Evaluation of binding and inhibition mechanism of dietary phytochemicals with sphingosine kinase 1: Towards targeted anticancer therapy

AbstractSphingosine kinase 1 (SphK1) has recently gained attention as a potential drug target for its association with cancer and other inflammatory diseases. Here, we have investigated the binding affinity of dietary phytochemicals viz., ursolic acid, capsaicin, DL-α tocopherol acetate, quercetin, vanillin, citral, limonin and simvastatin with the SphK1. Docking studies revealed that all these compounds bind to the SphK1 with varying affinities. Fluorescence binding and isothermal titration calorimetric measurements suggested that quercetin and capsaicin bind to SphK1 with an excellent affinity, and significantly inhibits its activity with an admirable IC50 values. The binding mechanism of quercetin was assessed by docking and molecular dynamics simulation studies for 100 ns in detail. We found that quercetin acts as a lipid substrate competitive inhibitor, and it interacts with important residues of active-site pocket through hydrogen bonds and other non-covalent interactions. Quercetin forms a stable complex with SphK1 without inducing any significant conformational changes in the protein structure. In conclusion, we infer that quercetin and capsaicin provide a chemical scaffold to develop potent and selective inhibitors of SphK1 after required modifications for the clinical management of cancer.

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Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy

Molecules ◽

10.3390/molecules24244589 ◽

2019 ◽

Vol 24 (24) ◽

pp. 4589 ◽

Cited By ~ 13

Author(s):

Taj Mohammad ◽

Sagar Batra ◽

Rashmi Dahiya ◽

Mohammad Hassan Baig ◽

Irfan Ahmad Rather ◽

...

Keyword(s):

Cancer Progression ◽

Conformational Changes ◽

Interaction Analysis ◽

Interaction Mechanism ◽

Structural Similarity ◽

Docking Studies ◽

Dynamics Simulation ◽

Cyclin Dependent Kinase ◽

Pubchem Database ◽

Cycle Regulation

Cyclin-dependent kinase 2 (CDK2) is an essential protein kinase involved in the cell cycle regulation. The abnormal activity of CDK2 is associated with cancer progression and metastasis. Here, we have performed structure-based virtual screening of the PubChem database to identify potent CDK2 inhibitors. First, we retrieved all compounds from the PubChem database having at least 90% structural similarity with the known CDK2 inhibitors. The selected compounds were subjected to structure-based molecular docking studies to investigate their pattern of interaction and estimate their binding affinities with CDK2. Selected compounds were further filtered out based on their physicochemical and ADMET properties. Detailed interaction analysis revealed that selected compounds interact with the functionally important residues of the active site pocket of CDK2. All-atom molecular dynamics simulation was performed to evaluate conformational changes, stability and the interaction mechanism of CDK2 in-complex with the selected compound. We found that binding of 6-N,6-N-dimethyl-9-(2-phenylethyl)purine-2,6-diamine stabilizes the structure of CDK2 and causes minimal conformational change. Finally, we suggest that the compound (PubChem ID 101874157) would be a promising scaffold to be further exploited as a potential inhibitor of CDK2 for therapeutic management of cancer after required validation.

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Design and Development of Novel Urea, Sulfonyltriurea, and Sulfonamide Derivatives as Potential Inhibitors of Sphingosine Kinase 1

Pharmaceuticals ◽

10.3390/ph13060118 ◽

2020 ◽

Vol 13 (6) ◽

pp. 118

Author(s):

Sonam Roy ◽

Amarjyoti Das Mahapatra ◽

Taj Mohammad ◽

Preeti Gupta ◽

Mohamed F. Alajmi ◽

...

Keyword(s):

Binding Affinity ◽

Drug Targets ◽

Inflammatory Diseases ◽

Cancer Therapeutics ◽

Sphingosine Kinase ◽

Binding Pocket ◽

Van Der Waals Interactions ◽

Titration Calorimetry ◽

Sphingosine Kinase 1

Sphingosine kinase 1 (SphK1) is one of the well-studied drug targets for cancer and inflammatory diseases. Recently discovered small-molecule inhibitors of SphK1 have been recommended in cancer therapeutics; however, selectivity and potency of first-generation inhibitors are great challenge. In search of effective SphK1 inhibitors, a set of small molecules have been designed and synthesized bearing urea, sulfonylurea, sulfonamide, and sulfonyltriurea groups. The binding affinity of these inhibitors was measured by fluorescence-binding assay and isothermal titration calorimetry. Compounds 1, 5, 6, and 7 showed an admirable binding affinity to the SphK1 in the sub-micromolar range and significantly inhibited SphK1 activity with admirable IC50 values. Molecular docking studies revealed that these compounds fit well into the sphingosine binding pocket of SphK1 and formed significant number of hydrogen bonds and van der Waals interactions. These molecules may be exploited as potent and selective inhibitors of SphK1 that could be implicated in cancer therapeutics after the required in vivo validation.

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4-Aminocoumarin based Aroylthioureas as Potential Jack Bean Urease Inhibitors; Synthesis, Enzyme Inhibitory Kinetics and Docking Studies

Medicinal Chemistry ◽

10.2174/1573406415666190715164834 ◽

2020 ◽

Vol 16 (2) ◽

pp. 229-243 ◽

Cited By ~ 1

Author(s):

Tanzeela A. Fattah ◽

Aamer Saeed ◽

Zaman Ashraf ◽

Qamar Abbas ◽

Pervaiz A. Channar ◽

...

Keyword(s):

Radical Scavenging ◽

Docking Studies ◽

Target Protein ◽

Dynamics Simulation ◽

Stable Complex ◽

Urease Inhibitors ◽

Jack Bean Urease ◽

Thiourea Derivatives ◽

Jack Bean ◽

Urease Enzyme

Background: Urease enzyme catalyzes the hydrolysis of urea into ammonia and CO2, excess ammonia causes global warming and crop reduction. Ureases are also responsible for certain human diseases such as stomach cancer, peptic ulceration, pyelonephritis, and kidney stones. New urease inhibitors are developed to get rid of such problems. Objective: This article describes the synthesis of a series of novel 1-aroyl-3-(2-oxo-2H-chromen-4- yl)thiourea derivatives (5a-j) as Jack bean urease inhibitors. Methods: Freshly prepared aryl isothiocyanates were reacted with 4-aminocoumarin in the same pot in an anhydrous medium of acetone. The structures of the title thioureas (5a-j) were ascertained by their spectroscopic data. The inhibitory effects against jack bean urease were determined. Results: It was found that compounds 5i and 5j showed excellent activity with IC50 values 0.0065 and 0.0293, µM respectively. Compound 5i bearing 4-methyl substituted phenyl ring plays a vital role in enzyme inhibitory activity. The kinetic mechanism analyzed by Lineweavere-Burk plots revealed that compound 5i inhibits the enzyme non-competitively. The Michaelis-Menten constant Km and inhibition constants Ki calculated from Lineweavere-Burk plots for compound 5i are 4.155mM and 0.00032µM, respectively. The antioxidant activity results displayed that compound 5j showed excellent radical scavenging activity. The cytotoxic effects determined against brine shrimp assay showed that all of the synthesized compounds are non-toxic to shrimp larvae. Molecular docking studies were performed against target protein (PDBID 4H9M) and it was determined that most of the synthesized compounds exhibited good binding affinity with the target protein. Molecular dynamics simulation (MDS) results revealed that compound 5i forms a stable complex with target protein showing little fluctuation. Conclusion: Based upon our investigations, it is proposed that 5i derivative may serve as a lead structure for devising more potent urease inhibitors.

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Transcriptional Regulation of Sphingosine Kinase 1

Cells ◽

10.3390/cells9112437 ◽

2020 ◽

Vol 9 (11) ◽

pp. 2437

Author(s):

Joseph Bonica ◽

Cungui Mao ◽

Lina M. Obeid ◽

Yusuf A. Hannun

Keyword(s):

Transcriptional Regulation ◽

Inflammatory Diseases ◽

Second Messengers ◽

Sphingosine Kinase ◽

Transcriptional Level ◽

Sphingosine Kinase 1 ◽

Micro Rnas ◽

Sphingosine 1 Phosphate ◽

Sphingosine Kinases ◽

Expression And Activity

Once thought to be primarily structural in nature, sphingolipids have become increasingly appreciated as second messengers in a wide array of signaling pathways. Sphingosine kinase 1, or SK1, is one of two sphingosine kinases that phosphorylate sphingosine into sphingosine-1-phosphate (S1P). S1P is generally pro-inflammatory, pro-angiogenic, immunomodulatory, and pro-survival; therefore, high SK1 expression and activity have been associated with certain inflammatory diseases and cancer. It is thus important to develop an understanding of the regulation of SK1 expression and activity. In this review, we explore the current literature on SK1 transcriptional regulation, illustrating a complex system of transcription factors, cytokines, and even micro-RNAs (miRNAs) on the post transcriptional level.

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

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy ◽

10.1016/j.saa.2019.117453 ◽

2020 ◽

Vol 225 ◽

pp. 117453 ◽

Cited By ~ 19

Author(s):

Preeti Gupta ◽

Faez Iqbal Khan ◽

Sonam Roy ◽

Saleha Anwar ◽

Rashmi Dahiya ◽

...

Keyword(s):

Conformational Changes ◽

Sphingosine Kinase ◽

Sphingosine Kinase 1 ◽

Functional Implications

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Kelch-like protein 5-mediated ubiquitination of lysine 183 promotes proteasomal degradation of sphingosine kinase 1

Biochemical Journal ◽

10.1042/bcj20190245 ◽

2019 ◽

Vol 476 (21) ◽

pp. 3211-3226 ◽

Cited By ~ 5

Author(s):

Jason A. Powell ◽

Melissa R. Pitman ◽

Julia R. Zebol ◽

Paul A.B. Moretti ◽

Heidi A. Neubauer ◽

...

Keyword(s):

Ubiquitin Ligase ◽

Conformational Changes ◽

Protein Turnover ◽

Expression System ◽

Proteasome Inhibitors ◽

Sphingosine Kinase ◽

Proteasomal Degradation ◽

Dominant Negative ◽

Sphingosine Kinase 1 ◽

Ubiquitin Ligase Complex

Sphingosine kinase 1 (SK1) is a signalling enzyme that catalyses the phosphorylation of sphingosine to generate the bioactive lipid sphingosine 1-phosphate (S1P). A number of SK1 inhibitors and chemotherapeutics can induce the degradation of SK1, with the loss of this pro-survival enzyme shown to significantly contribute to the anti-cancer properties of these agents. Here we define the mechanistic basis for this degradation of SK1 in response to SK1 inhibitors, chemotherapeutics, and in natural protein turnover. Using an inducible SK1 expression system that enables the degradation of pre-formed SK1 to be assessed independent of transcriptional or translational effects, we found that SK1 was degraded primarily by the proteasome since several proteasome inhibitors blocked SK1 degradation, while lysosome, cathepsin B or pan caspase inhibitors had no effect. Importantly, we demonstrate that this proteasomal degradation of SK1 was enabled by its ubiquitination at Lys183 that appears facilitated by SK1 inhibitor-induced conformational changes in the structure of SK1 around this residue. Furthermore, using yeast two-hybrid screening, we identified Kelch-like protein 5 (KLHL5) as an important protein adaptor linking SK1 to the cullin 3 (Cul3) ubiquitin ligase complex. Notably, knockdown of KLHL5 or Cul3, use of a cullin inhibitor or a dominant-negative Cul3 all attenuated SK1 degradation. Collectively this data demonstrates the KLHL5/Cul3-based E3 ubiquitin ligase complex is important for regulation of SK1 protein stability via Lys183 ubiquitination, in response to SK1 inhibitors, chemotherapy and for normal SK1 protein turnover.

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Investigating the binding mechanism of sphingosine kinase 1/2 inhibitors: Insights into subtype selectivity by homology modeling, molecular dynamics simulation and free energy calculation studies

Journal of Molecular Structure ◽

10.1016/j.molstruc.2020.127900 ◽

2020 ◽

Vol 1208 ◽

pp. 127900

Author(s):

Jinmiao Zhang ◽

Maoyu Zhang ◽

Jinying Yu ◽

Yanguo Shang ◽

Kaixuan Jiang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Sphingosine Kinase ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Sphingosine Kinase 1 ◽

Binding Mechanism ◽

Subtype Selectivity

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Analysis of small molecules against the NMDA receptor: an insight from virtual screening and molecular dynamics simulation based findings

10.21203/rs.3.rs-568180/v1 ◽

2021 ◽

Author(s):

Garima Sharma ◽

Rohit Shukla ◽

Tiratha Raj Singh

Keyword(s):

Neurodegenerative Disorder ◽

Docking Studies ◽

Dynamics Simulation ◽

Death Process ◽

Stable Complex ◽

Web Based ◽

Simulation Based ◽

Cell Death Process ◽

Experimental Validations ◽

Result Analysis

Abstract Alzheimer’s disease (AD) is a chronic intensifying neurodegenerative disorder and accounts for three-fourths of dementia cases. To date, there is no effective treatment available which can completely cure AD. The available medications can slower AD progression and can provide symptomatic relaxation. The N-methyl-d-aspartate receptor (NMDAR) plays a paramount role in the survival of neurons and synaptic plasticity. Although, excessive function of NMDAR cause excitotoxicity. Due to this the cell death process activated resulting into neurodegeneration and promotes AD. Hence in this study, we have screened 98,072 natural compounds by using Smina and idock. After that 154 compounds were selected and ADMET is predicted by using the pkCSM web-based server. From the ADMET analysis, 18 compounds were chosen and employed for the re-docking studies by using Autodock Vina. Then from the docking result, we have selected top three complexes (NMDAR-ZINC4258884, NMDAR-ZINC8635472, and NMDAR-ZINC15675934) and employed them for the 100 ns MDS studies. Based on MDS result analysis we have concluded that NMDAR-ZINC4258884 and NMDAR-ZINC15675934 are the best stable complex and can function as a lead compound against the NMDAR. Although this is a theoretical study while we have shortlisted only two compounds out of 98072 compounds and proposed them to the scientific community worldwide for further experimental validations.

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