Functional implications of pH-induced conformational changes in the Sphingosine kinase 1

Gupta, Preeti; Khan, Faez Iqbal; Roy, Sonam; Anwar, Saleha; Dahiya, Rashmi; Alajmi, Mohamed F.; Hussain, Afzal; Rehman, Tabish; Lai, Dakun; Hassan, Md. Imtaiyaz

doi:10.1016/j.saa.2019.117453

Cited by 48 publications

(31 citation statements)

References 72 publications

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“…The standard phosphate curve was prepared as per the manufacturer's protocol to calculate the kinase activity in terms of inorganic phosphate released from ATP upon catalysis. Measurements in triplicates were performed as described [ 52 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of Potential Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase IV from Bioactive Phytoconstituents

Gupta

Khan

Fakhar

et al. 2020

Oxidative Medicine and Cellular Longevity

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Calcium/calmodulin-dependent protein kinase IV (CaMKIV) is an upstream regulator of CaMKK-CaMKIV signaling cascade that activates various transcription factors, thereby regulating several cellular activities including, neuronal communication and immune response. Owing to the abnormal expression in cancer and neurodegenerative diseases, the CaMKIV has been considered a potential drug target. In the present study, we checked the binding affinity of plant-derived natural compounds viz., quercetin, ellagic acid (EA), simvastatin, capsaicin, ursolic acid, DL-α-tocopherol acetate, and limonin towards CaMKIV. Molecular docking and fluorescence binding studies showed that EA and quercetin bind to the CaMKIV with a considerable affinity in comparison to other compounds. Enzyme inhibition assay revealed that both EA and quercetin inhibit CaMKIV activity with their IC50 values in the micromolar range. To get atomistic insights into the mode of interactions, inhibition mechanism, and the stability of the CaMKIV-ligand complex, a 100 ns MD simulation analysis was performed. Both EA and quercetin bind to the catalytically important residues of active site pocket of CaMKIV forming enough stabilizing interactions presumably inhibiting enzyme activity. Moreover, no significant structural change in the CaMKIV was observed upon binding of EA and quercetin. In conclusion, this study illustrates the application of phytoconstituents in the development of therapeutic molecules targeting CaMKIV having implications in cancer and neurodegenerative diseases after in vivo validation.

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Section: Methodsmentioning

confidence: 99%

Identification of Potential Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase IV from Bioactive Phytoconstituents

Gupta

Khan

Fakhar

et al. 2020

Oxidative Medicine and Cellular Longevity

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“…The computational strategies like virtual screening have been used widely as effective approaches in order to discover and develop new compounds. Previously, we have studied structural and conformational changes in SphK1 at different pH using various spectroscopic techniques and computational methods 78 . SphK1 maintains its secondary and tertiary structure in the pH range of 7.5-10.0.…”

Section: Discussionmentioning

confidence: 99%

Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer

Khan

Lai

Anwer

et al. 2019

Journal of Enzyme Inhibition and Medicinal Chemistry

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Sphingosine kinase 1 (SphK1) is a promising therapeutic target against several diseases including mammary cancer. The aim of present work is to identify a potent lead compound against breast cancer using ligand-based virtual screening, molecular docking, MD simulations, and the MMPBSA calculations. The LBVS in molecular and virtual libraries yielded 20,800 hits, which were reduced to 621 by several parameters of drug-likeness, lead-likeness, and PAINS. Furthermore, 55 compounds were selected by ADMET descriptors carried forward for molecular interaction studies with SphK1. The binding energy (DG) of three screened compounds namely ZINC06823429 (-11.36 kcal/mol), ZINC95421501 (-11.29 kcal/mol), and ZINC95421070 (-11.26 kcal/mol) exhibited stronger than standard drug PF-543 (-9.9 kcal/mol). Finally, it was observed that the ZINC06823429 binds tightly to catalytic site of SphK1 and remain stable during MD simulations. This study provides a significant understanding of SphK1 inhibitors that can be used in the development of potential therapeutics against breast cancer.

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“…The charges on Agp2, PAiRFP1, and PAiRFP2 molecules were neutralized by addition of Na + and Cl − ions using gmx genion module to maintain neutrality, preserving a physiological concentration (0.15 M). The detailed methodology used to analyze the trajectories has been described in our previous communications [ 51 , 53 , 54 , 55 ]. All graphical presentations of the 3D models were prepared using PyMOL and VMD (Visual Molecular Dynamics) [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

“…The structural features and conformational profiles of a protein can be obtained by Gibbs free energy landscape using conformational sampling methods [ 55 ]. The structural information and conformations profiles attained by MD simulations are used for further analysis.…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2

et al. 2020

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Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of Agrobacterium tumefaciens C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm2) and PAiRFP2 (726.74 nm2) when compared with Agp2 (535.79 nm2). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.

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Functional implications of pH-induced conformational changes in the Sphingosine kinase 1

Cited by 48 publications

References 72 publications

Identification of Potential Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase IV from Bioactive Phytoconstituents

Identification of Potential Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase IV from Bioactive Phytoconstituents

Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer

Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2

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