AlteQ: a new complementarity principle-centered method for the evaluation of docking poses

Molecular docking is the most popular and widely used method for identifying novel molecules against a target of interest. However, docking procedures and their validation are still under intense development. In the present investigation, we evaluate a quantum free-orbital AlteQ method for evaluating docking complexes generated by taking EGFR complexes as an example. The AlteQ method calculates the electron density using Slater's type atomic contributions in the interspace between the receptor and the ligand. Since the interactions are determined by the overlap of electron clouds, they follow the complementarity principle, and an equation can be obtained that describes these interactions. The AlteQ method evaluates the quality of the interaction between the receptor and the ligand, how complementary the interactions are, and due to this, it is used to reject less realistic structures obtained by docking methods. Here, three different equations were used to determine the quality of the interactions in experimental complexes and docked complexes obtained using AutoDock Vina and AutoDock 4.2.6.Communicated by Ramaswamy H. Sarma.

A systems biology investigation of curcumin potency against TGF-β-induced EMT signaling in lung cancer

Curcumin (diferuloylmethane) is bioactive phenolic compound which exerts diverse antimetastatic effect. Several studies have reported the antimetastatic effect of curcumin by its ability to modulate the epithelial-to-mesenchymal transition (EMT) process in different cancers, but underlying molecular mechanism is poorly understood. EMT is a highly conserved biological process in which epithelial cells acquire mesenchymal-like characteristics by losing their cell-cell junctions and polarity. As a consequence, deviation in cellular mechanism leads to cancer metastasis and thereby death. In this perspective, we explored the antimetastatic potential and mechanism of curcumin on the EMT process by establishing in vitro EMT model in lungs cancer (A549) cells induced by TGF-β1. Our results showed that curcumin mitigates EMT by regulating the expression of crucial mesenchymal markers such as MMP2, vimentin and N-cadherin. Besides, the transcriptional analysis revealed that the curcumin treatment differentially regulated the expression of 75 genes in NanoString nCounter platform. Further protein-protein interaction network and clusters analysis of differentially expressed genes revealed their involvement in essential biological processes that plays a key role during EMT transition. Altogether, the study provides a comprehensive overview of the antimetastatic potential of curcumin in TGF-β1-induced EMT in lung cancer cells.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03360-7.

Anti-neoplastic pharmacophore benzophenone-1 coumarin (BP-1C) targets JAK2 to induce apoptosis in lung cancer

Reigning of the abnormal gene activation associated with survival signalling in lung cancer leads to the anomalous growth and therapeutic failure. Targeting specific cell survival signalling like JAK2/STAT3 nexus has become a major focus of investigation to establish a target specific treatment. The 2-bromobenzoyl-4-methylphenoxy-acetyl hydra acetyl Coumarin (BP-1C), is new anti-neoplastic agent with apoptosis inducing capacity. The current study was aimed to develop antitumor phramacophore, BP-1C as JAK2 specific inhibitor against lung neoplastic progression. The study validates and identifies the molecular targets of BP-1C induced cell death. Cell based screening against multiple cancer cell lines identified, lung adenocarcinoma as its specific target through promotion of apoptosis. The BP-1C is able to induce, specific hall marks of apoptosis and there by conferring anti-neoplastic activity. Validation of its molecular mechanism, identified, BP-1C specifically targets JAK2^Tyr1007/1008 phosphorylation, and inhibits its downstream STAT3^Tyr705 signalling pathway to induce cell death. As a consequence, modulation in Akt/Src survival signal and altered expression of interwoven apoptotic genes were evident. The results were reproducible in an in-vivo LLC tumor model and in-ovo xenograft studies. The computational approaches viz, drug finger printing confers, BP-1C as novel class JAK2 inhibitor and molecular simulations studies assures its efficiency in binding with JAK2. Overall, BP-1C is a novel JAK2 inhibitor with experimental evidence and could be effectively developed into a promising drug for lung cancer treatment.

Network Pharmacology Approach Uncovering Pathways Involved in Targeting Hsp90 Through Curcumin and Epigallocatechin to Control Inflammation

AIMS

To fetch pathways involved in targetting Hsp90 through Curcumin and Epigallocatechin through Network pharmacological approach.

BACKGROUND

Hsp90 is a molecular chaperone involved in stabilizing inflammatory protein which may lead to chronic diseases. The herbal compounds Curcumin and Epigallocatechin processing antiinflammatory properties are known to follow a common pathway and control the expression of Hsp90.

OBJECTIVE

To collect the gene targets of Hsp90, Curcumin and Epigallocatechin in order to understand protein-protein interactions of gene targets by constructing the interactome to identify the hub proteins. Hub proteins docking was performed with curcumin and epigallocatechin. Finally, hub proteins involvement with various human diseases were identified.

METHODS

The gene targets of Hsp90, Curcumin and Epigallocatechin were obtained from there respective databases. Protein-protein interactions of Pkcδ-Nrf2 and Tlr4 pathway gene targets were collected from String database. Protein interaction network was constructed and merged to get intercession network in cytoscape and Cluego was used to predict the disease related target genes. Docking of ligands to target proteins was carried out using Autodock vina tool.

RESULT

The main key regulators of Curcumin and Epigallocatechin were identified particularly from Pkcδ-Nrf2 and Tlr4 pathway.

CONCLUSION

The combined action of Curcumin and Epigallocatechin can reduce the expression of Hsp90 eventually controlling the inflammation.

Molecular docking analysis of curcumin analogues against kinase domain of ALK5

During metastasis, cancer cells transcend from primary site to normal cells area upon attaining epithelial to mesenchymal transition (EMT) causing malignant cancer disease. Increased expression of TGF-β and its receptor ALK5 is an important hallmark of malignant cancer. In the present study, efficacy of curcumin and its analogues as inhibitors of ALK5 (TGFβR-I) receptor was evaluated using in silico approaches. A total of 142 curcumin analogues and curcumin were retrieved from peer reviewed literature and constructed a combinatorial library. Further their drug-likeness was assessed using Molinspiration, cheminformatics and preADMET online servers. The interaction of 142 curcumin analogues and curcumin with ALK5 receptor was studied using Autodock Vina. This study revealed six curcumin analogues as promising ALK5 inhibitors with significant binding energy and H-bonding interaction.

Cytotoxicity of zinc nanoparticles fabricated by Justicia adhatoda L. on root tips of Allium cepa L.--a model approach

Zinc nanoparticles were synthesized using aqueous leaf extract of Justicia adhatoda L. The characterization of nanoparticles was done by ultraviolet-visible (UV-vis) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM), and high-resolution transmission electron microscopy (HR-TEM). The characteristic absorption peak of the UV spectrum was recorded at 379 nm. The FTIR data revealed the possible biomolecules involved in bioreduction and capping of zinc nanoparticles for efficient stabilization. AFM and HR-TEM images have shown that the size of zinc nanoparticles ranges from 55 to 83 nm and they are spherical in shape. The biogenic zinc nanoparticles were evaluated for their toxic effect on mitotic chromosomes of Allium cepa as a model system. Experiments were conducted in triplicate to assay the effect of 25, 50, 75, and 100 % of zinc nanoparticles on mitotic chromosomes at an interval of 6 h duration for 24 h. The investigation revealed that the mitotic index (MI) was decreased with increased concentration of zinc nanoparticles and exposure duration. The results revealed that zinc nanoparticles have induced abnormalities like anaphase bridge formation, diagonal anaphase, C-metaphase, sticky metaphase, laggards, and sticky anaphase at different percentages and times of exposure. It is evident from the observation that mitotic cell division becomes abortive at 100 % treatment of zinc nanoparticles.