Current computer-aided drug design最新文献

Background: Epidermal growth factor receptor tyrosine kinase [EGFR TK] is a primary target for inhibiting cellular signal transduction in several types of cancer. Numerous EGFR TK inhibitors have been developed and approved as standard therapy for cancer management. However, the development of drug resistance and significant adverse effects have encouraged the search for alternative EGFR TK inhibitors.

Objective: This study attempted to identify 2,4-diaryl-6-styrylpyridine derivatives as alternative orthosteric-allosteric EGFR TK inhibitors through molecular docking, molecular dynamic simulation, binding free energy calculation, and pharmacokinetic properties analysis.

Methods: Two series of 2,4-diaryl-6-styrylpyridine derivatives were docked in orthosteric and allosteric sites of EGFR TK. Docking results were validated through molecular dynamic simulation and binding free energy calculation using YASARA Structure. Pharmacokinetic properties were analyzed using web-based free servers SwissADME and ADMETLab 3.0.

Results: The molecular docking studies revealed relatively strong affinity, with binding energy ranging from -10.3 to -12.2 kcal/mol in the orthosteric site and from -8.3 to -10.9 kcal/mol in the allosteric site of EGFR TK. The proposed ligand complexes with the highest binding energy and proper hydrogen bonds showed comparable stability and binding free energy than native ligand complexes. The pharmacokinetic properties of the proposed ligands indicated relatively poor characteristics due to relatively high lipophilicity and certain toxicophores.

Conclusion: This study identified NASP06 and NASP01 as the most stable orthosteric and allosteric inhibitors of EGFR TK, respectively. These findings revealed a novel class of EGFR TK inhibitors capable of interacting with both orthosteric and allosteric sites.

Background: XueFuZhuYu pills (XFZY), a traditional Chinese herbal formula originated from the xuefuzhuyu decoction in Correction on Errors in Medical Classics, has a certain clinical effect on the treatment of hyperprolactinemia (HPRL) caused by antipsychotics. However, the active ingredients and mechanism by which XFZY contributes to the hyperprolactinemia caused by antipsychotics remain unclear.

Objectives: The aim of the study was to investigate the molecular basis of XFZY in the therapy of antipsychotic-induced HPRL and to establish a scientific foundation for its application.

Methods: First, the UHPLC-Q-TOF-MS/MS methodology was employed to perform chromatographic separation and gather mass spectrometry data. Subsequently, the preprocessed mass spectrometry data were uploaded to the Global Natural Products Social Molecular Networking (GNPS) platform for spectral library interrogation and molecular network analysis. Next, based on the detected chemical constituents and the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, the effective chemical components within XFZY were chosen. Swiss Target Prediction was employed to determine probable targets of components, and we used Cytoscape to create a network of components and their associated targets. After that, HPRL-related targets were found and filtered using four disease databases, and then a proteinprotein interaction (PPI) network was built using the STRING database. Cytoscape was utilized to conduct visualization and cluster analysis. Meanwhile, the Metascape database was adopted for the enrichment analysis of GO and KEGG. At last, Autodock Vina was applied to perform molecular docking between the principal components and target proteins.

Results: In total, 213 compounds were discovered in XFZY. Two hundred eight active chemical components, 622 probable targets, and 242 HPRL-related target genes were identified. There were 76 common targets between the XFZY and HPRL. Following analysis, 1371 GO biological process items and 162 KEGG signal pathways were identified. The primary chemicals and target proteins exhibited great affinity in molecular docking.

Conclusion: This research manifests that XFZY, as a traditional Chinese medicine formula, proffers a novel pathway for the treatment of antipsychotic-induced HPRL. We elucidated the specific molecular mechanisms underlying the anti-HPRL effects of XFZY and its active ingredients, laying a foundation for the subsequent clinical applications of this formula.

Background: Oral Squamous Cell Carcinoma (OSCC) is a multiple-phase carcinogenic disease that concurrently involves malignant lesions, invasion, and metastasis. It has been reported that Ubiquitin-conjugating enzymes play a significant role in the progression of OSCC and other fatal cancers through the process of ubiquitination. Among them, UBE2D1 represents a promising target for therapeutic intervention. Strategies aimed at inhibiting UBE2D1 could restore the function of tumor suppressors, such as p53, and potentially enhance the effectiveness of existing cancer therapies.

Objective: This study aims to discover the potential natural inhibitors of UBE2D1 from an extensive chemical library through computational techniques.

Methods: This study utilized in silico methods, such as virtual screening, molecular docking, analysis of pharmacokinetic parameters, and molecular dynamics simulation, to discover the most effective inhibitors for the ubiquitin-conjugating enzyme.

Results: Based on binding affinity, the top six compounds, ZINC15113777, ZINC225461658, ZINC107430641, ZINC259440, ZINC4025306, and ZINC107283931, were found to be the best for the selected target. Also, molecular dynamic simulation results showed that all these compounds form stable complexes with UBE2D1.

Conclusion: Based on our analysis of the results, we have determined that natural products, specifically ZINC15113777, ZINC4025306, and ZINC107283931, have the ability to inhibit UBE2D1 efficiently and could be utilized as potential drugs for the treatment of OSCC and other cancers. Such approaches may help to reinstate normal apoptotic pathways and improve overall treatment outcomes in patients with cancers characterized by UBE2D1 dysregulation. Additionally, conducting in-vitro/vivo studies on these molecules could be a prospective avenue in the realm of pharmaceutical research.

Introduction: Our group previously reported isatin-based hydrazones (ISB1-ISB6) were further evaluated for their in vitro acetylcholine esterase, butylcholinestrase and cytotoxic effects on cancer cell lines. The compounds successfully suppressed AChE and BChE, with Ki values ranging from 1.06±0.07 to 23.57±1.64 nM for AChE and 15.31±1.28 to 84.41±8.04 nM for BChE. However, the IC50 values of these compounds for AChE and BChE were found to be in the ranges of 1.45-25.51 nM and 16.38-92.90 nM, respectively.

Method: Furthermore, to explore the anti-tumor potential of our newly synthesized compounds, we conducted a cytotoxic MTT assay to assess their impact on two different cancer cell lines: MCF7 and A2780.

Results: Our findings highlight diverse cytotoxic profiles among the compounds. Specifically, ISB2, ISB3, and ISB4 demonstrated potential cytotoxicity in the A2780 cell line, while ISB6 exhibited significant cytotoxicity in the MCF7 cell line. This suggests that these compounds have different effects on cancer cell types, indicating the need for further investigation into their potential applications in cancer therapy.

Conclusion: Finally, molecular docking and dynamic study revealed that lead molecule ISB3 provides stability in the AChE and BChE protein-ligand complex.

Background: The global spread of Strongyloides stercoralis has escalated public health concerns, affecting over 600 million people worldwide. The rise in global migration has heightened the risk of transmission, underscoring the urgent need for effective treatment options.

Objective: This study aimed to investigate ten polyphenolic phytochemicals derived from Mangifera indica as potential alternatives to combat S. stercoralis.

Methods: The efficacy of these compounds was evaluated using computational techniques, including density functional theory (DFT) analysis, molecular docking, adsorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment, and molecular dynamics (MD) simulations.

Results: DFT calculations revealed significant chemical reactivity in compounds such as kaempferol, ellagic acid, quercetin, norathyriol, mangiferin, and ferulic acid. Molecular docking identified mangiferin, quercetin, kaempferol, and norathyriol as top candidates for targeting S. stercoralis. A 200-ns MD simulation of the protein-ligand complex demonstrated the stability and binding behavior of these compounds compared to the reference drug, thiabendazole. ADMET screening confirmed their drug-likeness. Notably, quercetin and mangiferin exhibited strong binding affinities (ΔGbind = -42.35 and -54.57 kcal/mol, respectively), outperforming thiabendazole (ΔGbind = -28.94 kcal/mol).

Conclusion: Quercetin and mangiferin emerge as promising alternatives to thiabendazole, offering favorable chemical reactivity, potent inhibition constants, and strong biological activity for the treatment of S. stercoralis.

Background: An important characteristic of the quality-by-design approach is defining risk, which is a combination of the probability of harm and its severity. During risk assessment, it is essential to determine how the formulation, properties of active ingredients and excipients, and process parameters can potentially affect critical quality attributes or critical process parameters.

Objective: to develop an algorithm and a mathematical model for predicting quality risks in the pharmaceutical development of bisoprolol fumarate tablets with indapamide.

Methods: The software programs "Microsoft Excel 2016" and "Statistica 10.0" (StatSoft, Inc.) were used to predict potential risks and to build a regression model of quality-related risks for bisoprolol fumarate tablets with indapamide.

Results: A mathematical model for predicting the tablet quality risk has been developed, incorporating significant predictors: Carr's index for powder mixtures (Х1), evaluation of the pressing process (Х2), uniformity of tablet weight (Х3), tablets hardness testing (Х4), disintegration time (Х6). Four levels of quality risk are defined: low risk [0.8-1.0], moderate risk [0.6-0.8], high risk [0.4-0.6], and critical risk [0-0.4]. The calculated coefficient of determination of the forecasting model (R2=0.8168) testifies to its high quality.

Conclusion: The developed algorithm and mathematical model for predicting tablet quality risks, proposed for the first time, are highly informative and qualitative. It makes it possible to assess and predict risks related to the quality of tablets, arising from the influence of multiple factors.

Background: The potency content of penicillin serves as a crucial indicator for measuring its pharmacological effects, playing a vital role in quality control and clinical applications. In recent years, with the continuous improvement of production efficiency and quality requirements in the pharmaceutical industry, the need for high-frequency monitoring of drug potency has become increasingly urgent. Infrared spectroscopy, as an emerging research tool, has demonstrated immense potential in the field of drug potency testing.

Objective: The objective of this study is to develop a real-time monitoring model for penicillin potency content utilizing near-infrared (NIR) spectroscopy data. This model aims to enable rapid and accurate detection of potency content during the penicillin production process, ultimately enhancing production efficiency and reducing costs.

Method: During the penicillin production process, NIR spectroscopy data from penicillin samples were scanned and collected to form a comprehensive dataset. Five distinct spectral preprocessing methods were combined with three regression models to construct detection models. By comparing the performance of different combinations, the optimal model configuration was identified.

Results: The optimal model configuration identified in this study integrates the Savitzky-Golay filtering method with ridge regression. Under this optimal model, the coefficient of determination for the test set reached 0.990669, indicating an extremely high degree of agreement between the model's predicted values and the actual measured values. This real-time monitoring model for penicillin potency content can be applied as a rapid and non-destructive monitoring method in factory settings.

Conclusion: This study successfully developed a real-time monitoring model for penicillin potency based on NIR spectroscopy technology. The research findings not only provide strong support for potency monitoring during the penicillin production process but also offer new insights and methodologies for non-destructive testing of other pharmaceuticals and chemicals.

Background: The function of HOXC antisense RNA 1 (HOXC-AS1) in lung adenocarcinoma (LUAD) remains largely unexplored.

Objective: The objective of this research was to examine the relationship between HOXC-AS1 levels and LUAD through both bioinformatics analysis and experimental validation.

Methods: We employed statistical methods and bioinformatics to evaluate the correlation between HOXC-AS1 expression and various clinical features, survival predictors, regulatory mechanisms, and immune cell infiltration in LUAD. The levels of HOXC-AS1 in LUAD cell lines were ascertained through quantitative reverse transcription PCR.

Results: HOXC-AS1 displayed significantly increased expression in individuals with LUAD. There was a significant correlation between high HOXC-AS1 levels and diminished overall survival in LUAD patients, characterized by a hazard ratio of 0.66, a 95% confidence interval of 0.49 to 0.88, and a statistically significant P-value (0.005). An elevated expression of HOXCAS1 was found to be a standalone predictor of poor overall survival in LUAD patients, with a Pvalue of 0.002. HOXC-AS1 was found to be implicated in various pathways, such as neuroactive ligand-receptor interaction and asthma, among others. The study revealed a substantial link between high HOXC-AS1 expression and unfavorable outcomes in LUAD, including poor survival and altered immune cell infiltration. LUAD cell lines exhibited a marked increase in HOXC-AS1 expression compared to the Beas-2B normal lung cell line.

Conclusion: The research indicated a strong association between higher levels of HOXC-AS1 and negative outcomes in LUAD, such as reduced survival rates and the presence of immune cell infiltration. HOXC-AS1 could potentially be utilized as a biomarker to anticipate patient prognosis and their likelihood of responding to immunotherapies in LUAD.

Introduction: The extended IL-1 activity is implicated in autoimmune disorders, such as rheumatoid arthritis, diabetes mellitus, and Parkinson's disease, as well as delayed wound healing. Additionally, it can result in cytokine storms during pathogenic infections.

Methods: The regulation was carried out by Interleukin-1 receptor antagonist (IL-1RA), a key anti-inflammatory molecule. IL-1RA serves as a decoy protein that competes with Interleukin-1 receptors (IL-1RI and IL-1RII) for binding, effectively counteracting the activity of Interleukin- 1 (IL-1). The deficiency was substantiated by commercially available recombinant IL-1RA called Anakinra. The main problem with the existing drug is that it has less pharmacokinetics and reduced binding affinity to its receptor, which requires frequent administration of the drug. To overcome these drawbacks, we have designed a new fusion protein by adding an Fc fragment of Human IgGI fused with IL-1RA using a linker in between, and the design aimed to transport the protein into the N-glycosylation pathway. These characteristic features increase the pharmacokinetics, solubility, and binding efficiency of the protein. As the protein was designed to be expressed in a eukaryotic system, to understand the possibility of the proposed hypothesis, we used machine learning-based AlphaFold2 to model the protein structure and molecular simulation studies to understand the functional integrity of the designed protein.

Results: The in silico results showed that the modeled fusion protein structure has very good binding to its receptor with the support of 21 H bonds and 7 salt bridges and maintained the binding stability over the MD simulations.

Conclusion: These findings support fusion protein's potential as a promising and stable therapeutic candidate.

Background: Acute pharyngitis (AP) is a prevalent ailment. Gynostemma pentaphylla (GP), a traditional Chinese medicine (TCM), may treat AP due to its anti-tumor and anti-inflammatory properties, but this remains unexplored.

Methods: This study utilized the TCMSP and Swiss Target Prediction databases to analyze GP's chemical composition and target proteins. The Genecards database was used to identify targets relevant to AP. A PPI network diagram of drug-disease intersection targets was created using the STRING database, and Cytoscape was utilized to create a network visualization diagram of "GP active components-targets-AP" in order to determine key active components of GP in treating AP. Gene ontology (GO) and biological pathway (KEGG) enrichment analyses were conducted on targets in the David database. Molecular docking verification of key targets and components was performed using AutoDock Vina software. In animal experiments, a rat model of AP was induced by a 15% concentrated ammonia solution, and HE staining was conducted to observe histopathological changes in the rat pharynx after intragastric administration of Houyanqing. ELISA was used to detect expression levels of serum interleukin-1-beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor (TNF-α).

Results: A total of 18 active ingredients were screened from GP, among which Ruvoside _ qt, Rhamnazin, 3 ' -methyleriodictyol, and sitosterol were five key active ingredients. The key targets involved EGFR, STAT3, MAPK3, SRC, AKT1, etc. KEGG enrichment analysis showed that GP mainly acted on Pathways in cancer, P13K-AKT signaling Pathways, JAK-STAT signaling pathways, and other signaling pathways. Molecular docking results showed that four core compounds and five key targets met the energy matching. Animal experiments showed that compared with the normal group, the expression levels of IL-1β, IL-6, and TNF-α in the AP model group were significantly up-regulated (P < 0.05). In addition, compared with the model group, intragastric administration of the dexamethasone group and gypenosides group could alleviate the up-regulation of inflammatory factors in model rats, and the levels of IL-1β, IL-6, and TNF-α were decreased (P < 0.05).

Conclusion: This study predicted the possible targets of GP in the treatment of AP through network pharmacology. The results suggest that gypenosides may inhibit the expression of inflammatory factors by regulating Pathways in cancer, P13K-AKT, and JAK-STAT signaling pathways to treat AP.