Journal Articles

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    A Negative Effect of Niobium-Doped Ceria on Soot Oxidation Activity‡
    (John Wiley and Sons Inc, 2022) Patil, S.S.; Naik, S.; Ramesh, M.D.; Harshini, H.; Prasad Dasari, H.P.
    Niobium-doped ceria catalysts were synthesized to study soot oxidation activity. X-Ray diffraction (XRD) and Raman analysis of the samples revealed the presence of a fluorite structure of CeO2 for all the doped samples. The T50 temperature of the pure CeO2 sample was more significant than that of bare soot. The high catalytic activity of the CeO2 catalyst can be attributed to the low crystallite size, high facet ratio, and the large Brunauer-Emmett-Teller (BET) surface area as compared to Nb-doped samples. The activation energy calculated by both Ozawa and KAS methods were found to be low for CeO2 when compared to Nb-doped samples. CeO2 resulted in better soot oxidation activity with low activation energy. © 2022 Wiley-VCH GmbH
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    In Silico Studies of (Z)-3-(2-Chloro-4-Nitrophenyl)-5-(4-Nitrobenzylidene)-2-Thioxothiazolidin-4-One Derivatives as PPAR-γ Agonist: Design, Molecular Docking, MM-GBSA Assay, Toxicity Predictions, DFT Calculations and MD Simulation Studies
    (World Scientific, 2024) Gowdru Srinivasa, M.G.; Naik, S.; Udayakumar, U.; Mehta, C.H.; Nayak, U.Y.; Revanasiddappa, B.C.
    Diabetes mellitus, a metabolic disorder, arises from insufficient insulin levels or increased insulin resistance. An alternative approach to address this pathogenesis involves targeting PPAR-γ, which activates glucose homeostasis and improves peripheral glucose utilization. In this study, we aimed to investigate the designed 2-thioxothiazolidin-4-one derivatives (T1-25) and assess their potential as PPAR-γ regulators by an in silico approach. Physicochemical properties and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) profiles were evaluated. Docking studies were performed using Schrödinger software, with the protein target being PPAR-γ (PDB ID: 2ZNO). Additionally, MD simulation studies were conducted, and the key interactions in the protein-ligand complexes were identified. The results demonstrate the drug-likeness of compounds T11, T24 and T25, with docking scores of -7.953 kcal/mol, -7.973 kcal/ mol and -8.212 kcal/mol, respectively, and exhibit significant activity against PPAR-γ agonist and compared with the standard drug Pioglitazone (-7.367 kcal/mol). The density functional calculations were also performed to determine the geometrical properties, thermal parameters, chemical reactivity descriptors and molecular electrostatic potential of the compounds using the B3LYP functional and 6-31G++ basis sets. The energy difference between the highest occupied molecular orbitals and lowest unoccupied molecular orbitals for all the investigated compounds is in the range of 2.8-3.4 eV which allows for easy transfer of electrons and reactivity. Further research and development of these designed compounds could contribute to the advancement of effective antidiabetic treatments. © 2024 World Scientific Publishing Company.
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    Mechanistic insights and DFT analysis of bimetal doped styrofoam-like LaFeO3 perovskites with in-built dual redox couples for enhanced Photo-Fenton degradation of Tetracycline
    (Elsevier B.V., 2024) James, A.; Naik, S.; Rodney, J.D.; Joshi, S.; Udayakumar, U.; Kim, B.C.; Udayashankar, N.K.
    The rising number of contaminants released into the environment and the inadequacies of traditional wastewater treatment techniques have led to the demand for enhanced oxidation technologies like photo-Fenton. In this study, bimetal co-doped lanthanum orthoferrite (BixLa1-xCuyFe1-yO3 (x = 0, 0.01, 0.05, 0.1; y = 0, 0.01, 0.05, 0.1, 0.15)) based photo-Fenton catalysts with the in-built redox couples Fe3+/Fe2+, Cu2+/Cu+ and oxygen vacancies have been successfully synthesised via a facile one-pot solution combustion route. Systematic studies show that the Bi0.05La0.95Cu0.1Fe0.9O3 (LFOBC) exhibits an optimal photo-Fenton degradation rate of 0.0497/min for Tetracycline (TC) removal, being ∼ 1.8 and ∼ 6.2 times greater than Bi0.05La0.95FeO3 (LFOB) and pristine LaFeO3 (LFO) respectively. DFT analysis confirmed the better adsorption and dissociation of H2O2 on a bimetal co-doped catalyst and identified the electron density difference in LFOBC, which can induce the H2O2 dissociation. A detailed investigation of various influencing reaction parameters is explored. The degradation pathway for the LFOBC catalyst with the toxicological characteristics of each intermediate is analysed. This study presents the Bi0.05La0.95Cu0.1Fe0.9O3 as a potential photocatalyst for enhanced photo-Fenton degradation with excellent efficiency observed for the degradation of various harmful pollutants for environmental remediation. © 2024 Elsevier B.V.
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    Synthesis and biological evaluation of novel hybrid compounds bearing pyrazine and 1,2,4-triazole analogues as potent antitubercular agents
    (Royal Society of Chemistry, 2024) Naik, S.; Puttachari, D.; Vanishree, A.L.; Udayakumar, U.; Shetty, V.P.; Prabhu, C.; Deekshit, V.K.
    In this study, we elucidate the conceptualization and synthesis of hybrid compounds (T1-T18) amalgamating pyrazine and 1,2,4-triazole scaffolds. A total of eighteen compounds were screened in vitro for their efficacy against the Mycobacterium tuberculosis H37Rv strain via the MABA assay. The results revealed that eight compounds (T4, T5, T6, T11, T14, T15, T16, and T18) manifested noteworthy activity against Mtb, with minimum inhibitory concentration (MIC) values of ≤21.25 μM. Furthermore, we also examined these compounds for their antibacterial and antifungal properties against various strains. Compounds T4, T9, T10, T16, and T18 displayed significant antibacterial activity, while compounds T12 and T14 demonstrated significant antifungal activity. Subsequently, the most potent compounds were evaluated for their potential cytotoxicity to the Vero cell line via the MTT assay, revealing IC50 values surpassing 375 μM, indicative of minimal cytotoxicity. Additionally, we conducted in silico studies on these target molecules to better understand their action mechanisms. The in silico investigations suggest that the target enzyme involved in the action of the compounds may be DprE1. However, further experimental validation is necessary to ascertain the target responsible for the whole cell activity. All the target compounds are docked within the active site of the DprE1 enzyme, demonstrating favorable binding interactions. Furthermore, we predicted the ADME properties, physicochemical characteristics, and drug-like qualities of the target compounds using in silico methods. We also performed DFT studies to examine their electronic properties. These findings collectively indicate that the active compounds hold substantial promise as prospective contenders for the development of novel antitubercular agents. © 2024 RSC.
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    Synthesis, Molecular Docking, MD Simulation and Evaluation of Anticancer Activity of Novel 1,3,4-Oxadiazole Derivatives against Ehrlich Ascites Carcinoma (EAC) Cell Lines
    (World Scientific, 2024) Deshpande, N.S.; Naik, S.; Udayakumar, U.; Prabhu, A.; Rani, V.; Dixit, S.R.; Singh, D.; Revanasiddappa, B.C.
    In this study, a new series of 1,3,4-oxadiazole derivatives (3a- 3h) was synthesized, characterized using various analytical techniques (FT-IR, 1H- and 13C-NMR, mass spectrometry), and tested for their effectiveness against Ehrlich's Ascites Carcinoma (EAC) cell lines in vitro. After 48 h of exposure to these test compounds, the EAC cells exhibited a dose-dependent reduction in their viability. Among the tested compounds, 3b and 3e demonstrated the most potent anticancer effects, with IC50 values of 352.69 μM and 177.44 μ M, respectively. Consequently, these compounds were chosen for further investigation into their mechanisms of action on EAC cell lines. The assessment included the induction of apoptosis and the analysis of DNA damage, which were evaluated using fluorescence staining and the comet assay. These assessments revealed distinctive apoptotic characteristics such as nuclear fragmentation, cytoplasmic shrinkage and DNA damage. As a result, these compounds hold promise as potential anticancer agents. The study also delved into the binding affinities of these compounds through molecular docking analysis, and the findings showed that compounds 3b and 3e exhibited a strong binding affinity with the receptor Transforming Growth Factor-Beta Receptor I (TGF-βRI) kinase (PDB ID: 1PY5), surpassing the reference compound 5-fluorouracil. Additionally, calculations related to Molecular Mechanics Generalized Born Surface Area (MM-GBSA) indicated favorable free binding energy. The compounds also displayed acceptable ADMET properties. To validate the stability of the bond between compounds 3b and 3e with the 1PY5 receptor, a molecular dynamics simulation lasting 100 ns was carried out. © 2024 World Scientific Publishing Company.
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    Synthesis and in vitro Screening of Pyrazine-2-Carbohydrazide Derivatives as Potential Antimicrobial Agents
    (World Scientific, 2024) Naik, S.; Dinesha, P.; Udayakumar, U.; Shetty, V.P.; Prabhu, C.; Deekshit, V.K.
    Herein, we report the design of a new set of pyrazine-2-carbohydrazide derivatives (T1-T20) and in silico investigations to evaluate their inhibition activity against the enzyme, decaprenylphosphoryl-β-D-ribose 2′-epimerase (DprE1). The derivatives interact with the Cys387 residue of the enzyme's active site through hydrogen bonds. Further, we synthesized these compounds and evaluated their efficacy against the M. tuberculosis H37Rv strain. Compounds T16 and T19 displayed promising antitubercular activity, boasting a minimal inhibitory concentration of 1.56 μg/mL. Furthermore, we assessed the antibacterial activity of these compounds against a range of pathogens, including S. aureus, S. mutans, E. coli and S.Typhi. Additionally, we evaluated their antifungal potency against A. niger. Notably, compounds T4, T8, T9, T16 and T19 exhibited noteworthy antibacterial activity against tested bacterial strains. Compounds T4, T9, T16, T17, T18 and T19 showed significant inhibition activity against A. niger. Importantly, all active compounds demonstrated low cytotoxicity, with IC50 values exceeding 300 μM, ensuring no harm to normal cells. To gain a deeper understanding of these compounds, we conducted in silico investigations to evaluate their pharmacokinetics and pharmacochemical properties. Additionally, we employed DFT studies to explore the electronic characteristics of these compounds, providing valuable insights into their potential applications in the pharmaceutical field. © 2024 World Scientific Publishing Company.
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    Design, synthesis, characterization, and biological evaluation of novel pyrazine-1,3,4-oxadiazole/[1,2,4] triazolo[3,4-b][1,3,4]thiadiazine hybrids as potent antimycobacterial agents
    (Elsevier B.V., 2024) Naik, S.; Dinesha, P.; Udayakumar, U.; Shetty, V.P.; Deekshit, V.K.
    In this study, we present novel pyrazine-1,3,4-oxadiazole hybrids (T1-T9) and [1,2,4]triazolo[3,4-b][1,3,4]thiadiazine derivatives (T10-T18), which possess remarkable antimicrobial activity. These compounds have been meticulously scrutinized for their efficacy in combatting the M. tuberculosis H37Rv strain. Three compounds T7, T8, and T17 showed promising antitubercular activity with MIC of 1.56 µg/mL. The target compounds are also evaluated for their antibacterial activity against S. aureus, S. mutans, E. coli, and S. Typhi, and antifungal activity against A. niger. Most of the compounds showed significant antibacterial and antifungal activity. All the active compounds exhibited very low toxicity and none of the active compounds were toxic to the normal cells. To deepen our understanding of these compounds, an in-silico ADME, and molecular docking analysis against the DprE1 enzyme were conducted, followed by DFT studies to shed some light on their electronic properties, and enhance our grasp of their pharmacological potential. © 2024 Elsevier B.V.
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    Elucidating mechanisms and DFT analysis of monometallic Vanadium incorporated nanoporous TiO2 as advanced material for enzyme-free electrochemical blood glucose biosensors with exceptional performance tailored for point-of-care applications
    (Elsevier Inc., 2024) Rao, L.; Rodney, J.D.; Naik, S.; Udayakumar, U.; Udayashankar, N.K.; Kim, B.C.; Badekai Ramachandra, B.R.
    Diabetes is a chronic condition that can last a lifetime and has claimed a great number of lives in recent years. This motivated scientists to design a glucose biosensor to monitor and control blood glucose levels in diabetic patients. Herein, hydrothermal derived Vanadium (V), Nickel (Ni), and Cobalt (Co)-doped TiO2 (MxTi1-xO2 (x = 0.01, 0.02, and 0.03)) was synthesized to achieve the best material to answer the pertaining problem. Of all the materials synthesized, V0.03Ti0.97O2@NF demonstrated the highest level of sensitivity, and selectivity, and has higher electrochemical cycling stability in 0.1 M KOH. It exhibits a very high sensitivity of 1129.31 μAmM-1cm-2 and Limits of Detection (LOD) and Limits of Quantification (LOQ) of 1.8 μM (S/N = 3) and 6.2 μM, respectively, with a broad linear range from 20 μM to 2 mM. The DFT approach was employed computationally to analyze the adsorption of glucose on surfaces of pure TiO2 and TiO2 doped with V, Ni, and Co respectively. The research findings highlight that when it comes to its interaction with glucose, pure TiO2 exhibits significantly less reactivity compared to transition metal-doped TiO2. Experimentally it shows that the V0.03Ti0.97O2@NF surface has the most sensitive glucose detection capability and it also exhibited significant selectivity towards glucose in the presence of additional interference. It demonstrated 100% retention after cycling stability and had a shelf life of ≃30 days. The V0.03Ti0.97O2@NF-based sensor exhibits accurate glucose sensing, even for human serum samples. © 2024 Elsevier B.V.
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    A novel and ultrasensitive high-surface porous carbon-based electrochemical biosensor for early detection of dengue virus
    (Elsevier Ltd, 2024) Hegde, S.S.; Naik, S.; Badekai Ramachandra, B.R.; Mishra, P.; Udayakumar, D.; Ahmed, M.U.; Santos, G.N.
    Dengue fever, a mosquito-borne viral infection, poses a significant global health threat, and early diagnosis is crucial for effective disease management. The utilization of advanced materials in the design ensures an improved surface area, facilitating a heightened interaction between the sensor and the target. In this study, the incorporation of biomass-derived high-surface porous carbon-based materials not only contributed to the sensor's sensitivity but also ensured a cost-effective and scalable manufacturing process. The electrochemical nature of the biosensor added a layer of precision to the detection process and offered a reliable, rapid method for identifying the infection of the dengue virus. The enhanced sensitivity of the biosensor allowed the detection of even trace amounts of the NS1 protein, enabling early diagnosis in the initial stages of dengue infection. The system exhibited a high sensitivity with a wide linear range between 1 pg/mL and 100 μg/mL, and the extremely low detection limit of 0.665 pg/mL ranks this as one of the most efficient biosensors for the detection of dengue virus NS1 protein. Selectivity studies, coupled with computational insights, showcased the biosensor's prowess in distinguishing NS1 protein from potential interfering substances, laying the foundation for reliable diagnostics in complex biological matrices. Real sample analysis using human serum spiked with NS1 protein offers a tantalizing glimpse into the transformative potential of biosensors in real-world scenarios. This innovative biosensor holds great promise for addressing the pressing need for early detection of dengue virus infections. © 2024 The Authors
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    Structure-based drug design and characterization of novel pyrazine hydrazinylidene derivatives with a benzenesulfonate scaffold as noncovalent inhibitors of DprE1 tor tuberculosis treatment
    (Springer Nature, 2024) Naik, S.; Dinesha, P.; Udayakumar, D.
    In this study, we present a novel series of (E)-4-((2-(pyrazine-2-carbonyl) hydrazineylidene)methyl)phenyl benzenesulfonate (T1-T8) and 4-((E)-(((Z)-amino(pyrazin-2-yl)methylene)hydrazineylidene)methyl)phenyl benzenesulfonate (T9-T16) derivatives which exert their inhibitory effects on decaprenylphosphoryl-?-D-ribose 2'-epimerase (DprE1) through the formation of hydrogen bonds with the pivotal active site Cys387 residue. Their effectiveness against the M. tuberculosis H37Rv strain was examined and notably, three compounds (namely T4, T7, and T12) exhibited promising antitubercular activity, with a minimum inhibitory concentration (MIC) of 1.56 µg/mL. The target compounds were screened for their antibacterial activity against a range of bacterial strains, encompassing S. aureus, B. subtilis, S. mutans, E. coli, S. typhi, and K. pneumoniae. Additionally, their antifungal efficacy against A. fumigatus and A. niger also was scrutinized. Compounds T6 and T12 demonstrated significant antibacterial activity, while compound T6 exhibited substantial antifungal activity. Importantly, all of these active compounds demonstrated exceedingly low toxicity without any adverse effects on normal cells. To deepen our understanding of these compounds, we have undertaken an in silico analysis encompassing Absorption, Distribution, Metabolism, and Excretion (ADME) considerations. Furthermore, molecular docking analyses against the DprE1 enzyme was conducted and Density-Functional Theory (DFT) studies were employed to elucidate the electronic properties of the compounds, thereby enhancing our understanding of their pharmacological potential. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024.