Determining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study

Elucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach

In the present study, we have analyzed the interaction of a phytochemical, stigmasterol (Stig), with human serum albumin (HSA) under physiological conditions using fluorescence quenching, circular dichroism and molecular modeling methods. Cytotoxic studies with Stig in mouse macrophages (RAW 246.7) and HeLa cell lines showed anti-inflammatory and anti-cancer properties. Further, the intrinsic fluorescence of HSA was quenched by Stig, which was considered a static quenching mechanism. The site-specific marker experiments revealed that Stig binds to the IIIA subdomain of HSA with a binding constant of K_Stig=1.8 ± 0.03 × 10⁵ M^-1 and free energy of -7.26 ± 0.031 Kcal/mol. The secondary structure of HSA was partially unfolded after binding of Stig, which indicates an alteration in the microenvironment of the protein binding site. Molecular docking experiments found that Stig binds strongly with HSA at the IIIA domain of the hydrophobic pocket with one hydrogen bond. The rigidity of the protein-Stig complex and free energies were analyzed by molecular dynamic simulation (MDS) for 100 ns, where the HSA-Stig was stabilized after 40 ns. MDS studies revealed that HSA does not significantly change the secondary structure when it binds with Stig, which is in agreement with the circular dichroism data. Overall, the results obtained gave qualitative and quantitative insight into the binding interaction between HSA and Stig, which is essential in understanding the latter as a therapeutic molecule.Communicated by Ramaswamy H. Sarma.

Berberine as a potential agent for breast cancer therapy

Breast cancer (BC) is a common malignancy that mainly occurred in women and it has become the most diagnosed cancer annually since 2020. Berberine (BBR), an alkaloid extracted from the Berberidacea family, has been found with broad pharmacological bioactivities including anti-inflammatory, anti-diabetic, anti-hypertensive, anti-obesity, antidepressant, and anticancer effects. Mounting evidence shows that BBR is a safe and effective agent with good anticancer activity against BC. However, its detailed underlying mechanism in BC treatment remains unclear. Here, we will provide the evidence for BBR in BC therapy and summarize its potential mechanisms. This review briefly introduces the source, metabolism, and biological function of BBR and emphasizes the therapeutic effects of BBR against BC via directly interacting with effector proteins, transcriptional regulatory elements, miRNA, and several BBR-mediated signaling pathways. Moreover, the novel BBR-based therapeutic strategies against BC improve biocompatibility and water solubility, and the efficacies of BBR are also briefly discussed. Finally, the status of BBR in BC treatment and future research directions is also prospected.

Molecular insights into the crystalline nanocellulose and human lysozyme interactions: An experimental and theoretical research

In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.

Modulation of Long Non-Coding RNAs by Different Classes of Secondary Metabolites from Plants: A Mini-Review on Antitumor Effects

The broad pharmacological spectrum of plants is related to their secondary metabolism, which is responsible for the synthesis of different compounds that have multiple effects on cellular physiology. Among the biological effects presented by phytochemicals, their use for the prevention and treatment of cancer can be highlighted. This occurs due to several mechanisms of antitumor action demonstrated by these compounds, including regulation of the cell signaling pathways and inhibition of tumor growth. In this way, long non-coding RNAs (lncRNAs) appear to be promising targets for the treatment of cancer. Their deregulation has already been related to a variety of clinical-pathological parameters. However, the effects of secondary metabolites on lncRNAs are still restricted. For this reason, the present review aimed to gather data on phytochemicals with action on lncRNAs in order to confirm their possible antitumor potential. According to the literature, terpenoid and flavonoid are the main examples of secondary metabolites involved with lncRNAs activity. In addition, the lncRNAs H19, CASC2, HOTAIR, NKILA, CCAT1, MALAT1, AFAP1-AS1, MEG3, and CDKN2B-AS1 can be highlighted as important targets in the search for new anti-tumor agents since they act as modulating pathways related to cell proliferation, cell cycle, apoptosis, cell migration and invasion. Finally, challenges for the use of natural products as a commercial drug were also discussed. The low yield, selectivity index and undesirable pharmacokinetic parameters were emphasized as a difficulty for obtaining these compounds on a large scale and for improving the potency of its biological effect. However, the synthesis and/or development of formulations were suggested as a possible approach to solve these problems. All of these data together confirm the potential of secondary metabolites as a source of new anti-tumor agents acting on lncRNAs.

Revealing the binding properties between resorcinol and DNA

Resorcinol (1,3-dihydroxybenzene) is a common coupling agent in permanent hair dyes, and has arrested people's attention for its potential hazard to human health. However, the action mechanism of resorcinol and human DNA has not been elucidated. In this research, the binding properties between resorcinol and calf thymus DNA (ct-DNA) were studied for the first time through various spectral and molecular docking techniques. Spectral studies showed that the initial fluorescence quenching of resorcinol against DNA was a static one. The result of ΔH < 0 and ΔS > 0 was produced from thermodynamic experimental data, therefore it could be concluded that electrostatic force was the major driving force, while binding constant K_b was 1.56 × 10⁴  M^-1 at 298 K. The electrostatic binding network between resorcinol and ct-DNA was established explicitly through competitive substitution analysis and other spectral approaches. The results of FT-IR absorption spectra indicated that resorcinol had bound to the DNA phosphate skeleton. Molecular docking clearly revealed that binding occurred between hydroxyl groups of resorcinol and phosphorus oxygen bonds (P-O) of the DNA skeleton. These findings may deepen our understanding of the action mechanism between resorcinol and ct-DNA and provide some useful data on the effect of resorcinol on human diseases.

Effects of Berberine on the Gastrointestinal Microbiota

The gastrointestinal microbiota is a multi-faceted system that is unraveling novel contributors to the development and progression of several diseases. Berberine has been used to treat obesity, diabetes mellitus, atherosclerosis, and metabolic diseases in China. There are also clinical trials regarding berberine use in cardiovascular, gastrointestinal, and endocrine diseases. Berberine elicits clinical benefits at standard doses and has low toxicity. The mechanism underlying the role of berberine in lipid‐lowering and insulin resistance is incompletely understood, but one of the possible mechanisms is related to its effect on the gastrointestinal microbiota. An extensive search in electronic databases (PubMed, Scopus, Embase, Web of Sciences, Science Direct) was used to identify the role of the gastrointestinal microbiota in the berberine treatment. The aim of this review was to summarize the pharmacologic effects of berberine on animals and humans by regulation of the gastrointestinal microbiota.

Pharmacokinetic-Pharmacodynamic Modeling of the Antioxidant Activity of Quzhou Fructus Aurantii Decoction in a Rat Model of Hyperlipidemia

BACKGROUND

Quzhou Fructus Aurantii (QFA) is an herb that is commonly used to alleviate inflammation in individuals dealing with obesity.To date, however, no systematic pharmacokinetic (PK) or pharmacodynamic (PD) analyses of the clinical efficacy of QFA under hyperlipemia-associated oxidative stress conditions have been conducted. The present study, was therefore designed to construct a PK-PD model for this herb, with the goal of linking QFA PK profiles to key therapeutic outlines to guide the therapeutic use of this herb in clinical settings.

METHODS

Rats were fed a high-fat diet in order to establish a model of hyperlipidemia, after which they were randomized into a normal control group (NCG), a normal treatment group (NTG), a model control group (MCG), and a model treated group (MTG) (n = 6 each). QAF decoction was used to treat rats in the NTG and MTG groups (25 g/kg), while equivalent volumes of physiological saline were administered to rats in the NCG and MCG groups. Plasma samples were collected from the mandibular vein for animals at appropriate time points and analyzed via high-performance liquid chromatography (HPLC). We evaluated PK properties for three QAF components and compared these dynamics between the NTG and MTG groups, while also measuring levels of lipid peroxidation (LPO) in the plasma of rats in all four treatment groups. We then constructed a PK-PD model based upon plasma neohesperidin, luteolin, and nobiletin concentrations and LPO levels using a three-compartment PK model together with a Sigmoid E_max PD model. This model thereby enabled us to assess the antioxidative impact of neohesperidin, luteolin, and nobiletin on hyperlipidemia in rats.

RESULTS

When comparing the NTG and MTG groups, we detected significant differences in the following parameters pertaining to neohesperidin, luteolin, and nobiletin:t_1/2β, V1,  t_1/2γ, CL1 (p < 0.01) and AUC_0-t, T_max, C_max (p < 0.05). Relative to NTG group rats, AUC_0-t, T_maxandC_maxvalues significantly higher for MTG group rats (p < 0.01), while t_1/2β, V1, and  t_1/2γ values were significantly lower in MTG group rats (p < 0.01) in MTG rats. QAF decoction also exhibited excellent PD efficacy in MTG rats, with significant reductions in plasma LPO levels relative to NTG rats (p < 0.01) following treatment. This therapeutic efficacy may be attributable to the activity of neohesperidin, luteolin, and nobiletin, as LPO levels and plasma concentrations of these compounds were negatively correlated in treated rats. Based upon Akaike Information Criterion (AIC) values, we determined that neohesperidin, luteolin, and nobiletin PK processes were consistent with a three-compartment model. Together, these findings indicated that three active components in QAF decoction (neohesperidin, luteolin, and nobiletin) may exhibit antioxidant activity in vivo.

CONCLUSION

Our in vivo data indicated that neohesperidin, luteolin and nobiletin components of QAF decoctions exhibit distinct PK and PD properties. Together, these findings suggest that hyperlipidemia-related oxidative stress can significantly impact QFA decoction PK and PD parameters. Our data additionally offer fundamental insights that can be used to design appropriate dosing regimens for individualized clinical QAF decoction treatment.

Anterior gradient 2 is a novel pro-tumor factor in pancreatic cancer under NF-κB subunit RelA trans-regulation that can be suppressed by eugenic acid

This study aimed to examine eugenic acid (EA) as an alternative therapeutic approach against pancreatic cancer. The pancreatic cancer xenograft mouse model was employed to determine the impacts of treatment with EA on the growth of tumors. Expressions of NF-κB subunit RelA as well as Anterior gradient 2 (AGR2) were quantified in pancreatic cells treated with EA. Chromatin immunoprecipitation and luciferase report assay were performed to examine the regulation of AGR2 by RelA. The function of AGR2 as a downstream effector EA treatment was further assessed through overexpression of AGR2 in pancreatic cells. EA suppressed the growth of xenograft pancreatic tumor, and promoted the overall survival of animals with xenograft tumors. Furthermore, EA downregulated the expression of AGR2 in pancreatic cancer cells via the RelA binding site. Ectopic AGR2 overexpression attenuated the EA-elicited inhibition on the growth of xenograft pancreatic tumor, and negated the EA-induced enhancement of mouse survival. EA ameliorates pancreatic cancer through suppression of AGR2 expression, and future studies in clinical settings are needed to further assess the anti-cancer efficacy of EA.

Modulatory effects of Xihuang Pill on lung cancer treatment by an integrative approach

Lung cancer has a rapidly increasing incidence and remains the highest ranked cancer in terms of mortality worldwide. Xihuang Pill(XHW), a famous four-herb traditional Chinese formulation, has been used to treat lung cancer in China for more than 100 years. It is usually prescribed as a complementary and alternative medicine for cancer therapy. However, the main active ingredients of XHW that treat lung cancer and their regulatory effects remain unclear. Here, we revealed modulatory effects effects of XHW on lung cancer in a mouse model of Lewis lung cancer (LLC) by a comprehensive strategy combining network pharmacology with metabolomics. The results demonstrated that XHW inhibited tumour growth in this model. Additionally, 11 differentially expressed metabolites were identified in the XHW group compared to those in the model group or normal group by untargeted metabolomics. They were enriched in amino acid-related metabolic pathways, and the top three pathways were phenylalanine metabolism; phenylalanine, tyrosine and tryptophan biosynthesis; and aminoacyl-tRNA biosynthesis. A total of 107 active components derived from Niuhuang, Shexiang, Ruxiang and Moyao, directly acted on 13 important targets (NR3C2, AKR1D1, MPO, PNP, NT5E, TAAR1, ADRB2, ADRB1, ADRA1A, ADRA2B, ADRA2A, MAOA and MAOB) to regulate 4 metabolites (L-phenylalanine, l-adrenaline, corticosterone and guanosine). Our results suggested that the key metabolites of XHW involved in the treatment of lung cancer were regulated by a multi-component and multi-target interaction network. This research elucidated the modulatory effect and therapeutic advantages of XHW treatment for lung tumours through an integrated approach.

Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods

Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (K_b ) was 0.78 × 10⁴ L·mol^-1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP-DNA were 67.92 kJ·mol^-1 and 302.96 J·mol^-1 ·K^-1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.

Multispectroscopic analysis, atomic force microscopy, molecular docking and molecular dynamic simulation studies of the interaction between [SnMe2Cl2(Me2phen)] complex and ct-DNA in the presence of glucose

In this study, the spectroscopic methods (UV-vis, fluorimetric), Atomic force microscopy, and computational studies (molecular docking and molecular dynamic simulation) were used to investigate the interaction of [SnMe₂Cl₂(Me₂phen)] complex with CT-DNA in the presence of glucose. The results showed the complex in the medium containing glucose has less effect on calf thymus DNA (ct-DNA) than the medium without glucose. Cytotoxicity of [SnMe₂Cl₂(Me₂phen)] complex on MCF-7 cells was examined and showed Sn(IV) complex possesses potential cytotoxicity against this cell line. Molecular docking study showed that Sn(IV) complex interacts with DNA by groove binding mode. Radius of gyration (Rg) was smaller upon binding of the Sn(IV) complex suggesting a more compact structure of DNA in the presence of Sn(IV) complex.Communicated by Ramaswamy H. Sarma.

New aryl Schiff bases of thiadiazole derivative of ibuprofen as DNA binders and potential anticancer drug candidates

The work presented in this paper describes the synthesis of two new aryl Schiff bases [(E)-N-(4-(benzyloxy)-3-methoxybenzylidene)-5-(1-(4-isobutylphenyl)ethyl)-1,3,4-thiadiazol-2-amine] (ASB-1) and [(E)-N-(4-(benzyloxy)benzylidene)-5-(1-(4-isobutylphenyl)ethyl)-1,3,4-thiadiazol-2-amine] (ASB-2). These compounds were characterized by different analytical techniques and then studied for DNA binding. Binding studies were carried out at neutral pH (7.0) and at 37 °C by theoretical and experimental methods including DFT, molecular docking, spectroscopy (UV-visible, fluorescence), cyclic voltammetry (CV) and viscometry. Further investigations of these compounds were done on hepatocellular carcinoma; Huh-7 cancer cell line. Binding constant, free energy change and binding site size, i.e. K_b, ΔG and n were evaluated which indicated that both ASB-1 and ASB-2 bind significantly and spontaneously with the DNA. However, data revealed relatively greater binding of ASB-1 with DNA. Spectral and voltammetric results were found supportive of each other. Binding site sizes and viscosity measurements verified the mixed binding mode of interactions as observed in molecular docking analysis, i.e. intercalation with groove binding. DNA binding studies were very well correlated with the in-vitro studies performed on Huh-7 cell line as well as normal HEK-293 cell lines. The compound ASB-1 not only showed greater binding affinity toward DNA but also showed greater anticancer potency with least IC₅₀ value as compared to ASB-2.

Synthesis, characterization, photoluminescence, anti-tumor activity, DFT calculations and molecular docking with proteins of zinc(ii) halogen substituted terpyridine compounds

Study on the synthesis, characterization, photoluminescence and anti-tumor activity of a series of zinc(ii) halogen substituted terpyridine complexes.