Department of Biological Sciences

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Anti-adipogenic and anti-steatotic potential of edible pigment bixin and annatto seed extracts: LC-MS based bioactive profiling and in vitro biochemical validation
(Elsevier, 2025-02) Sharma, Pankaj Kumar; Deepa, P.R.
The rising prevalence of metabolic syndrome (MetS), such as obesity and its hepatic complication, and non-alcoholic fatty liver disease (NAFLD), necessitates safe, effective, and protective interventions. Natural products, such as carotenoids, including bixin derived from annatto seeds, have emerged as promising candidates due to their multifaceted pharmacological properties. This study aimed to characterize the edible food pigment bixin and other co-existing bioactives in acetone- and ethyl lactate-extracts of Bixa Orellana L. seeds, followed by their anti-adipogenic and anti-steatotic assessments using in-vitro models of obesity and NAFLD. LC-MS analysis revealed the presence of various phytochemicals in the bixin rich solvent extracts. In vitro studies demonstrated differential and significant anti-adipogenic and anti-steatotic effects of bixin (pure pigment) and solvent extracts of annatto seeds (P < 0.05). The LC-MS profiling of annatto seed extracts revealed the presence of bixin and several bixinoids. Other key phytochemicals that were identified were eicosatrienoic acid, geranylgeraniol, hypolatein, δ-tocotrienol, caffeoyl acid derivative, and zeaxanthin, which were differentially abundant in each solvent extract. Bixin and coexisting bioactives in the annatto seed extracts demonstrated significant anti-oxidant, anti-inflammatory, and anti-lipidemic effects (P < 0.05) in the present in vitro MetS models. Further studies may be directed toward evaluating the nutraceutical potential of bixin in combination with the implicated phytochemicals in the extracts for treating metabolic disorders.
Anti-obesity and anti-steatotic effects of bixin (apocarotenoid from bixa orellana l. Seeds): dose-dependent correlations with bioactivity
(MDPI, 2024-12) Sharma, Pankaj Kumar; Deepa, P.R.
Annatto, a tropical shrub from Central and South America and parts of India, contains Bixin, an apocarotenoid pigment. Bixin is conventionally used as a natural food colorant and is now receiving attention for its health-promoting nutraceutical properties, particularly in chronic diseases (metabolic syndrome—MetS—and cancers). This study investigates the dose-dependent anti-obesity and anti-steatotic effects of Bixin in in vitro cell culture models. The anti-adipogenic and anti-steatotic effects of Bixin were examined in well-established in vitro models of obesity and non-alcoholic fatty liver disease (NAFLD/steatosis) using 3T3-L1 preadipocytes (by a differentiation protocol) and HepG2cells (steatosis-induced with oleic acid), respectively. Bixin was administered in the following concentration range: 1 μg mL−1–20 μg mL−1 (obesity model) and 2.5 μg mL−1–10 μg mL−1 (NAFLD/steatosis model). The neutral lipid content was estimated by Oil Red O staining; ROS/RNS were quantified by 2′,7′-dichlorofluorescein diacetate (DCFDA) and nitrite assays; and malondialdehyde (MDA), the biochemical marker of lipid peroxidation, was assessed by TBARS assay. At lower concentrations, 5 μg mL−1 in steatotic cells and 10 μg mL−1 in matured adipocytes, Bixin significantly reduced lipid accumulation in both hepatocytes and adipocytes (p < 0.05), demonstrating its potential as an anti-steatotic and anti-obesity agent. This beneficial effect was correlated with a reduction in oxidative stress levels (decreased MDA and ROS/RNS levels). Strikingly, at higher concentrations (>10 μg mL−1), Bixin showed increased lipid accumulation and oxidative stress. Bixin exhibits anti-obesity and anti-steatotic effects at lower doses, which correlates with its antioxidant properties. However, its bioactivity is dose-dependent, meaning that at higher concentrations, it ceases to inhibit adipogenesis. This opposing response is accompanied by elevated oxidative stress levels, indicating a pro-oxidant effect at higher doses, which suggests its anti-cancer potential. The present study highlights the significance of dosage optimization of nutraceuticals and dietary ingredients with respect to their intended biological applications, such as MetS and cancer treatment.
Arid/semi-arid flora as a treasure trove of bioactives and bioenergy: the case for underutilized desert legumes towards environmental sustainability
(Springer, 2024) Deepa, P.R.; Sharma, Pankaj Kumar
As the spectre of climate change gains in strength with each passing moment, many of our mundane food crops like rice face the heat, leading to uncertain yields and unforeseen disease outbreaks. Subsequently, mankind is forced to look for alternative food choices that should primarily come from indigenous plants that are less demanding in terms of usage of water and application of chemical-based fertilizers/pesticides. There are plants growing in the wild in the arid and semi-arid zones of Rajasthan, India, that can come to the rescue, with an added potential for development into valuable functional foods—i.e., not only as source of carbohydrates, proteins, and micro-nutrients but also that of health benefiting nutraceuticals (like antioxidant flavonoids) and relevant enzymes. The other parts (non-edible) of these plants have often also been traditionally validated via diverse ethnomedicinal practices; these could also be useful bioenergy sources. Keeping in mind the broader aim of looking at future functional foods that are also required to be environmentally sustainable, the current report: (a) reviews the extant literature on underutilized legumes from arid/semi-arid zones, (b) discusses current status with respect to biological activities present therein, and (c) suggests pertinent research questions and solution paths in the domains of bioactives, bioenergy, and sustainable environment.
Atheroprotective effect of exogenous heparin-derivative treatment on the aortic disturbances and lipoprotein oxidation in hypercholesterolemic diet fed rats
(Elsiever, 2005) Deepa, P.R.
The present work explores the myriad of biochemical and cellular changes that are featured in the early stages of atherosclerosis; if unchecked these changes lead to the complicated atherosclerotic plaque formation. The influence of a low-molecular-weight heparin derivative on the aortic aberrations and lipoprotein oxidation has been assessed in an experimental model of hypercholesterolemic atherogenesis.
Beneficial cardio-renovascular effects of a low-molecular-weight heparin-derivative on adriamycin-induced glycosaminoglycanuria and tissue lipid abnormalities
(Elsiever, 2005) Deepa, P.R.
The present work includes a study on the glycosaminoglycanuric condition induced by adriamycin (ADR, a chemotherapeutic agent) and the accompanying secondary hyperlipidemia, wherein the treatment with a low-molecular-weight heparin-derivative (LMWH), certoparin, is evaluated for its protective role (if any) on these parameters. Two groups of male albino rats of the Wistar strain (140 ± 10 g) received a single intravenous injection of adriamycin (7.5 mg/kg), and one of these groups was treated with a low-molecular-weight heparin-derivative (Certoparin Sodium, Troparin®; 300 μg/day/rat s.c.), commencing on day 8, for a week. Urinary total glycosaminoglycans excretion of the untreated ADR-induced group was found to increase on the 8th and the 15th days of observation, when compared with the controls. The LMWH treatment commencing on day 8 resulted in minimising the glycosaminoglycans (GAGs) excretion by day 15 (p < 0.001). Plasma, cardiac, hepatic and renal lipids (cholesterol, triglycerides and phospholipids) showed a sharp increase in the pathologic group, along with a rise in plasma LDL and VLDL cholesterol and drop in HDL cholesterol levels, paralleled by abnormal activities of the enzymes involved in lipid metabolism. LMWH treated group showed a normalised lipid profile and the activities of the lipid-metabolising enzymes was close to that of controls. It is concluded herein that adriamycin administration resulted in severe nephropathy manifested by increased glycosaminoglycanuria and abnormal lipid metabolism, and that LMWH treatment afforded substantial protection by restoring glomerular structure and function, and normalised the plasma and tissue lipid levels, lipoprotein profile and the activities of lipid-metabolising enzymes.
A Bio-mathematical Approach to Evaluate the Risk Burden of Hypertension and Hyperlipidemia in Diabetic Cardiovascular Disease
(Scientific & Academic Publishing, 2012) Deepa, P.R.
Cardiovascular disease (CVD) is a major cause of mortality in both developed and developing countries, owing to significant increase in the intake of high-energy foods, reduced physical activity, and an increase in psychosocial stress, which in turn lead to dysglycemia, hypertension, and dyslipidemia. The incidence of CVD in diabetics is very high that is further aggravated by co-morbidities such as hyperlipidemia and/or hypertension. The purpose of this study is to mathematically model the dynamics of CVD in diabetic population with hyperlipidemia and hypertension. Here, the mathematical model is a system of ordinary differential equations (ODEs). The steady states of the model are computed and their stability is studied. Numerical simulations are performed on the model, and conditions for controlling CVD in diabetics are derived. The results of this analysis suggest that the extent of control of hyperlipidemia and hypertension directly correlates with decrease in CVD development in the diabetic population. Early diagnosis of the modifiable risk factors such as hyperlipidemia and hypertension, followed by effective clinical management to regulate blood lipid levels and blood pressure in diabetics would greatly reduce the burden of cardiovascular complications in diabetic populations
Bioactivity-guided purification and characterization of antioxidant, anti-gout and anti-diabetic polyphenols from Panchkuta: a traditional food combination of (semi) arid regions
(Elsevier, 2024-12) Deepa, P.R.; Sharma, Pankaj Kumar
Desert ecosystems have thrived in part because of the contribution of local traditions, along with conventional knowledge passed down through generations. Panchkuta, a combination of five plants, including Prosopis cineraria, Cordia dichotoma, Capparis decidua, Acacia senegal, and Mangifera indica, is a classic example of ethnic desert food and how communities utilize existing food resources to ensure nutritional security. In this study, we determined the total phenolic content, total flavonoid content, antioxidant, anti-gout, and anti-diabetic activities of crude and purified (using Amberlite XAD7HP and Sephadex LH-20) fractions of Panchkuta. Further, the phenolic compounds (quercetin, tiliroside, myricetin-3-O-galactoside, and others) responsible for these activities were identified by analytical techniques, including TLC, LC-MS, and HR-MS. The purified fraction showing maximum antioxidant activity in DPPH assay (Fraction 16, IC50–156.65 ± 12.6 μg/ml) was validated for its cytoprotective and anti-lipid peroxidative effects in the in vitro cell culture system (murine fibroblast cells). Fraction 9 showed the maximum anti-gout activity in xanthine oxidase assay (IC50- 80.59 ± 9.89 μg/ml) and fraction 11 showed the maximum anti-diabetic activity in α-amylase assay (IC50 of 101.54 ± 14.7 μg/ml). The study reinforces the understanding of traditional knowledge, relevance to One Health, and authenticates the potential medicinal value of Panchkuta through scientific validation.
Biochemical changes accompanying apoptotic cell death in retinoblastoma cancer cells treated with lipogenic enzyme inhibitors
(Elsiever, 2013) Deepa, P.R.
Retinoblastoma (RB) is a malignant intra-ocular neoplasm that affects children (usually below the age of 5 years). In addition to conventional chemotherapy, novel therapeutic strategies that target metabolic pathways such as glycolysis and lipid metabolism are emerging. Fatty acid synthase (FASN), a lipogenic multi-enzyme complex, is over-expressed in retinoblastoma cancer. The present study evaluated the biochemical basis of FASN inhibition induced apoptosis in cultured Y79 RB cells. FASN inhibitors (cerulenin, triclosan and orlistat) significantly inhibited FASN enzyme activity (P < 0.05) in Y79 RB cells. This was accompanied by a decrease in palmitate synthesis (end-product depletion), and increased malonyl CoA levels (substrate accumulation). Differential lipid profile was biochemically estimated in neoplastic (Y79 RB) and non-neoplastic (3T3) cells subjected to FASN inhibition. The relative proportion of phosphatidyl choline to neutral lipids (triglyceride + total cholesterol) in Y79 RB cancer cells was found to be higher than the non-neoplastic cells, indicative of altered lipid distribution and utilization in tumor cells. FASN inhibitor treated Y79 RB and fibroblast cells showed decrease in the cellular lipids (triglyceride, cholesterol and phosphatidyl choline) levels. Apoptotic DNA damage induced by FASN inhibitors was accompanied by enhanced lipid peroxidation.
Biochemical evaluation of the inflammatory changes in cardiac, hepatic and renal tissues of adriamycin-administered rats and the modulatory role of exogenous heparin-derivative treatment
(Elsiever, 2005) Deepa, P.R.
The aim of the present work is to evaluate the role of a heparin derivative, low molecular weight heparin (LMWH), certoparin on the inflammatory changes in adriamycin (ADR) cytotoxicity on a biochemical basis. Male Wistar rats (140 ± 10 g) were divided into four groups: untreated control, ADR group (a single dose intravenous injection of 7.5 mg/kg ADR), LMWH control (300 μg/(day rat) s.c. for 1 week) and ADR plus LMWH group (7.5 mg/kg ADR on day 1 of study period followed by LMWH treatment, 300 μg/(day rat) commencing on day 8 and continued for 1 week). At the end of the 2-week experimental period, biochemical assessment of the inflammatory status was carried out in the plasma, cardiac, hepatic and renal tissues. Increased concentrations of plasma C-reactive protein (CRP) and fibrinogen indicated severe inflammation in the ADR cytotoxic rats. These acute-phase inflammatory markers diminished significantly in the LMWH treated group, when compared with the cytotoxic group (p < 0.001). Tissue damage was marked by elevated levels of plasma and tissue hexose, hexosamine, hexuronic acid and sialic acid, which were reversed on LMWH administration (p < 0.001). The activities of lysosomal enzymes was measured in the experimental groups, and it was observed that the ADR induced rats showed a marked increase in the enzymic activities, while LMWH treated rats revealed normal activities. The present study throws light on the inflammatory changes in the ADR-challenged heart, liver and kidney tissues, and projects the biochemical basis for the anti-inflammatory property of the LMWH, certoparin.
Biochemical evaluation of wound healing efficacy of cold plasma-conditioned media under different operational conditions
(IOP, 2024) Deepa, P.R.
Wound healing is a dynamic and intricate biological process crucial for tissue repair and regeneration. This study explores the potential therapeutic impact of non-thermal plasma generated by a hand-held cold atmospheric pressure plasma jet (C-APPJ) source on fibroblast cells (NIH/3T3) in vitro. The sequential phases of wound healing—inflammation, cell proliferation, and tissue remodelling, were assessed in the context of cell migration and oxidative stress dynamics. Typically, plasma generates a mixture of several reactive oxygen/nitrogen (ROS/RNS) species. The present study investigates the safety and efficacy of C-APPJ under distinct operating conditions (argon (GI) and argon + nitrogen (GII)) and exposure times (1 min and 3 min). Cell viability assays confirmed the non-cytotoxic nature of the cold plasma conditioned medium. The levels of ROS/RNS and malondialdehyde (biomarker of oxidative stress) in the plasma-treated samples remained comparable with the control fibroblast cells grown in normal media, suggesting the favourable modulation of ROS by the cellular antioxidant mechanisms. Accelerated wound-closure rates from 6th hour to 24th hour in all the treated groups ranged from 38.76% to 45.66%, when compared to 34.25% in the control cells. Substantial cell migration leading to 51.59% of wound closure was recorded in the argon + nitrogen (GII) group exposed for 3 min. Taken together, the potential of cold plasma to effectively heal wounds without causing prolonged oxidative stress and chronic inflammation is implicated. These outcomes suggest scope for clinical application of C-APPJ as safe and cost-effective treatment of wounds (ulcers, burns, diabetic foot) and wound disinfection.
Biokinetics of fed-batch production of poly (3-hydroxybutyrate) using microbial co-culture
(Springer, 2019) Deepa, P.R.
A novel fed-batch strategy based on carbon/nitrogen (C/N) ratio in a microbial co-culture production medium broth was carried out in a biocalorimeter for improved production of poly (3-hydroxybutyrate) (PHB). Shake flask study suggested that the C/N ratio of 10 increased the yield of PHB by 2.8 times. Online parameters monitored during the C/N ratio of 10 in biocalorimeter (BioRC1e) indicated that the heat profile was maintained in the fed-batch mode resulting in a PHB yield of 30.3 ± 1.5 g/L. The oxy-calorific heat yield coefficient during the fed-batch strategy was found to be 394.24 ± 18.71 kJ/O2 due to the oxidative metabolism of glucose. The reported heat-based model adapted for PHB concentration prediction in the present fed-batch mode. The heat-based model has a Nash-Sutcliffe efficiency of 0.9758 for PHB prediction. PHB obtained by fed-batch-mode was characterized using gas chromatography-mass spectrometry (GC-MS) for the monomer-acid analysis, Thermogravimetric analysis (TGA) for thermal stability of PHB, and Fourier transform infrared spectroscopy (FT-IR) for confirmation of functional groups. Here, we establish a favorable C/N ratio for achieving optimal PHB yield and a predictive heat-based model to monitor its production.
Chemical inhibition of fatty acid synthase: molecular docking analysis and biochemical validation in ocular cancer cells
(Springer, 2011) Deepa, P.R.
Fatty acid biosynthesis is an attractive target for anti-cancer therapeutics. The ocular cancer, retinoblastoma cells were treated with fatty acid synthase (FASN) enzyme inhibitors: cerulenin, triclosan and orlistat. The IC50 and dose-dependent sensitivity of cancer cells to FASN inhibitors decrease in biologic enzyme activity, and cell morphology alterations were analysed. Molecular interactions of enzyme-inhibitor complexes were studied by molecular modelling and docking simulations. The crystal structures of ketoacyl synthase (PDB ID:3HHD) (cerulenin) and thioesterase (PDB ID:2PX6) (orlistat) domains of human FASN were utilized for docking, while for the non-crystallised human FASN enoyl reductase domain (triclosan), homology model was built and used for docking. All three inhibitors showed significant binding energy indicating stable complex formation with their respective FASN subunits. The predicted Ki value of the FASN inhibitors corroborated well with their corresponding anti-cancer effects.
Chromatographic analysis of bioactive metabolites from a traditional food combination of (semi) arid regions—panchkuta: insights for sustainable functional foods development
(MDPI, 2024-10) Sharma, Pankaj Kumar; Deepa, P.R.
Conventional agriculture may not meet the needs of the growing human population and sustainable development. These issues necessitate a shift towards traditional foods and underutilized desert plants, offering promising sustainable agricultural and food security alternatives. ‘Panchkuta’, a blend of five plants (Prosopis cineraria, Acacia senegal, Capparis decidua, Cordia dichotoma, and Mangifera indica), is a traditional food combination from (semi) arid regions. In this study, the bioactive metabolites were identified through analytical techniques, including TLC and GC-MS analysis. Tapping these underexplored plants can help design and develop healthy functional foods and nutraceutical products.
Clinico-Pathological Association of Delineated miRNAs in Uveal Melanoma with Monosomy 3/Disomy 3 Chromosomal Aberrations
(Plos One, 2016) Deepa, P.R.
To correlate the differentially expressed miRNAs with clinico-pathological features in uveal melanoma (UM) tumors harbouring chromosomal 3 aberrations among South Asian Indian cohort.
Clinico-pathological correlations of fatty acid synthase expression in retinoblastoma: An Indian cohort study
(Elsiever, 2011) Deepa, P.R.
Retinoblastoma (RB), the most common intra-ocular malignancy in children under 5 years of age, has an estimated incidence of about 2000 a year in India, where most cases are in advanced stage at the time of diagnosis. Newer therapeutic approaches would reduce the morbidity of chemotherapy in children with RB. Fatty Acid Synthase (FASN), a lipogenic multi-enzyme complex, is minimally expressed in normal human tissues and over expressed in many cancers, making it an attractive target for cancer therapy. We analyzed RB tissues for FASN protein expression by immunohistochemistry, western blot, and ELISA, and FASN mRNA expression by RT-PCR. FASN expression was correlated with the clinico-pathological characteristics of the tumors. FASN immunostaining was positive in all the 44 RB tissues analyzed (100%). However, FASN expression was heterogeneous within the tumor samples. Tumors with invasion of choroid, optic nerve, orbit and/or retinal pigment epithelium showed significantly higher FASN immunoreactivity than the tumors without invasion (P < 0.05), supported by western analysis (P < 0.05). FASN expression was significantly high in poorly differentiated retinoblastomas (P < 0.05). FASN protein and FASN mRNA estimated by ELISA and RT-PCR respectively showed multi-fold expression over the non-neoplastic muller glial cells that varied quantitatively between tumor tissues. FASN mRNA over-expression was substantially lower than the corresponding FASN protein expression values. The present study reports (i) markedly high expression of FASN protein in poorly differentiated and in invasive retinoblastomas, and (ii) multi-fold over-expression of FASN mRNA and protein in RB tissues, although at varying levels, indicating FASN to be a potential therapeutic target in retinoblastoma management.
A clustering and graph deep learning-based framework for COVID-19 drug repurposing
(Elsevier, 2024-09) Agarwal, Vinti; Deepa, P.R.
Drug repurposing (or repositioning) is the process of finding new therapeutic uses for drugs already approved by drug regulatory authorities (e.g., the Food and Drug Administration (FDA) and Therapeutic Goods Administration (TGA)) for other diseases. This involves analysing the interactions between different biological entities, such as drug targets (genes/proteins and biological pathways) and drug properties, to discover novel drug–target or drug–disease relations. Machine learning and deep learning models have successfully analysed complex heterogeneous data with applications in the biomedical domain, and have also been used for drug repurposing. This study presents a novel unsupervised machine learning framework that utilizes a graph-based autoencoder for multi-feature type clustering on heterogeneous drug data. The dataset consists of 438 drugs, of which 224 are under clinical trials for COVID-19 (category A). The rest are systematically filtered to ensure the safety and efficacy of the treatment (category B). The framework solely relies on reported drug data, including its pharmacological properties, chemical/physical properties, interaction with the host, and efficacy in different publicly available COVID-19 assays. Our machine-learning framework revealed three clusters of interest and provided recommendations featuring the top 15 drugs for COVID-19 drug repurposing, which were shortlisted based on the predicted clusters that were dominated by category A drugs. Our framework can be extended to support other datasets and drug repurposing studies with the availability of our open-source code.
Comparative bioactivity assessment of bixin pigment and associated phytochemicals extracted from annatto seeds using conventional and green solvents
(JFDA, 2024-06) Sharma, Pankaj Kumar; Deepa, P.R.
Nutraceuticals, that include food ingredients and bioactives from natural products, confer physiological health benefits and protection against chronic diseases. Annatto is a tropical shrub grown in Central and South America and parts of India. Its seeds are rich in the edible carotenoid-derived apocarotenoid pigment, bixin, which is used as a natural colorant in food, textiles, and cosmetics, and is now gaining attention for its potential health-promoting attributes. Here, we compared a green solvent (ethyl lactate) based extraction of bixin and associated metabolites in annatto seeds (crushed and seed coat) with two other conventional solvents (acetone and acid-base). Bixin was characterized in the extracts using UV-visible- and FTIR- spectroscopy and thin-layer chromatography. The bixin-containing solvent extracts were then profiled for other co-existing metabolites using GC-MS analysis, which were found to be sesquiterpenes, terpenes, terpenoids, phytosterols, and tocotrienols. Their bioactivity was evaluated based on antioxidant and wound-healing efficacies and compared with pure bixin, using NIH-3T3 fibroblast cells in-vitro. Pure bixin, as well as the annatto solvent extracts, showed strong antioxidant and wound healing properties, wherein pure bixin and green solvent extract (ethyl lactate coat) exhibited higher levels of antioxidant activity, achieving 46.00% and 44.60% reduction in MDA levels, respectively, as well as enhanced wound-healing activity, with 54.09% and 53.60% wound closure within 24 h. The green solvent extracts of annatto seeds revealed: (a) differential bioactive profiles in annatto seeds (crushed and seed coat) in comparison with other solvents, and (b) strong antioxidant and wound healing properties. Thus, ethyl lactate extraction shows strong potential for sustainable environmental friendly production of functional foods/nutraceuticals from annatto seeds
Comparative docking of dual conformations in human fatty acid synthase thioesterase domain reveals potential binding cavity for virtual screening of ligands
(Taylor & Francis, 2017) Deepa, P.R.
Human fatty acid synthase (hFASN), a homo dimeric lipogenic enzyme with seven catalytic domains, is an important clinical target in cancer, metabolic syndrome and infections. Here, molecular modelling and docking methods were implemented to examine the inter-molecular interactions of thioesterase (TE) domain in hFASN with its physiological substrate, and to identify potential chemical inhibitors. TE catalyses the hydrolysis of thioester bond between palmitate and the 4’ phosphopantetheine of acyl carrier protein, releasing 16-carbon palmitate. The crystal structure of hFASN TE in two inhibitory conformations (A and B) were geometry-optimized and used for molecular docking with palmitate, orlistat (a known FASN inhibitor) and virtual screening against compounds from National Cancer Institute (NCI) database. Relatively, low binding affinity was observed during the complex formation of palmitate with A (−.164 kcal/mol) and B (−.332 kcal/mol) forms of TE, when compared with orlistat-docked TE (A form: −5.872 kcal/mol and B form: −5.484 kcal/mol), clearly indicating that the native inhibited conformation (crystal structure) was unfavourable for substrate binding. We used these orlistat dual binding modes as positive controls for prioritizing the ligands during virtual screening. From 2, 31,617 molecules in the NCI database, 916 high-scoring compounds (hit ligands) were obtained for A-form and 4582 for B-form of the TE-domain, which were then ranked according to glide docking score, XP H bond score, absorption, distribution, metabolism and excretion and binding free energy (Prime/MM-GBSA). Consequently, two top scoring ligands (NSC: 319661 and NSC: 153166) emerged as promising drug candidates that may be tested in FASN-over-expressing diseases.
Comparative Modeling and Molecular Dynamics Simulation of Substrate Binding in Human Fatty Acid Synthase: Enoyl Reductase and β-Ketoacyl Reductase Catalytic Domains
(Korea Genome Organization, 2015) Deepa, P.R.
Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and β-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and β-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.
Comparative proteomic analysis of differentially expressed proteins in primary retinoblastoma tumors
(Wiley, 2010) Deepa, P.R.
To understand the disease mechanism and to identify the potential tumor markers that would help in therapeutics, comparative proteomic analysis of 29 retinoblastoma (RB) tumors was performed using 14 non-neoplastic retinas (age ranged from 45 to 89 years) as control tissues.