Browsing by Author "Chakraborty, Sudip"

Now showing 1 - 6 of 6
  • No Thumbnail Available
    Item
    Caesium carbonate promoted regioselective O-functionalization of 4,6-diphenylpyrimidin-2(1H)-ones under mild conditions and mechanistic insight
    (Royal Society of Chemistry, 2023-06-05T00:00:00) Kumar, Vijay; Singh, Praval Pratap; Dwivedi, Ashish Ranjan; Kumar, Naveen; Rakesh kumar, None; Chandra Sahoo, Subash; Chakraborty, Sudip; Kumar, Vinod
    A facile one-step catalyst free methodology has been developed for the regioselective functionalization of 4,6-diphenylpyrimidin-2(1H)-ones under mild conditions. Selectivity towards the O-regioisomer was achieved by using Cs2CO3 in DMF without use of any coupling reagents. A total of 14 regioselective O-alkylated 4,6-diphenylpyrimidines were synthesized in 81-91% yield. In the DFT studies it was observed that the transition state for the formation of the O-regioisomer is more favourable with Cs2CO3 as compared to K2CO3. Furthermore, this methodology was extended to increase the O/N ratio for the alkylation of 2-phenylquinazolin-4(3H)-one derivatives. � 2023 The Royal Society of Chemistry.
  • No Thumbnail Available
    Item
    Combing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface
    (Academic Press Inc., 2023-11-08T00:00:00) Yadav, Hemendra; Algaonkar, Prashant S.; Chakraborty, Sudip; Ramakrishna, Wusirika
    DNA combing is a powerful technique for studying replication profile, fork-directionality and fork velocity. At present, there is requirement of a methodology to comb DNA present in a single human cell for studying replication dynamics at early embryonic stage. In our study, a surface having dual characteristics i.e., affinity towards negatively charged single DNA molecules and a hydrophobic gradient for self propelled droplet motion of combing solution was developed. The surface was made by coating of TCOS (trichloro-octylsilane) by vapor diffusion on APTES (Aminopropyl-triethoxysilane) coated glass slides. A gradient surface having high deposition efficiency (DE) was developed on which 5 picogram DNA equivalent to genomic DNA present in one single human cell can be combed. The gradient surface was thermostable in nature having the ability to sustain boiling temperature for two hours and sustain anisotropy in 70 % ethanol for 80 h. Applicability for multiple runs was enhanced such that the surface can be used for 13�14 times. Factors associated with gradient surface are unidirectional movement of combing solution droplet over the gradient surface for combing straight DNA molecules and a longer gradient surface of more than 1 cm such that long size DNA molecules can be combed. Ellipsometry and contact angle hysteresis confirmed the presence of hydrophobic gradient. XPS (X-ray photoelectron spectroscopy) and FTIR (Fourier Transform Infrared Spectroscopy) confirmed the presence of characteristic affinity towards negatively charged DNA molecules on the gradient surface. Combing solution was optimized for increasing deposition efficiency and for increasing the applicability of gradient surface for multiple runs. High temperature of combing solution was found to increase Deposition Efficiency. Combing solution was also optimized for combing single DNA molecules over the gradient surface. Single DNA molecules were combed by reducing pH and lowering concentration of triton-X in the combing solution. Dye: bp ratio was optimized for high fluorescent intensity and low surface background. � 2023 Elsevier Inc.
  • No Thumbnail Available
    Item
    Genomic Variation Affecting MPV and PLT Count in Association with Development of Ischemic Stroke and Its Subtypes
    (Springer, 2023-07-15T00:00:00) Ludhiadch, Abhilash; Sulena; Singh, Sandeep; Chakraborty, Sudip; Sharma, Dixit; Kulharia, Mahesh; Singh, Paramdeep; Munshi, Anjana
    Platelets play a significant role in the pathophysiology of ischemic stroke since they are involved in the formation of intravascular thrombus after erosion or rupture of the atherosclerotic plaques. Platelet (PLT) count and mean platelet volume (MPV) are the two significant parameters that affect the functions of platelets. In the current study, MPV and PLT count was evaluated using flow cytometry and a cell counter. SonoClot analysis was carried out to evaluate activated clot timing (ACT), clot rate (CR), and platelet function (PF). Genotyping was carried out using GSA and Sanger sequencing, and expression analysis was performed using RT-PCR. In silico analysis was carried out using the GROMACS tool and UNAFold. The interaction of significant proteins with other proteins was predicted using the STRING database. Ninety-six genes were analyzed, and a significant association of THPO (rs6141) and ARHGEF3 (rs1354034) was observed with the disease and its subtypes. Altered genotypes were associated significantly with increased MPV, decreased PLT count, and CR. Expression analysis revealed a higher expression in patients bearing the variant genotypes of both genes. In silico analysis revealed that mutation in the THPO gene leads to the reduced compactness of protein structure. mRNA encoded by mutated ARHGEF3 gene increases the half-life of mRNA. The two significant proteins interact with many other proteins, especially the ones involved in platelet activation, aggregation, erythropoiesis, megakaryocyte maturation, and cytoskeleton rearrangements, suggesting that they could be important players in the determination of MPV values. In conclusion, the current study demonstrated the role of higher MPV affected by genetic variation in the development of IS and its subtypes. The results of the current study also indicate that higher MPV can be used as a biomarker for the disease and altered genotypes, and higher MPV can be targeted for better therapeutic outcomes. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
  • No Thumbnail Available
    Item
    Identification of 1,3,4-oxadiazoles as tubulin-targeted anticancer agents: a combined field-based 3D-QSAR, pharmacophore model-based virtual screening, molecular docking, molecular dynamics simulation, and density functional theory calculation approach
    (Taylor and Francis Ltd., 2023-09-11T00:00:00) Das, Agnidipta; Sarangi, Manaswini; Jangid, Kailash; Kumar, Vijay; Kumar, Amit; Singh, Praval Pratap; Kaur, Kamalpreet; Kumar, Vinod; Chakraborty, Sudip; Jaitak, Vikas
    Cancer is one of the most prominent causes of death worldwide and tubulin is a crucial protein of cytoskeleton that maintains essential cellular functions including cell division as well as cell signalling, that makes an attractive drug target for cancer drug development. 1,3,4-oxadiazoles disrupt microtubule causing G2-M phase cell cycle arrest and provide anti-proliferative effect. In this study, field-based 3D-QSAR models were developed using 62 bioactive anti-tubulin 1,3,4-oxadiazoles. The best model characterized by PLS factor 7 was rigorously validated using various statistical parameters. Generated 3D-QSAR model having high degree of confidence showed favourable and unfavourable contours around 1,3,4-oxadiazole core that assisted in defining proper spatial positioning of desired functional groups for better bioactivity. A five featured pharmacophore model (AAHHR_1) was developed using same ligand library and validated through enrichment analysis (BEDROC160.9 value = 0.59, Average EF 1% = 27.05, and AUC = 0.74). Total 30,212 derivatives of 1,3,4-oxadiazole obtained from PubChem database was prefiltered through validated pharmacophore model and docked in XP mode on binding cavity of tubulin protein (PDB code: 1SA0) which led into the identification of 11 HITs having docking scores between ?7.530 and ?9.719 kcal/mol while the reference compound Colchicine exerted docking score of ?7.046 kcal/mol. Following the analysis of MM-GBSA and ADME studies, HIT1 and HIT4 emerged as the two promising hits. To verify their thermodynamic stability at the target site, molecular dynamic simulations were carried out. Both HITs were further subjected to DFT analysis to determine their HOMO-LUMO energy gap for ensuring their biological feasibility. Finally, molecular docking based structural exploration for 1,3,4-oxadiazoles to set up a lead of Formula I for further advancements of tubulin polymerization inhibitors as anti-cancer agents. Communicated by Ramaswamy H. Sarma. � 2023 Informa UK Limited, trading as Taylor & Francis Group.
  • No Thumbnail Available
    Item
    Recent advances and challenges of carbon nano onions (CNOs) for application in supercapacitor devices (SCDs)
    (Elsevier Ltd, 2023-06-26T00:00:00) Kaur, Simran; Krishnan, Abhinand; Chakraborty, Sudip
    Since the discovery of CNOs, the number of publications and citations related to these carbon nanostructures research are still growing, indicating their strange behavior attracting the attention of the scientific community. As far as, the reviews published on CNOs have paid attention to the synthesis, characterization, surface functionalization and biomedical applications. However, very few works have summarized the advances and challenges of CNOs for application in SCDs. In this review, our objective is to summarize the recent advancement and challenges of the synthetic strategy, morphology, and electrochemical performance of different CNOs based materials along with their application in SCDs. The review commence with a short description of CNOs history and its structure, followed by the CNOs based supercapacitors and its recent advancement for the capacitance value augmentation. Then emphasized the synthetic procedure of Doped CNOs and its applications. After a critical analysis of the literature, we have discussed the molecular mechanism behind the improved electrochemical behavior of doped CNOs as compared with the pristine CNOs. A common guidance for selecting dopants based on their specific applications in supercapacitors have been explored. Further, the physico-chemical and electrochemical properties of CNO-composites are also discussed. We summarized the DFT based studies for CNOs based materials, and the advantages of Molecular Modeling/ReaxFF based simulation techniques for modeling of CNOs based electrodes and task specific electrolyte design for SCDs. The CNOs based materials are very good candidates for supercapacitor electrode design, with various challenges, more specifically the structural ordering of CNOs, electrochemical performance and condition of supercapacitor health. The Artificial Intelligence (AI)/Machine Learning (ML) based literatures are discussed and recommended several AI/ML based algorithms in the field of supercapacitors and energy storage devices (ESDs) to predict the specific capacitance value and the supercapacitors condition of health. We have outlined the current challenges and opportunities in this field. To the best of our knowledge, the review will be useful to provide a systematic framework for CNOs based research in the field of supercapacitor devices. � 2023 Elsevier Ltd
  • No Thumbnail Available
    Item
    Wheat grain proteomic and protein�metabolite interactions analyses provide insights into plant growth promoting bacteria�arbuscular mycorrhizal fungi�wheat interactions
    (Springer Science and Business Media Deutschland GmbH, 2022-04-09T00:00:00) Yadav, Radheshyam; Chakraborty, Sudip; Ramakrishna, Wusirika
    Key message: Proteomic, protein�protein and protein�metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant�s metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein�protein and protein�metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat�PGPB�AMF interactions leading to higher yield and biofortification. � 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.