Inhibition of the ATPase Domain of Human Topoisomerase IIa on HepG2 Cells by 1, 2-benzenedicarboxylic Acid, Mono (2-ethylhexyl) Ester: Molecular Docking and Dynamics Simulations

Characterization and biological applications of gonadal extract of Paracentrotus lividus collected along the Mediterranean coast of Alexandria, Egypt

Marine invertebrates represent a valuable reservoir of pharmaceutical bioactive compounds with potential relevance to various medical applications. These compounds exhibit notable advantages when compared to their terrestrial counterparts, in terms of their potency, activity, and mechanism of action. Within this context, the present work aimed to extract, chemically characterize, and investigate the bioactivity of the gonadal extract of the sea urchin Paracentrotus lividus (P. lividus) collected along the Mediterranean coast of Alexandria, Egypt. Fractions of the gonadal extract were characterized by Spectrophotometry and gas chromatography-mass spectrometry (GC-MS), and their bioactivities were investigated in vitro. The analysis supported the extract richness of carotenoids and bioactive compounds. The extract showed promising anticancer activity against three different breast cancer cell lines with different levels of aggressiveness and causative factors, namely MDA-MB-231, MDA-MB-453, and HCC-1954. Gene expression analysis using RT-qPCR showed that P. lividus extract inhibited the expression of crucial factors involved in cell cycle regulation and apoptosis. In addition, the extract significantly inhibited the lipo-polysaccharides (LPS) induced inflammation in the RAW264.7 macrophage cell line and exerted anti-bacterial activity against the Gram-negative bacteria Klebsiella pneumoniae and Pseudomonas aeruginosa. Collectively, these results demonstrated the chemical richness and the wide-scale applicability of P. lividus gonadal extract as an anti-cancer, anti-bacterial, and anti-inflammatory natural extract.

Chemical profiling, cytotoxic activities through apoptosis induction in MCF-7 cells and molecular docking of Phyllostachys heterocycla bark nonpolar extract

The chemical constituents of the nonpolar fractions of the bamboo shoot skin Phyllostachys heterocycla were extensively studied. The phytochemical study was divided into two parts: the first deals with isolation of the chemical constituents using different chromatographic techniques that resulted in isolation of four compounds. The chemical structures of the pure isolated compounds were elucidated using different spectroscopic data. The second part deals with identification of the rest of the constituents using the GC technique. Additionally, both crude extract and the pure isolated compounds were investigated for cytotoxic activity. One of the isolated compounds; namely glyceryl 1-monopalmitate showed highly promising effect against the MCF-7 cells with (IC₅₀ = 19.78 µM) compared to 5-FU (26.98 µM), and it remarkably stimulated apoptotic breast cancer cell death with 31.6-fold (16.13% compared to 0.51 for the control) at pre-G1 and G2/M-phase cell cycle arrest and blocked the progression of MCF-7 cells. Moreover, the identified compounds especially 1 were found to have high binding affinity towards both TPK and VEGFR-2 through the molecular docking studies which highlight its mode of action. HighlightsChemical profiling of Phyllostachys heterocycla bark nonpolar extract was fully identified.Glyceryl 1-monopalmitate showed highly promising effect against the MCF-7 cells with (IC₅₀ = 19.78 µM) compared to 5-FU (26.98 µM).Glyceryl 1-monopalmitate significantly stimulated apoptotic breast cancer cell death with 31.6-fold by arresting cell cycle at G2/M and preG1 phases.Molecular docking simulation showed good binding affinities towards TPK and VEGFR-2 proteins.Communicated by Ramaswamy H. Sarma.

Crosstalk between biological and chemical diversity with cytotoxic and cytostatic effects of Aphanothece halophytica in vitro

Different solvent extracts from Aphanothece halophytica (A. halophytica) were evaluated for their cytotoxic effects against four human cancer cell lines. The samples demonstrated different percentages of cyanobacteria species populations. The samples containing 100% A. halophytica and 90% A. halophytica showed a significant cytotoxic effect in human breast cancer cells MDA231. The cytostatic effect was demonstrated in MDA231 and human glioblastoma T98G cells regardless of the treatment, resulting in a significant cell cycle arrest in the S phase. The chemical profiles of the extracts were proven to be diverse in qualitative and quantitative compositions. This variability was dependent on the A. halophytica´s abundance in each extract. The 100% A. halophytica extract induced cytotoxic and cytostatic effects in breast cancer cells, and those could be associated with the predominance of fatty acids, hydrocarbons and phthalates, indicating that A. halophytica is an interesting source of novel compound with anticancer effect.

Structural characterization and conformational dynamics of alpha-1 antitrypsin pathogenic variants causing alpha-1-antitrypsin deficiency

Background: Alpha-1 antitrypsin deficiency (A1ATD) is a progressive lung disease caused by inherited pathogenic variants in the SERPINA1 gene. However, their actual role in maintenance of structural and functional characteristics of the corresponding α-1 anti-trypsin (A1AT) protein is not well characterized. Methods: The A1ATD causative SERPINA1 missense variants were initially collected from variant databases, and they were filtered based on their pathogenicity potential. Then, the tertiary protein models were constructed and the impact of individual variants on secondary structure, stability, protein-protein interactions, and molecular dynamic (MD) features of the A1AT protein was studied using diverse computational methods. Results: We identified that A1ATD linked SERPINA1 missense variants like F76S, S77F, L278P, E288V, G216C, and H358R are highly deleterious as per the consensual prediction scores of SIFT, PolyPhen, FATHMM, M-CAP and REVEL computational methods. All these variants were predicted to alter free energy dynamics and destabilize the A1AT protein. These variants were seen to cause minor structural drifts at residue level (RMSD = <2Å) of the protein. Interestingly, S77F and L278P variants subtly alter the size of secondary structural elements like beta pleated sheets and loops. The residue level fluctuations at 100 ns simulation confirm the highly damaging structural consequences of all the six missense variants on the conformation dynamics of the A1AT protein. Moreover, these variants were also predicted to cause functional deformities by negatively impacting the binding energy of A1AT protein with NE ligand molecule. Conclusion: This study adds a new computational biology dimension to interpret the genotype-protein phenotype relationship between SERPINA1 pathogenic variants with its structural plasticity and functional behavior with NE ligand molecule contributing to the Alpha-1-antitrypsin deficiency. Our results support that A1ATD complications correlates with the conformational flexibility and its propensity of A1AT protein polymerization when misfolded.

LC-MS/MS Phytochemical Profiling, Antioxidant Activity, and Cytotoxicity of the Ethanolic Extract of Atriplex halimus L. against Breast Cancer Cell Lines: Computational Studies and Experimental Validation

Atriplex halimus L., also known as Mediterranean saltbush, and locally as "Lgtef", an halophytic shrub, is used extensively to treat a wide variety of ailments in Morocco. The present study was undertaken to determine the antioxidant activity and cytotoxicity of the ethanolic extract of A. halimus leaves (AHEE). We first determined the phytochemical composition of AHEE using a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) technique. The antioxidant activity was evaluated using different methods including DPPH scavenging capacity, β-carotene bleaching assay, ABTS scavenging, iron chelation, and the total antioxidant capacity assays. Cytotoxicity was investigated against human cancer breast cells lines MCF-7 and MDA-MB-231. The results showed that the components of the extract are composed of phenolic acids and flavonoids. The DPPH test showed strong scavenging capacity for the leaf extract (IC₅₀ of 0.36 ± 0.05 mg/mL) in comparison to ascorbic acid (IC₅₀ of 0.19 ± 0.02 mg/mL). The β-carotene test determined an IC₅₀ of 2.91 ± 0.14 mg/mL. The IC₅₀ values of ABTS, iron chelation, and TAC tests were 44.10 ± 2.92 TE µmol/mL, 27.40 ± 1.46 mg/mL, and 124 ± 1.27 µg AAE/mg, respectively. In vitro, the AHE extract showed significant inhibitory activity in all tested tumor cell lines, and the inhibition activity was found in a dose-dependent manner. Furthermore, computational techniques such as molecular docking and ADMET analysis were used in this work. Moreover, the physicochemical parameters related to the compounds' pharmacokinetic indicators were evaluated, including absorption, distribution, metabolism, excretion, and toxicity prediction (Pro-Tox II).

Protective Effects of Green Tea Supplementation against Lead-Induced Neurotoxicity in Mice

The use of natural products as therapeutic agents is rapidly growing recently. In the current study, we investigated the protective effects of green tea supplementation on lead-induced toxicity in mice. Forty albino mice were divided into four groups as follows: A: control group; B: green tea receiving group; C: lead-intoxicated group; and D: lead-intoxicated group supplemented with green tea. At the end of the experiment, the animals were tested for neurobehavioral and biochemical alterations. Green tea was analyzed through Gas Chromatography–Mass Spectrometry (GC/MS) analysis. We found that supplementation with green tea ameliorated the lead-associated increase in body weight and blood glucose. Green tea supplementation also changed the blood picture that was affected due to lead toxicity and ameliorated lead-induced dyslipidemia. The group of mice that were supplemented with green tea has shown positive alterations in locomotory, anxiety, memory, and learning behaviors. The GC/MS analysis revealed many active ingredients among which the two most abundant were caffeine and 1,2-benzenedicarboxylic acid, mono(2-ethylhexyl) ester. We concluded that green tea supplementation has several positive effects on the lead-induced neurotoxicity in mice and that these effects may be attributed to its main two active ingredients.

Topoisomerase Assays

Topoisomerases are enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of DNA topoisomerases: type I enzymes, which make single-stranded cuts in DNA, and type II enzymes, which cut and decatenate double-stranded DNA. DNA topoisomerases are important targets of approved and experimental anti-cancer agents. Provided in this article are protocols to assess activities of topoisomerases and their inhibitors. Included are an assay for topoisomerase I activity based on relaxation of supercoiled DNA; an assay for topoisomerase II based on the decatenation of double-stranded DNA; and approaches for enriching and quantifying DNA-protein covalent complexes formed as obligatory intermediates in the reactions of type I and II topoisomerases with DNA; and assays for measuring DNA cleavage in vitro. Topoisomerases are not the only proteins that form covalent adducts with DNA in living cells, and the approaches described here are likely to find use in characterizing other protein-DNA adducts and exploring their utility as targets for therapy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Assay of topoisomerase I activity Basic Protocol 2: Assay of topoisomerase II activity Basic Protocol 3: In vivo determination of topoisomerase covalent complexes using the in vivo complex of enzyme (ICE) assay Support Protocol 1: Preparation of mouse tissue for determination of topoisomerase covalent complexes using the ICE assay Support Protocol 2: Using recombinant topoisomerase standard for absolute quantification of cellular TOP2CC Basic Protocol 4: Quantification of topoisomerase-DNA covalent complexes by RADAR/ELISA: The rapid approach to DNA adduct recovery (RADAR) combined with the enzyme-linked immunosorbent assay (ELISA) Basic Protocol 5: Analysis of protein-DNA covalent complexes by RADAR/Western Support Protocol 3: Adduct-Seq to characterize adducted DNA Support Protocol 4: Nuclear fractionation and RNase treatment to reduce sample complexity Basic Protocol 6: Determination of DNA cleavage by purified topoisomerase I Basic Protocol 7: Determination of inhibitor effects on DNA cleavage by topoisomerase II using a plasmid linearization assay Alternate Protocol: Gel electrophoresis determination of topoisomerase II cleavage.

Chemical, Nutrient and Physicochemical Properties of Brown Seaweed, Sargassum polycystum C. Agardh (Phaeophyceae) Collected from Port Dickson, Peninsular Malaysia

Recent increased interest in seaweed is motivated by attention generated in their bioactive components that have potential applications in the functional food and nutraceutical industries. In the present study, nutritional composition, metabolite profiles, phytochemical screening and physicochemical properties of freeze-dried brown seaweed, Sargassum polycystum were evaluated. Results showed that the S. polycystum had protein content of 8.65 ± 1.06%, lipid of 3.42 ± 0.01%, carbohydrate of 36.55 ± 1.09% and total dietary fibre content of 2.75 ± 0.58% on dry weight basis. The mineral content of S. polycystum including Na, K, Ca, Mg Fe, Se and Mn were 8876.45 ± 0.47, 1711.05 ± 0.07, 1079.75 ± 0.30, 213.85 ± 0.02, 277.6 ± 0.12, 4.70 ± 0.00 and 4.45 ± 0.00 mg 100/g DW, respectively. Total carotenoid, chlorophyll a and b content in S. polycystum were detected at 45.28 ± 1.77, 141.98 ± 1.18 and 111.29 µg/g respectively. The total amino acid content was 74.90 ± 1.45%. The study revealed various secondary metabolites and major constituents of S. polycystum fibre to include fucose, mannose, galactose, xylose and rhamnose. The metabolites extracted from the seaweeds comprised n-hexadecanoic acid, 1,2-benzenedicarboxylic acid, mono(2-ethylhexyl) ester, benzenepropanoic acid, 3,5-bis(1,1-dimethylethyl)-4-hydroxy- methyl ester, 1-dodecanol, 3,7,11-trimethyl-, which were the most abundant. The physicochemical properties of S. polycystum such as water-holding and swelling capacity were comparable to several commercial fibre-rich products. In conclusion, results of this study indicate that S. polycystum is a potential candidate as functional food sources for human consumption and its cultivation needs to be encouraged.

Pseudo-ginsenoside Rh2 Induces Protective Autophagy in Hepatocellular Carcinoma HepG2 Cells

BACKGROUND

Pseudo-ginsenoside-Rh2 (pseudo-G-Rh2), a novel derivative of ginsenoside Rh2, is reported to exert a pro-apoptotic effect on various malignancies. However, whether this anti-cancer action of pseudo-G-Rh2 involves autophagy remains to be determined and explored.

OBJECTIVES

Investigation of pseudo-G-Rh2-induced apoptosis and autophagy and the underlying mechanism.

METHODS

In the present study, the MTT assay was used for evaluating cell viability and the lactate dehydrogenase (LDH) assay was performed to assess cell toxicity. Autophagy evaluation was performed using monodansylcadaverine (MDC) staining and transmission electron microscopy (TEM). The levels of autophagy-associated and apoptosis-associated proteins were determined using Western blotting. The Annexin V FITC/propidium iodide (PI) assay was used to assess apoptosis.

RESULTS

The Annexin V FITC/PI assay revealed that the percentage of apoptotic cells in HepG2 cells at concentrations 0, 20, 40, and 60 μM was 3.75%±1.37%, 5.70%±1.04%, 12.30%±2.10%, and 34.26%±4.73%, respectively. Pseudo-G-Rh2 was observed to significantly increase the expressions of BAX, cleaved-caspase-3, and cleaved-caspase-9, while it decreased the Bcl-2 expression. MDC and TEM analyses revealed that pseudo-G-Rh2 at concentrations 20, 40, and 60 μM significantly facilitated the accumulation of autophagosomes and autolysosomes within the HepG2 cells. Moreover, pseudo-G-Rh2 significantly increased the expressions of LC3 Ⅱ/LC3 Ⅰ, and Beclin-1 and decreased the expression of p62. The Annexin V FITC/PI assay also revealed that in comparison to the pseudo-G-Rh2 group, the concurrent treatment with pseudo-G-Rh2 and an autophagy inhibitor (CQ or 3-MA) significantly induced distinct apoptosis. In addition, pseudo-G-Rh2 activated AMPK and inhibited the PI3K/Akt/mTOR pathway in a concentration-dependent manner. Pseudo-G-Rh2 is similar to the current patents, which enhanced its anti-cancer activity by combining with autophagy inhibitors.

CONCLUSION

Pseudo-G-Rh2 could induce protective autophagy in HepG2 cells, at least in part, via AMPK and the PI3K/Akt/mTOR pathway.

Chemical Composition and Evaluation of the α-Glucosidase Inhibitory and Cytotoxic Properties of Marine Algae Ulva intestinalis, Halimeda macroloba, and Sargassum ilicifolium

Seaweed has tremendous potentials as an alternative source of high-quality food products that have attracted research in recent times, due to their abundance and diversity. In the present study, three selected seaweed species commonly found in the Malaysian Peninsular, Ulva intestinalis, Halimeda macroloba, and Sargassum ilicifolium, were subjected to preliminary chemical screening and evaluated for α-glucosidase inhibitory and cytotoxic activities against five cancer cell lines. Chemical composition of U. intestinalis, H. macroloba, and S. ilicifolium methanolic extracts was evaluated by Gas Chromatography-Mass Spectrometry (GC-MS) analysis. Our results revealed the highest total carotenoids (162.00 μg g-1 DW), chlorophyll a (313.09 ± 2.53 μg g-1 DW), and chlorophyll b (292.52 ± 8.84 μg g-1 DW) concentrations in U. intestinalis. In the α-glucosidase inhibitory activity, S. ilicifolium demonstrated the lowest efficacy with an IC50 value of 38.491 ppm compared to other species of seaweed. H. macroloba extract, on the other hand, was found to be the most cytotoxic toward MCF-7 and HT 29 cells with IC50 of 37.25 ± 0.58 and 21.32 ± 0.25 μg/mL, respectively, compared to other cell lines evaluated. Furthermore, H. macroloba extract was also found to be less toxic to normal cell (3T3) with IC50 of 48.80 ± 0.11 μg/mL. U. intestinalis extract exhibited the highest cytotoxicity toward Hep G2 cells with IC50 of 23.21 ± 0.11 μg/mL, whereas S. ilicifolium was less toxic to MDA- MB231 cell with IC50 of 25.23 ± 0.11 μg/mL. Subsequently, the GC-MS analysis of the methanolic extracts of these seaweed samples led to the identification of 27 metabolites in U. intestinalis, 22 metabolites in H. macroloba, and 24 metabolites in S. ilicifolium. Taken together, the results of this present study indicated that all the seaweed species evaluated are good seaweed candidates that exhibit potential for cultivation as functional food sources for human consumption and need to be promoted.

Discovery of new promising USP14 inhibitors: computational evaluation of the thumb-palm pocket

Ubiquitin-specific protease 14 (USP14) is a member of the deubiquitinating enzymes (DUBs) involved in disrupting the ubiquitin-proteasome regulation system, responsible for the degradation of impaired and misfolded proteins, which is an essential mechanism in eukaryotic cells. The involvement of USP14 in cancer progression and neurodegenerative disorders has been reported. Thereof USP14 is a prime therapeutic target; hence, designing efficacious inhibitors against USP14 is central in curbing these conditions. Herein, we relied on structural bioinformatics methods incorporating molecular docking, molecular mechanics generalized born surface area (MM-GBSA), molecular dynamics simulation (MD simulation), and ADME to identify potential allosteric USP14 inhibitors. A library of over 733 compounds from the PubChem repository with >90% match to the IU1 chemical structure was screened in a multi-step framework to attain prospective drug-like inhibitors. Two potential lead compounds (CID 43013232 and CID 112370349) were shown to record better binding affinity compared to IU1, but with subtle difference to IU1-47, a 10-fold potent compound when compared to IU1. The stability of the lead molecules complexed with USP14 was studied via MD simulation. The molecules were found to be stable within the binding site throughout the 50 ns simulation time. Moreover, the protein-ligand interactions across the simulation run time suggest Phe331, Tyr476, and Gln197 as crucial residues for USP14 inhibition. Furthermore, in-silico pharmacological evaluation revealed the lead compounds as pharmacological sound molecules. Overall, the methods deployed in this study revealed two novel candidates that may show selective inhibitory activity against USP14, which could be exploited to produce potent and harmless USP14 inhibitors.Communicated by Ramaswamy H. Sarma.

Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors

The enzyme phospholipase C gamma 1 (PLCγ1) has been identified as a potential drug target of interest for various pathological conditions such as immune disorders, systemic lupus erythematosus, and cancers. Targeting its SH3 domain has been recognized as an efficient pharmacological approach for drug discovery against PLCγ1. Therefore, for the first time, a combination of various biophysical methods has been employed to shed light on the atomistic interactions between PLCγ1 and its known binding partners. Indeed, molecular modeling of PLCγ1 with SLP76 peptide and with previously reported inhibitors (ritonavir, anethole, daunorubicin, diflunisal, and rosiglitazone) facilitated the identification of the common critical residues (Gln805, Arg806, Asp808, Glu809, Asp825, Gly827, and Trp828) as well as the quantification of their interaction through binding energies calculations. These features are in agreement with previous experimental data. Such an in depth biophysical analysis of each complex provides an opportunity to identify new inhibitors through pharmacophore mapping, molecular docking and MD simulations. From such a systematic procedure, a total of seven compounds emerged as promising inhibitors, all characterized by a strong binding with PLCγ1 and a comparable or higher binding affinity to ritonavir (∆G_bind < -25 kcal/mol), one of the most potent inhibitor reported till now.