In Silico Study on the Interactions, Molecular Docking, Dynamics and Simulation of Potential Compounds from Withania somnifera (L.) Dunal Root against Cancer by Targeting KAT6A

Impact of mutations on KAT6A enzyme and inhibitory potential of compounds from Withania somnifera using computational approaches

KAT6A is an enzyme that regulates biological processes that are linked to cancer cell proliferation and metastasis. Recent studies suggest that certain compounds from Withania somnifera may inhibit cancer growth by targeting KAT6A. However, the impact of mutations on KAT6A's structure and the inhibitory potential of compounds obtained from W. somnifera remain unclear. This study investigated three mutations, K181N, R242P and R325C, using molecular docking, molecular dynamics simulations and network pharmacology to assess their effects on KAT6A's interaction with its coenzyme, acetyl-CoA (CoA), and inhibitors (WM8014, withasomniferol B, withanolide E and sitoindoside IX). The results showed that R242P and R325C mutations significantly reduced binding affinity (from -12.94 kcal/mol to -9.96 and -7.00 kcal/mol, respectively) and increased RMSD values (from 1.860 to 2.296 and 2.373, respectively) compared to K181N (-11.86 kcal/mol and 1.698), suggesting altered enzyme activity. Notably, these mutations enhanced the inhibitory effects of the compounds from W. somnifera, particularly withanolide E, which showed reduced RMSD values (2.259-2.211, 2.045 and 1.985 for K181N, R242P, and R325C, respectively). Additionally, mutant complexes showed higher binding energies, including R325C-WM8014 (-90.53 kcal/mol), K181N-CoA (-90.50 kcal/mol) and R242P-withanolide E (-82.06 kcal/mol) compared to their corresponding wild-type complexes, which exhibited -85.25 kcal/mol, -69.30 kcal/mol and -57.08 kcal/mol, respectively. Network pharmacology also revealed that the compounds from Withania somnifera target KAT6A through multiple cancer pathways like PI3K-Akt signaling, apoptosis and chemical carcinogenesis. These findings suggest that specific KAT6A mutations may enhance the efficacy of the compounds from W. somnifera. However, further research is needed to validate these results, which could advance clinical applications and drug development for KAT6A-targeted cancer therapies.

Exploring the efficacy of Benincasa hispida extract on obesity linked inflammatory bowel disease by integrating computational analysis and experimental validations

The association of obesity with inflammatory bowel disease (IBD) can be understood by the intricate role of pro- and anti-inflammatory cytokines, especially adipokines, which are secreted by adipose tissue and are responsible for IBD because of their structural similarity with tumor necrosis factor-alpha (TNF-α), an important cytokine involved in IBD pathogenesis. The current study was carried out to evaluate the therapeutic potential of Benincasa hispida in obesity-associated IBD. Approximately 18 compounds sourced from Benincasa hispida (Thunb.) were comprehensively analyzed, among which 11 presented favorable drug-likeness scores and adherence to Lipinski's Rule of Five. Various methodologies, including compound-gene set pathway enrichment analysis, network pharmacology, docking studies, and molecular dynamics simulations, have been employed. Safety assessments via Protox confirmed the nontoxic nature of these compounds, which is crucial for their therapeutic potential. Through Venn diagram analysis of the Gene Card and OMIM databases, proteins associated with obesity and IBD management were pinpointed. Pathway enrichment analysis revealed 810 targets across 192 distinct pathways, with 8 directly related to the pathogenesis of obesity and IBD. Notable therapeutic targets, such as MTOR, were identified through STRING and KEGG pathway database analyses, shedding light on the molecular pathways modulated by these protein targets. Interactions among compounds, proteins, and pathways were visualized via Cytoscape 3.6.1. Furthermore, the compounds were docked with the protein target via AutoDock 4.2, and the compound ajmalin exhibited the highest binding affinity with the MTOR protein, with a binding energy of -7.8 kcal/mol; later, a dynamic study was performed for the ajmaline and protein complex. These findings shed light on the potential efficacy of Benincasa hispida in targeting crucial pathways for managing obesity and IBD. Hence, in vivo studies involving Wistar rats exposed to microplastics and monosodium glutamate (MSG) were carried out to evaluate the potential of Benincasa hispida extracts in mitigating obesity-related IBD. Fecal lipid analysis revealed alterations associated with these conditions, whereas histopathological examinations of the liver and intestine revealed the inflammatory changes induced by MSG and microplastics. The protective effects of this extract on liver and intestinal histology suggest promising avenues for further investigations, emphasizing its potential as a therapeutic intervention for IBD and obesity.

ERα status of invasive ductal breast carcinoma as a result of regulatory interactions between lysine deacetylases KAT6A and KAT6B

Breast cancer (BC) is the leading cause of death among cancer patients worldwide. In 2020, almost 12% of all cancers were diagnosed with BC. Therefore, it is important to search for new potential markers of cancer progression that could be helpful in cancer diagnostics and successful anti-cancer therapies. In this study, we investigated the potential role of the lysine acetyltransferases KAT6A and KAT6B in the outcome of patients with invasive breast carcinoma. The expression profiles of KAT6A/B in 495 cases of IDC and 38 cases of mastopathy (FBD) were examined by immunohistochemistry. KAT6A/B expression was also determined in the breast cancer cell lines MCF-7, BT-474, SK-BR-3, T47D, MDA-MB-231, and MDA-MB-231/BO2, as well as in the human epithelial mammary gland cell line hTERT-HME1 - ME16C, both at the mRNA and protein level. Statistical analysis of the results showed that the nuclear expression of KAT6A/B correlates with the estrogen receptor status: KAT6ANUC vs. ER r = 0.2373 and KAT6BNUC vs. ER r = 0.1496. Statistical analysis clearly showed that KAT6A cytoplasmic and nuclear expression levels were significantly higher in IDC samples than in FBD samples (IRS 5.297 ± 2.884 vs. 2.004 ± 1.072, p < 0.0001; IRS 5.133 ± 4.221 vs. 0.1665 ± 0.4024, p < 0.0001, respectively). Moreover, we noticed strong correlations between ER and PR status and the nuclear expression of KAT6A and KAT6B (nucKAT6A vs. ER, p = 0.0048; nucKAT6A vs. PR p = 0.0416; nucKAT6B vs. ER p = 0.0306; nucKAT6B vs. PR p = 0.0213). Significantly higher KAT6A and KAT6B expression was found in the ER-positive cell lines T-47D and BT-474, whereas significantly lower expression was observed in the triple-negative cell lines MDA-MB-231 and MDA-MB-231/BO2. The outcomes of small interfering RNA (siRNA)-mediated suppression of KAT6A/B genes revealed that within estrogen receptor (ER) positive and negative cell lines, MCF-7 and MDA-MB-231, attenuation of KAT6A led to concurrent attenuation of KAT6A, whereas suppression of KAT6B resulted in simultaneous attenuation of KAT6A. Furthermore, inhibition of KAT6A/B genes resulted in a reduction in estrogen receptor (ER) mRNA and protein expression levels in MCF-7 and MDA-MMB-231 cell lines. Based on our findings, the lysine acetyltransferases KAT6A and KAT6B may be involved in the progression of invasive ductal breast cancer. Further research on other types of cancer may show that KAT6A and KAT6B could serve as diagnostic and prognostic markers for these types of malignancies.

Covalent binding of withanolides to cysteines of protein targets

Withanolides represent an important category of natural products with a steroidal lactone core. Many of them contain an α,β-unsaturated carbonyl moiety with a high reactivity toward sulfhydryl groups, including protein cysteine thiols. Different withanolides endowed with marked antitumor and anti-inflammatory have been shown to form stable covalent complexes with exposed cysteines present in the active site of oncogenic kinases (BTK, IKKβ, Zap70), metabolism enzymes (Prdx-1/6, Pin1, PHGDH), transcription factors (Nrf2, NFκB, C/EBPβ) and other structural and signaling molecules (GFAP, β-tubulin, p97, Hsp90, vimentin, Mpro, IPO5, NEMO, …). The present review analyzed the covalent complexes formed through Michael addition alkylation reactions between six major withanolides (withaferin A, physalin A, withangulatin A, 4β-hydroxywithanolide E, withanone and tubocapsanolide A) and key cysteine residues of about 20 proteins and the resulting biological effects. The covalent conjugation of the α,β-unsaturated carbonyl system of withanolides with reactive protein thiols can occur with a large set of soluble and membrane proteins. It points to a general mechanism, well described with the leading natural product withaferin A, but likely valid for most withanolides harboring a reactive (electrophilic) enone moiety susceptible to react covalently with cysteinyl residues of proteins. The multiplicity of reactive proteins should be taken into account when studying the mechanism of action of new withanolides. Proteomic and network analyses shall be implemented to capture and compare the cysteine covalent-binding map for the major withanolides, so as to identify the protein targets at the origin of their activity and/or unwanted effects. Screening of the cysteinome will help understanding the mechanism of action and designing cysteine-reactive electrophilic drug candidates.

Antitumor Activity and Mechanism of Terpenoids in Seaweeds Based on Literature Review and Network Pharmacology

Seaweeds are a treasure trove of natural secondary metabolites. Terpenoids extracted from seaweeds are shown to possess a variety of antitumor cellular activities. However, due to the complex and diverse structures of terpenoids, their therapeutic targets and complex mechanisms of action have not been clarified. The present study summarises the research on terpenoids from seaweeds in oncological diseases over the last 20 years. Terpenoids show different degrees of inhibitory effects on different types of tumor cells, suggesting that terpenoids in seaweeds may have potential antitumor disease potential. Terpenoids with potential antitumor activity and their mechanism of action are investigated using network pharmacology. A total of 125 terpenoids and 286 targets are obtained. Proto-oncogene tyrosine-protein kinase Src(SRC), Signal transducer and activator of transcription 3 (STAT3), Mitogen-activated protein kinase (MAPK3, MAPK1), Heat shock protein HSP 90-alpha (HSP90AA1), Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and RAC-alpha serine/threonine-protein kinase (AKT1) are defined as core targets. According to GO function and Kyoto encyclopedia of genes and genomes(KEGG) enrichment analysis, terpenoids may affect the Phoshatidylinositol 3'-kinase (PI3K)-Akt signaling pathway, Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor resistance, Prostate cancer, MAPK signaling pathway, and Proteoglycans in cancer. In addition, the molecular docking results show that the selected terpenoids are all able to bind strongly to the active protein. Terpenoids may slow down the progression of cancer by controlling apoptosis, proliferation, and protein and enzyme binding.

Investigation of alpha amylase inhibitors from Bidens pilosa L. by in silico and in vitro studies

Bidens pilosa L. has been traditionally used as an anti-diabetic herbal medicine; however, its mechanism of action remains elusive. In this study, the potential role of B. pilosa compounds on alpha-amylase inhibition and regulation of multiple pathways was investigated via computational and experimental studies. The phytocompounds were retrieved from plant databases and published literature. The druggability profile of these compounds was predicted using MolSoft. The probable targets of these phytocompounds were predicted using BindingDB (similarity index ≥ 0.7). Further, compound-gene set-pathway and functional enrichment analysis were performed using STRING and KEGG pathway databases. The network between compound-protein-pathway was constructed using Cytoscape. Molecular docking was performed using AutoDock Vina, executed through the POAP pipeline. The stability of the best docked complex was subjected to all-atom molecular dynamics (MD) simulation for 100 ns to investigate their structural stabilities and intermolecular interactions using GROMACS software. Finally, B. pilosa hydroalcoholic extract was subjected to LC-MS and tested for dose- and time-dependent alpha-amylase inhibitory activity. Out of 31 bioactive compounds, 13 were predicted to modulate the human pancreatic alpha-amylase (AMY2A) and 12 pathways associated with diabetes mellitus. PI3K-Akt signaling pathway (hsa04151) scored the lowest false discovery rate by triggering 15 genes. Further intermolecular interaction analysis of the docked complex revealed that Brassidin had the highest active site interaction and lowest binding energy compared to standard acarbose, and MD reveals the formation of a stable complex throughout 100 ns production run. LC-MS analysis revealed the presence of 13 compounds (targeting AMY2A) in B. pilosa hydroalcoholic extract, which showed potent AMY2A inhibition by in vitro studies that corroborate in silico findings for its anti-diabetic activity. Based on these findings, enriched fractions/pure compounds inhibitory activity that can be performed in future for drug discovery.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00187-9.

Pharmacoinformatics-Based Approach for Uncovering the Quorum-Quenching Activity of Phytocompounds against the Oral Pathogen, Streptococcus mutans

Streptococcus mutans, a gram-positive oral pathogen, is the primary causative agent of dental caries. Biofilm formation, a critical characteristic of S. mutans, is regulated by quorum sensing (QS). This study aimed to utilize pharmacoinformatics techniques to screen and identify effective phytochemicals that can target specific proteins involved in the quorum sensing pathway of S. mutans. A computational approach involving homology modeling, model validation, molecular docking, and molecular dynamics (MD) simulation was employed. The 3D structures of the quorum sensing target proteins, namely SecA, SMU1784c, OppC, YidC2, CiaR, SpaR, and LepC, were modeled using SWISS-MODEL and validated using a Ramachandran plot. Metabolites from Azadirachta indica (Neem), Morinda citrifolia (Noni), and Salvadora persica (Miswak) were docked against these proteins using AutoDockTools. MD simulations were conducted to assess stable interactions between the highest-scoring ligands and the target proteins. Additionally, the ADMET properties of the ligands were evaluated using SwissADME and pkCSM tools. The results demonstrated that campesterol, meliantrol, stigmasterol, isofucosterol, and ursolic acid exhibited the strongest binding affinity for CiaR, LepC, OppC, SpaR, and Yidc2, respectively. Furthermore, citrostadienol showed the highest binding affinity for both SMU1784c and SecA. Notably, specific amino acid residues, including ASP86, ARG182, ILE179, GLU143, ASP237, PRO101, and VAL84 from CiaR, LepC, OppC, SecA, SMU1784c, SpaR, and YidC2, respectively, exhibited significant interactions with their respective ligands. While the docking study indicated favorable binding energies, the MD simulations and ADMET studies underscored the substantial binding affinity and stability of the ligands with the target proteins. However, further in vitro studies are necessary to validate the efficacy of these top hits against S. mutans.