In Silico docking studies of selected flavonoids--natural healing agents against breast cancer

Molecular docking studies, DFT, and ADMET calculations of some flavonoids and their characteristic structural features involved in inhibition of pro-inflammatory enzymes

Inflammation is an immune system response triggered by pathogens, damaged cells, or stimuli. Some regulatory enzymes, such as phosphodiesterase, hyaluronidase, collagenase, and lipoxygenase, play an essential role in the inflammatory process. Polyphenolic compounds, such as flavonoids, are active suppressors of inflammatory cytokines, modulators of transcription factors, and inflammation-related pathways. A set of flavonoid structures was screened and docked against inflammation pathway enzymes. Amentoflavone has been shown to cause interactions with phosphodiesterase enzymes, while Bilobetin and Silibinin demonstrated an increase in binding energy with collagenase enzymes. The retrieved compounds from the docking study were subjected to DFT theory. The results showed that the LUMO orbital is located on the flavonoid part. The thermochemical parameters indicated that Silibinin is more stable than other compounds. The ADMET profile predicted that Silibinin can be used orally among the compounds. Silibinin can be introduced as a promising anti-inflammatory agent demonstrating phosphodiesterase and collagenase inhibitory properties.

Pearlin, K. Ponmozhi. Phytocompounds from Withania somnifera against breast cancer: An in-silico study

Introduction and Aim: Withania somnifera, called as Indian Ginseng is a very important plant in traditional medicinal practices. The plant possesses a wide range of activity and has been used to treat multiple diseases. Ginseng possesses anti-inflammatory, neuroprotective, hypoglycemic, antiarthritic, hepatoprotective, antioxidant, anti-stress, immunostimulatory and anti-cancer therapeutic activities. Cancer is a health burden prevalent worldwide and, breast cancer is the top major cause of death among women and people in the low and middle-income countries are affected in higher number because they have low treatment access. This is an in-silico study and focused on studying the interaction between five phytocompounds namely, anaferine, isopelletierin, sitoindoside IX, somniferine, withanone present in W.somnifera and the 3 proteins involved in breast cancer pathway viz., C-Raf, AKt 2 and GSK 3? through molecular docking. Methodology: We retrieved the above three proteins from PDB, retrieved five ligands from PubChem, and docking was done. Docking of the phytocompounds against the target proteins were carried out using Auto dock vina. Results: From the docking results, we found that the phytocompounds; sitoindoside IX, somniferine, withanone from Withania somnifera are effective in inhibiting the proteins causing breast cancer whereas anaferine and isopelletierin are less effective in inhibiting the breast cancer.  Conclusion: This study concludes that the phytocompounds sitoindoside IX, somniferine, withanone from W. somnifera have the potential ability to treat breast cancer. These findings will aid in the development of natural based therapy against breast cancer.

Morelloflavone as Potential Anticancer Agent Against MCF-7 Breast Cancer Cell Lines: In vitro and In silico Studies

Background:

Breast cancer is most commonly reported to contribute to people's death. Nowadays, cancer treatment is focused on investigating anticancer drugs from natural compounds. Various methods, including in vitro, in vivo, and in silico methods, are used to assess the potential of anticancer compounds. The efficacy of bioactive compounds from medicinal plant origin lies in their affordability and minimized side effects. The Garcinia genus contains bioactive compounds, such as xanthones, benzophenones, triterpenes, biflavonoids, and benzoquinones.

Purpose:

The study aimed at investigating an active compound that can inhibit cancer cell growth and proteins that contribute to cancer cell growth, such as Caspase-9, TNF-α, ER-α, and HER-2.

Methods:

This study is divided into three steps. The first step is the isolation of the active compound from G. cymosa. The second step is an assessment of cytotoxic activity against MCF-7 cell by using MTT assay, and the last one is an investigation of the molecular mechanism of an active compound against Caspase-9, TNF-α, ER-α, and HER-2 by using in silico studies utilizing various programs, such as PyRx 0.8, PYMOL, and Discovery Studio.

Results:

Morelloflavone from G. cymosa stem barks has exhibited anticancer activity (55.84 μg/mL) eight times lower than doxorubicin (6.99 μg/mL), but it can block the activity of Caspase-9, TNF-α, ER- α, and HER-2. The binding affinity of morelloflavone is the strongest of all ligands.

Conclusion:

The natural flavonoid, morelloflavone, may be a new lead candidate for anticancer agent inhibiting action mechanism of Caspase-9, TNF-α, ER-α, and HER-2, respectively.

Effectiveness and Anticancer Activity of a Novel Phenolic Compound from Garcinia porrecta Against the MCF-7 Breast Cancer Cell Line in vitro and in silico

Background

Cancer is a leading cause of death worldwide, with breast cancer being the most common invasive cancer type in women. Several therapeutic strategies have been explored to reduce the mortality rates of breast cancer. Chemotherapy is the most commonly used systemic treatment, but associated with numerous side-effects. Development of anticancer agents with high efficacy and minimal negative effects is therefore an important focus of research. Natural materials provide an excellent source of bioactive compounds. For instance, Garcinia porrecta from the Clusiaceae family has multiple pharmacological activities, including antioxidant, anti-inflammatory, antibacterial, antiviral, anti-HIV, antidepressant, and anticancer properties.

Purpose

The main objective of this study was to investigate the potential anticancer effects of compounds extracted from the bark of G. porrecta.

Materials and Methods

Our experiments were divided into three steps: (1) chromatographic isolation of compounds using various separation techniques, such as extraction, separation and purification, (2) characterization via infrared (IR), nuclear magnetic resonance (NMR) and mass spectroscopy, and (3) evaluation of anticancer activity in vitro (MTT assay) and in silico (via analysis of molecular docking against caspase-9, tumor necrosis factor alpha (TNF-α), estrogen receptor alpha (ER-α), and human epidermal growth factor receptor 2 (HER-2)).

Results

Depsidone (1) and benzophenone (2) from the ethyl acetate extract of bark of G. porrecta were identified as bioactive components. Examination of the activities of these compounds against MCF-7 cells revealed an IC₅₀ value of 119.3 µg/mL for benzophenone, whereas IC₅₀ for depsidone could not be estimated. Benzophenone activity was lower than that of the positive control doxorubicin (6.9 µg/mL). Depsidone showed the highest binding affinity for HER-2 (−9.2 kcal.mol-1) and benzophenone for ER-α (−8.0 kcal.mol-1).

Conclusion

Benzophenone displays potency as an anticancer agent through blocking ER-α.

Anticancer drug discovery from Iranian Chrysanthemum cultivars through system pharmacology exploration and experimental validation

Breast cancer is the most common carcinoma in women, and natural products would be effective preventing some side effects of cancer treatment. In the present study, cytotoxic activities of different Iranian Chrysanthemum morifolium cultivars were evaluated in human breast cancer cell lines (MCF-7) and human lymphocytes. A systems pharmacology approach was employed between major compounds of these cultivars (chlorogenic acid, luteolin, quercetin, rutin, ferulic acid, and apigenin) and known breast cancer drugs (tucatinib, methotrexate, tamoxifen, and mitomycin) with 22 breast cancer-related targets to analyze the mechanism through which Chrysanthemum cultivars act on breast cancer. Target validation was performed by the molecular docking method. The results indicated that Chrysanthemum extracts inhibited the proliferation of MCF7 cells in a dose- and cultivar-dependent manner. In all studied cultivars, the most effective extract concentration with the lowest viability of MCF-7 cells, was as much as 312 µg ml^-1. Also, higher concentrations of the extracts (> 1000 µg ml^-1) reduced the lymphocyte cell viability, demonstrating that these doses were toxic. The gene ontology analysis revealed the therapeutic effects of Chrysanthemum's active compounds on breast cancer by regulating the biological processes of their protein targets. Moreover, it has been documented that rutin, owing to its anticancer effects and several other health benefits, is a promising multi-targeted herbal ingredient. Finally, the present study compared different Iranian Chrysanthemum cultivars to provide new insights into useful pharmaceutical applications.

In-silico protein-ligand docking studies against the estrogen protein of breast cancer using pharmacophore based virtual screening approaches

Breast cancer in woman is the most common cancer and in 2018 there were around 2 million new cases recorded. The maximum rate of breast cancer is reported in Belgium followed by Luxembourg. It is the second most general cancer, Lung cancer being the first. If the cancer tumor is located only in the breast, the survival rate would be 99%. If the tumor has wide to lymph nodes around the survival rate would be 85% and if the tumor had extend to distant parts, the survival rate would come down to 27%. Mammary gland is an important organ in mammals which has potential function to secrete, synthesize and deliver milk to the infants for nourishment, improvement and protection. Generally, cancer is named after the body part in which it originated; thus, breast cancer refers to the erratic development and proliferation of cells that originate in the breast tissue (7). There are some kinds of tumors that may grow within various areas of the breast. Most tumors are the outcome of benign (non-cancerous) alters within the breast. The estrogen receptors (ER) in ordinary and diseased states are significant for the improvement of relevant therapeutic strategies. Two main forms of ER exist, ERα and ERβ, which are encoded by separate genes. Estrogens play a central role in breast cancer improvement with ERα status being the mainly significant predictor of breast cancer prognosis. The potent lead molecule binding mode, residue-interaction patterns and docking energy were examined by molecular docking and binding free energy studies. The lead compounds and 3ERT complex structural stability and dynamic behavior were monitored by molecular dynamics analysis. The drug-likeness properties of lead compounds were predicted ADME analysis.

Synthesized chrysin-loaded nanoliposomes improves cadmium-induced toxicity in mice

In this study, chrysin as a natural flavonoid was encapsulated in nanoliposomal structures, and the synthesized nanoliposome-loaded chrysin (NLC) was further characterized for its physical properties and cytoprotective effects in mice that received cadmium-containing water. The results showed that the synthesized NLC is possessed spherical structure with the size of 185.1 nm and negative surface charge of - 26 mV with a poly dispersity index of 0.26. The mice received cadmium (2 mg/kg body weight/day) through drinking water showed weight loss and decease in the feed intake significantly (p ≤ 0.05). The cadmium notably (p ≤ 0.05) increased the liver enzymes including aspartate aminotransferase, alanine transaminase, and alkaline phosphatase; altered the liver metal deposition (cadmium, copper, manganese, selenium, and zinc); and induced hepatic oxidative stress (inducible nitric oxide synthase, catalase, superoxide dismutase, and glutathione peroxidase genes) with no remarkable histopathological changes. Furthermore, the cadmium impaired the morphology of jejunum through reducing villus height and villus width and increasing the crypt depth. Providing NLC as a dietary supplement at the concentrations of 2.5 and 5 mg/kg mice body weight significantly (p ≤ 0.05) improved the feed intake and body weight gain, modulated the liver enzymes, and alleviated the hepatic oxidative stress. The NLC also improved the antioxidant mineral deposition in the liver and morphohistological structure of jejunum. Consequently, the NLC is suggested as a potential dietary supplement to alleviate the symptoms of cadmium-induced toxicity in mice.

Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach

The proteins encoded by the two major breast cancer genes (BRCA1 and BRCA2), ensure the stability of DNA and prevent uncontrolled cell growth; mutation of these genes is linked to the development of hereditary breast cancers. Exploration of human breast cancer inhibitors plays a vital role in the drug discovery process. In the current work, in silico studies were performed which involves a computational approach for the identification of active phytocompounds from the diverse set of medicinal plant products against the BRCA receptor. The in silico study through pharmacokinetics and pharmacodynamics properties shown promising outcomes for these phytocompounds data set as breast cancer inhibitors. It was observed that the compounds conformed to the Lipinski's rule of five and had good bioavailability. The drug-likeness model score and ADMET profile of the designed ligands also established their potential as a drug candidate. The docking study provided useful insights on potential target-lead interactions and indicated that the newly designed leads had a good binding affinity for BRCA targets. A pharmacophore model was built to explore the scaffolds for BRCA inhibitory activity. An effort is made to screen an inhibitor against BRCA targets by combining the use of ADMET, docking score, and pharmacophore model.Communicated by Ramaswamy H. Sarma.

A New Class of Pure Estrogen Alpha Receptor Antagonists; Design, Synthesis and in-vitro Screening

Background:

In view of the estrogenic receptor inhibitory properties of coumarin nucleus, long chain nature of fatty acid and anti-breast cancer activity of fatty acids, it was proposed to attach long chain fatty acids at 3rd,4th and 7th position of coumarin nucleus and evaluate for their anti-breast cancer activity through suitable in-vitro methods.

Methods:

The present study focuses a library of fatty acid coumarin conjugates as ligands to the ligand-binding domain of the human estrogen receptor α (PDB ID 2IOG) and their binding affinities using GLIDE module of Schrodinger after ascertaining their drug-likeness with QIKPROP. The compounds LNAC 8, SAC 1 and OAC 5 are the best hits based on their docking scores as well as the Prime MM-GBSA free energy of binding. Based on the in-silico results and synthetic feasibility the compounds SAC 1 PAC 1 and OAC 1 are synthesized, characterized and investigated for their time interval growth inhibitory effect on MCF-7 which is an ER positive breast cancer cell lines.

Results:

SAC 1, showed better in vitro growth inhibitory effect in sub micromolar range as compared to Tamoxifen, a standard estrogen receptor modulator.

Conclusion:

Conclusively, in silico molecular docking studies have been very useful in predicting the pharmacokinetic profiles and the binding affinities of new hits before a detailed preclinical and clinical evaluation.

Development of leads targeting ER-α in breast cancer: An in silico exploration from natural domain

The steroid, estrogen has been recognized as being important for stimulating the growth of breast cancers primarily mediated via the steroidal estrogen receptor-α (ER-α). Inhibition of estrogen activity by small molecules with increased target specificity has proven to be an effective treatment for breast cancer. After the success stories of SERMs and fulvestrant, there is a need for the development of new small molecule modulating ER-α is due to developing resistance and side effects to current breast cancer therapy. In this pursuit, we virtually screened 227 chemically diverse bioactive natural products to get the best hits having an ER-α binding affinity. The docking scores and protein-ligand interactions of the obtained hits were emulated with the clinically used selective estrogen modulators and ER-antagonists. The results revealed 18 potential hits, which were putatively classified as hits belonging to ER agonists, modulators, and antagonists. Furthermore, as most of the hits were found to comprise the chromene nucleus, the 2D and 3D QSAR studies were performed using a set of natural products and synthesized compounds containing this scaffold, to understand the structural requirements for improving activity against breast cancer. Additionally, a pharmacophore model was generated to investigate the pharmacophoric features of the explored scaffolds for an optimal anticancer activity. The results signify that these compounds with structural modification could serve as potential leads in the drug discovery process for the treatment of breast cancer.

Nanoscale modification of chrysin for improved of therapeutic efficiency and cytotoxicity

Chrysin, as a flavone, is a promising drug candidate because of its multifaceted properties, such as anti-inflammatory, antioxidant and anticancer. However, its poor bioavailability is a bottleneck for pharmaceutical applications. To enhance the bioactive effects, chrysin-loaded poly (D,L-lactic-co-glycolic acid) and polyvinyl alcohol were successfully prepared to overcome problems associated with chrysin. The properties of modified nanochrysin were analysed by in vitro dissolution study, XRD, FTIR and SEM. Free radical scavenging potentials of the modified nanochrysin against DPPH were confirmed based on its stable antioxidant effects. A DNA instability enhancement was observed after H₂O₂ exposure, whereas chrysin decreased the H₂O₂ activity, and modified nanochrysin was more potent in this regard. Blood compatibility on red blood cells was confirmed by haemolytic and in vitro cytotoxicity assays. The in vitro anticancer activity of the modified nanochrysin towards MCF-7 and SKOV-3 cell lines using various parameters was investigated. The nanochrysin was found to exert cell growth arrest against both cancer cells in a dose-dependent manner. IC₅₀ value was significantly decreased in nanochrysin in comparison with pure chrysin and induced apoptotic cell death pathway. The results of this study suggest that the nanochrysin might be used for medical applications and offer a beneficial formulation for chemotherapy.

Structure Based docking studies towards exploring potential anti-androgen activity of selected phytochemicals against Prostate Cancer

Prostate cancer (PCa) is the second most common malignancy amongst men worldwide. Under PCa maintenance therapy drugs acting as antagonists/partial agonists of hormone receptors against the prostate tissue are used in clinical practices. Prominent drugs being Cyproterone acetate, Flutamide, Bicalutamide, they not only cause acute and long-term toxicity, but also develops drug resistance among patients. Our focus has been on phytochemicals which do not exhibit any cytotoxicity and have significant androgen receptor (AR) inhibition activity. As Protein- Ligand interactions play a key role in structure based drug design, so by using molecular docking, we screened 803 phytochemicals and investigated their binding affinity against AR. The three dimensional (3D) structure of AR was retrieved from Protein Data Bank, and docked with 3D Pubchem structures of 803 phytochemicals using Argus Lab. Molecular docking and drug likeness studies were made using ADMET properties while Lipinski's rule of five was performed for the phytochemicals to evaluate their anti-prostate cancer activity. The results showed that Isobavachin exhibited best binding affinity of -13.73 kcal/mol with AR followed by Glabranin, Anthocyanin and Eriosemation. Our studies therefore reveal that these four phytochemicals could be promising candidates for further evaluation for PCa prevention or management.

Artonin E and Structural Analogs from Artocarpus Species Abrogates Estrogen Receptor Signaling in Breast Cancer

The increasing rate of mortality ensued from breast cancer has encouraged research into safer and efficient therapy. The human Estrogen receptor α has been implicated in the majority of reported breast cancer cases. Molecular docking employing Glide, Schrodinger suite 2015, was used to study the binding affinities of small molecules from the Artocarpus species after their drug-like properties were ascertained. The structure of the ligand-binding domain of human Estrogen receptor α was retrieved from Protein Data Bank while the structures of compounds were collected from PubChem database. The binding interactions of the studied compounds were reported as well as their glide scores. The best glide scored ligand, was Artonin E with a score of -12.72 Kcal when compared to other studied phytomolecules and it evoked growth inhibition of an estrogen receptor positive breast cancer cells in submicromolar concentration (3.8-6.9 µM) in comparison to a reference standard Tamoxifen (18.9-24.1 µM) within the tested time point (24-72 h). The studied ligands, which had good interactions with the target receptor, were also drug-like when compared with 95% of orally available drugs with the exception of Artoelastin, whose predicted physicochemical properties rendered it less drug-like. The in silico physicochemical properties, docking interactions and growth inhibition of the best glide scorer are indications of the anti-breast cancer relevance of the studied molecules.

Novel DOT1L ReceptorNatural Inhibitors Involved in Mixed Lineage Leukemia: a Virtual Screening, Molecular Docking and Dynamics Simulation Study

BACKGROUND

The human protein methyl-transferase DOT1L catalyzes the methylation of histone H3 on lysine 79 (H3K79) at homeobox genes and is also involved in a number of significant processes ranging from gene expression to DNA-damage response and cell cycle progression. Inhibition of DOT1L activity by shRNA or small-molecule inhibitors has been established to prevent proliferation of various MLL-rearranged leukemia cells in vitro, establishing DOT1L an attractive therapeutic target for mixed lineage leukemia (MLL). Most of the drugs currently in use for the MLL treatment are reported to have low efficacy, hence this study focused on various natural compounds which exhibit minimal toxic effects and high efficacy for the target receptor.

MATERIALS AND METHODS

Structures of human protein methyl-transferase DOT1L and natural compound databases were downloaded from various sources. Virtual screening, molecular docking, dynamics simulation and drug likeness studies were performed for those natural compounds to evaluate and analyze their anti-cancer activity.

RESULTS

The top five screened compounds possessing good binding affinity were identified as potential high affinity inhibitors against DOT1L's active site. The top ranking molecule amongst the screened ligands had a Glide g-score of -10.940 kcal/mol and Glide e-model score of -86.011 with 5 hydrogen bonds and 12 hydrophobic contacts. This ligand's behaviour also showed consistency during the simulation of protein-ligand complex for 20000 ps, which is indicative of its stability in the receptor pocket.

CONCLUSIONS

The ligand obtained out of this screening study can be considered as a potential inhibitor for DOT1L and further can be treated as a lead for the drug designing pipeline.

Preparation and Evaluation of Chrysin Encapsulated in PLGA- PEG Nanoparticles in the T47-D Breast Cancer Cell Line

BACKGROUND

Polymeric nanoparticles are attractive materials that have been widely used in medicine for drug delivery, with therapeutic applications. In our study, polymeric nanoparticles and the anticancer drug, chrysin, were encapsulated into poly (D, L-lactic-co-glycolic acid) poly (ethylene glycol) (PLGA-PEG) nanoparticles for local treatment.

MATERIALS AND METHODS

PLGA: PEG triblock copolymers were synthesized by ring-opening polymerization of D, L-lactide and glycolide as an initiator. The bulk properties of these copolymers were characterized using 1H nuclear magnetic resonance spectroscopy and Fourier transform infrared spectroscopy. In addition, the resulting particles were characterized by scanning electron microscopy.

RESULTS

The chrysin encapsulation efficiency achieved for polymeric nanoparticles was 70% control of release kinetics. The cytotoxicity of different concentration of pure chrysin and chrysin loaded in PLGA-PEG (5-640μM) on T47-D breast cancer cell line was analyzed by MTT-assay.

CONCLUSIONS

There is potential for use of these nanoparticles for biomedical applications. Future work should include in vivo investigation of the targeting capability and effectiveness of these nanoparticles in the treatment of breast cancer.

Sequence to structure approach of estrogen receptor alpha and ligand interactions

Estrogen receptors (ERs) are steroid receptors located in the cytoplasm and on the nuclear membrane. The sequence similarities of human ERα, mouse ERα, rat ERα, dog ERα, and cat ERα are above 90%, but structures of ERα may different among species. Estrogen can be agonist and antagonist depending on its target organs. This hormone play roles in several diseases including breast cancer. There are variety of the relative binding affinity (RBA) of ER and estrogen species in comparison to 17β-estradiol (E2), which is a natural ligand of both ERα and ERβ. The RBA of the estrogen species are as following: diethyl stilbestrol (DES)>hexestrol>dienestrol>17β-estradiol (E2)>17-estradiol>moxestrol>estriol (E3)>4-OH estradiol>estrone-3-sulfate. Estrogen mimetic drugs, selective estrogen receptor modulators (SERMs), have been used as hormonal therapy for ER positive breast cancer and postmenopausal osteoporosis. In the postgenomic era, in silico models have become effective tools for modern drug discovery. These provide three dimensional structures of many transmembrane receptors and enzymes, which are important targets of de novo drug development. The estimated inhibition constants (Ki) from computational model have been used as a screening procedure before in vitro and in vivo studies.