Traditional treatments of cancer have faced various challenges, including toxicity, medication resistance, and financial burdens. On the other hand, bioactive phytochemicals employed in complementary alternative medicine have recently gained interest due to their ability to control a wide range of molecular pathways while being less harmful. As a result, we used a network pharmacology approach to study the possible regulatory mechanisms of active constituents of Cordia myxa for the treatment of liver cancer (LC). Active constituents were retrieved from the IMPPAT database and the literature review, and their targets were retrieved from the STITCH and Swiss Target Prediction databases. LC-related targets were retrieved from expression datasets (GSE39791, GSE76427, GSE22058, GSE87630, and GSE112790) through gene expression omnibus (GEO). The DAVID Gene Ontology (GO) database was used to annotate target proteins, while the Kyoto Encyclopedia and Genome Database (KEGG) was used to analyze signaling pathway enrichment. STRING and Cytoscape were used to create protein–protein interaction networks (PPI), while the degree scoring algorithm of CytoHubba was used to identify hub genes. The GEPIA2 server was used for survival analysis, and PyRx was used for molecular docking analysis. Survival and network analysis revealed that five genes named heat shot protein 90 AA1 (HSP90AA1), estrogen receptor 1 (ESR1), cytochrome P450 3A4 (CYP3A4), cyclin-dependent kinase 1 (CDK1), and matrix metalloproteinase-9 (MMP9) are linked with the survival of LC patients. Finally, we conclude that four extremely active ingredients, namely cosmosiin, rosmarinic acid, quercetin, and rubinin influence the expression of HSP90AA1, which may serve as a potential therapeutic target for LC. These results were further validated by molecular dynamics simulation analysis, which predicted the complexes with highly stable dynamics. The residues of the targeted protein showed a highly stable nature except for the N-terminal domain without affecting the drug binding. An integrated network pharmacology and docking study demonstrated that C. myxa had a promising preventative effect on LC by working on cancer-related signaling pathways.

Phosphatidylinositol 3,4,5‐trisphosphate‐ (PIP3‐) dependent Rac exchanger 1 (P‐Rex1) functions as Rho guanine nucleotide exchange factor and is activated by synergistic activity of Gβγ and PIP3 of the heterotrimeric G protein. P‐Rex1 activates Rac GTPases for regulating cell invasion and migration and promotes metastasis in several human cancers including breast, prostate, and skin cancer. The protein is a promising therapeutic target because of its multifunction roles in human cancers. Herein, the present study attempts to identify selective P‐Rex1 natural inhibitors by targeting PIP3‐binding pocket using large‐size multiple natural molecule libraries. Each library was filtered subsequently in FAF‐Drugs4 based on Lipinski’s rule of five (RO5), toxicity, and filter pan assay interference compounds (PAINS). The output hits were virtually screened at the PIP3‐binding pocket through PyRx AutoDock Vina and cross‐checked by GOLD. The best binders at the PIP3‐binding pocket were prioritized using a comparative analysis of the docking scores. Top‐ranked two compounds with high GOLD fitness score (>80) and lowest AutoDock binding energy (< ‐12.7 kcal/mol) were complexed and deciphered for molecular dynamics along with control‐P‐Rex1 complex to validate compound binding conformation and disclosed binding interaction pattern. Both the systems were seen in good equilibrium, and along the simulation time, the compounds are in strong contact with the P‐Rex1 PIP3‐binding site. Hydrogen bonding analysis towards simulation end identified the formation of 16 and 22 short‐ and long‐distance hydrogen bonds with different percent of occupancy to the PIP3 residues for compound I and compound 2, respectively. Radial distribution function (RDF) analysis of the key hydrogen bonds between the compound and the PIP3 residues demonstrated a strong affinity of the compounds to the mentioned PIP3 pocket. Additionally, MMGB/PBSA energies were performed that confirmed the dominance of Van der Waals energy in complex formation along with favorable contribution from hydrogen bonding. These findings were also cross‐validated by a more robust WaterSwap binding energy predictor, and the results are in good agreement with a strong binding affinity of the compounds for the protein. Lastly, the key contribution of residues in interaction with the compounds was understood by binding free energy decomposition and alanine scanning methods. In short, the results of this study suggest that P‐Rex1 is a good druggable target to suppress cancer metastasis; therefore, the screened druglike molecules of this study need in vitro and in vivo anti‐P‐Rex1 validation and may serve as potent leads to fight cancer.

Klebsiella pneumoniae is a Gram-negative encapsulated opportunistic pathogen, which presents a major threat to public health due to its ability for multi-antibiotic drug resistance. It is responsible for 30% of Gram-negative bacterial infections, including nosocomial infections, pneumonia, septicemia, and urinary tract infections. The study aimed to analyze the key phenotypic and genetic features of clinical K. pneumoniae isolates. Between 2022 and 2023, a total of 91 strains of Klebsiella pneumoniae were collected from Al-Imamian Al-Kadhimiyain Medical City (IKMC) and characterized using the VITEK-2 technique. Whole-genome sequencing (WGS) was employed to characterize the extreme drug-resistant strain. The whole genome was extracted and sequenced using the Next Generation Sequencing (NGS) technique. The genome of our bacterial isolate was analyzed using different bioinformatics tools such as Galaxy workflow, SPAdes, PROKKA, and Staramr. The analysis identified Klebsiella pneumoniae serotype K36:O2a and sequencing type ST-437, containing 15 different plasmids carrying 54 resistance genes and more than 100 virulence genes with one region of CRISPR and no Cas. The sample obtained four intact bacteriophages and two questionable ones. Seven insertion sequences were revealed in the analysis as part of Other Mobile Genetic Elements (OMG). Additionally, the 16SrRNA phylogenetic tree identified a higher relationship of the bacteria to the strains from the USA and India than from Iraq. It is the first study in Iraq to utilize WGS to comprehensively characterize an opportunistic pathogen. The study emphasizes the need for WGS to track the development of resistance and virulence patterns in clinical strains of K. pneumoniae.