Navneeta Bharadvaja

Computational design of novel flavonoid analogues as potential AChE inhibitors: analysis using group-based QSAR, molecular docking and molecular dynamics simulations

Acetyl cholinesterase (AChE) is an enzyme associated with the loss of cholinergic neurones in Alzheimer’s disease. Acetylcholine is an important neurotransmitter found in the brain and the levels of which decrease significantly in Alzheimer’s patients due to increased expression of AChE. In this study, a novel fragment-based QSAR model has been developed using twenty-seven flavonoid-derived compounds exhibiting inhibitory activity against AChE. This fragment-based method gives the advantage of studying the effect of individual fragments on the biological activity of the compound by evaluating the descriptors. The compounds were divided into training and test sets, where the test set was used for cross-validation of the model. The QSAR model exhibited good statistical values for the training set (r2xa0=xa00.8070, q2xa0=xa00.7088, F-ratioxa0=xa031.3616) and test set (pred_r2xa0=xa00.8131). The regression equation obtained had three descriptors describing effect of substitutions in terms of quantitative values. Evaluation of the model implied that electronegative substitution at R1 position lowers the inhibitory activity, while the presence of hydroxyl group improves the same. The presence of rings increased the activity of the compounds. The model thus generated was used to obtain six combinatorial libraries and predicts the activity of these compounds. These compounds were selected for docking and molecular dynamics simulation studies and two leads were identified against AChE.

Mechanistic analysis elucidating the relationship between Lys96 mutation in Mycobacterium tuberculosis pyrazinamidase enzyme and pyrazinamide susceptibility

Background Pyrazinamide (PZA) is one of the most effective first line treatments against tuberculosis disease. The drug generally has bacteriostatic action. It also acts on bacterial spores which eliminates the chances of resurfacing of the infection. However, in recent years there has been a major increase in the occurrence of drug resistant bacterial strains. Resistance against PZA is caused by mutations in pyrazinamidase (PncA) protein which is the activator of the prodrug PZA. In the present study, we have tried to gain insights into the mechanism by which resistance develops due to K96R mutation occurring in the PncA catalytic region Results The binding cavity analysis showed an increase of 762.3 A 3 in the volume of the mutant protein. Docking studies revealed that PZA has a greater binding affinity for the native protein in comparison to the mutant protein. Molecular dynamics simulations further showed the role of flap region, which is present in PncA protein, in development of resistance to the drug. Conclusion The residues of flap region acquire more flexibility in mutant form of protein and thus move away from the active site. This leads to weak binding of the drug to the target residues which might interfere with the activation of the drug to functional form thereby giving rise to drug resistant bacterial strains. Background

Identification of chebulinic acid as potent natural inhibitor of M. tuberculosis DNA gyrase and molecular insights into its binding mode of action

Drug resistant tuberculosis has threatened all the advances that have been made in TB control at the global stage in the last few decades. DNA gyrase enzymes are an excellent target for antibacterial drug discovery as they are involved in essential functions like DNA replication. Here we report, a successful application of high throughput virtual screening (HTVS) to identify an inhibitor of Mycobacterium DNA gyrase targeting the wild type and the most prevalent three double mutants of quinolone resistant DNA gyrase namely A90V+D94G, A74S+D94G and A90V+S91P. HTVS of 179.299 compounds gave five compounds with significant binding affinity. Extra presicion (XP) docking and MD simulations gave a clear view of their interaction pattern. Among them, chebulinic acid (CA), a phytocompound obtained from Terminalia chebula was the most potent inhibitor with significantly high XP docking score, -14.63, -16.46, -15.94 and -15.11 against wild type and three variants respectively. Simulation studies for a period of 16 ns indicated stable DNA gyrA-CA complex formation. This stable binding would result in inhibition of the enzyme by two mechanisms. Firstly, binding of CA causes displacement of catalytic Tyr129 away from its target DNA-phosphate molecule from 1.6 Å to 3.8-7.3 Å and secondly, by causing steric hindrance to the binding of DNA strand at DNA binding site of enzyme. The combined effect would result in loss of cleavage and religation activity of enzyme leading to bactericidal effect on tuberculosis. This phytocompound displays desirable quality for carrying forward as a lead compound for anti-tuberculosis drug development. The results presented here are solely based on computations and need to be validated experimentally in order to assert the proposed mechanism of action.

Effect of Different Media and Growth Hormones on Shoot Multiplication of In Vitro Grown Centella asiatica Accessions

Centella asiatica also known as Gotu Kola is an important medicinal plant which contains several bioactive compounds such as triterpenoid saponins including asiaticoside, madecassoside, centelloside, asiatic acid, etc. In addition, Centella sp. contains other components including flavonoids, phytosterols, tannins, amino acids, sugars, etc. Due to its medicinal importance, this plant is being overexploited and it is essential to conserve this plant. In the present investigation, comparative study of different accessions of Centella asiatica for shoot multiplication in different media and growth hormones was performed. Shoot multiplication and phytocompounds production from different accessions is required to be assessed to choose an accession giving optimum production of phytocompounds. For this, different media containing different combinations of macro and micro nutrients have to be tested that influence the growth of the plant. Assessment of best culture media and concentrations of plant hormone for shoot culture are some of the critical culture conditions to achieve. So there is a need to optimise such conditions that will enhance the growth of the plant. For shoot culture, explant of different accession of Centella asiatica were inoculated in different media i.e. Murashige and Skoog (MS), Gamborg’s B5 and Nitsch medium which were supplemented with standard concentrations of plant growth hormones. The cultures were incubated at 25 ± 2°C with photoperiod of 16 hours. After six week of incubation period, highest growth was found in MS media in all accessions. Further MS medium was supplemented with different combinations of growth hormones. After six week of incubation, MS medium supplemented with 1mg/l BAP showed the highest growth of the plant followed by 2mg/l BAP+0.5 NAA.

Curcumin-based IKKβ inhibiting anticancer lead design using novel fragment-based group QSAR modelling

AbstractNF-κB transcription factor plays a vital role in the protection of transformed cells from apoptosis, thus resulting in the onset/progression nof cancer. Activation of NF-κB is strictly controlled by IκB kinase, and therefore IκB kinase inhibition forms the basis for anticancer drug research. We present here a novel fragment-based QSAR model using 4-arylidene curcumin analogues having IκB kinase inhibitory properties. The insights into the contribution of each chemical fragment of the analogues in IκB kinase inhibitory activity were used to generate a combinatorial library containing 167,828 molecules and their inhibitory activities were predicted by the reported G-QSAR model. We report top two scoring compounds BEP and BHP possessing high docking scores of −9.21 and −8.98xa0kcal/mol, respectively. Molecular dynamics simulations studies showed that the trajectories of the IκB kinase complexed with BEP and BHP were stable over a considerably long time period (16xa0ns). The two compounds reported here showed high binding affinity and stability with IκB kinase and thus can be taken forward as promising anticancer leads. The G-QSAR model reported here will pave way for the development of novel leads by high-throughput activity prediction of similar compounds.

Effect of Different Carbon Sources and Elicitors on Shoot Multiplication inAccessions of Centella asiatica

Centella asiatica is a medicinal herb which has been extensively used in the treatment of nervous disorders and skin diseases. It is distributed throughout the tropical and sub-tropical region of the world. This plant contains various bioactive constituents such as asiaticoside, madecassic acid, flavonoids etc. Centella is in huge demand in International market for the preparation of pharmaceuticals and cosmetics which has resulted in its overexploitation. This situation demands the use of biotechnological methods to conserve as well as increase the production of biomass and bioactive compounds. The present study focused the use of different carbon sources (sucrose and fructose) and elicitors (Malt extract, Salicylic acid and Jasmonic acid) for the enhancement of biomass in five accessions of Centella asiatica. It was concluded that Murashige and Skoog (MS) medium supplemented with 1 mg/L concentration of Malt extract and 1.5 mg/L concentration of 6-Benzyl amino purine (BAP) showed highest biomass production among all elicitors. Among two carbon sources, MS media supplemented with Sucrose (3 mg/L) along with BAP (1.5 mg/L) showed better result than fructose.

Identification of Potential Culture Conditions for Enhancing the Biomass Production of Microalga Chlorella minutissima

Identification of Potential Culture Conditions for Enhancing the Biomass Production of Microalga Chlorella minutissima nMicroalgae have been considered as appropriate source of various commercial products due to their enormous potential of growth, higher content of biochemical product like sugars, lipids, proteins and pigments, high CO2 tolerance etc. But these organisms are easily affected by environmental factors due to their minute size. So it is necessary to find potential culture conditions of microalgae so maximum biomass can be achieved in short duration of time under lab settings. In this study, effects of various components of culture conditions on biomass of microalga Chlorella minutissima were recorded. Based on the result of biomass production, potential culture conditions have been summarized for microalgae Chlorella minutissima. Among six different media tested, N-11, BBM and BG-11 media were found suitable for this microalga. Although with nitrogen starvation, BBM and BG-11 were found to be the potential media. Potential source of nitrogen, phosphorus and carbon were sodium & potassium nitrate, di-potassium hydrogen phosphate & potassium di hydrogen phosphate and glycerol respectively. The suitable concentration of nitrate, phosphate, and glycerol were 0.375 g/l, 0.16 g/l and 12.5 g/l. Alkaline pH was found suitable for this microalgae to provide higher biomass. Chlorella minutissima has shown better biomass production in 24 hours of illumination of white light of 20 W tube light and shaking period of 2 hours in Erlenmeyer flasks.

Molecular Interaction Studies of Shrimp Antiviral Protein, PmAV with WSSV RING Finger Domain in silico

Molecular Interaction Studies of Shrimp Antiviral Protein, PmAV with WSSV RING Finger Domain in silicoxa0Mathematical Assessment of Prognosis nDiagnosis is the result of combined clinical and biological examinations. In most cases, it is refined by a classification of the patient in a disease group, which in turn contributes to prognostic assessment. Prognosis has long been the subjective result of experience. With the appearance of new technologies combining numerous samples with large-scale quantitative biological marker measurements, molecular assessment supplied new possibilities in cancer diagnosis and prognosis.

Medicinal Plants as a Potential Source of Chemopreventive Agents

Cancer is one of the most common deadly diseases and remains as one of the leading causes of death worldwide. High mortality and incidence make it an important public health and economic issue which requires an effective prevention. Radiotherapy, immunotherapy, and chemotherapy are the most common methods used for the treatment of cancer, but these techniques adversely affect the healthy cells. Thus, inhibition of damaging behavior to the healthy tissues with the use of commonly used therapies motivates to explore the new safe methods to treat cancer. Chemoprevention is a novel approach to control cancer; it involves utilization of specific natural or synthetic agents to suppress, prevent, or reverse the malignancy before development of invasive cancer. Products from natural sources such as medicinal plants and herbs and their phytocompounds including flavonoids, alkaloids, carotenoids, etc. show protective effects against various forms of cancers. Chemoprevention of cancer using phytocompounds may be one of the feasible approaches to control this disease. An herbal medicine which refers to the medicinal product of plant stem, roots, leaves, bark, seed, flower, and fruit is one of the best sources for extraction of chemopreventive agents as they are nontoxic in nature and cause less or no side effect to the patients. Consumption of chemopreventive agents containing phytocompounds shows an important insight to fight against cancer and yield promising outcomes. The aim of this chapter is to provide an overview of various scientific evidences that support the utilization of medicinal plants and chemopreventive agents for the treatment of cancer.

Fatty Acid Methyl Ester Profile Analysis of In-Vitro Grown Accessions of Plumbago zeylanica

Plumbago zeylanica is a pharmaceutically important plant which belongs to Plumbaginaceae family. It possesses wide range of pharmacological activities which includes antibacterial central nervous system stimulatory activity, anti-fungal, anti-inflammatory, anti-hyperglycemic, anti-cancer and anti-atherosclerotic activity. Fatty acid methyl ester analysis reveals the presence of various fatty acids in the plant. The present study deals with Fatty acid methyl ester profile of five different accession of Plumbago zeylanica. Results reveal that these accessions are rich in Octadecadienoic acid (8-22%), Octadecatrienoic acid (7-24%) and Pentadecanoic acid (11-22%) fatty acids. Accession number 421418 is contains the highest amount of Pentadecanoic acid and 9,12,15 Octadecatrienoic acid. Accession number 439212 contains highest amount of Hexadecanoic acid. Highest amount of 9,12 Octadecadienoic acid was present in accession number 524441.