In-silico identification of novel DDI2 inhibitor in glioblastoma via repurposing FDA approved drugs using molecular docking and MD simulation study.

Glioblastoma, the most severe form of brain tumor and a leading cause of death within a year of diagnosis, is characterized by excessive protein synthesis and folding in the lumen of the endoplasmic reticulum (ER), leading to increased ER stress in the cells of GBM tissues. To mitigate this stress the cancer cells have intelligently adopted a plethora of response mechanisms and Unfolded Protein Response (UPR) is one of those. To bear with this exhaustive situation cells upregulate a strong protein degradation system in form of 26S proteasome and blocking of proteasomal gene synthesis may be a potential therapeutic action against GBM. Proteasomal gene synthesis is exclusively dependent on the transcription factor Nuclear respiratory factor 1 (NRF1) and its activating enzyme DNA damage inducible 1 homolog 2 (DDI2). Here in this study, we performed molecular docking against DDI2 with the 20 FDA-approved drugs and identified Alvimopan and Levocabastine as the top two compounds with the best binding score along with the standard drug Nelfinavir. MD simulation (100 ns) of these protein-ligand docked complexes reveals that the stability and compactness of Alvimopan are high in comparison with Nelfinavir. Our in-silico (Molecular docking and Molecular dynamics simulation) studies pointed out that Alvimopan may be repurposed as a DDI2 inhibitor and can be used as a potential anticancer agent for the treatment of brain tumors.Communicated by Ramaswamy H. Sarma.

A computational analysis to evaluate deleterious SNPs of GSK3ß, a multifunctional and regulatory protein, for metabolism, wound healing, and migratory processes.

This study focused on GSK-3ß, a critical serine/threonine kinase with diverse cellular functions. However, there is limited understanding of the impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on its structure and function. Through an exhaustive in-silico investigation 12 harmful nsSNPs were predicted from a pool of 172 acquired from the NCBI dbSNP database using 12 established tools that detects deleterious SNPs. Consistently, these nsSNPs were discovered in locations with high levels of conservation. Notably, the three harmful nsSNPs F67C, A83T, and T138I were situated in the active/binding site of GSK-3ß, which may affect the protein's capacity to bind to substrates and other proteins. Molecular dynamics simulations revealed that the F67C and T138I mutants had stable structures, indicating rigidness, whereas the A83T mutant was unstable. Analysis of secondary structures revealed different modifications in all mutant forms, which may affect the stability, functioning, and interactions of the protein. These mutations appear to alter the structural dynamics of GSK-3ß, which may have functional ramifications, such as the formation of novel secondary structures and variations in coil-to-helix transitions. In conclusion, this study illuminates the possible structural and functional ramifications of these GSK-3 nsSNPs, revealing how protein compactness, stiffness, and interactions may affect biological activities.

Selective ADA2 inhibition for enhancing anti-tumor immune response in glioma: Insights from computational screening of flavonoid compounds.

Brain tumors, particularly gliomas, remain difficult to treat due to their complex and dynamic microenvironment and high mortality rate. The presence of tumor-associated macrophages (TAMs) is considered one of the primary factors contributing to a poor prognosis in Glioma. Previous reports have linked elevated levels of Adenosine deaminase 2 (ADA2) with immunosuppression, tumor progression, and angiogenesis via MAPK, PDGFß signaling pathway in the glioma microenvironment. In contrast, Adenosine deaminase 1 (ADA1), another type of adenosine deaminase, plays a pivotal role in purine metabolism, which is essential for lymphocyte survival. Hence, selectively targeting ADA2 while preserving ADA1 activity could offer a viable approach for regulating macrophage polarization and enhancing the anti-tumor immune response. In pursuit of this objective, our study employed a computational approach, unveiling the remarkable attributes of Daidzin, characterized by its exceptional specificity, and binding affinity towards ADA2 while displaying minimal affinity towards ADA1. Furthermore, Define Secondary Structure of Proteins (DSSP) analysis revealed that Daidzin elicits conspicuous conformational alterations within the dimerization domain of the ADA2 receptor, which could have a crucial impact on its activity. However, the ADA1 structure remained unaltered. Our study offers the potential use of Daidzin as a specific therapeutic agent for modulating the tumor microenvironment and revolutionizing glioma management.

Effects of the pathological E200K mutation on human prion protein: A computational screening and molecular dynamics approach.

The human prion protein gene (PRNP) is mapped to the short arm of chromosome 20 (20pter-12). Prion disease is associated with mutations in the prion protein-encoding gene sequence. Earlier studies found that the mutation G127V in the PRNP increases protein stability. In contrast, the mutation E200K, which has the highest mutation rate in the prion protein, causes Creutzfeldt-Jakob disease (CJD) in humans and induces protein aggregation. We aimed to identify the structural mechanisms of E200k and G127V mutations causing CJD. We used a variety of bioinformatic algorithms, including SIFT, PolyPhen, I-Mutant, PhD-SNP, and SNP& GO, to predict the association of the E200K mutation with prion disease. MD simulation is performed, and graphs for root mean square deviation, root mean square fluctuation, radius of gyration, DSSP, principal component analysis, porcupine, and free energy landscape are generated to confirm and prove the stability of the wild-type and mutant protein structures. The protein is analyzed for aggregation, and the results indicate more fluctuations in the protein structure during the simulation owing to the E200K mutation; however, the G127V mutation makes the protein structure stable against aggregation during the simulation.

TGF-ß1 induced autophagy in cancer associated fibroblasts during hypoxia contributes EMT and glycolysis via MCT4 upregulation.

The Transforming growth factor-ß1 (TGF- ß1) in the tumor microenvironment (TME) is the major cytokine that acts as a mediator of tumor-stroma crosstalk, which in fact has a dual role in either promoting or suppressing tumor development. The cancer-associated fibroblasts (CAFs) are the major cell types in the TME, and the interaction with most of the epithelial cancers is the prime reason for cancer survival. However, the molecular mechanisms, associated with the TGF- ß1 induced tumor promotion through tumor-CAF crosstalk are not well understood. In the Reverse Warburg effect, CAFs feed the adjacent cancer cells by lactate produced during the aerobic glycolysis. We hypothesized that the monocarboxylate transporter, MCT4 which is implicated in lactate efflux from the CAFs, must be overexpressed in the CAFs. Contextually, to explore the role of TGF- ß1 in the hypoxia-induced autophagy in CAFs, we treated CoCl2 and external TGF- ß1 to the human dermal fibroblasts and L929 murine fibroblasts. We demonstrated that hypoxia accelerated the TGF- ß1 signaling and subsequent transformation of normal fibroblasts to CAFs. Moreover, we elucidated that synergistic induction of autophagy by hypoxia and TGF- ß1 upregulate the aerobic glycolysis and MCT4 expression in CAFs. Furthermore, we showed a positive correlation between glucose consumption and MCT4 expression in the CAFs. Autophagy was also found to be involved in the EMT in hypoxic CAFs. Collectively, these findings reveal the unappreciated role of autophagy in TME, which enhances the CAF transformation and that promotes tumor migration and metastasis via the reverse Warburg effect.

A computational study to assess the polymorphic landscape of matrix metalloproteinase 3 promoter and its effects on transcriptional activity.

BACKGROUND: Matrix metalloproteinase 3 (MMP3) plays a crucial role in cancer progression and development by proteolyzing extracellular matrix substrates. Primarily, the expression of MMP3 is regulated at the transcriptional level. The minute interplay of various transcription factor binding motifs at the promoter region is responsible for the altered expression of the genes. Single nucleotide polymorphism (SNP) at the transcription factor binding sites shows specific effects on gene expressions. Genome-wide association study (GWAS) strongly reported the association of common SNPs (rs3025058, rs522616, and rs617819) of MMP3 promoter with disease progression. The insufficient functional analysis of these promoter SNPs indicates the need for extensive mechanistic analysis on the effects of allelic variants upon transcription factor binding at MMP3 promoter. METHODS: The binding of transcription factors on the MMP3 promoter sequence was investigated by a virtual laboratory. The interaction between the specific transcription factor and promoter DNA with allelic variants was analyzed by computational tools. RESULTS: It was found that transcription factor c-Myb and Smad4 binding on MMP3 promoter were altered due to the presence of rs522616 and rs617819 SNPs, respectively. Further, the binding affinity of Smad4 to the MMP3 promoter containing C allele at -375 region is higher than that of its allelic variant G. CONCLUSION: This study presented that the complex of Smad4-DNA fragment containing C allele has higher binding affinity and stability as compared with its allelic variant. Hence, it is predicted that rs617819 polymorphism directly affects the Smad4 binding motif on MMP3 promoter and alters its gene expression.

Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach.

A new strain of coronavirus (CoV) has been identified as SARS-CoV-2, which is responsible for the recent COVID-19 pandemic. Currently, there is no approved vaccine or drug available to combat the pandemic. COVID-19 main protease (Mpro) is a key CoV enzyme, which plays an important role in triggering viral replication and transcription, turns it into an attractive target. Therefore, we aim to screen natural products library to find out potential COVID-19 Mpro inhibitors. Plant-based natural compounds from Sigma-Aldrich plant profiler chemical library have been screened through virtual molecular docking and molecular dynamics simulation to identify potential inhibitors of COVID Mpro. Our virtual molecular docking results have shown that there are twenty-eight natural compounds with a greater binding affinity toward the COVID-19 Mpro inhibition site as compared to the co-crystal native ligand Inhibitor N3 (-7.9 kcal/mol). Also, molecular dynamics simulation results have confirmed that Peonidin 3-O-glucoside, Kaempferol 3-O-ß-rutinoside, 4-(3,4-Dihydroxyphenyl)-7-methoxy-5-[(6-O-ß-D-xylopyranosyl-ß-D-glucopyranosyl)oxy]-2H-1-benzopyran-2-one, Quercetin-3-D-xyloside, and Quercetin 3-O-α-L-arabinopyranoside (selected based on the docking score) possess a significant amount of dynamic properties such as stability, flexibility and binding energy. Our In silco results suggests that all the above mention natural compounds have the potential to be developed as a COVID-19 Mpro inhibitor. But before that, it must go through under the proper preclinical and clinical trials for further scientific validation.Communicated by Ramaswamy H. Sarma.

Screening of the Prime bioactive compounds from Aloe vera as potential anti-proliferative agents targeting DNA.

BACKGROUND: Aloe vera extract and its bioactive compounds possess anti-proliferative properties against cancer cells. However, no detailed molecular mechanism of action studies has been reported. We have now employed a computational approach to scrutinize the molecular mechanism of lead bioactive compounds from Aloe vera that potentially inhibit DNA synthesis. METHODS: Initially, the anti-proliferative activity of Aloe vera extract was examined in human breast cancer cells (in vitro/in vivo). Later on, computational screening of bioactive compounds from Aloe vera targeting DNA was performed by molecular docking and molecular dynamics simulation. RESULTS: In-vitro and in-vivo studies confirm that Aloe vera extract effectively suppresses the growth of breast cancer cells without significant cytotoxicity towards non-cancerous normal immortal cells. Computational screening predicts that growth suppression may be due to the presence of DNA intercalating bioactive compounds (riboflavin, daidzin, aloin, etc.) contained in Aloe vera. MM/PBSA calculation showed that riboflavin has a higher binding affinity at the DNA binding sites compared to standard drug daunorubicin. CONCLUSIONS: These observations support the hypothesis that riboflavin may be exploited as an anti-proliferative DNA intercalating agent to prevent cancer and is worthy of testing for the management of cancer by performing more extensive pre-clinical and if validated clinical trials.

Natural products based nanoformulations for cancer treatment: current evolution in Indian research.

The use of medicinal plants is as ancient as human civilization. The development of phytochemistry and pharmacology facilitates the identification of natural bioactive compounds and their mechanisms of action, including against cancer. The efficacy and the safety of a bioactive compound depend on its optimal delivery to the target site. Most natural bioactive compounds (phenols, flavonoids, tannins, etc) are unable to reach their target sites due to their low water solubility, less cellular absorption, and high molecular weight, leading to their failure into clinical translation. Therefore, many scientific studies are going on to overcome the drawbacks of natural products for clinical applications. Several studies in India, as well as worldwide, have proposed the development of natural products-based nanoformulations to increase their efficacy and safety profile for cancer therapy by improving the delivery of natural bioactive compounds to their target site. Therefore, we are trying to discuss the development of natural products-based nanoformulations in India to improve the efficacy and safety of natural bioactive compounds against cancer.

Paracrine TGF-ß1 from breast cancer contributes to chemoresistance in cancer associated fibroblasts via upregulation of the p44/42 MAPK signaling pathway.

Conventionally, Cancer-associated fibroblasts (CAFs) are considered as an inducer of chemoresistance in cancer cells. However, the underlying mechanism by which carcinomas induce chemoresistance in CAFs through tumor-stroma cross-talk is largely unknown. Henceforth, we uncovered a network of paracrine signals between carcinoma and CAFs that drives chemoresistance in CAFs. Acquired tamoxifen and 5-Fu resistant cell lines MCF-7 and MDA-MB-468 respectively showed higher apoptotic resistance compared to the parental cell. Besides, chemoresistant breast cancer cells showed overexpression of TGF-ß1 and have the higher potential to induce CAF phenotype in the normal dermal fibroblasts in a paracrine manner through the TGF-ß1 cytokine, compared to their parental cell. Moreover, the chemoresistant cancer cells augmented the EMT markers with a reduction of E-cadherin in the CAFs. Importantly we found out that the TGF- ß1 enriched conditioned media from both of the resistant cells triggered chemoresistance in the CAFs by p44/42 MAPK signaling axis. Mechanistically, pharmacological and genetic blockade of TGF-ß1 inhibits p44/42 MAPK activation with the subsequent restoration of chemosensitivity in the CAFs. Altogether we ascertained that chemoresistant cancer cells have tremendous potential to modulate the CAFs compared to the parental counterpart. Targeting TGF-ß1 and p44/42 MAPK signaling in the future may help to abrogate the chemoresistance in the CAFs.

In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis.

The recent outbreak of the coronavirus disease COVID-19 is putting the world towards a great threat. A recent study revealed COVID-19 main protease (Mpro) is responsible for the proteolytic mutation of this virus and is essential for its life cycle. Thus inhibition of this protease will eventually lead to the destruction of this virus. In-Silico Molecular docking was performed with the Native ligand and the 15 flavonoid based phytochemicals of Calendula officinals to check their binding affinity towards the COVID-19 main protease. Finally, the top 3 compounds with the highest affinity have been chosen for molecular dynamics simulation to analyses their dynamic properties and conformational flexibility or stability. In-Silico Docking showed that major phytochemicals of Calendula officinals i.e. rutin, isorhamnetin-3-O-ß-D, calendoflaside, narcissin, calendulaglycoside B, calenduloside, calendoflavoside have better binding energy than the native ligand (inhibitor N3). MD simulation of 100 ns revealed that all the protease-ligand docked complexes are overall stable as compare to Mpro-native ligand (inhibitor N3) complex. Overall, rutin and caledoflaside showed better stability, compactness, and flexibility. Our in silico (Virtual molecular docking and Molecular dynamics simulation) studies pointed out that flavonoid based phytochemicals of calendula (rutin, isorhamnetin-3-O-ß-D, calendoflaside) may be highly effective for inhibiting Mpro which is the main protease for SARS-CoV-2 causing the deadly disease COVID-19. Rutin is already used as a drug and the other two compounds can be made available for future use. Thus the study points a way to combat COVID-19 by the use of major flavonoid based phytochemicals of Calendula officinals. Communicated by Ramaswamy H. Sarma.

In vitro and in silico study of Aloe vera leaf extract against human breast cancer.

Aloe vera leaf contains some bioactive compounds that have a strong binding affinity toward estrogen receptor as compared to standard drug tamoxifen. In this study, we have found that the IC50 of Aloe vera leaf extract against breast cancer cell line (MCF-7) is 23 µg/mL which is much lower than the IC50 (332 µg/mL) of Aloe vera leaf extract against non-cancerous cell line (NIH-3T3). We have also calculated the total concentration of phenolic acid (385.662 µg/mL), flavonoids (160.402 µg/mL) and alkaloids (276.754 µg/mL) in Aloe vera leaf extract. The free radical scavenging activity of Aloe vera leaf extract is 67% to 89% (at 50 to 300 µg/ml). Our virtual molecular docking study suggests that bioactive compounds like Aloe-emodin (-8.8 Kcal/mol), 7-hydroxy-2,5 dimethylchromone (-7.5 Kcal/mol), Beta-sitosterol (-7.3 Kcal/mol) etc. have a greater binding affinity toward estrogen alpha receptor as compared to standard drug Tamoxifen (-6.4 Kcal/mol). [Formula: see text].

Lead bioactive compounds of Aloe vera as potential anticancer agent.

Aloe vera (Aloe barbadensis Miller) is a perennial succulent medicinal plant. It has been used as a traditional or folk medicine for thousands of years and claimed that it possesses wound and burn healing activities, and anti-inflammatory as well as immunomodulatory effects. In recent years, the use of Aloe vera has been growing as a dietary supplement. The pre-clinical studies over the last couple of decades uncover the potential therapeutic activities of Aloe vera and its bioactive compounds, especially against neoplastic disease. Such investigations indicate the possible preventive as well as therapeutic effects of Aloe vera against cancer. Here, we discuss the crucial bioactive compounds of Aloe vera that have been harnessed against cancer and also address several mechanisms of action of these lead bioactive compounds compared to other standard drugs involved in cancer prevention and treatment.