Anti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation

Exploring the potential of Andrographis paniculata for developing novel HDAC inhibitors: an in silico approach

Cancer is one of the dreaded diseases of the twentieth century, emerging the major global causes of human morbidity. Cancer research in the last 15 years has provided unprecedented information on the role of epigenetics in cancer initiation and progression. Histone deacetylases (HDACs) are recognized as important epigenetic markers in cancer, whose overexpression leads to increased metastasis and angiogenesis. In the current study, thirty-four (34) compounds from Andrographis paniculata were screened for the identification of potential candidate drugs, targeting three Class I HDACs (Histone deacetylases), namely HDAC1 (PDB id 5ICN), HDAC3 (PDB id 4A69) and HDAC8 (PDB id 5FCW) through computer-assisted drug discovery study. Results showed that some of the phytochemicals chosen for this study exhibited significant drug-like properties. In silico molecular docking study further revealed that out of 34 compounds, the flavonoid Andrographidine E had the highest binding affinities towards HDAC1 (-9.261 Kcal mol-1) and 3 (-9.554 Kcal mol-1) when compared with the control drug Givinostat (-8.789 and -9.448 Kcal mol-1). The diterpenoid Andrographiside displayed the highest binding affinity (-9.588 Kcal mol-1) to HDAC8 compared to Givinostat (-8.947 Kcal mol-1). Statistical analysis using Principal Component Analysis tool revealed that all 34 phytocompounds could be clustered in four statistical groups. Most of them showed high or comparable inhibitory potentials towards HDAC target protein. Finally, the stability of top-ranked complexes (Andrographidine E-HDAC1 and HDAC3; Andrographiside-HDAC8) at the physiological condition was validated by Molecular Dynamic Simulation and MM-PBSA study.Communicated by Ramaswamy H. Sarma.

Nature's arsenal unleashed: Senegalia modesta derived thymol halts cancer progression by suppressing proangiogenic genes

Inhibiting angiogenesis with plant-derived bioactive compounds can inhibit tumour progression. Antiangiogenic potential of Senegalia modesta was analysed by preparing and analysing ethanolic extracts of S.modesta by GC-MS and HPLC to identify bioactive components. In-vivo blood vessel formation assays in mice and chorioallantoic membrane assays (CAM) in eggs were employed to assess the antiangiogenic effects. qPCR was performed to elucidate mRNA expression of proangiogenic genes in MDA-MB-231 cells after exposure to S.modesta and thymol. Molecular docking analysis highlighted the interaction of thymol with VEGF receptors. S.modesta treatment significantly delayed wound healing in mice compared to control group. GC-MS and HPLC analyses thymol as a bioactive compound in S.modesta extract. CAM assay indicated reduced angiogenesis in thymol-treated groups, further confirmed by downregulation of proangiogenic genes. Molecular docking of thymol with VEGFR1/VEGFR2 revealed strong binding affinity, suggesting thymol-mediated receptor blocking. Thymol exhibits antiangiogenic potential and may serve as a promising therapeutic agent against cancer.

Flavone-C-glycosides from Cassia auriculata L. as possible inhibitors of phosphodiesterase-5 (PDE5): in vitro, molecular docking and molecular dynamics studies

Phosphodiesterase-5 (PDE5) is a homodimeric enzyme that specifically targets cyclic guanosine monophosphate (cGMP), that mediates many downstream effects such as vasodilation, neurotransmission, and calcium homeostasis. Considering the functions of cGMP, inhibition of PDE5 has been established to have several therapeutic effects in disease conditions such as cancer, cardiovascular diseases and Alzheimer's disease. Consequently, many PDE5 inhibitors were developed but with severe adverse effects such as non-arteritic anterior ischemic optic neuropathy (NAION), priapism, etc. Hence, in our study for the identification of new PDE5 inhibitors from alternative sources, Cassia auriculata L. was identified as a potential PDE5 inhibitors with 56.23% inhibition at 100 μg/mL in vitro. In addition, the respective phytoconstituents were evaluated through molecular docking, interaction studies and MM/GBSA binding free energy calculations, identifying two potential flavone C-glycosides, lucenin-II (-15.977, dG bind = -38.8), stellarin-II (-15.099, dG bind = -34.59), and a flavan derivative (2S)-7,4-dihydroxyflavan(4β-8)-catechin, in comparison to sildenafil (-10.890, dG bind = -75.4) and having frequent contacts with Phe 786, Phe 820, Ser 663, Tyr 664, and other crucial residues at the catalytic site of PDE5. Molecular dynamics simulations performed for 100 ns showed structural stability and compactness of the candidates through RMSD, RMSF which showed less fluctuations. The ADMET analysis revealed favorable pharmacokinetics, and pharmacodynamic properties with no subsequent toxicity in normal cells. The biological target class prediction identified enzymes with similar properties and icariin, which is a well-established natural PDE5 inhibitor was identified as a structurally similar analogue. These findings could lead to the development of novel natural product based PDE5 inhibitors.

Potential mechanism of Laportea bulbifera on treating inflammation and tumor via metabolomics, network pharmacology and molecular docking

This study aimed to utilize metabolomics, network pharmacology, and molecular docking techniques to identify the major active components of Laportea bulbifera and investigate their anti-inflammatory and potential anti-tumor mechanisms. The metabolic constituents of L. bulbifera were examined utilizing UPLC-ESI-MS/MS. PPI networks and compound-target-pathway networks were established using resources such as TCMSP, Swiss Target Prediction, DAVID, STRING database, and Cytoscape software. Molecular docking analysis of the most important compounds and targets was conducted using Autodock4, followed by validation of the molecular docking results' stability using GROMACS. The UPLC-ESI-MS/MS analysis identified a total of 798 compounds. A network pharmacology-based analysis was conducted, revealing that eight compounds and four molecular targets-namely, TNF, IL6, PIK3CA, and HDAC1-were enriched in the network. Pathway analysis of the identified targets demonstrated enrichment in 217 KEGG pathways. Molecular docking analysis and molecular dynamics simulations demonstrated strong therapeutic potential of N-feruloyltyramine, N-feruloylagmatine, and Ellagic acid against various inflammatory and tumor diseases. This study, for the first time, employed an integrated strategy of metabolomics, network pharmacology, molecular docking, and molecular dynamics, elucidating the mechanisms underlying the anti-inflammatory and potential anti-tumor effects of L. bulbifera, laying the foundation for subsequent drug development endeavors.

In Silico Repurposing of a Novel Inhibitor (drug) of EGFR and VEGFR-2 Kinases of Cancer by Pharmacokinetics, Toxicity, Molecular Docking, and Molecular Dynamics Simulation

Vascular endothelial growth factor is an angiogenic that promotes the development and metastasis of tumors (VEGF). The epidermal growth factor receptor, or EGFR, controls the division, growth, and death of cells via several signaling pathways. It has been found that most of the tyrosine kinase EGFR/VEGFR-2 inhibited by drugs that the FDA has approved are so far. The main objective of the present study was to identify an efficacious and selective dual inhibitor of VEGFR-2/EGFR for the treatment of cancer. Out of the 400 ligands tested against the kinases, 12 compounds demonstrated the best docking scores through molecular docking for the two kinases. Of these, only compound SCHEMBL2435814 inhibited the kinases with the highest score values when compared to a reference, vandetanib, as a dual inhibitor of EGFR/VEGFR-2 kinases through interaction with the identified active sites pocket. Following drug-likeness score toxicity and pharmacokinetic testing, the two compounds, SCHEMBL2435814 and vandetanib, were analyzed to determine how the two kinases interacted with each other. The results of calculations of π-cation interactions, hydrogen bonds, and hydrophobic interactions demonstrated a strong interaction between the two kinases and SCHEMBL2435814. Eventually, molecular dynamic modeling was used to assess the stability of complexes. This demonstrated many characteristics, including RMSF, RMSD, SASA, RG, and H-bond analysis, which demonstrated that SCHEMBL2435814 with the two kinases was more stable than vandetanib over a 100ns simulation period. By suppressing EGFR/VEGFR-2, chemical SCHEMBL2435814 may be able to postpone the signaling pathway of proteins that are essential to the advancement of cancer.

'In silico' repurposing new inhibitors of EGFR and VEGFR-2 kinases via biophysical mechanisms

Epidermal growth factor receptor (EGFR) controls cell growth, death, and proliferation through a variety of signaling mechanisms. The expression of vascular endothelial growth factor receptor-2 (VEGFR-2) by endothelial cells from malignant tissues triggers a series of signaling pathways that lead to tumor angiogenesis and increase cancer cell survival, proliferation, migration, and vascular permeability. The aim is to find novel inhibitors for EGFR and VEGFR-2 kinases by molecular docking drug-likeness models, pharmacokinetic, interaction analysis, and molecular dynamic simulation. Over 482 ligands were tested against the kinases, there are about 20 compounds that had the best docking scores for the 2 kinases but only compound 2C inhibited them with the highest score values by binding to active sites pocket established through molecular docking study. Secondly, the drug-likeness score of 2C was very good compared to the other compounds. The pharmacokinetics, physicochemical properties, and toxicity of 2C were much better than sorafenib and erlotinib as references. Analysis of interaction showed a strong interaction between 2C and active sites of EGFR and VEGFR-2 kinases illustrated by calculation of halogen bonds, π-Cation Interactions, Hydrogen Bonds, and Hydrophobic Interactions. Finally, the molecular dynamic simulation was also used to assess the stability of the EGFR and VEGFR-2 kinases-2C complexes. The complexes' stability was validated by RMSD, Rg, RMSF, SASA, and several hydrogen bonds analysis. 2C was shown to interact stably with pocket residues after MD simulation. Compound 2C may be a promising way to slow the signaling cascade of proteins that are significant contributors to the spread of cancer.Communicated by Ramaswamy H. Sarma.

From Flora to Pharmaceuticals: 100 new additions to angiosperms of Gafargaon subdistrict in Bangladesh and unraveling antidiabetic drug candidates targeting DPP4 through in silico approach

Addition to the angiosperm flora provides essential insights into the biodiversity of a region, contributing to ecological understanding and conservation planning. Gafargaon subdistrict under Mymensingh district in Bangladesh represents a diverse population of angiosperms with a multifaceted ecosystem that demands re-evaluation of the existing angiosperm diversity of Gafargaon to update the status of angiosperm taxa and facilitate their conservation efforts. With this endeavor, a total of 100 angiosperm taxa belonging to 90 genera and 46 families were uncovered as additional occurrence in Gafargaon. The species in the area showcased a variety of life forms, including 63 herbs, 14 shrubs, 14 trees, and 9 climbers. Among the recorded taxa, Chamaecostus cuspidatus (Nees & Mart.) C.D. Specht & D.W. Stev. was selected for antidiabetic drug design endeavor based on citation frequency and ethnomedicinal evidence. A total of 41 phytochemicals of C. cuspidatus were screened virtually, targeting the Dipeptidyl peptidase 4 protein through structure-based drug design approach, which unveiled two lead compounds, such as Tigogenin (-9.0 kcal/mol) and Diosgenin (-8.5 kcal/mol). The lead candidates demonstrated favorable pharmacokinetic and pharmacodynamic properties with no major side effects. Molecular dynamics simulation revealed notable stability and structural compactness of the lead compounds. Principal component analysis and Gibbs free energy landscape further supported the results of molecular dynamics simulation. Molecular mechanics-based MM/GBSA approach unraveled higher free binding energies of Diosgenin (-47.36 kcal/mol) and Tigogenin (-46.70 kcal/mol) over Alogliptin (-46.32 kcal/mol). The outcome of the present investigation would enrich angiosperm flora of Gafargaon and shed light on the role of C. cuspidatus to develop novel antidiabetic therapeutics to combat diabetes.

Synergistic therapeutic strategies and engineered nanoparticles for anti-vascular endothelial growth factor therapy in cancer

Angiogenesis is one of the defining characteristics of cancer. Vascular endothelial growth factor (VEGF) is crucial for the development of angiogenesis. A growing interest in cancer therapy is being caused by the widespread use of antiangiogenic drugs in treating several types of human cancer. However, this therapeutic approach can worsen resistance, invasion, and overall survival. As we proceed, refining combination strategies and addressing the constraint of targeted treatments are paramount. Therefore, major challenges in using novel combinations of antiangiogenic agents with cytotoxic treatments are currently focused on illustrating the potential of synergistic therapeutic strategies, alongside advancements in nanomedicine and gene therapy, present opportunities for more precise interference with angiogenesis pathways and tumor environments. Nanoparticles have the potential to regulate several crucial activities and improve several drug limitations such as lack of selectivity, non-targeted cytotoxicity, insufficient drug delivery at tumor sites, and multi-drug resistance based on their unique features. The goal of this updated review is to illustrate the enormous potential of novel synergistic therapeutic strategies and the targeted nanoparticles as an alternate strategy for t treating a variety of tumors employing antiangiogenic therapy.

Insight into novel inhibitors from Sterculia urens against Cholera via pharmacoinformatics and molecular dynamics simulation approaches

The underdeveloped countries with large populations are facing a grave global threat in the form of cholera. Vibrio cholerae, the etiologic agent of Cholera has drawn attention recently due to antimicrobial resistance and resulting outbreaks that necessitates establishment of novel medications to counteract virulence and viability of the pathogen. Sterculia urens Roxb. (Malvaceae) is an ethnomedicinally important tree, which harbors a good number of bioactive phytocompounds. In the present study, 53 phytocompounds of S. urens were screened against the promising target ToxT of V. cholerae employing structure-based drug design approach that revealed three lead compounds, viz., 4,4,5,8-Tetramethylchroman-2-ol (-8.2 kcal/mol), Beta-Bisabolol (-8.2 kcal/mol) and Ledol (-8.7 kcal/mol) with satisfactory ADMET properties. Molecular dynamics simulation for 150 ns unveiled notable compactness and structural stability for the lead compounds considering RMSD, RMSF, Rg, MolSA, PSA and protein-ligand contacts parameters. Molecular mechanics-based MM/GBSA binding energy calculation revealed Beta-Bisabolol (-66.74 kcal/mol) to have better scores than 4,4,5,8-Tetramethylchroman-2-ol (-47.42 kcal/mol) and Ledol (-65.79 kcal/mol). Enzymes were mostly found as drug target class, and Nabilone was found as a structurally similar analog for 4,4,5,8-Tetramethylchroman-2-ol. These discoveries could aid in revealing new antibacterial medications targeting ToxT to combat Cholera.Communicated by Ramaswamy H. Sarma.

Pharmacoinformatics and molecular dynamics simulation approach to identify anti-diarrheal potentials of Centella asiatica (L.) Urb. against Vibrio cholerae

Vibrio cholerae, the etiological agent of cholera, causes dehydration and severe diarrhea with the production of cholera toxin. Due to the acquired antibiotic resistance, V. cholerae has drawn attention to the establishment of novel medications to counteract the virulence and viability of the pathogen. Centella asiatica is a medicinal herb native to Bangladesh that has a wide range of medicinal and ethnobotanical applications including anti-bacterial properties. In the present investigation, a total of 25 bioactive phytochemicals of C. asiatica have been screened virtually through molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses, and molecular dynamics simulation. Our results revealed four lead compounds as Viridiflorol (-8.7 Kcal/mol), Luteolin (-8.1 Kcal/mol), Quercetin (-8.0 Kcal/mol) and, Geranyl acetate (-7.1 Kcal/mol) against V. cholerae Toxin co-regulated pilus virulence regulatory protein (ToxT). All the lead compounds have been found to possess favorable pharmacokinetic, pharmacodynamics, and molecular dynamics properties. Toxicity analysis revealed satisfactory results with no major side effects. Molecular dynamics simulation was performed for 100 ns that revealed noteworthy conformational stability and structural compactness for all the lead compounds, especially for Quercetin. Target class prediction unveiled enzymes in most of the cases and some experimental and investigational drugs were found as structurally similar analogs of the lead compounds. These findings could aid in the development of novel therapeutics targeting Cholera disease and we strongly recommend in vitro trials of our experimental findings.Communicated by Ramaswamy H. Sarma.