Concurrent inhibition of IR, ITGB1, and CD36 perturbated the interconnected network of energy metabolism and epithelial-to-mesenchymal transition in breast cancer cells.

Altered energy metabolism is an emerging hallmark of cancer and plays a pivotal in cell survival, proliferation, and biosynthesis. In a rapidly proliferating cancer, energy metabolism acts in synergism with epithelial-to-mesenchymal transition (EMT), enabling cancer stemness, dissemination, and metastasis. In this study, an interconnected functional network governing energy metabolism and EMT signaling pathways was targeted through the concurrent inhibition of IR, ITGB1, and CD36 activity. A novel multicomponent MD simulation approach was employed to portray the simultaneous inhibition of IR, ITGB1, and CD36 by a 2:1 combination of Pimozide and Ponatinib. Further, in-vitro studies revealed the synergistic anticancer efficacy of drugs against monolayer as well as tumor spheroids of breast cancer cell lines (MCF-7 and MDA-MB-231). In addition, the combination therapy exerted approximately 40% of the apoptotic population and more than 1.5- to 3-fold reduction in the expression of ITGB1, IR, p-IR, IRS-1, and p-AKT in MCF-7 and MDA-MB-231 cell lines. Moreover, the reduction in fatty acid uptake, lipid droplet accumulation, cancer stemness, and migration properties were also observed. Thus, targeting IR, ITGB1, and CD36 in the interconnected network with the combination of Pimozide and Ponatinib represents a promising therapeutic approach for breast cancer.

Amyloid Targeting Red Emitting AIE Dots for Diagnostic and Therapeutic Application against Alzheimer's Disease.

The emergence of neurodegenerative diseases is connected to several pathogenic factors, including metal ions, amyloidogenic proteins, and reactive oxygen species. Recent studies suggest that cytotoxicity is caused by the small, dynamic, and metastable nature of early stage oligomeric species. This work introduces a small molecule-based red-emitting probe with smart features such as increased reactivities against multiple targets, metal-free amyloid-ß (Aß), and metal-bound amyloid-ß (Aß), and most importantly, early stage oligomeric species which are associated with the most common and widespread type of dementia, Alzheimer's disease (AD). Theoretical analyses like molecular dynamics simulation and molecular docking were performed to confirm the reactivity of the molecule toward Aß and found some excellent interactions between the molecule and the peptide. The in vitro and cellular studies demonstrated that this highly biocompatible molecule effectively reduces the structural damage to mitochondria while shielding cells from apoptosis, scavenges ROS (reactive oxygen species), and attenuates multifaceted amyloid toxicity.

Targeting AR-positive breast cancer cells via drug repurposing approach.

Androgen Receptor (AR) is overexpressed in almost all the molecular subtypes of breast cancer. Besides aiding the tumorigenic environment of cancer by abnormal cell proliferation, AR also takes part in promoting cancer signaling pathways, thereby promoting aggressiveness. In this study, AR was selected as the target protein in breast cancer cells. Following this, a library of 1293 FDA-approved drugs was screened via molecular docking, MD simulation, and MMPBSA binding energy. Amongst the library of compounds, Adapalene exhibited the least binding energy of (-10.2 kCal/mol) in comparison to that of the chosen reference compound, Nilutamide (-8.6 kCal/mol). Furthermore, the in vitro efficacy of Adapalene was also determined in two different breast cancer cell lines such as MCF7 (AR-positive/ER-positive) and MDA-MB-231 (AR negative/TNBC). Initially, the cell viability assay (MTT) was performed, which endowed us with a lesser IC50 value of Adapalene in comparison to Nilutamide in both cell lines. The IC50 of Adapalene was found to be 12 µM and 39.4 µM in MCF7 and MDA-MB-231 cells, respectively. Furthermore, Adapalene also induced cellular ROS and apoptosis by 3.5-fold and 26.58% in MCF7 cells. However, the overall effect of Adapalene was significantly lower in the case of MDA-MB-231 cell lines, which could be attributed to its inherent nature of the absence of hormone receptors. Conclusively, Adapalene possesses greater therapeutic efficacy in comparison to the control drug, thereby hinting towards the potential use of Adapalene in the treatment of AR-positive breast cancer.

Apigenin exerts anti-cancer effects in colon cancer by targeting HSP90AA1.

Apigenin, a flavonoid, has shown early promise in colon cancer (CC); thus, exploring potential mechanisms of Apigenin is obligatory. In this study, shared targets of Apigenin and CC were identified through online tools, which were then subjected to functional enrichment analyses, Gene Ontology and KEGG. Further, the protein-protein interaction network of the shared targets was developed (via STRING). The top targets of Apigenin in CC were identified by molecular docking; further investigated for differential gene and protein expression in CC and their influence on CC patient survival (using TCGA data). Out of 13 hub genes, the top 3 targets (HSP90AA1, MMP9, PTGS2) were selected based on docking score. Their expression was significantly elevated and related to poor overall survival in CC (except PTGS2). Molecular dynamics simulation further validated protein-ligand interactions and divulged HSP90AA1 as the best target of Apigenin in CC. Finally, the anti-cancer effects of Apigenin and its major metabolite, luteolin, were investigated in CC, which is involved in the cytotoxicity of CC cells (COLO-205) by reducing HSP90AA1 expression revealed by real-time PCR. Thus, HSP90AA1 was identified as one of the prime targets of Apigenin in CC, and Apigenin could be effective against CC.Communicated by Ramaswamy H. Sarma.

In silico screening and identification of potential drug against p300 acetyltransferase activity in breast cancer via drug repurposing approach.

Emerging evidence portray the involvement of epigenomic reprogramming in the onset and progression of several malignancies, including breast cancer. Histone acetyltransferase (HAT) p300 is a critical epigenetic regulator that acts as a transcription co-activator and regulates various cellular processes. p300 is overexpressed in breast cancer and promotes cellular invasion and survival, making it a promising druggable target. In this study, the relevance of p300 in different cancer pathways was established. Virtual screening of the FDA-approved drug library was carried out using molecular docking, and the top 10 potential repurposed drugs were identified. Further, recalculation of binding free energy of drug-p300 complexes was carried out using molecular mechanics Poisson-Boltzmann and surface area (MM-PBSA) method after molecular dynamic simulation. Based on molecular dynamic simulation parameters and binding free energy analysis, two drugs, namely Netarsudil (-305.068 kJ/mol) and Imatinib (-260.457 kJ/mol), were identified as potential repurposed drugs to inhibit the activity of p300. In conclusion, these findings suggest, Netarsudil and Imatinib might be a potential repurposed drug to combat breast cancer via p300 inhibition.Communicated by Ramaswamy H. Sarma.

Synthesis of 3-sulfenylindole derivatives from 4-hydroxy-2H-chromene-2-thione and indole using oxidative cross-dehydrogenative coupling reaction and anti-proliferative activity study of some of their sulfone derivatives.

The synthesis of hitherto unreported 3-sulfenylindole derivatives is achieved from 4-hydroxy-2H-chromene-2-thione (1) and indole (2) by employing an oxidative cross-dehydrogenative coupling reaction using a combination of 10 mol% of molecular iodine and 1 equivalent of TBHP in DMSO at room temperature. Then, the 3-sulfenylindole derivatives 3a, 3b, 3d, 3f, 3 h, and 3 k were converted into their corresponding sulfone derivatives because of lead likeness properties. Subsequently, a target prediction and docking study of six sulfone derivatives (5a-f) was performed, and four sulfones, namely 5a, 5d, 5e, and 5f, were selected for further in-vitro studies. The four sulfones mentioned above exhibited prominent anti-proliferative activity on breast cancer (MCF7) cell lines. In addition, this reaction was exergonic through quantum chemical analysis of the mechanistic steps. The salient features of this reaction are mild reaction conditions, good yields, and broad substrate scope.

Multi-targeting TACE/ADAM17 and gamma-secretase of notch signalling pathway in TNBC via drug repurposing approach using Lomitapide.

The aberrant expression of the Notch signalling pathway genes aids in potentiating the belligerent characteristics of numerous malignancies. Besides imparting abnormal proliferation and metastasis, the Notch also aids in the metabolic reprogramming of tumor cells. Since the activation of the Notch pathway is mediated via TACE/ADAM protease and the γ-secretase complex, hence it is crucial in determining a multi-targeted therapeutic approach to target these major proteases to downregulate the aberrant Notch signalling pathway. In this study, Lomitapide was chosen based on its binding score (-305.108 kJ/mol and - 173.174 kJ/mol) against the crucial proteases, TACE and γ-secretase, respectively. Further, the remarkable antitumor properties of Lomitapide were established on the TNBC cell lines (MDA-MB-231 and MDA-MB-468), along with the EMT-induced MDA-MB-468 cells. Apart from inducing ∼2 to 2.5-fold increase in the cellular ROS levels, Lomitapide treatment induced significant apoptosis, arrested cell cycle progression and reduced sphere and colony forming abilities of the TNBC cells. Differentiated epithelial phenotype with diminished CD44-stem cell marker was also observed upon treatment. Furthermore, reduction of migration potential, decrease in the gene expression profile of the EMT markers, along with downregulation of the Notch signalling genes were evident in the treated TNBC cells. Altogether, the present study attributes the repurposing of Lomitapide as an effective therapeutic agent against the major proteases of the Notch pathway to combat TNBC progression and dissemination.

Targeting UNC-51-like kinase 1 and 2 by lignans to modulate autophagy: possible implications in metastatic colorectal cancer.

Colorectal cancer (CRC), especially metastatic (mCRC) form, becomes a major reason behind cancer morbidity worldwide, whereas the treatment strategy is not optimum. Several novel targets are under investigation for mCRC including the autophagy pathway. Natural compounds including dietary lignans are sparsely reported as autophagy modulators. Nonetheless, the interaction between dietary lignans and core autophagy complexes are yet to be characterised. We aimed to describe the interaction between the dietary lignans from flaxseed (Linum usitatissimum) and sesame seeds (Sesamum indicum) along with the enterolignans (enterodiol and enterolactone) and the UNC-51-like kinase 1 and 2 (ULK1/2), important kinases required for the autophagy. A range of in-silico technologies viz. molecular docking, drug likeness, and ADME/T was employed to select the best fit modulator and/or inhibitor of the target kinases from the list of selected lignans. Drug likeness and ADME/T studied further selected the best-suited lignans as potential autophagy inhibitor. Molecular dynamic simulation (MDS) analyses were used to validate the molecular docking results. Binding free energies of the protein-ligand interactions by MM-PBSA method further confirmed best-selected lignans as ULK1 and/or ULK2 inhibitor. In conclusion, three dietary lignans pinoresinol, medioresinol, and lariciresinol successfully identified as dual ULK1/2 inhibitor/modifier, whereas enterodiol emerged as a selective ULK2 inhibitor/modifier.

Designing of disruptor molecules to restrain the protein-protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques.

Governing protein-protein interaction networks are the cynosure of cell signaling and oncogenic networks. Multifarious processes when aligned with one another can result in a dysregulated output which can result in cancer progression. In the current research, one such network of proteins comprising VANG1/SCRIB/NOS1AP, which is responsible for cell migration, is targeted. The proteins are modeled using in-silico approaches, and the interaction is visualized utilizing protein-protein docking. Designing drugs for the convoluted protein network can serve as a challenging task that can be overcome by fragment-based drug designing, a recent game-changer in the computational drug discovery strategy for protein interaction networks. The model is exposed to the extraction of hotspots, also known as the restrained regions for small molecular hits. The hotspot regions are subjected to a library of generated fragments, which are then recombined and rejoined to develop small molecular disruptors of the macromolecular assemblage. Rapid screening methods using pharmacokinetic tools and 2D interaction studies resulted in four molecules that could serve the purpose of a disruptor. The final validation is executed by long-range simulations of 100 ns and exploring the stability of the complex using several parameters leading to the emergence of two novel molecules VNS003 and VNS005 that could be used as the disruptors of the protein assembly VANG1/SCRIB/NOS1AP. Also, the molecules were explored as single protein targets approbated via molecular docking and 100 ns molecular dynamics simulation. This concluded VNS003 as the most suitable inhibitor module capable of acting as a disruptor of a macromolecular assembly as well as acting on individual protein chains, thus leading to the primary hindrance in the formation of the protein interaction complex.

Dual therapeutic approach to modulate Glycogen Synthase kinase -3 beta (GSK-3Β) and inhibitor of nuclear factor kappa kinase-beta (IKK-ß) receptors by in silico designing of inhibitors.

Cancer malignancies require the application of advanced strategies leading to the development of novel theranostic. Quite often drugs target a variety of receptors in the cell signaling cascades that could be explored to combat aggressive tumors. Herein, two receptors that are over-expressed during the diagnosis of breast cancer are used as the primary drug targets, inclusively Glycogen Synthase kinase -3 beta (GSK-3Β) and Inhibitor of nuclear factor kappa kinase-beta (IKK-ß). Dual-targeting inhibitors pave the way for a challenging pathway in the treatment of aberrant tumor progression. The present study involves the observation of similarities in the structure of the receptors, along with the designing of novel therapeutics that act on them by molecular docking followed by a pharmacokinetic screening approach. A 3D QSAR modeling study is performed to approach the functionality of the bioactive conformer molecules. Additionally, Molecular Dynamic Simulation parameters are used for the validation of the drug complexes. Already available inhibitors are used as reference compounds and a library of analogs generated for these compounds from the PubChem database has been used for in silico designing of novel inhibitors. Molecular Docking and ADME analysis narrowed down the vast library of compounds to two specific classes of chemical compounds. Molecular Dynamic simulation studies used for the selection of the novel moieties showed significant superiority in their stability studies and binding trajectories resulted in two novel molecules A6 and B3 that could inhibit the kinase receptors. The current work involves computational designing of therapeutics targeting two major oncogenic proteins.

Multi-targeted Drug Repurposing Approach for Breast Cancer via Integrated Functional Network Analysis.

The present study focuses on the interconnected functional network of altered metabolism and EMT (epithelial to mesenchymal transition) signaling in breast cancer. We have interlinked the metabolic and EMT signaling circuits and selected Insulin receptor (IR), Integrin beta 1 (ITGB1), and CD36 as target proteins based on network analysis. Extensive computational approaches discerned the potential drug molecules from the library of 1293 FDA-approved drugs to block all three target proteins. Using molecular docking, molecular dynamics simulation, and MMPBSA binding free energy studies, Capmatinib, Ponatinib, Naldemedine, and Pimozide were identified as potential repurposed drugs to block the function of all three target proteins. Among in silico selected candidate drugs, Pimozide, a known anti-psychotic drug, was further validated using in-vitro studies for its anti-cell proliferative potential on breast cancer cell lines (namely, MCF7, MDAMB231 and MDAMB468). The inhibitory concentration (IC50 ) values of MCF7, MDAMB231 and MDAMB468 was found to be 16.26 µM, 20.82 µM and 13.10 µM, respectively. The effect of Pimozide on EMT-induced MDAMB231 and MDAMB468 cells was evident from their IC50 values of 7.85 µM and 6.83 µM, respectively. The potent anti-cancer property of Pimozide has opened up avenues for drug repurposing towards 'multi-targeted therapy' in EMT dynamics.

Targeting protein tyrosine phosphatase 1B in obesity-associated colon cancer: Possible role of sweet potato (Ipomoea batatas).

Protein tyrosine phosphatase 1B (PTP1B) has emerged as one of the links between obesity and colon cancer (CC). Anti-obesity and anti-CC attributes of sweet potato (Ipomoea batatas) reported sparsely. Here, we aimed to study the potential of PTP1B as a target in CC, particularly in obese population. Expression and genomic alteration frequency of PTPN1 (PTP1B) were checked in CC. Interacting partners of PTP1B through STRING and hub genes through Cytoscape (MCODE) were identified. Hub genes were subjected to functional enrichment analyses (via Metascape), differential gene expression, copy number variation, and single nucleotide variation analyses (GSCA database). Cancer-related pathways and associated immune infiltrates of the hub genes were checked too. Eleven sweet potato-derived compounds selected through drug likeness (DL) and toxicity filters were explored via molecular docking (AutoDock Vina) to reveal the interactions with PTP1B. Genomic alteration frequency of the PTPN1 was highest in CC compared to all the other TCGA cancers, and a high expression (RNA and protein) is also observed in CC that correlated well to a poor overall survival (OS). Furthermore, PTP1B and related proteins were enriched in different biological processes and signaling pathways related to carcinogenesis including epithelial-mesenchymal transition. Overall, PTP1B identified as a potential target in obesity-linked CC and sweet potato might exert its protective action by targeting the PTP1B. Sweet potato compounds (e.g., pelargonidin and luteolin) interacted with the catalytic P loop and the WPD loop of the PTP1B. Furthermore, MD simulation study ascertained that luteolin has the highest affinity against the PTP1B, whereas pelargonidin and quercetin showed good binding affinity too, thus can be explored further.

In silico approach to target PI3K/Akt/mTOR axis by selected Olea europaea phenols in PIK3CA mutant colorectal cancer.

Worldwide disease burden of colorectal cancer (CRC) increasing alarmingly, but a suitable therapeutic strategy is not available yet. Abnormal activation of the PI3K/Akt/mTOR signalling because of mutation in the PIK3CA gene is a driving force behind CRC development. Therefore, this study aimed to comprehensively characterise the potential of phenolic compounds from Olea europaea against the PI3K/Akt/mTOR axis by using in silico methodologies. Molecular docking was utilised to study key interactions between phenolic compounds of O. europaea and target proteins PI3K, Akt, mTOR with reference to known inhibitor of target. Drug likeness and ADME/T properties of selected phenols were explored by online tools. Dynamic properties and binding free energy of target-ligand interactions were studied by molecular dynamic simulation and MM-PBSA method respectively. Molecular docking revealed apigenin, luteolin, pinoresinol, oleuropein, and oleuropein aglycone as the top five phenolic compounds which showed comparable/better binding affinity than the known inhibitor of the respective target protein. Drug likeness and ADME/T properties were employed to select the top three phenols namely, apigenin, luteolin, and pinoresinol which shown to bind stably to the catalytic cleft of target proteins as confirmed by molecular dynamics simulations. Therefore, Apigenin, luteolin, and pinoresinol have the potential to be used as the non-toxic alternative to synthetic chemical inhibitors generally used in CRC treatment as they can target PI3K/Akt/mTOR axis. Particularly, pinoresinol showed great potential as dual PI3K/mTOR inhibitor. However, this study needs to be complemented with future in vitro and in vivo studies to provide an alternative way of CRC treatment. Communicated by Ramaswamy H. Sarma.

In-silico evidence of ADAM metalloproteinase pathology in cancer signaling networks.

Lack of effective targeted therapies often contributes to poor clinical outcomes of aggressive malignancies associated with drug resistance, angiogenesis and metastasis. Literature mining portrays the major role of ADAM17 in cancer and inflammatory diseases. However, it is quite challenging to design a candidate drug for targeting ADAM17 due to its structural similarity with the catalytic domain of the matrix metalloproteases (MMPs). The present study reports the protein-protein interaction analysis of ADAM17, along with the molecular docking and MD simulation studies for the screened compounds. Our analysis confirms the association of ADAM17 with numerous oncogenes that facilitates cancer progression and inflammation, especially the members of the Notch, receptor tyrosine kinase (RTK) and TNFα pathways. The outcome provides evidence that the prevalent protease ADAM17 could attribute to cancer signaling regulation though the shedding of various inflammatory and oncogenic molecules. We have also exploited the analogues of the existing inhibitors, with an aim at discovering a potent molecule, which could be repurposed as a drug against ADAM17 inflicted cancer progression. Upon stringent screening, we delineated our choice into two specific compounds (I6 and I9; analogues of IK862, a type of y-lactam hydroxamates), possessing the lowest binding energy (-9.1 Kcal/mol), stable MD-simulation studies and superior pharmacodynamic properties. The current information illustrates the avenue to persuade further research on targeting ADAM17 with small molecular compounds (I6 and I9) in cancer therapeutics.Communicated by Ramaswamy H. Sarma.

Designing of RNA aptamer against DNA binding domain of the glucocorticoid receptor: A response element-based in-silico approach.

Virtual screening, a conventional in-silico approach to design an RNA aptamer against target proteins require huge RNA library containing 1010 to 1015 combination of RNA oligomers and high-performance computing systems. However, in the case of nuclear receptor proteins, screening can be narrowed down by using response element sequences rather than random RNA oligomer library. In this study, we used a novel method to design RNA aptamer against the DNA binding domain of the glucocorticoid receptor α (GRα). GRα plays a vital role in cancer metastasis such as colon, cervical and breast cancer by activating the S100A8 calcium-binding protein, which makes it a potential drug target for those cancers. We started the screening of 24 RNA aptamers (16 nucleotides long), all of which are glucocorticoid response elements (GRE) of S100A8. Among the aptamers screened, Apt-2, Apt-5, Apt-6 and Apt-15 are found to be most suitable by molecular docking and dynamic studies. The stability and compactness of the aptamer-protein complexes were assessed by GROMACS. The binding energies were rescored using the MM-PBSA method, which were -3679.581, -3690.892, -8246.052 and -3412.802 KJ/mol, respectively for Apt-2, Apt- 5, Apt-6 and Apt-15. The designed RNA aptamer may directly bind to the DNA binding domain of GR and prevent the trans-activation of the S100A8 gene by blocking the binding of GR to its response element. Thus, this novel approach of design the response elements-based RNA aptamer against GRα like nuclear receptor proteins will help to generate target-specific RNA aptamers with minimal efforts and cost.Communicated by Ramaswamy H. Sarma.

Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain.

Bromodomains are evolutionarily conserved reader modules that recognize acetylated lysine residues on the histone tails to facilitate gene transcription. The bromodomain and PHD finger containing protein 3 (BRPF3) is a scaffolding protein that forms a tetrameric complex with HBO1 histone acetyltransferase (HAT) and two other subunits, which is known to regulate the HAT activity and substrate specificity. However, its molecular mechanism, histone ligands, and biological functions remain unknown. Herein, we identify mono- (H4K5ac) and di- (H4K5acK12ac) acetylated histone peptides as novel interacting partners of the BRPF3 bromodomain. Consistent with this, pull-down assays on purified histones from human cells confirm the interaction of BRPF3 bromodomain with acetylated histone H4. Further, MD simulation studies highlight the binding mode of acetyllysine (Kac) and the stability of bromodomain-histone peptide complexes. Collectively, our findings provide a key insight into how histone targets of the BRPF3 bromodomain direct the recruitment of HBO1 complex to chromatin for downstream transcriptional regulation.

Rational design of Shewanella sp. l-arabinose isomerase for d-galactose isomerase activity under mesophilic conditions.

d-Tagatose, a potential low calorific substitute for sucrose, can be produced by bioconversion of d-galactose catalysed by l-arabinose isomerase. l-Arabinose isomerase from Shewanella sp. ANA-3 is unique for its ability to catalyse bioconversion reactions under mesophilic conditions. However, d-galactose not being a natural substrate for l-arabinose isomerase is catalysed at a slower rate. We attempted to increase the biocatalytic efficiency of Shewanella sp. l-arabinose isomerase by rational design to enhance galactose isomerisation activity. In silico molecular docking, analysis has revealed that F279 is sterically hindering the binding of d-galactose at the C6 position. Substitution of bulky Phe residue with smaller hydrophilic residues such as Asn and Thr increased the galactose isomerase activity by 86 % and 12 % respectively. At mesophilic conditions, F279N mutant catalysed the bioconversion of d-galactose more efficiently than l-arabinose, indicating a shift in substrate preference.