The Experts below are selected from a list of 67545 Experts worldwide ranked by ideXlab platform
Nyshadham S. N. Chaitanya - One of the best experts on this subject based on the ideXlab platform.
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TargetIng SARS CoV2 (Indian isolate) genome with miRNA: An In Silico Study.
Iubmb Life, 2020Co-Authors: Arpita Devi, Nyshadham S. N. ChaitanyaAbstract:The newly identified SARS CoV2 has become a global pandemic sInce December 2019. Various researchers are tryIng to design a vaccIne candidate agaInst the virus. On the other hand, another group is focussIng on repurposIng approved or clInically tested drugs for treatment. However, there is always a search for alternative therapies. Thus, we propose an alternative approach apart from chemotherapy that is the usage of miRNA as novel antisense therapy to cure SARS CoV2 Infected patients. To address the objective, miRNAs have been designed by targetIng the genome of SARS CoV2 (Indian isolate). First, the open readIng frames In the viral genome have been identified, and the proteIns encoded by those open readIng frames have been predicted. UsIng computational biology, several miRNAs have been designed and their probability to bInd to a viral gene has been predicted. In addition, miRNA target mInIng In the host cell has been done to rule out the possibility of non-specific bIndIng of the miRNAs. The miRNAs havIng the highest chances to bInd to the viral genome have been converted Into pre-miRNAs, and their Interaction with dicer endoribonuclease has been studied by molecular dockIng. Results revealed that the pre-miRNAs Interact with the RNAse III 2 domaIn of dicer. Thus, it is predicted that the pre-miRNAs after delivery to the Infected host cell will be processed by dicer to generate mature miRNAs that will target the SARS CoV2 viral genome. Therefore, miRNA therapy can be an alternative approach for the treatment of SARS CoV2 Infection.
Assem Barakat - One of the best experts on this subject based on the ideXlab platform.
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synthesis In vitro biological activities and In Silico Study of dihydropyrimidInes derivatives
Bioorganic & Medicinal Chemistry, 2015Co-Authors: Assem Barakat, Mohammad Shahidul Islam, Abdullah Mohammed Almajid, Hazem A Ghabbour, Hoongkun Fun, Kulsoom Javed, Rehan Imad, Sammer YousufAbstract:We describe here the synthesis of dihydropyrimidInes derivatives 3a-p, and evaluation of their α-glucosidase enzyme Inhibition activities. Compounds 3b (IC50=62.4±1.5 μM), 3c (IC50=25.3±1.26 μM), 3d (IC50=12.4±0.15 μM), 3e (IC50=22.9±0.25 μM), 3g (IC50=23.8±0.17 μM), 3h (IC50=163.3±5.1 μM), 3i (IC50=30.6±0.6 μM), 3m (IC50=26.4±0.34 μM), and 3o (IC50=136.1±6.63 μM) were found to be potent α-glucosidase Inhibitors In comparison to the standard drug acarbose (IC50=840±1.73 μM). The compounds were also evaluated for their In vitro cytotoxic activity agaInst PC-3, HeLa, and MCF-3 cancer cell lInes, and 3T3 mouse fibroblast cell lIne. All compounds were found to be non cytotoxic, except compounds 3f and 3m (IC50=17.79±0.66-20.44±0.30 μM), which showed a weak cytotoxic activity agaInst the HeLa, and 3T3 cell lInes. In molecular dockIng simulation Study, all the compounds were docked Into the active site of the predicted homology model of α-glucosidase enzyme. From the dockIng result, it was observed that most of the synthesized compounds showed Interaction through carbonyl oxygen atom and polar phenyl rIng with active site residues of the enzyme.
Rienk Van Grondelle - One of the best experts on this subject based on the ideXlab platform.
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steady state spectroscopy of zInc bacteriopheophytIn contaInIng lh1 an In vitro and In Silico Study
Principles and Practice of Constraint Programming, 2002Co-Authors: M Wendling, Frank Van Mourik, Karine Lapouge, Vladimir I. Novoderezhkin, Bruno Robert, Rienk Van GrondelleAbstract:Abstract By reversible dissociation of the light-harvestIng complex 1 (LH1) of Rhodospirillum rubrum it is possible to (partly) exchange the bacteriochlorophyll (BChl) a by zInc-bacteriopheophytIn (Zn-BPheo). After reassociation of the proteIn a complex is formed which can have different percentages of Zn-BPheo bound to the polypeptides [Biochemistry 39 (2000) 1091]. Low-temperature absorption spectra show a shift of the absorption maximum from 886 to 863 nm, when the native LH1 complex is compared to a modified complex contaInIng 90% Zn-BPheo, whereas the positions of the absorption maxima of BChl a and Zn-BPheo differ by only 6 nm, when the pigments are bound to the isolated polypeptides. UsIng an exciton model with static disorder of site energies based on the rIng-like structure of LH1 we can describe this shift by assumIng a difference In the excitonic couplIng origInatIng solely from the different dipole strength of the exchanged Zn-BPheo compared with the origInal BChl a . We estimate that In LH1 the nearest-neighbour Interaction energy of two BChl a molecules is around 400 cm −1 and the diagonal disorder is around 600 cm −1 . Furthermore, we determIned if the energy transfer In pigment-modified complexes is similar to native LH1. This can be observed by selectively excitIng electronic states dependIng on their energy and measurIng the polarized emission spectra at low temperature. The native complex was compared to a complex contaInIng 70% Zn-BPheo. The fluorescence anisotropy and the shift of the emission maximum In native LH1 and 70%-Zn-BPheo–LH1 dependIng on the excitation wavelength can generally be described withIn the same disordered exciton model, extended In a simple way with lIne shapes. The model proved to be simple and robust when applied to these engIneered light-harvestIng complexes.
Arpita Devi - One of the best experts on this subject based on the ideXlab platform.
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TargetIng SARS CoV2 (Indian isolate) genome with miRNA: An In Silico Study.
Iubmb Life, 2020Co-Authors: Arpita Devi, Nyshadham S. N. ChaitanyaAbstract:The newly identified SARS CoV2 has become a global pandemic sInce December 2019. Various researchers are tryIng to design a vaccIne candidate agaInst the virus. On the other hand, another group is focussIng on repurposIng approved or clInically tested drugs for treatment. However, there is always a search for alternative therapies. Thus, we propose an alternative approach apart from chemotherapy that is the usage of miRNA as novel antisense therapy to cure SARS CoV2 Infected patients. To address the objective, miRNAs have been designed by targetIng the genome of SARS CoV2 (Indian isolate). First, the open readIng frames In the viral genome have been identified, and the proteIns encoded by those open readIng frames have been predicted. UsIng computational biology, several miRNAs have been designed and their probability to bInd to a viral gene has been predicted. In addition, miRNA target mInIng In the host cell has been done to rule out the possibility of non-specific bIndIng of the miRNAs. The miRNAs havIng the highest chances to bInd to the viral genome have been converted Into pre-miRNAs, and their Interaction with dicer endoribonuclease has been studied by molecular dockIng. Results revealed that the pre-miRNAs Interact with the RNAse III 2 domaIn of dicer. Thus, it is predicted that the pre-miRNAs after delivery to the Infected host cell will be processed by dicer to generate mature miRNAs that will target the SARS CoV2 viral genome. Therefore, miRNA therapy can be an alternative approach for the treatment of SARS CoV2 Infection.
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A Comparative In Silico Study of the Glucose Transporters Predicts UbiquitInation of the Transporters at the C-TermInal End
2018Co-Authors: Arpita DeviAbstract:Glucose Transporters are a family of membrane spannIng proteIns that transports glucose from exterior of the cell to the Interior of the cell through the plasma membrane. There are 14 glucose transporters known till now. Although the transporters belong to the same family but not all function In glucose transport. They are different from each other In primary amIno acid sequence. However, there is similarity In the secondary as well as tertiary structure. In this Study, we have modelled the tertiary structure of all the glucose transporters. The process of degradation of GLUTs has not been studied till now. In this Study, it is predicted that GLUTs are ubiquitInated and the site for ubiquitInation is conserved across all members of the family. Keywords: Glucose transporters; ubiquitInation; dockIng; bIndIng energy Cite this Article Arpita Devi. A comparative In Silico Study of the Glucose Transporters predicts ubiquitInation of the transporters at the C-termInal end. Research & Reviews: A Journal of BioInformatics . 2018; 5(2): 15–24p.
Sammer Yousuf - One of the best experts on this subject based on the ideXlab platform.
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synthesis In vitro biological activities and In Silico Study of dihydropyrimidInes derivatives
Bioorganic & Medicinal Chemistry, 2015Co-Authors: Assem Barakat, Mohammad Shahidul Islam, Abdullah Mohammed Almajid, Hazem A Ghabbour, Hoongkun Fun, Kulsoom Javed, Rehan Imad, Sammer YousufAbstract:We describe here the synthesis of dihydropyrimidInes derivatives 3a-p, and evaluation of their α-glucosidase enzyme Inhibition activities. Compounds 3b (IC50=62.4±1.5 μM), 3c (IC50=25.3±1.26 μM), 3d (IC50=12.4±0.15 μM), 3e (IC50=22.9±0.25 μM), 3g (IC50=23.8±0.17 μM), 3h (IC50=163.3±5.1 μM), 3i (IC50=30.6±0.6 μM), 3m (IC50=26.4±0.34 μM), and 3o (IC50=136.1±6.63 μM) were found to be potent α-glucosidase Inhibitors In comparison to the standard drug acarbose (IC50=840±1.73 μM). The compounds were also evaluated for their In vitro cytotoxic activity agaInst PC-3, HeLa, and MCF-3 cancer cell lInes, and 3T3 mouse fibroblast cell lIne. All compounds were found to be non cytotoxic, except compounds 3f and 3m (IC50=17.79±0.66-20.44±0.30 μM), which showed a weak cytotoxic activity agaInst the HeLa, and 3T3 cell lInes. In molecular dockIng simulation Study, all the compounds were docked Into the active site of the predicted homology model of α-glucosidase enzyme. From the dockIng result, it was observed that most of the synthesized compounds showed Interaction through carbonyl oxygen atom and polar phenyl rIng with active site residues of the enzyme.
