Structure based molecular inhibition of Caspase-8 for treatment of multi-neurodegenerative diseases using known natural compounds

Acacia Honey-derived Bioactive Compounds Exhibit Induction of p53-dependent Apoptosis in the MCF-7 Human Breast Cancer Cell Line

Background

Research studies have focused on discovering new anti-proliferative and pro-apoptotic agents derived from natural products from which honey constitutes a prominent candidate. The Acacia honey (AH) is known to display anticancer activity, but the mechanisms of action are still not well defined.

Objectives

Using in vitro and computational approaches, we aimed to assess the interaction among selected bioactive compounds derived from AH, with the apoptotic protein p53, which could trigger apoptosis.

Methods

The phytocompounds of AH were investigated via gas chromatography–mass spectrophotometry analysis. The cytotoxic effect and induced apoptosis on the MCF-7 breast cancer cell line were assessed by 3-(4,5-dimethylthiazolyl-2)-2,5 diphenyltetrazolium bromide and acridine orange-ethidium bromide staining approaches. The molecular docking analysis between AH compounds and p53 was carried out.

Results

The drug-likeness prediction revealed that most of the identified compounds meet Lipinski’s rules. We demonstrate that AH exerts an interesting cytotoxic effect in a dose-dependent manner against the MCF-7 cell line with IC50 5.053µg/mL. Significant cell alterations and notable induced apoptosis were detected when cells were treated with AH. The molecular docking analysis revealed that melezitose is among the most important potential bioactive compounds that interact with p53 leading to apoptosis. The binding affinity was −8.1 kcal/mol, and the closest molecular interactions in the active site included 10 residues, which could explain the potential biological activity.

Conclusion

This work sheds light on AH as a significant source of bioactive chemicals with potential for promoting apoptosis that may be exploited as an alternative therapy for breast cancer.

Carvacrol instigates intrinsic and extrinsic apoptosis with abrogation of cell cycle progression in cervical cancer cells: Inhibition of Hedgehog/GLI signaling cascade

Recent times have seen a strong surge in therapeutically targeting the hedgehog (HH)/GLI signaling pathway in cervical cancer. HH signaling pathway is reported to be a crucial modulator of carcinogenesis in cervical cancer and is also associated with recurrence and development of chemoresistance. Moreover, our previous reports have established that carvacrol (CAR) inhibited the proliferation of prostate cancer cells via inhibiting the Notch signaling pathway and thus, it was rational to explore its antiproliferative effects in cervical cancer cell lines. Herein, the present study aimed to investigate the anticancer and apoptotic potential of CAR on C33A cervical cancer cells and further explore the underlying mechanisms. We found that CAR significantly suppressed the growth of C33A cells, induced cell cycle arrest, and enhanced programmed cell death along with augmentation in the level of ROS, dissipated mitochondrial membrane potential, activation of caspase cascade, and eventually inhibited the HH signaling cascade. In addition, CAR treatment increased the expression of pro-apoptotic proteins (Bax, Bad, Fas-L, TRAIL, FADDR, cytochrome c) and concomitantly reduced the expression of anti-apoptotic proteins (Bcl-2 and Bcl-xL) in C33A cells. CAR mediates the activation of caspase-9 and -3 (intrinsic pathway) and caspase-8 (extrinsic pathway) accompanied by the cleavage of PARP in cervical cancer cells. Thus, CAR induced apoptosis by both the intrinsic and extrinsic apoptotic pathways. CAR efficiently inhibited the growth of cervical cancer cells via arresting the cell cycle at G0/G1 phase and modulated the gene expression of related proteins (p21, p27, cyclin D1 and CDK4). Moreover, CAR inhibited the HH/GLI signaling pathway by down regulating the expression of SMO, PTCH and GLI1 proteins in cervical carcinoma cells. With evidence of the above results, our data revealed that CAR treatment suppressed the growth of HPV^-C33A cervical cancer cells and further elucidated the mechanistic insights into the functioning of CAR.

Pharmacology Mechanism of Polygonum Bistorta in Treating Ulcerative Colitis Based on Network Pharmacology

Aim. Ulcerative colitis (UC) is a refractory gastrointestinal disease. The study aimed to expound the mechanism of Polygonum bistorta (PB) in treating UC by network pharmacology, molecular docking, and experiment verification. Methods. The compositions and targets of PB and UC-associated targets were obtained by searching the websites and the literature. The potential mechanism of PB in the treatment of UC was predicted by protein-protein interaction network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Molecule docking was performed by AutoDock. In vitro experiments explored the mechanism of quercetin (Que), the main active composition of PB, in treating UC. Results. Six compositions, 139 PB targets, and 934 UC-associated targets were obtained. 93 overlapping targets between PB and UC were identified, and 18 of them were the core targets. 467 biological processes, 10 cell components, and 30 molecular functions were obtained by GO analysis. 102 pathways were enriched through KEGG analysis. Among them, the IL-17 signaling pathway had high importance. The core targets FOS, JUN, IL-1β, CCL2, CXCL8, and MMP9 could dock with Que successfully. Act1, TRAF6, FOS, and JUN were identified by KEGG as the key proteins of the IL-17 signaling pathway. The expressions of the abovementioned proteins were increased in Caco-2 cells stimulated by Dextran sulfate sodium and decreased after being treated by Que. Conclusion. PB might treat UC by downregulating the IL-17 signaling pathway. It is worth doing further research on PB treating UC in vivo.

Garlic Extract: Inhibition of Biochemical and Biophysical Changes in Glycated HSA

Glycation of various biomolecules contributes to structural changes and formation of several high molecular weight fluorescent and non-fluorescent, advanced glycation end products (AGEs). AGEs and glycation are involved in various health complications. Synthetic medicines, including metformin, have several adverse effects. Natural products and their derivatives are used in the treatment of various diseases due to their significant therapeutic qualities. Allium sativum (garlic) is used in traditional medicines because of its antioxidant, anti-inflammatory, and anti-diabetic properties. This study aimed to determine the anti-glycating and AGEs inhibitory activities of garlic. Biochemical and biophysical analyses were performed for in vitro incubated human serum albumin (HSA) with 0.05 M of glucose for 1, 5, and 10 weeks. Anti-glycating and AGEs inhibitory effect of garlic was investigated in glycated samples. Increased biochemical and biophysical changes were observed in glycated HSA incubated for 10 weeks (G-HSA-10W) as compared to native HSA (N-HSA) as well as glycated HSA incubated for 1 (G-HSA-1W) and 5 weeks (G-HSA-5W). Garlic extract with a concentration of ≥6.25 µg/mL exhibited significant inhibition in biophysical and biochemical changes of G-HSA-10W. Our findings demonstrated that garlic extract has the ability to inhibit biochemical and biophysical changes in HSA that occurred due to glycation. Thus, garlic extract can be used against glycation and AGE-related health complications linked with chronic diseases in diabetic patients due to its broad therapeutic potential.

Targeting apoptosis and autophagy following spinal cord injury: Therapeutic approaches to polyphenols and candidate phytochemicals

Spinal cord injury (SCI) is a neurological disorder associated with the loss of sensory and motor function. Understanding the precise dysregulated signaling pathways, especially apoptosis and autophagy following SCI, is of vital importance in developing innovative therapeutic targets and treatments. The present study lies in the fact that it reveals the precise dysregulated signaling mediators of apoptotic and autophagic pathways following SCI and also examines the effects of polyphenols and other candidate phytochemicals. It provides new insights to develop new treatments for post-SCI complications. Accordingly, a comprehensive review was conducted using electronic databases including, Scopus, Web of Science, PubMed, and Medline, along with the authors' expertise in apoptosis and autophagy as well as their knowledge about the effects of polyphenols and other phytochemicals on SCI pathogenesis. The primary mechanical injury to spinal cord is followed by a secondary cascade of apoptosis and autophagy that play critical roles during SCI. In terms of pharmacological mechanisms, caspases, Bax/Bcl-2, TNF-α, and JAK/STAT in apoptosis along with LC3 and Beclin-1 in autophagy have shown a close interconnection with the inflammatory pathways mainly glutamatergic, PI3K/Akt/mTOR, ERK/MAPK, and other cross-linked mediators. Besides, apoptotic pathways have been shown to regulate autophagy mediators and vice versa. Prevailing evidence has highlighted the importance of modulating these signaling mediators/pathways by polyphenols and other candidate phytochemicals post-SCI. The present review provides dysregulated signaling mediators and therapeutic targets of apoptotic and autophagic pathways following SCI, focusing on the modulatory effects of polyphenols and other potential phytochemical candidates.

Study of Caspase 8 Inhibition for the Management of Alzheimer's Disease: A Molecular Docking and Dynamics Simulation

Alzheimer’s disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer’s potential against caspase 8.

Molecular docking based design of Dengue NS5 methyltransferase inhibitors

Dengue is a viral infection caused by RNA infection of the family Flaviviridae and spread by the Aedes mosquitoes. Dengue NS5 methyltransferase is a known drug target for the disease. Therefore, it is of interest to design potential inhibitors for the target using molecular docking analysis. Our analysis shows the binding of compounds STOCK1N-98943, STOCK1N-98872, STOCK1N-98956, STOCK1N-98865, and STOCK1N-98950 with the protein drug target with optimal binding features for further in vitro and in vivo evaluations.

Targeting Caspase 8: Using Structural and Ligand-Based Approaches to Identify Potential Leads for the Treatment of Multi-Neurodegenerative Diseases

Caspase 8 is a central player in the apoptotic cell death pathway and is also essential for cytokine processing. The critical role of this protease in cell death pathways has generated research interest because its activation has also been linked with neural cell death. Thus, blocking the activity of caspase 8 is considered a potential therapy for neurodegenerative diseases. To extend the repertoire of caspase 8 inhibitors, we employed several computational approaches to identify potential caspase 8 inhibitors. Based on the structural information of reported inhibitors, we designed several individual and consensus pharmacophore models and then screened the ZINC database, which contains 105,480 compounds. Screening generated 5332 candidates, but after applying stringent criteria only two candidate compounds, ZINC19370490 and ZINC04534268, were evaluated by molecular dynamics simulations and subjected to Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis. These compounds were stable throughout simulations and interacted with targeted protein by forming hydrogen and van der Waal bonds. MM-PBSA analysis showed that these compounds were comparable or better than reported caspase 8 inhibitors. Furthermore, their physical properties were found to be acceptable, and they are non-toxic according to the ADMET online server. We suggest that the inhibitory efficacies of ZINC19370490 and ZINC04534268 be subjected to experimental validation.

Molecular docking and pharmacokinetic evaluation of natural compounds as targeted inhibitors against Crz1 protein in Rhizoctonia solani

Crz1p regulates Calcineurin, a serine-threonine-specific protein phosphatase, in Rhizoctonia solani. It has attracted consideration as a novel target of antifungal therapy based on studies in numerous pathogenic fungi, including, Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus. To investigate whether Calcineurin can be a useful target for the treatment of Crz1 protein in R. solani causing wet root rot in Chickpea. The work presented here reports the in-silico studies of Crz1 protein against natural compounds. This study Comprises of quantitative structure-toxicity relationship (QSTR) and quantitative structure-activity relationship (QSAR). All compounds showed high binding energy for Crz1 protein through molecular docking. Further, a pharmacokinetic study revealed that these compounds had minimal side effects. Biological activity spectrum prediction of these compounds showed potential antifungal properties by showing significant interaction with Crz1. Hence, these compounds can be used for the prevention and treatment of wet root rot in Chickpea.

Knockdown of APPL mimics transgenic Aβ induced neurodegenerative phenotypes in Drosophila

A variety of Drosophila mutant lines have been established as potential disease-models to study various disease mechanisms including human neurodegenerative diseases like Alzheimer's disease (AD), Huntington's disease (HD) and Parkinson's disease (PD). The evolutionary conservation of APP (Amyloid Precursor Protein) and APPL (Amyloid Precursor Protein-Like) and the comparable detrimental effects caused by their metabolic products strongly implies the conservation of their normal physiological functions. In view of this milieu, a comparative analysis on the pattern of neurodegenerative phenotypes between Drosophila APPL-RNAi line and transgenic Drosophila line expressing eye tissue specific human Aβ (Amyloid beta) was undertaken. Our results clearly show that Drosophila APPL-RNAi largely mimics transgenic Aβ in various phenotypes which include eye degeneration, reduced longevity and motor neuron deficit functions, etc. The ultra-structural morphological pattern of eye degeneration was confirmed by scanning electron microscopy. Further, a comparative study on longevity and motor behaviour between Aβ expressing and APPL knockdown lines revealed similar kind of behavioural deficit and longevity phenotypes. Therefore, it is suggested that APPL-knockdown approach can be used as an alternative approach to study neurodegenerative diseases in the fly model. To the best of our knowledge this is the first report showing comparable phenotypes between APPL and Aβ in AD model of Drosophila.

Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxukn and STOP-Toxukk tests

Stem cell-based in vitro test systems can recapitulate specific phases of human development. In the UKK test system, human pluripotent stem cells (hPSCs) randomly differentiate into cells of the three germ layers and their derivatives. In the UKN1 test system, hPSCs differentiate into early neural precursor cells. During the normal differentiation period (14 days) of the UKK system, 570 genes [849 probe sets (PSs)] were regulated >fivefold; in the UKN1 system (6 days), 879 genes (1238 PSs) were regulated. We refer to these genes as 'developmental genes'. In the present study, we used genome-wide expression data of 12 test substances in the UKK and UKN1 test systems to understand the basic principles of how chemicals interfere with the spontaneous transcriptional development in both test systems. The set of test compounds included six histone deacetylase inhibitors (HDACis), six mercury-containing compounds ('mercurials') and thalidomide. All compounds were tested at the maximum non-cytotoxic concentration, while valproic acid and thalidomide were additionally tested over a wide range of concentrations. In total, 242 genes (252 PSs) in the UKK test system and 793 genes (1092 PSs) in the UKN1 test system were deregulated by the 12 test compounds. We identified sets of 'diagnostic genes' appropriate for the identification of the influence of HDACis or mercurials. Test compounds that interfered with the expression of developmental genes usually antagonized their spontaneous development, meaning that up-regulated developmental genes were suppressed and developmental genes whose expression normally decreases were induced. The fraction of compromised developmental genes varied widely between the test compounds, and it reached up to 60 %. To quantitatively describe disturbed development on a genome-wide basis, we recommend a concept of two indices, 'developmental potency' (D _p) and 'developmental index' (D _i), whereby D _p is the fraction of all developmental genes that are up- or down-regulated by a test compound, and D _i is the ratio of overrepresentation of developmental genes among all genes deregulated by a test compound. The use of D _i makes hazard identification more sensitive because some compounds compromise the expression of only a relatively small number of genes but have a high propensity to deregulate developmental genes specifically, resulting in a low D _p but a high D _i. In conclusion, the concept based on the indices D _p and D _i offers the possibility to quantitatively express the propensity of test compounds to interfere with normal development.