The Impact of Software Used and the Type of Target Protein on Molecular Docking Accuracy

Zhongfeng decoction attenuates cerebral ischemia-reperfusion injury by inhibiting autophagy via regulating the AGE-RAGE signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Tackling phlegm and improving blood circulation is vital in the treatment of ischemic stroke (IS), culminating in the development of Zhongfeng Decoction (ZFD), a method grounded in this approach and serving as an effective therapy for IS. Nonetheless, the defensive mechanism of the ZFD in preventing cerebral ischemia-reperfusion damage remains ambiguous.

AIM OF THE STUDY

Determine the active ingredients in ZFD that have neuroprotective effects, and identify its mechanism of action against IS.

MATERIALS AND METHODS

A cerebral ischemia model in rats was developed, utilizing TTC, Nissl staining, and an oxidative stress kit to evaluate the neuroprotective impact of ZFD on this rat model. Following this, an amalgamation of LC-MS and network pharmacology techniques was employed to pinpoint potential active components, primary targets, and crucial action mechanisms of ZFD in treating IS. Finally, key targets and signaling pathways were detected using qRT-PCR, ELISA, Western blotting, electron microscopy, and other methods.

RESULTS

Through LC-MS and network analysis, 15 active ingredients and 6 hub targets were identified from ZFD. Analysis of pathway enrichment revealed that ZFD predominantly engages in the AGE-RAGE signaling route. Kaempferol, quercetin, luteolin, baicalein, and nobiletin in ZFD are the main active ingredients for treating IS. In vivo validation showed that ZFD can improve nerve damage in cerebral ischemic rats, reduce the mRNA expression of IL6, SERPINE1, CCL2, and TGFB1 related to inflammation. Furthermore, we also confirmed that ZFD can inhibit the protein expression of AGEs, RAGE, p-IKBα/IKBα, p-NF-κB p65/NF-κB p65, reduce autophagy levels, and thus decrease neuronal apoptosis.

CONCLUSIONS

The mechanism of action of ZFD in treating IS primarily includes inflammation suppression, oxidative stress response alleviation, post-stroke cell autophagy and apoptosis regulation, and potential mediation of the AGE-RAGE signaling pathway. This study elucidates how ZFD functions in treating IS, establishing a theoretical basis for its clinical application.

Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors

Human dihydroorotate dehydrogenase (hDHODH) is a flavin mononucleotide-dependent enzyme that can limit de novo pyrimidine synthesis, making it a therapeutic target for diseases such as autoimmune disorders and cancer. In this study, using the docking structures of complexes generated by AutoDock Vina, we integrate interaction features and ligand features, and employ support vector regression to develop a target-specific scoring function for hDHODH (TSSF-hDHODH). The Pearson correlation coefficient values of TSSF-hDHODH in the cross-validation and external validation are 0.86 and 0.74, respectively, both of which are far superior to those of classic scoring function AutoDock Vina and random forest (RF) based generic scoring function RF-Score. TSSF-hDHODH is further used for the virtual screening of potential inhibitors in the FDA-Approved & Pharmacopeia Drug Library. In conjunction with the results from molecular dynamics simulations, crizotinib is identified as a candidate for subsequent structural optimization. This study can be useful for the discovery of hDHODH inhibitors and the development of scoring functions for additional targets.

Interactions of memantine and rivastigmine with graphene oxide nanocarrier and beta-amyloid protein using molecular docking and in-silico methods

Alzheimer's disease is characterized by the accumulation of beta-amyloid plaques and neurofibrillary tangles. Effective therapeutic strategies involve inhibiting the formation of beta-amyloid aggregates and destabilizing existing ones. A significant challenge in current treatments is the inability of therapeutic agents to cross the blood-brain barrier, a limitation addressed by employing drug nanocarriers. This study investigates the interactions between memantine, rivastigmine, beta-amyloid structures, and graphene oxide nanocarriers using molecular docking and in silico methods. The goal is to enhance drug development through cost-effective and efficient computational techniques. Results indicate that the binding energies for memantine-beta-amyloid and rivastigmine-beta-amyloid complexes are -9.03 kcal/mol and -7.81 kcal/mol, respectively, suggesting superior stability for the memantine-beta-amyloid complex. The electrostatic energies are -1.91 kcal/mol for memantine and -0.81 kcal/mol for rivastigmine, further supporting the greater stability of the memantine complex. Additionally, memantine's interaction with graphene oxide results in more negative adsorption energy (-92.47 kJ/mol) compared to rivastigmine (-86.36 kJ/mol), indicating a stronger binding affinity. The charge transfer (Q) values are -0.41 kJ/mol for memantine and -0.33 kJ/mol for rivastigmine. The negative enthalpy (ΔH) of -85.71 kJ/mol and Gibbs free energy (ΔG) of -41.52 kJ/mol for the memantine-graphene oxide interaction suggest a spontaneous process. Both memantine and rivastigmine display similar electronic properties, but memantine shows a more effective interaction with graphene oxide, likely due to its amine functional group and spatial configuration. The adsorption energy analysis confirms that memantine forms a more stable complex with graphene oxide than rivastigmine.

In vitro antibacterial activities, DPPH radical scavenging, and molecular simulation of isolated compounds from the leaves of Rhus ruspolii

Rhus ruspolii Engl. plant is traditionally used in Ethiopia to treat various diseases. However, the biological and phytochemical properties of the leaves are not well documented. Hence, this study aimed to isolate phytochemicals from R. ruspolii leaves and evaluate their antibacterial and DPPH radical scavenging activities. GC-MS analysis identified 16 compounds from combined fractions 6-10. Chromatographic separation and NMR analysis resulted in the isolation and characterization of palmitic acid (7), 3,4-dihydroxybenzoic acid (17), cupressuflavone (18), amentoflavone (19), shikimic acid (20), avicularin (21), and myricetin-3-O-5''-acetylarabinofuranoside (22). The inhibition zones of extracts (100 mg/mL) and isolated compounds (5 mg/mL) ranged from 8.33 ± 0.50 to 16.33 ± 0.47 mm against all evaluated bacteria. Of all isolated compounds, compounds 18 and 21 showed good activity against Gram-negative (supported by in silico molecular docking studies) and Gram-positive bacteria, respectively. The lowest (49.1 %) and the highest (91.3 %) DPPH radicals were inhibited by combined fractions 6-10 and compound 17, respectively, at 62.5 μg/mL. The SwissADME online analysis showed compounds 17 and 20 have good solubility and permeability. The Pro Tox 3.0 online analysis revealed none of the isolated compounds are fatal if swallowed. Therefore, the findings of this study support the traditional use of the plant for treating bacteria diseases.

Identification of potential sclerostin inhibiting flavonoids from Oroxylum indicum: an insilico approach

Flavonoids are secondary metabolites that are widely found in various medicinal plants. They are known for their medicinal benefits and have been extensively used in healthcare industries and in the management of age-related diseases. This paper focuses on flavonoids from Oroxylum indicum, a significant medicinal tree in the practice of traditional Indian medicine. O. indicum has been utilized in a variety of polyherbal formulations for the management of musculoskeletal disorders, however the mechanism of action of its bioactive flavonoids remains unknown. The present study aimed to identify the flavonoids of O. indicum with the potential to target sclerostin, an antagonist of canonical Wnt signaling pathway for the treatment of bone-related disorders. Molecular docking, coarse-grained and molecular dynamics simulations were performed to screen the major flavonoids and investigate their interaction with sclerostin. Flavonoids with highest binding affinity and interacting with at least one of the amino acids of the PNAIG motif residues were selected from docking studies and subjected to further drug likeness and ADMET screening. Further screening from coarse-grained and molecular dynamic simulations results showed that baicalein, compared to other screened flavonoids, stably binds with the important residues of the LRP6 binding site of sclerostin, resulting in pronounced structural changes in the protein. These findings suggest that baicalein from O. indicum can potentially inhibit sclerostin and can elicit skeletal protective effects, providing an insight for further in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.

Pantothenate kinase: A promising therapeutic target against pathogenic Clostridium species

Current treatment of clostridial infections includes broad-spectrum antibiotics and antitoxins, yet antitoxins are ineffective against all Clostridiumspecies. Moreover, rising antimicrobial resistance (AMR) threatens treatment effectiveness and public health. This study therefore aimed to discover a common drug target for four pathogenic clostridial species, Clostridium botulinum, C. difficile, C. tetani, and C. perfringens through an in-silico core genomic approach. Using four reference genomes of C. botulinum, C. difficile, C. tetani, and C. perfringens, we identified 1484 core genomic proteins (371/genome) and screened them for potential drug targets. Through a subtractive approach, four core proteins were finally identified as drug targets, represented by type III pantothenate kinase (CoaX) and, selected for further analyses. Interestingly, the CoaX is involved in the phosphorylation of pantothenate (vitamin B5), which is a critical precursor for coenzyme A (CoA) biosynthesis. Investigation of druggability analysis on the identified drug target reinforces CoaX as a promising novel drug target for the selected Clostridium species. During the molecular screening of 1201 compounds, a known agonist drug compound (Vibegron) showed strong inhibitory activity against targeted clostridial CoaX. Additionally, we identified tazobactam, a beta-lactamase inhibitor, as effective against the newly proposed target, CoaX. Therefore, identifying CoaX as a single drug target effective against all four clostridial pathogens presents a valuable opportunity to develop a cost-effective treatment for multispecies clostridial infections.

Tanreqing injection demonstrates anti-dengue activity through the regulation of the NF-κB-ICAM-1/VCAM-1 axis

BACKGROUND

Tanreqing injection (TRQ) has been employed in clinical practice as a treatment for dengue fever (DF). Nevertheless, the precise pharmacological mechanism underlying its efficacy remains elusive.

METHOD

Network pharmacology, molecular docking, transcriptome sequencing, and experimental evaluation were employed to analyze and study the inhibitory potential of TRQ against dengue virus (DENV).

RESULT

We found that TRQ inhibited the replication of DENV in human umbilical vein endothelial cells, Huh-7 cells, and Hep3B cells. In addition, TRQ prolonged the survival duration of AG129 mice infected with DF, decreased the viral load in serum and organs, and alleviated organ damage. Subsequently, ultra-high-performance liquid chromatography-tandem mass spectrometry analysis of TRQ was performed to identify 314 targets associated with 36 active compounds present in TRQ. Integration of multiple databases yielded 47 DF-related genes. Then, 15 hub targets of TRQ in DF were determined by calculating the network topology parameters (Degree). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these pathways were primarily enriched in the processes of cytokine activation and leukocyte cross-endothelial migration, with significant enrichment of cell adhesion molecules. Molecular docking revealed favorable binding affinity between TRQ's key active compounds and the predicted hub targets. Transcriptome sequencing results showed TRQ's ability to restore the expression of vascular cell adhesion molecule-1 (VCAM-1) post-DENV infection. Finally, TRQ was found to modulate the immune status by regulating the nuclear factor kappa-B (NF-κB)- intercellular cell adhesion molecule-1 (ICAM-1)/VCAM-1 axis, as well as reduce immune cell alterations, inflammatory factor secretion, vascular permeability, and bleeding tendencies induced by DENV infection.

CONCLUSION

Our research suggests that TRQ exerts therapeutic effects on DF by regulating the NF-κB-ICAM-1/VCAM-1 axis.

Synthesis, Characterization, DFT, and In Silico Investigation of Two Newly Synthesized β-Diketone Derivatives as Potent COX-2 Inhibitors

Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains largely unexplored. β-Diketones and their complexes find broad applications as biologically active compounds. In this study, in silico molecular docking results revealed that two β-diketone derivatives, namely 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione, exhibit anti-COX-2 activities. However, recent docking results indicated that the relative anti-COX-2 activity of these two studied β-diketones was influenced by the employed docking programs. For improved design of COX-2 inhibitors from β-diketones, we conducted molecular dynamics simulations, density functional theory (DFT) calculations, Hirshfeld surface analysis, energy framework, and ADMET studies. The goal was to understand the interaction mechanisms and evaluate the inhibitory characteristics. The results indicate that 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione shows greater anti-COX-2 activity compared to 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione.

Benchmarking different docking protocols for predicting the binding poses of ligands complexed with cyclooxygenase enzymes and screening chemical libraries

Introduction

Non-steroidal anti-inflammatory drugs (NSAIDs) constitute an important class of pharmaceuticals acting on cyclooxygenase COX-1 and COX-2 enzymes. Due to their numerous severe side effects, it is necessary to search for new selective, safe, and effective anti-inflammatory drugs. In silico design of novel therapeutics plays an important role in nowadays drug discovery pipelines. In most cases, the design strategies require the use of molecular docking calculations. The docking procedure may require case-specific condition for a successful result. Additionally, many different docking programs are available, which highlights the importance of identifying the most proper docking method and condition for a given problem.

Methods

In the current work, the performances of five popular molecular docking programs, namely, GOLD, AutoDock, FlexX, Molegro Virtual Docker (MVD) and Glide to predict the binding mode of co- crystallized inhibitors in the structures of known complexes available for cyclooxygenases were evaluated. Furthermore, the best performers, Glide, AutoDock, GOLD and FlexX, were further evaluated in docking-based virtual screening of libraries consisted of active ligands and decoy molecules for cyclooxygenase enzymes and the obtained docking scores were assessed by receiver operating characteristics (ROC) analysis.

Results

The results of docking experiments indicated that Glide program outperformed other docking programs by correctly predicting the binding poses (RMSD less than 2 Å) of all studied co-crystallized ligands of COX-1 and COX-2 enzymes (i.e., the performance was 100%). However, the performances of the other studied docking methods for correctly predicting the binding poses of the ligands were between 59% to 82%. Virtual screening results treated by ROC analysis revealed that all tested methods are useful tools for classification and enrichment of molecules targeting COX enzymes. The obtained AUCs range between 0.61-0.92 with enrichment factors of 8 - 40 folds.

Conclusion

The obtained results support the importance of choosing appropriate docking method for predicting ligand-receptor binding modes, and provide specific information about docking calculations on COXs ligands.

Phytochemical Screening of Ultrasonic Extracts of Salix Species and Molecular Docking Study of Salix-Derived Bioactive Compounds Targeting Pro-Inflammatory Cytokines

Willow bark (Salix spp., Salicaceae) is a traditional analgesic and antirheumatic herbal medicine. The aim of this study was to evaluate and compare the phytochemical and antioxidant profiles of leaf and bark extracts of six species of the genus Salix obtained by ultrasound-assisted extraction (UAE) and to examine the inhibitory potential of target bioactive compounds against two inflammatory mediators, tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6), through in silico molecular docking. The total phenolic and flavonoid content of the extracts was estimated using spectrophotometric methods and the antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH^•) and hydroxyl radical (^•OH) scavenging assays. Chemical profiling of extracts was carried out using high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). Principal component analysis (PCA) was performed to differentiate the sample extracts based on their phytochemical profiles and amounts of target bioactive compounds. Chemical composition varied among the analyzed willow species and also among the plant organs of the same species. The major bioactive compounds of the extracts were salicin, chlorogenic acid, rutin and epicatechin. The extracts exhibited significant DPPH^● and ^●OH scavenging activities. Results of molecular docking revealed that chlorogenic acid had the highest binding affinity toward TNF-α and IL-6. UAE extracts represent valuable sources of antioxidant and anti-inflammatory compounds.