebral and hippocampal expression of HDAC in experimental AD rats. Intracerebroventricular injection of STZ (3 mg/kg) induced experimental AD and the rats were treated with low dose (200 mg/kg), high dose (400 mg/kg) of ORV and donepezil (10 mg/kg) for 21 days. The STZ-induced AD caused cognitive and behavioural deficits demonstrated by considerable increases in acetylcholinesterase activity and escape latency compared to sham control. The levels of malondialdehyde (MDA) and HDAC activity were significantly increased in AD disease group comparison to the sham. Interestingly, the ORV reversed the cognitive-behavioural deficit and prominently reduced the MDA and HDAC levels comparable to the effect of the standard drug, donepezil. The findings suggest anti-AD role of ORV via antioxidant effect and inhibition of HDAC in the hippocampal and frontal cortical area of rats for AD. [ABSTRACT FROM AUTHOR]

Widespread usage of antifungals has led to the development of antifungal resistance, causing a change in the epidemiology of the responsible agents from albicans to non-Candida albicans species. Pharmaceutical repurposing is an alternate strategy that has provided a cost-effective method to address the increasing resistance to antifungal medications. The objective of this work was to examine the antifungal properties of Alexidine dihydrochloride (AXD) and Hexachlorophene (HCP) against a non-Albicans Candida model, C. glabrata. The lowest inhibitory doses of AXD and HCP against C. glabrata were determined by in vitro methods to be 0.69-1.03 µM and 14.75-19.66 µM, respectively. The minimum doses of AXD and HCP that caused fungicidal effects were defined as 1.375 µM and 61.44 µM, respectively. Three proteins involved in crucial physiological pathways, namely cell wall production (Kre1p, Kre2p, Ecm33p), membrane calcium channel (Mid1p, Ecm7p), and ergosterol biosynthesis (Erg5p), were chosen as potential targets for the medications due to their functions in survival and disease development. SWISS MODEL was used to create the 3D structures of predicted targets of C. glabrata. The quality of these structures was assessed using Ramachandran plot statistics. AXD and HCP were analyzed by docking software AutoDock Vina against these targets. The findings of computational investigations have shown that both medicines exhibit interaction affinities with all the selected protein types. The binding energy profiles of AXD and HCP showed that Mid1p had the lowest binding energies at -10.1 kcal/mol and -9.2 kcal/mol, respectively. Kre2p had binding energies of -7.9 kcal/mol and -7.1 kcal/mol, respectively. Erg5p had binding energies of -6.6 kcal/mol and -6.2 kcal/mol, respectively. Ecm7p had binding energies of -6.6 kcal/mol and -6.1 kcal/mol, respectively. Recm7p had binding energies of -4.8 kcal/mol and -7.7 kcal/mol, respectively. These results suggest that these genes are likely targets of the two drugs in C. glabrata.

Abstract The number of infections and deaths caused by multidrug resistant (MDR) tuberculosis is increasing globally. One of the efflux pumps, that makes Mycobacterium tuberculosis resistant to a number of antibiotics and results in unfavourable treatment results is Tap or Rv1258c. In our study, we tried to utilize a rational drug design technique using in silico approach to look for an efficient and secure efflux pump inhibitor (EPI) against Rv1258c. The structure of Rv1258c was built using the homology modeling tool MODELLER 9.24. 210 phytocompounds were used for blind and site-specific ligand docking against the modelled structure of Rv1258c using AutoDock Vina software. The best docked plant compounds were further analysed for druglikeness and toxicity. In addition to having excellent docking scores, two plant compounds—ellagic acid and baicalein—also exhibited highly desirable drug-like qualities. These substances outperform more well-known EPIs like piperine and verapamil in terms of effectiveness. This data shows that these two compounds might be further investigated for their potential as Rv1258c inhibitors.

Diabetes remains an important disease worldwide with about 500 million patients globally. In tropical Africa, Morus mesozygia is traditionally used in the treatment of diabetes. Biological and phytochemical investigation of the root bark extracts of the plant led to the isolation of a new prenylated arylbenzofuran named 7-(3-hydroxy-3-methylbutyl)moracin M (1) and two congeners, moracins P (2) and M (3). When compared to acarbose (IC50 = 486 µM), all the isolated compounds are better inhibitors of α-glucosidase with in vitro IC50 values of 16.9, 16.6, and 40.9 µM, respectively. However, they were not active against α-amylase. The compounds also demonstrated moderate inhibition of dipeptidyl peptidase-4 (DPP4). Based on in silico docking studies, all isolates (1, 2, and 3) exhibit binding affinities of -8.7, -9.5, and -8.5 kcal/mol, respectively against α-glucosidase enzyme (PDB: 3AJ7). They are stabilized within the α-glucosidase active site through hydrogen bonds, pi interactions, and hydrophobic interactions. This study provides scientific support for the traditional use of Morus mesozygia in the treatment of diabetes as well as adding to the repository of α-glucosidase inhibitory agents. [ABSTRACT FROM AUTHOR]

Ammodaucus leucotrichus exhibits promising pharmacological activity, hinting at anti-inflammatory and anti-arthritic effects. This study investigated seed extracts from Ammodaucus leucotrichus using methanol and n-hexane, focusing on anti-inflammatory and anti-arthritic properties. The methanol extract outperformed the n-hexane extract and diclofenac, a reference anti-inflammatory drug, in trypsin inhibition (85% vs. 30% and 64.67% at 125 μg/mL). For trypsin inhibition, the IC50 values were 82.97 μg/mL (methanol), 202.70 μg/mL (n-hexane), and 97.04 μg/mL (diclofenac). Additionally, the n-hexane extract surpassed the methanol extract and diclofenac in BSA (bovine serum albumin) denaturation inhibition (90.4% vs. 22.0% and 51.4% at 62.5 μg/mL). The BSA denaturation IC50 values were 14.30 μg/mL (n-hexane), 5408 μg/mL (methanol), and 42.30 μg/mL (diclofenac). Gas chromatography–mass spectrometry (GC–MS) revealed 59 and 58 secondary metabolites in the methanol and n-hexane extracts, respectively. The higher therapeutic activity of the methanol extract was attributed to hydroxyacetic acid hydrazide, absent in the n-hexane extract. In silico docking studies identified 28 compounds with negative binding energies, indicating potential trypsin inhibition. The 2-hydroxyacetohydrazide displayed superior inhibitory effects compared to diclofenac. Further mechanistic studies are crucial to validate 2-hydroxyacetohydrazide as a potential drug candidate for rheumatoid arthritis treatment. [ABSTRACT FROM AUTHOR]

One of the most important factors limiting the growth and development of children is gastrointestinal helminths. A conscious anthelmintic herbal cure is a rational approach to establishing a sustainable public health program in the treatment of oxyurid infections that are mostly seen in children, disrupt development, frequently recur and are asymptomatic. This study aims to investigate the molecular mechanisms of the anthelmintic features of Artemisia annua L. and to compare the antinematodal effect of A. annua L. n-hexane extract with Albendazole (ABZ) in naturally infected mice. For this purpose, A. annua L. n-hexane extract was extracted and orally administered to Balb-c mice infected with Syphacia obvelata oxyurid species at 300, 600, and 1200 mg/kg doses for seven days. Mice were examined for changes in S. obvelata egg numbers on days -7, -1, 1, 3, 5, and 7 by the anal tape method. As a reference drug, ABZ was administered at a dose of 5 mg/kg for three days, and as solvent control, corn oil was given in the same way and time as the extract. Some components of A. annua L. were investigated for possible chemical interactions and free energy of binding in Haemonchus contortus β-tubulin (Hcβ-tubulin) protein and rat Carnitine Palmitoyltransferase II (RnCPT II) enzyme by in silico docking simulations. Stigmasterol and friedelin inhibit the RnCPT II enzyme in silico with 9.43 nM and 13.07 nM Ki values, respectively, while not binding to Hcβ-tubulin. Arteannuin-B and scopoletin inhibited both RnCPT II and Hcβ-tubulin. A. annua L. n-hexane extract at 1200 mg/kg dose reduced oxyurid eggs by 88% on the 7th day. ABZ caused a 65.58% reduction. As the result, arteannuin-B, scopoletin, stigmasterol and friedelin are worthy of isolation and investigation in vitro and in vivo in terms of their anthelmintic effect. They can be evaluated as potential anthelmintic molecules. [ABSTRACT FROM AUTHOR]

Summary: The present work investigated the antioxidant activity and inhibitory effects towards α‐amylase and α‐glucosidase of phenolic compounds in Elaeocarpus braceanus fruits and clarified their possible mechanisms based on molecular docking and dynamic analysis. A total of 12 phenolic compounds were identified and quantified in the extracts of E. braceanus fruits using UHPLC‐ESI‐HRMS/MS. The TPC and TFC were 229.18 ± 5.76 mg GAE/g and 144.85 ± 1.17 mg RE/g, respectively. In vitro analyses, E. braceanus fruits extracts exhibited good antioxidant activities and demonstrated strong inhibitory effects towards α‐amylase and α‐glucosidase. Molecular docking and molecular dynamics results showed that quercetin and myricetin can stably form hydrogen bonds and van der Waals forces with the active amino acid residues of α‐amylase and α‐glucosidase, and thereby inhibiting their enzymatic activities. The findings might provide a good potential natural resource for improving oxidative stress damage and controlling blood glucose in diabetes. [ABSTRACT FROM AUTHOR]

The present investigation entails the encapsulation of Apium graveolens essential oil into chitosan nanobiopolymer (AGEO-Ne) and assessment of its efficacy against Fusarium verticillioides contamination and fumonisins biosynthesis in stored rice (Oryza sativa L.) samples. The AGEO was encapsulated through ionic gelation process and characterized by scanning electron microscopy (SEM), Dynamic light scattering (DLS), X-ray diffractometry (XRD), and Fourier transform infrared spectroscopy (FTIR) analyses. The AGEO exhibited bi-phasic delivery pattern from chitosan matrix. The AGEO caused complete inhibition of F. verticillioides growth at 1.2 μL/mL, while fumonisin B1 (FB1) and B2 (FB2) biosynthesis at 1.2 and 1.0 μL/mL, respectively. On the other hand, nanoencapsulated AGEO (AGEO-Ne) exhibited improved efficacy, caused complete inhibition of fungal growth at 0.8 μL/mL, and FB1 and FB2 production at 0.8 and 0.6 μL/mL, respectively. AGEO-Ne caused 100 % inhibition of ergosterol synthesis at 0.8 μL/mL and exhibited greater efflux of Ca2+, Mg2+, K+ ions (18.99, 21.63, and 25.38 mg/L) as well as 260 and 280 nm absorbing materials from exposed fungal cells. The in silico interaction of granyl acetate and linalyl acetate with FUM 21 protein validated the molecular mechanism for inhibition of FB1 and FB2 biosynthesis. Further, improvement in antioxidant activity of AGEO-Ne was observed after encapsulation with IC50 values of 12.08 and 6.40 μL/mL against DPPH and ABTS radicals, respectively. During in situ investigation, AGEO caused 82.09 and 86.32 % protection of rice against F. verticillioides contamination in inoculated and uninoculated rice samples, respectively, while AGEO-Ne exhibited 100 % protection of fumigated rice samples against F. verticillioides proliferation as well as FB1 and FB2 contamination. The AGEO-Ne also caused better retardation of lipid peroxidation (41.35 and 37.52 μM/g FW malondialdehyde in inoculated and uninoculated treatment) and acceptable organoleptic properties in rice samples, which strengthen its application as plant based novel preservative in food and agricultural industries.

Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX464 or obefazimod, as a nematocidal candidate; synthesised a series of analogues which were assessed for activity against the free-living nematode Caenorhabditis elegans; and predicted compound-target relationships by thermal proteome profiling (TPP) and in silico docking. Here, we logically extended this work and critically evaluated the anthelmintic activity of ABX464 analogues on Haemonchus contortus (barber's pole worm) – a highly pathogenic nematode of ruminant livestock. First, we tested a series of 44 analogues on H. contortus (larvae and adults) to investigate the nematocidal pharmacophore of ABX464, and identified one compound with greater potency than the parent compound and showed moderate activity against a select number of other parasitic nematodes (including Ancylostoma, Heligmosomoides and Strongyloides species). Using TPP and in silico modelling studies, we predicted protein HCON_00074590 (a predicted aldo-keto reductase) as a target candidate for ABX464 in H. contortus. Future work aims to optimise this compound as a nematocidal candidate and investigate its pharmacokinetic properties. Overall, this study presents a first step toward the development of a new nematocide.

Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5-ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein-protein interaction.

Abstract Background Artemisiae Scopariae Herba (ASH) has been widely used as plant medicine in East Asia with remarkable antitumor activity. However, the underlying mechanisms have not been fully elucidated. Methods This study aimed to construct a multi-disciplinary approach to screen topoisomerase I (topo I) inhibitors from ASH extract, and explore the antitumor mechanisms. Bioaffinity ultrafiltration-UFLC-ESI-Q/TOF-MS/MS was used to identify chemical constitution of ASH extract as well as the topo I inhibitors, and in silico docking coupled with multiple complex networks was applied to interpret the molecular mechanisms. Results Crude ASH extract exhibited toxicogenetic and antiproliferative activities on A549 cells. A series of 34 ingredients were identified from the extract, and 6 compounds were screened as potential topo I inhibitors. Docking results showed that the formation of hydrogen bond and π-π stacking contributed most to their binding with topo I. Interrelationships among the 6 compounds, related targets and pathways were analyzed by multiple complex networks model. These networks displayed power-law degree distribution and small-world property. Statistical analysis indicated that isorhamnetin and quercetin were main active ingredients, and that chemical carcinogenesis-reactive oxygen species was the critical pathway. Electrophoretic results showed a therapeutic effect of ASH extract on the conversion of supercoiled DNA to relaxed forms, as well as potential synergistic effect of isorhamnetin and quercetin. Conclusions The results improved current understanding of Artemisiae Scopariae Herba on the treatment of tumor. Moreover, the combination of multi-disciplinary methods provided a new strategy for the study of bioactive constituents in medicinal plants.

Abstract Methanol, ethanol, acetone and chloroform extracts of powdered Hypericum heterophyllum prepared from leafs were investigated for their (i) phytochemical constituents, which was evaluated by LC-ESI-MS/MS and various known total bioactive methods; (ii) antioxidant capacity, which was evaluated by several in vitro assays such as DPPH, ABTS, H2O2, superoxide radical, and metal chelating; (iii) acetylcholinesterase (AChE) inhibitory activity; (iv) active constituents of the extracts with AChE in silico docking. Phytochemical analysis revealed that none of the extracts contained hypericin, pseudohypericin and hyperforin. Among the identified compounds, ethanol and acetone extracts had the highest number of compounds. The highest value of total phenolic content (132.7 mg GAE/g) was obtained with methanol extract, whereas the highest values of total flavonoid (61.8 mg QE/g) and flavanol (0.89 mg CE/g) content were recorded in acetone extract. Methanol extract displayed the most DPPH activity (24.9 mg TE/g), but ethanol extract (59.8 mg TE/g) showed the highest ABTS activity. Acetone extract displayed the best hydroxyl and superoxide radical scavenging activities with the values of 351.5 mg AAE/g, and 197.3 mg TE/g respectively. The chloroform extract exhibited the best AChE inhibition activity (11.07 µg/ml). In the docking study, quercetin-7-O-glucoside, diosgenin, and quercetin-3-glucoside were calculated to have a stronger MolDock Score than the reference ligand Donepezil. Our docking results have indicated that extracts contain compounds with a high affinity against the acetylcholinesterase enzyme. These data suggest that these extracts can be potentially important antioxidant supplements and drug candidates for AChE inhibition activity.

OBJECTIVE: Hepatic ischemia-reperfusion (H I/R) injury arises due to a temporary obstruction followed by the re-establishment of blood supply to the liver. Linalool (LIN), a main volatile constituent of essential oils in numerous aromatic plant species, exhibited various medicinal and pharmacological actions. This study investigated the protective effect of LIN on the status of H I/R, with the study of the possible mechanisms. In addition, linalool's antagonistic effects were tested against several metabolic targets using in silico molecular docking technique. MATERIALS AND METHODS: Wistar rats were allocated into five groups. Sham and LIN + Sham groups in which animals were administered either vehicle (1% CMC) or LIN (200 mg/kg/day) orally for two weeks. H I/R group in which rats were administered 1% CMC for two weeks and then experienced hepatic ischemia for 60 min followed by 6 hours of reperfusion. LIN 100 + H I/R and LIN 200 + H I/R groups in which rats were pretreated with LIN (100, 200 mg/kg/day) respectively for two weeks, then subjected to H I/R. RESULTS: H I/R-induced injury resulted in impaired liver function and activated Keap1/Nrf2/HO-1/NQO1 and HMGB1/TLR4/RAGE/NFB pathways with subsequent oxidative stress, inflammation, and apoptosis. LIN pretreatment alleviated I/R-induced impairment in liver function, promoted Keap1/Nrf2/HO-1/NQO1, and mitigated the HMGB1/TLR4/RAGE/NFB pathway. LIN pre-administration deterred adhesion molecule, neutrophils infiltration, RAGE, IL-1ß, IL-6, TNF-a, and apoptosis. CONCLUSIONS: LIN demonstrated hepato-protective effects against H I/R via instigation Keap1/Nrf2/HO-1/NQO1 and mitigating the HMGB1/TLR4/RAGE/NFB pathways with subsequent deterring oxidative stress, inflammation, and apoptosis. [ABSTRACT FROM AUTHOR]

• Marine brown agae (Sargassum wightii) has revealed its potential effects. • Palmitic acid scored good docking values against α-amylase and α-glucosidase. • ADME score of palmitic acid has recorded good activity. • Non-target toxicity assays proved that potential pharmaceutical effects. Jeopardized glucose hemostasis leads to cronic metaboic disorder like Diabetes mellitus and it is predicted to occur in ∼700 million people in the coming 20 years. Our study aims to isolate Palmitic acid (C 16 H 32 O 3), 9-Hydroxyhexadecanoic acid metabolite from Sargassum wightii to inhibit alpha-amylase and alpha-glucosidase to reduce postprandial hyperglycemia and decline the risk of diabetes. High docking score of palmitic acid with both α-amylase and α-glucosidase is observed in in-silico molecular docking analysis, in comparison to commercially available drug acarbose. The three hydrogen bond in palmitic acid interacts with the important amino acids like Arg195, Lys200 and Asp300 in Glide XP docking mode for alpha-amylase. For α-glucosidase, quantum-polarized ligand docking (QPLD) was used with similar three hydrogen bond interactions. Both docking studies showed significant binding interaction of palmitic acid with α-amylase (− 5.66 and −5.14 (Kcal/mol)) and with α-glucosidase (−4.52 and −3.51(Kcal/mol)) with respect to the standard, acarbose docking score. The bioactive palmitic acid isolated from the brown alga, Sargassum wightii is already seen to inhibit digestive enzyme with non-target property in Artemia nauplii and zebra fish embryos. Further studies are required to investigate its role in in vivo antidiabetic effects due to its non-toxic and digestive enzyme inhibitory properties. It can be recommended in additional pharmaceutical studies to develop novel therapeutics to manage diabetes mellitus. [ABSTRACT FROM AUTHOR]

Abstract MauG catalyzes the six-electron oxidation of pre-tryptophan tryptophylquinone (preTTQ) cofactor in methylamine dehydrogenase (MADH) to form mature tryptophan tryptophylquinone (TTQ) via long-range electron transfer. To identify alternative substrates for MauG, docking models for 10 tryptophan-like compounds were constructed using Autodock Vina. These demonstrated spontaneous binding to the preTTQ binding site of MauG, with hydroxyindoles most frequently sharing the natural substrate binding site of MauG. To confirm the result of in silico analysis, 7-hydroxyindole was reacted with bis-FeIV of MauG. The spectroscopic change, representing the reactivity of MauG, revealed the highly increased reaction rate (k 3 ) toward 7-hydroxyindole, suggesting that bis-FeIV MauG extracted an electron from the 7-hydroxyindole and then oxidized to di-ferric MauG.

Abstract Background CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in metagenomic data. Results CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRNA sequence: a structure-based method (in silico docking) and a sequence-based method (machine learning classification). For the structure-based method, users can either provide experimentally determined 3D structures of these macromolecules or use an integrated pipeline to generate 3D-predicted structures for in silico docking experiments. Conclusion CRISPR-Cas-Docker addresses the need of the CRISPR-Cas community to predict RNA–protein interactions in silico by optimizing multiple stages of computation and evaluation, specifically for CRISPR-Cas systems. CRISPR-Cas-Docker is available at www.crisprcasdocker.org as a web server, and at https://github.com/hshimlab/CRISPR-Cas-Docker as an open-source tool.

Background: The identification of novel therapeutic strategies for ovarian cancer (OC), the most lethal gynecological neoplasm, is of utmost urgency. Here, we have tested the effectiveness of the compound 2c (4-hydroxy-2,6-bis(4-nitrobenzylidene)cyclohexanone 2). 2c interferes with the cysteine-dependent deubiquitinating enzyme (DUB) UCHL5, thus affecting the ubiquitin-proteasome-dependent degradation of proteins. Methods: 2c phenotypic/molecular effects were studied in two OC 2D/3D culture models and in a mouse xenograft model. Furthermore, we propose an in silico model of 2c interaction with DUB-UCHL5. Finally, we have tested the effect of 2c conjugated to several linkers to generate 2c/derivatives usable for improved drug delivery. Results: 2c effectively impairs the OC cell line and primary tumor cell viability in both 2D and 3D conditions. The effectiveness is confirmed in a xenograft mouse model of OC. We show that 2c impairs proteasome activity and triggers apoptosis, most likely by interacting with DUB-UCHL5. We also propose a mechanism for the interaction with DUB-UCHL5 via an in silico evaluation of the enzyme-inhibitor complex. 2c also reduces cell growth by down-regulating the level of the transcription factor E2F1. Eventually, 2c activity is often retained after the conjugation with linkers. Conclusion: Our data strongly support the potential therapeutic value of 2c/derivatives in OC.

Bisphenol A (BPA) is a chemical used in the production of certain plastics and resins. Recent research has found that BPA can inhibit the activity of 3β-hydroxysteroid dehydrogenase/Δ5,4-isomerases (3β-HSDs). Whether benzene ring BPA substitutes can inhibit human, rat, and mouse gonadal 3β-HSDs, the structure-activity relationship and the underlying mechanism remain unclear. In this study, we compared 6 benzene ring BPA substitutes to BPA in the inhibition of human, rat, and mouse gonadal 3β-HSDs and conducted structure-activity relationship and in silico docking analysis. The inhibitory activity (IC50) of human 3β-HSD2 in KGN cells ranged from about 0.02 μM for bisphenol H to 8.75 μM for BPA, that of rat 3β-HSD1 in testicular microsomes ranged from 0.099 μM for bisphenol H to 31.32 μM for BPA, and that of mouse 3β-HSD6 ranged from 0.021 μM for BPH to ineffectiveness for 100 μM BPA. These compounds acted as mixed inhibitors with LogP inversely correlated with IC50 and ΔG positively correlated with IC50 value. Docking analysis showed that these compounds bind to the steroid active site of the 3β-HSD enzymes. In conclusion, some benzene ring BPA substitutes potently inhibit gonadal 3β-HSD in various species, and lipophilicity and binding affinity determine their inhibitory strength.

Background: Artemisiae Scopariae Herba (ASH) has been widely used as plant medicine in East Asia with remarkable antitumor activity. However, the underlying mechanisms have not been fully elucidated. Methods: This study aimed to construct a multi-disciplinary approach to screen topoisomerase I (topo I) inhibitors from ASH extract, and explore the antitumor mechanisms. Bioaffinity ultrafiltration-UFLC-ESI-Q/TOF-MS/MS was used to identify chemical constitution of ASH extract as well as the topo I inhibitors, and in silico docking coupled with multiple complex networks was applied to interpret the molecular mechanisms. Results: Crude ASH extract exhibited toxicogenetic and antiproliferative activities on A549 cells. A series of 34 ingredients were identified from the extract, and 6 compounds were screened as potential topo I inhibitors. Docking results showed that the formation of hydrogen bond and π-π stacking contributed most to their binding with topo I. Interrelationships among the 6 compounds, related targets and pathways were analyzed by multiple complex networks model. These networks displayed power-law degree distribution and small-world property. Statistical analysis indicated that isorhamnetin and quercetin were main active ingredients, and that chemical carcinogenesis-reactive oxygen species was the critical pathway. Electrophoretic results showed a therapeutic effect of ASH extract on the conversion of supercoiled DNA to relaxed forms, as well as potential synergistic effect of isorhamnetin and quercetin. Conclusions: The results improved current understanding of Artemisiae Scopariae Herba on the treatment of tumor. Moreover, the combination of multi-disciplinary methods provided a new strategy for the study of bioactive constituents in medicinal plants. [ABSTRACT FROM AUTHOR]

Binding interactions between Cibacron Blue‐F3GA (CB‐F3GA) and human serum albumin (HSA, at physiologically ten‐fold lower concentration) was studied by isothermal titration calorimetry (ITC) and in‐silico docking computations. ITC experiments revealed two separate binding sites on HSA with different binding affinities for CB‐F3GA. The high‐affinity binding site (PBS‐II) on HSA binds CB‐F3GA at nanomolar scale (KD1 = 118 ± 107 nM) with favorable binding enthalpy (ΔHo1 = − 6.47 ± 0.44 kcal/mol) and entropy (−TΔSo1 = −2.98 kcal/mol) energies. CB‐F3GA binds to the low‐affinity binding site (PBS‐I) at μM scale (KD2 = 31.20 ± 18.40 μM) with favorable binding enthalpy (ΔHo1 = − 5.03 ± 3.86 × 10−2 kcal/mol) and entropy (−TΔSo1 = −1.12 kcal/mol) energies. ITC binding data strongly suggest that CB‐F3GA binding to PBS‐II site increases the formation of dimeric‐HSA clusters (N1 = 2.43 ± 0.50), while binding to PBS‐I leads to tetrameric‐HSA clusters (N2 = 4.61 ± 0.90). These results suggest that a higher degree of HSA aggregation upon drug binding may be expected under physiological conditions, a notion that should be further investigated for the delivery and toxicity of drug−HSA interactions. [ABSTRACT FROM AUTHOR]

Background: Although the GABAA receptor (GABAAR) has been proposed as the main action site for sevoflurane, isoflurane, halothane, enflurane, propofol, and benzodiazepines (BZDs), binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses. Moreover, various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR. Methods: We performed in silico docking analysis to compare the binding modes of sevoflurane, isoflurane, halothane, enflurane, propofol, and BZDs to the GABAAR based on one of the most recently provided 3D structures. We performed the docking analysis and the affinity-based ranking of the binding sites. Results: Our docking studies revealed that isoflurane, halothane, and enflurane docked in an extracellular domain (ECD) on GABAARs, in contrast to sevoflurane. Conclusion: Our results supported a multi-site mechanism for the allosteric modulation of propofol. Propofol was bound to the pore or favored various subsites in the transmembrane domain (TMD). Our result confirmed that different chemically related BZD ligands interact via distinct binding modes rather than by using a common binding mode, as previously suggested. [ABSTRACT FROM AUTHOR]

Abstract RNA–protein interactions are crucial for diverse biological processes. In prokaryotes, RNA–protein interactions enable adaptive immunity through CRISPR-Cas systems. These defence systems utilize CRISPR RNA (crRNA) templates acquired from past infections to destroy foreign genetic elements through crRNA-mediated nuclease activities of Cas proteins. Thanks to the programmability and specificity of CRISPR-Cas systems, CRISPR-based antimicrobials have the potential to be repurposed as new types of antibiotics. Unlike traditional antibiotics, these CRISPR-based antimicrobials can be designed to target specific bacteria and minimize detrimental effects on the human microbiome during antibacterial therapy. In this study, we explore the potential of CRISPR-based antimicrobials by optimizing the RNA–protein interactions of crRNAs and Cas13 proteins. CRISPR-Cas13 systems are unique as they degrade specific foreign RNAs using the crRNA template, which leads to non-specific RNase activities and cell cycle arrest. We show that a high proportion of the Cas13 systems have no colocalized CRISPR arrays, and the lack of direct association between crRNAs and Cas proteins may result in suboptimal RNA–protein interactions in the current tools. Here, we investigate the RNA–protein interactions of the Cas13-based systems by curating the validation dataset of Cas13 protein and CRISPR repeat pairs that are experimentally validated to interact, and the candidate dataset of CRISPR repeats that reside on the same genome as the currently known Cas13 proteins. To find optimal CRISPR-Cas13 interactions, we first validate the 3-D structure prediction of crRNAs based on their experimental structures. Next, we test a number of RNA–protein interaction programs to optimize the in silico docking of crRNAs with the Cas13 proteins. From this optimized pipeline, we find a number of candidate crRNAs that have comparable or better in silico docking with the Cas13 proteins of the current tools. This study fully automatizes the in silico optimization of RNA–protein interactions as an efficient preliminary step for designing effective CRISPR-Cas13-based antimicrobials.

Background: Mushroom-derived components have immense potential to become a safe alternative in identifying lead anti-cancer molecules. Termitomyces heimii Natarajan (T. heimii) is a traditionally used edible mushroom with no previous record of anti-hepatocarcinoma activity. Methods: The anti-proliferative efficacy of the mushroom ethyl acetate extract was screened against a panel of seven cancer cell lines, namely Hep G2, MCF-7, MDA-MB-231, MAD-MB-436, MOLT-4, Reh, and K-562, and against peripheral blood mononuclear cells isolated from normal healthy donors by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction assay. The impact of the extract on nuclear morphology was examined by 4′,6-diamidino-2-phenylindole staining and the apoptotic potential of the extract was evaluated through flow cytometry and Annexin V-PI dual staining, followed by an in vitro scratch assay to elucidate the anti-migratory potential of the extract. The apoptotic and anti-migratory effects were further validated using in silico molecular docking with four compounds, ergosterol, ergosta-5,8-dien-3-ol, lanosterol, and eburicol, against two anti-apoptotic proteins, Bcl-2 and Bcl-XL, and two angiogenic receptors, VEGFR-1 and VEGFR-2. Results: The screening data revealed that ethyl acetate extract exhibited remarkable anti-proliferative efficacy against Hep G2 cells, with a half maximal inhibitory concentration (IC50) value of 263.53 (8.09) μg/mL, followed by MCF-7 cell lines and showed a negligible effect on peripheral blood mononuclear cells. A clear alteration of the cellular and nuclear morphology was concentration-dependently observed in Hep G2 cells. The extract induced robust apoptosis and a significant concentration-dependent increase in the scratch area. The results of in silico docking revealed that compared to standard drug sunitinib, both ergosterol and ergosta-5,8-dien-3-ol displayed lower binding energy, and satisfactory drugability and absorption, distribution, metabolism, excretion, and toxicity properties. Conclusions: T. heimii is a potential source for isolating lead anticancer molecules in the future. Ergosterol and ergosta-5,8-dien-3-ol hold great promise as new drugs against hepatocarcinoma.

Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering. [ABSTRACT FROM AUTHOR]

COVID-19 and its causative organism SARS-CoV-2 paralyzed the world and was designated a pandemic by the World Health Organization in March 2020. The worldwide health system is trying to discover an effective therapeutic measure since no clinically authorized medications are present. Screening of plant-derived pharmaceuticals may be a viable technique to fight COVID-19 in this vital situation. This review discusses the potential application of in silico approaches in developing new therapeutic molecules related to preventing SARS-CoV-2 infection. Also, it describes the binding affinity of various phytoconstituents with distinct SARS-CoV-2 target sites. In this perspective, an extensive literature survey was carried out to find the potential phytoconstituents to develop new therapeutic entities to treat COVID-19 in different online academic databases and books. Data retrieved from databases were analyzed and interpreted to conclude that many phytochemicals will bind with the 3-chymotrypsin-like (3CLpro) and papain-like proteases (PLpro), spike glycoprotein, ACE-2, NSP15-endoribonuclease, and E protein targets of SARS-CoV-2 main protease using in silico molecular docking approach. The present investigations reveal that phytoconstituents such as curcumin, apigenin, chrysophanol, and gingerol are significantly binding with spike glycoprotein; laurolistine, acetoside, etc. are bound with Mpro for anti-SARS-CoV-2 therapies. Using virtual applications of in silico studies, the current study constitutes a progressive data analysis on the mechanism of binding efficiency of distinct classes of plant metabolites against the active sites of SARS-CoV-2. Furthermore, the current review also demonstrates the fundamental necessity of the alternative and complementary medicine for future therapeutic uses of phytoconstituents by phytochemists in the fight against COVID-19. [ABSTRACT FROM AUTHOR]

A series of derivative benzimidazol‐2‐thione compounds (2 a–2 l) had been synthesized, screened for their antimicrobial activities by dish diffusion and dilution assays, anti‐tumor against breast, rhabdomyosarcoma, and liver human cancer cell lines via MTT assay, followed by carrying out in silico docking model. Entries 2 i–2 j, 2 l, and 2 g are novel compounds, among them, compound 2i manifested the highest antibacterial activity against both Methicillin‐resistant Staphylococcus aureus and Streptococcus faecalis; meanwhile, entries 2 i–2 j and 2 l showed significant antifungal activity toward Trichophyton mentagrophytes, Trichophyton rubrum, and Microsporum gypseum. Through in vitro approach, entry 2 i is the best derivative against human rhabdomyosarcoma cell line. Additionally, via in silico approach, entry 2 i reasonably explained drug delivery ligand against bacterium Streptococcus faecalis, moreover, entries 2 i–2 j and 2 l showed excellent antifungal activity, explained via enzyme inhibition mechanism against 2VF5. In silico, 2 i was proved to inhibit against sarcoma cancer cell line. [ABSTRACT FROM AUTHOR]

MauG catalyzes the six-electron oxidation of pre-tryptophan tryptophylquinone (preTTQ) cofactor in methylamine dehydrogenase (MADH) to form mature tryptophan tryptophylquinone (TTQ) via long-range electron transfer. To identify alternative substrates for MauG, docking models for 10 tryptophan-like compounds were constructed using Autodock Vina. These demonstrated spontaneous binding to the preTTQ binding site of MauG, with hydroxyindoles most frequently sharing the natural substrate binding site of MauG. To confirm the result of in silico analysis, 7-hydroxyindole was reacted with bis-FeIV of MauG. The spectroscopic change, representing the reactivity of MauG, revealed the highly increased reaction rate (k3) toward 7-hydroxyindole, suggesting that bis-FeIV MauG extracted an electron from the 7-hydroxyindole and then oxidized to di-ferric MauG. [ABSTRACT FROM AUTHOR]

Background: CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in metagenomic data. Results: CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRNA sequence: a structure-based method (in silico docking) and a sequence-based method (machine learning classification). For the structure-based method, users can either provide experimentally determined 3D structures of these macromolecules or use an integrated pipeline to generate 3D-predicted structures for in silico docking experiments. Conclusion: CRISPR-Cas-Docker addresses the need of the CRISPR-Cas community to predict RNA–protein interactions in silico by optimizing multiple stages of computation and evaluation, specifically for CRISPR-Cas systems. CRISPR-Cas-Docker is available at www.crisprcasdocker.org as a web server, and at https://github.com/hshimlab/CRISPR-Cas-Docker as an open-source tool. [ABSTRACT FROM AUTHOR]

Ammodaucus leucotrichus exhibits promising pharmacological activity, hinting at anti-inflammatory and anti-arthritic effects. This study investigated seed extracts from Ammodaucus leucotrichus using methanol and n-hexane, focusing on anti-inflammatory and anti-arthritic properties. The methanol extract outperformed the n-hexane extract and diclofenac, a reference anti-inflammatory drug, in trypsin inhibition (85% vs. 30% and 64.67% at 125 μg/mL). For trypsin inhibition, the IC50 values were 82.97 μg/mL (methanol), 202.70 μg/mL (n-hexane), and 97.04 μg/mL (diclofenac). Additionally, the n-hexane extract surpassed the methanol extract and diclofenac in BSA (bovine serum albumin) denaturation inhibition (90.4% vs. 22.0% and 51.4% at 62.5 μg/mL). The BSA denaturation IC50 values were 14.30 μg/mL (n-hexane), 5408 μg/mL (methanol), and 42.30 μg/mL (diclofenac). Gas chromatography–mass spectrometry (GC–MS) revealed 59 and 58 secondary metabolites in the methanol and n-hexane extracts, respectively. The higher therapeutic activity of the methanol extract was attributed to hydroxyacetic acid hydrazide, absent in the n-hexane extract. In silico docking studies identified 28 compounds with negative binding energies, indicating potential trypsin inhibition. The 2-hydroxyacetohydrazide displayed superior inhibitory effects compared to diclofenac. Further mechanistic studies are crucial to validate 2-hydroxyacetohydrazide as a potential drug candidate for rheumatoid arthritis treatment.

Toxoplasmosis and cancer are life-threatening diseases with worldwide distribution. However, currently used chemosynthetic treatments are not devoid of their own intrinsic problems. Natural metabolites are gaining attention due to their lower side effects. In this study, we investigated for the first time Zamia floridana leaves extract and its different fractions for their toxoplasmocidal activity, using Virulent RH Toxoplasma gondii, and cytotoxic activity against MCF-7 and HCT-116 cancer cell lines using MTT assay. The n-butanol fraction was the most potent fraction against T. gondii with an EC50 of 7.16 ± 0.4 µg/mL compared to cotrimoxazole (4.18 ± 0.3 µg/mL). In addition, the n-BuOH fraction showed a significant cytotoxicity against MCF-7 and HCT-116 with IC50 of 12.33 ± 1.1 and 17.88 ± 1.4 µg/mL, respectively, compared to doxorubicin (4.17 ± 0.2 and 5.23 ± 0.3 µg/mL, respectively), with higher safety index against normal cell line (WISH). Therefore, the n-BuOH fraction was investigated for its phytochemicals using extensive chromatographic techniques, which led to the isolation of six compounds that were fully characterized using different spectroscopic techniques. Three biflavonoids (1, 2 and 4) in addition to two phenolic acid derivatives (3 and 5) and a flavonoid glycoside (6) were isolated. Compounds (1, 3, 5 and 6) were reported for the first time from Z. floridana. In silico docking studies for toxoplasmocidal and cytotoxic effects of these compounds revealed that compounds (1, 2, 4 and 6) have promising inhibition potential of either thymidylate synthase-dihydrofolate reductase (TS-DHFR) or cyclin dependent kinase 2 (CDK2) target proteins. This study is considered the first report of chemical and biological investigation of Z. floridana leaves. [ABSTRACT FROM AUTHOR]

[Display omitted] • Thirty-seven pyrazolines were measured to identify inhibitory effects against the Early Growth Response-1 DNA-binding domain. • The binding mode between the title compound and EGR-1 was elucidated using in silico docking. • Pharmacophores derived from quantitative structure–activity relationship calculations were matched to the binding modes. • Compound 2 effectively reduced the mRNA expression of EGR-1-regulated inflammatory genes. To identify compounds inhibiting the activity of the Early Growth Response (EGR)-1 DNA-binding domain, thirty-seven pyrazolines were prepared and their EGR-1 DNA-binding activities were measured. Pharmacophores were derived based on quantitative structure–activity relationship calculations. As compound 2 , 1-(5-(4-methoxyphenyl)-4,5-dihydro-1 H -pyrazol-3-yl)naphthalen-2-ol, showed the best inhibitory effects against the activity of the EGR-1 DNA-binding domain, the binding mode between compound 2 and EGR-1 was elucidated using in silico docking. The pharmacophores were matched to the binding modes. Electrophoretic mobility shift assays confirmed that compound 2 dose-dependently inhibited TNFα-induced EGR-1-DNA complex formation in HaCaT cells. Reverse transcription-polymerase chain reaction demonstrated that compound 2 effectively reduced the mRNA expression of EGR-1-regulated inflammatory genes, including thymic stromal lymphopoietin (TSLP), interleukin (IL)-1β, IL-6, and IL-31, in TNFα-stimulated HaCaT cells. Therefore, compound 2 could be developed as an agent that inhibits the activity of the EGR-1 DNA-binding domain. [ABSTRACT FROM AUTHOR]

The marine ecosystem contains an assorted range of organisms, among which macroalgae stands out marine resources as an invaluable reservoir of structurally diverse bioactive compounds. Marine macroalgae are considered as primary consumers have gained more attention for their bioactive components. Sulfated polysaccharides (SPs) are complex polymers found in macroalgae that play a crucial role in their cell wall composition. This review consolidates high-tech methodologies employed in the extraction of macroalgal SPs, offering a valuable resource for researchers focuses in the pharmacological relevance of marine macromolecules. The pharmacological activities of SPs, focusing on their therapeutic action by encompassing diverse study models are summarized. Furthermore, in silico docking studies facilitates a comprehensive understanding of SPs interactions with their binding sites providing a valuable insight for future endeavors. The biological properties of algal SPs, along with a brief reference to mode of action based on different targets are presented. This review utilizes up-to-date research discoveries across various study models to elucidate the biological functions of SPs, focusing on their molecular-level mechanisms and offering insights for prospective investigations. Besides, the significance of SPs from seaweeds is highlighted, showcasing their potential beneficial applications in promoting human health. With promising biomedical prospects, this review explores the extensive uses and experimental evidence supporting the important roles of SPs in various fields. [Display omitted] [ABSTRACT FROM AUTHOR]

Fucoidan, a polymer derived from seaweed, poses a broad range of biological applications, and its potential medicinal benefits have been widely studied over the past decade. In this study, fucoidan was extracted from marine macroalga Sargassum ilicifolium and its bioactive potential for in silico molecular docking was investigated. Additionally, the computational in silico docking studies were applied on the fucoidan against anticancer and antioxidant target proteins by using Glide ligand docking, Schrodinger software. The FT-IR analysis revealed that fucoidan mainly consisted of the fucose residues (59.1%) and a few monosaccharides, such as uronic acid (11.7%) and sulphate (18.3%). The in vitro tests revealed that fucoidan possessed various antioxidative properties and anticoagulant activities. Fucoidans played an inhibitory role in the colony formation of HepG2 cells. The NADPH oxidase (−7.169 Kcal/mol) and cellular tumor antigen p53 protein (−6.205 Kcal/mol) exhibited the highest antioxidant and anticancer proteins, respectively. Overall, the present study results provide a theoretical foundation for broadening the application of fucoidan from S. ilicifolium as a pharmaceutical ingredient. [ABSTRACT FROM AUTHOR]