scholarly journals Study on the influence of G82S RAGE polymorphism on RAGE-Amyloid interaction in AD pathology

2019 ◽  
Author(s):  
Rani Cathrine. C ◽  
Bincy Lukose ◽  
P. Rani
Keyword(s):  
Cell Line ◽  
Binding Affinity ◽  
Structural Changes ◽  
Md Simulations ◽  
Binding Pocket ◽  
Enhanced Expression ◽  
Shsy5y Cell ◽  
High Affinity Receptor ◽  
Aβ42 Peptide

AbstractReceptor for advanced glycation end products (RAGE) has been implicated in the pathophysiology of AD due to its ability to bind amyloid-beta and mediate inflammatory response. G82S RAGE polymorphism is associated with AD but the molecular mechanism for this association is not understood. Our previous in silico study indicated a higher binding affinity for mutated G82S RAGE, which could be caused due to changes in N linked glycosylation at residue N81. To confirm this hypothesis, in the present study molecular dynamics (MD) simulations were used to simulate the wild type (WT) and G82S glycosylated structures of RAGE to identify the global structural changes and to find the binding efficiency with Aβ42 peptide. Binding pocket analysis of the MD trajectory showed that cavity/binding pocket in mutant G82S glycosylated RAGE variants is more exposed and accessible to external ligands compared to WT RAGE, which can enhance the affinity of RAGE for Aβ. To validate the above concept, an in vitro binding study was carried using SHSY5Y cell line expressing recombinant WT and mutated RAGE variant individually to which HiLyte Fluor labeled Aβ42 was incubated at different concentrations. Saturated binding kinetics method was adopted to determine the Kd values for Aβ42 binding to RAGE. The Kd value for Aβ42-WT and Aβ42-mutant RAGE binding were 92±40 nM (95% CI-52 to 152nM; R2-0.92) and 45±20 nM (95% CI −29 to 64nM; R2-0.93), respectively. The Kd value of <100nM observed for both variants implicates RAGE as a high-affinity receptor for Aβ42 and mutant RAGE has higher affinity compared to WT. The alteration in binding affinity is responsible for activation of the inflammatory pathway as implicated by enhanced expression of TNFα and IL6 in mutant RAGE expressing cell line which gives a mechanistic view for the G82S RAGE association with AD.

Potent Anticancer Activities of Beauvericin against KB cells In Vitro by Inhibiting the Expression of ACAT1 and Exploring Binding Affinity

2021 ◽  
Vol 21 ◽  
Author(s):  
Haiming Zhou ◽  
Jing Zhang ◽  
Xiaoqing Chen ◽  
Shili Guo ◽  
Huimei Lin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Cell Line ◽  
Binding Affinity ◽  
X Ray Diffraction ◽  
Kb Cells ◽  
Anticancer Activities ◽  
Monoclinic Crystal ◽  
X Ray ◽  
Multiple Tumor

Background and Objective: Beauvericin (BEA), a cyclic hexadepsipeptide mycotoxin, is a potent inhibitor of the acyl-CoA: cholesterol acyltransferase enzyme 1 (ACAT1) which involved in multiple tumor-correlated pathways. However, the binding mechanisms between BEA and ACAT1 were not elucidated. Methods: BEA was purified from a mangrove entophytic Fusarium sp. KL11. Single-crystal X-ray diffraction was used to determine the structure of BEA. Wound healing assays of BEA against KB cell line and MDA-MB-231 cell line were evaluated. Inhibitory potency of BEA against ACAT1 was determined by ELISA assays. Molecular docking was carried out to illuminate the bonding mechanism between BEA and ACAT1. Results: The structure of BEA was confirmed by X-ray diffraction, indicating a monoclinic crystal system with P21 space group (α = 90°, β = 92.2216(9)o, γ= 90o). BEA displayed migration-inhibitory activities against KB cells and MDA-MB-231 cells in vitro. ELISA assays revealed the protein expression level of ACAT1 in KB cells was significantly decreased after BEA treatment (P ＜0.05). Molecular docking demonstrated that BEA formed hydrogen bond with His425 and pi-pi staking with Tyr429 in ACAT1. Conclusions: BEA sufficiently inhibited the proliferation and migration of KB cells and MDA-MB-231 cells by downregulating ACAT1 expression. In addition, BEA potentially possessed a strong binding affinity with ACAT1. BEA may serve as a potential lead compound for the development of a new ACAT1-targeted anticancer drug.

scholarly journals SUSTAINED RELEASE TABLETS OF SORAFENIB-SILIBININ COMBINATIONS FOR THE TREATMENT OF HEPATOCELLULAR CARCINOMA

2018 ◽  
Vol 10 (5) ◽  
pp. 117
Author(s):  
Savita Mishra ◽  
Sandhya Hora ◽  
Vibha Shukla ◽  
Mukul Das ◽  
Harsha Kharkwal ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Drug Release ◽  
Sustained Release ◽  
Cell Line ◽  
Binding Affinity ◽  
Drug Combination ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Weight Variation

Objective: The aim of this study was to develop polymer coated sustained release tablet using sorafenib and silibinin combination for the treatment of hepatocellular carcinoma.Methods: The qualitative analysis such as weight variation, friability, hardness, interaction studies, disintegration and in vitro release were performed to validate formulated tablets. We have maintained the acceptable official limits for weight variation, friability, hardness and disintegration time according to prescribed pharmacopoeial recommendation. In vitro drug release studies were performed using USP-II (paddle type) dissolution apparatus. The MTT assay was performed for assessment of Cell viability of drug combination for tablet formulation. Molecular docking studies have been performed to determine the combinatorial mode of action for the tablet formulation.Results: Friability and weight variation were less than 1% for each formulation, which were within range of prescribed pharmacopoeial recommendation. The hardness of 20 tablets showed 5-6.5Kg/cm2 for all formulations 5-6.5Kg/cm2. The optimized formulation resulted in 98% drug release after 28 h. The present study reports the synergistic effects of drug combination to inhibit cell growth in HepG2 cell line. Molecular docking studies showed that sorafenib has high binding affinity for B-Raf vascular endothelial growth factor receptor β and protein kinase B. Silibinin showed binding affinity with MAP kinase-11, protein phosphatase 2 A and tankyrase.Conclusion: The present study reports for the first time a novel formulation for sustained release and reduced toxicity of sorafenib with enhanced inhibitory effect of the drug combination on cancerous hepatic cell line as well collaborative mechanism of action for the formulation.

scholarly journals OR24-01 Mutational Study of the GPR119 Receptor Binding Site

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Matthew D Rosales ◽  
Frank Dean ◽  
Evangelia Kotsikorou
Keyword(s):  
Hydrogen Bonding ◽  
Binding Site ◽  
Specific Activity ◽  
Md Simulations ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Receptor Model ◽  
Wild Type

Abstract The GPR119 receptor, a class A G-protein coupled receptor located in the pancreatic β cells, induces insulin production when activated. Due to its specific activity, the pharmaceutical industry has identified GPR119 as a target for the treatment for type 2 diabetes. The lack of a GRP119 crystal structure has hindered the study of the receptor so our laboratory developed GPR119 active and inactive homology models. Docking studies with the inactive receptor model indicated that two leucine residues facing the binding pocket, L5.43(169) and L6.52(242), may be involved in ligand activation. Additionally, a serine at the extracellular end of the pocket, S1.32(4), may help orient of the ligand in the binding pocket via hydrogen bonding. To gain further insight into the role of these residues and the receptor activation mechanism, molecular dynamics (MD) simulations and in vitro cAMP assays of the wild type and mutant receptors were employed. The software NAMD employing the CHARMM force field was used to carry out MD simulations of the active receptor model bound with the agonist AR231453 embedded in a hydrated lipid bilayer. Preliminary results indicate that L6.52(242), located on transmembrane helix (TMH) 6, does not face directly into the binding site and does not interact with the ligand, while L5.43(169), located on TMH5, does face into the binding site, potentially interacting directly with the ligand. Also, S1.32(4), because of its extracellular location, is solvated instead of interacting with the ligand. The in vitro studies overall support the MD simulations. The mutations L6.52(242)M and L6.52(242)A appear to have minimal to no effect on agonist-induced cAMP production, compared to the wild type. In contrast, the L5.43(169)M and L5.43(169)A mutations decrease the potency of activation by AR231453, indicating that L5.43(169) changes the shape of the binding pocket, affecting ligand binding and activation. Finally, the cAMP assays show that the S1.32(4)A mutant also shows decreased activity compared to the wild type, implying that the ligand may be losing a hydrogen bonding interaction when S1.32(4) is mutated to alanine.

scholarly journals Effect of identified non-synonymous mutations in DPP4 receptor binding residues among highly exposed human population in Morocco to MERS-CoV through computational approach

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258750
Author(s):  
Anass Abbad ◽  
Latifa Anga ◽  
Abdellah Faouzi ◽  
Nadia Iounes ◽  
Jalal Nourlil
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Md Simulation ◽  
Structural Changes ◽  
Computational Approach ◽  
Dipeptidyl Peptidase 4 ◽  
Synonymous Mutations ◽  
Binding Residues ◽  
Cellular Entry

Dipeptidyl peptidase 4 (DPP4) has been identified as the main receptor of MERS-CoV facilitating its cellular entry and enhancing its viral replication upon the emergence of this novel coronavirus. DPP4 receptor is highly conserved among many species, but the genetic variability among direct binding residues to MERS-CoV restrained its cellular tropism to humans, camels and bats. The occurrence of natural polymorphisms in human DPP4 binding residues is not well characterized. Therefore, we aimed to assess the presence of potential mutations in DPP4 receptor binding domain (RBD) among a population highly exposed to MERS-CoV in Morocco and predict their effect on DPP4 –MERS-CoV binding affinity through a computational approach. DPP4 synonymous and non-synonymous mutations were identified by sanger sequencing, and their effect were modelled by mutation prediction tools, docking and molecular dynamics (MD) simulation to evaluate structural changes in human DPP4 protein bound to MERS-CoV S1 RBD protein. We identified eight mutations, two synonymous mutations (A291 =, R317 =) and six non-synonymous mutations (N229I, K267E, K267N, T288P, L294V, I295L). Through docking and MD simulation techniques, the chimeric DPP4 –MERS-CoV S1 RBD protein complex models carrying one of the identified non-synonymous mutations sustained a stable binding affinity for the complex that might lead to a robust cellular attachment of MERS-CoV except for the DPP4 N229I mutation. The latter is notable for a loss of binding affinity of DPP4 with MERS-CoV S1 RBD that might affect negatively on cellular entry of the virus. It is important to confirm our molecular modelling prediction with in-vitro studies to acquire a broader overview of the effect of these identified mutations.

scholarly journals In silico, in vitro: antioxidant and antihepatotoxic activity of gnetol from Gnetum ula Brongn

Bioimpacts ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 239-249 ◽  
Author(s):  
Preetham Jinadatta ◽  
Sharath Rajshekarappa ◽  
Kiran Sundera Raja Rao ◽  
Sujan Ganapathy Pasura Subbaiah ◽  
Sudhesh Shastri
Keyword(s):  
Antioxidant Activity ◽  
Cell Line ◽  
Binding Affinity ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Reducing Power ◽  
Column Fraction ◽  
Fourth Column ◽  
Isolated Compound

Introduction: Gnetum ula is a notable medicinal plant used to cure various ailments. The stem part of the plant is used traditionally to treat jaundice and other disorders. The present work is to investigate the in vitro hepatoprotective and antioxidant activity of ethanol extract of stem of G. ula (GUE) and its isolated compound gnetol. Methods: Column chromatography was carried out for GUE and various column fractions were obtained. DPPH and reducing power assays were performed for GUE and column fractions. The potent fraction was characterized, interpreted and tested for in vitro hepatoprotective activity on the BRL3A cell line. In silico docking studies of gnetol compound on the protein TGF-β (transforming growth factor – β) and Peroxisome proliferator-activated receptor α (PPARα) was carried out. Results: DPPH scavenging and reducing power assay showed that the fourth column fraction has antioxidant potential than other fractions. The fourth column fraction was characterized to obtain gnetol compound. BRL3A cell line was used for the toxicity study of GUE and gnetol. Both, the extract and the isolated compound were found to be nontoxic with CTC50 value more than 1000 µg/mL. At the concentration of 200 µg/mL, GUE and gnetol offered cell protection of 50.2% and 54.3%, however, silymarin showed 77.15% protection at 200 µg/mL concentration against CCl4 treated BRL3A cell line. The docking results of the ligand molecule TGF-β showed that gnetol has the binding affinity of -7.0 and standard silymarin being -6.8. TGF-β showed good hydrophobic interactions and formed two hydrogen bonds with the amino acids. For PPARα protein, gnetol showed the binding affinity of -8.4 and silymarin with -6.5. Hydrogen bonding and good hydrophobic interactions against the amino acid molecules in relation to the PPARα protein are shown. Conclusion: Gnetum ula stem extract and its isolated compound are safe and offered significant hepatoprotection against CCl4 induced toxicity. Isolated compound gnetol exhibited a potent antioxidant activity offering protection to liver damage. However, in vivo studies need to be carried out to validate the traditional use of G. ula.

scholarly journals Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2908 ◽  
Author(s):  
Preethi Seelam Prabhakar ◽  
Richard A. Manderville ◽  
Stacey D. Wetmore
Keyword(s):  
Binding Affinity ◽  
Structural Changes ◽  
Experimental Studies ◽  
Local Environment ◽  
Md Simulations ◽  
Fine Tuning ◽  
Dna Aptamer ◽  
Solvent Exposure ◽  
Chemically Modified ◽  
Target Binding

Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.

Synthesis of Dual Target CPT-Ala-Nor Conjugates and Their Biological Activity Evaluation

2019 ◽  
Vol 19 (4) ◽  
pp. 502-508 ◽  
Author(s):  
Chang K. Zhao ◽  
Lang Xu ◽  
Xian H. Wang ◽  
Yu J. Bao ◽  
Yuhe Wang
Keyword(s):  
Cell Growth ◽  
Cell Line ◽  
Binding Affinity ◽  
Cancer Cell ◽  
Protein Phosphatase ◽  
Cancer Cell Growth ◽  
Strong Activity ◽  
Target Drug ◽  
Dual Target

Background: Target therapy has been one of the important strategies in new drug discovery and the resulting drug resistance has also been a serious problem for concern. At the same time, there are several cancer genes or pathways operating within a given cancer. Given these two things, the combination therapy will be needed for optimal therapeutic effect. Objective: Camptothecin and norcantharidin were thus chosen to construct a dual anticancer drugs assemblies mainly because CPT was the DNA-topoisomerase I inhibitor and norcantharidin could also suppress the cancer cell growth by inhibiting protein phosphatase. The designed conjugate of camptothecin and norcantharidin linked by alanine was expected to have dual target drug properties. Methods: EDCI/DMAP was chosen as a coupling agent for the coupling of CPT with substituted norcantharidin derivatives and CCK-8 method was used to test the cytotoxicity and intensity on human hepatoma cell line HepG2. Two kinds of enzymes, Top I and CDC 25B were selected to screen the binding affinity in molecular level. Results: Nine of dual targets camptothecin derivatives were smoothly synthesized by twice coupling in the condition of EDCI/DMAP in moderate yield. All of the synthesized compounds were characterized by 1HNMR and 13CNMR spectrum and exhibited strong potent inhibition against Hep G2, SW480, BGC803, and PANC-1 cell line in vitro. The newly synthesized camptothecin compounds, such as 3j and 3i have strengthened inhibition activity compared to camptothecin and norcantharidin. Conclusion: We have successfully synthesized a series of novel camptothecin derivatives constructed from three components of camptothecin, alanine and norcantharidin. These compounds not only preserved strong activity against several cancer cell lines in vitro, but also exhibited potential binding affinity to target Top I and CDC 25B. Therefore, these conjugates linked by alanine could suppress cancer cell growth by inhibiting Top I and protein phosphatase simultaneously, which makes it much valuable as a novel bi-functional target drug candidate to develop in vivo.

scholarly journals The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

2021 ◽  
Vol 12 (15) ◽  
pp. 5555-5565
Author(s):  
Veronica Macaluso ◽  
Giacomo Salvadori ◽  
Lorenzo Cupellini ◽  
Benedetta Mennucci
Keyword(s):  
Structural Changes ◽  
Md Simulations ◽  
Binding Pocket ◽  
Computational Investigation ◽  
Signaling Mechanism

A combination of MD simulations and a polarizable QM/MM description of a bacteriophytochrome in solution reveals the changes in the chromophore-binding pocket and in the overall structure of the phytochrome involved in the signaling mechanism.

scholarly journals Tocilizumab (TCZ) Decreases Angiogenesis in Rheumatoid Arthritis through its Regulatory Effect on miR-146a-5p and EMMPRIN/CD147

2021 ◽  
Author(s):  
Devy Zisman ◽  
Mirna Safieh ◽  
Elina Simanovich ◽  
Joy Feld ◽  
Amalia Kinarty ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Tube Formation ◽  
Angiogenic Factors ◽  
Angiogenic Factor ◽  
Serum Samples ◽  
Expression Levels ◽  
Enhanced Expression

Abstract BackgroundAngiogenesis is an important contributor to the development of Rheumatoid arthritis (RA). Tocilizumab (TCZ), an anti-IL-6 receptor antibody, is used in the treatment of RA patients, and has been shown to exert anti-inflammatory effects. However, its effects on angiogenesis are not fully elucidated, and the molecular mechanisms regulating this effect are unknown. MethodsWe evaluated the concentrations of several pro- and anti-angiogenic factors and the expression levels of several microRNA molecules that are associated with RA and angiogenesis in serum samples obtained from 40 RA patients, before and 4 months after the initiation of TCZ treatment. Additionally, we used an in vitro co-culture system of fibroblasts (the HT1080 cell line) and monocytes (the U937 cell line) to explore the mechanisms of TCZ action. ResultsSerum samples from RA patients treated with TCZ exhibited reduced levels of EMMPRIN/CD147, enhanced expression of miR-146a-5p and miR-150-5p, and reduced angiogenesis as was manifested by the reduced number of tube-like structures formed by EaHy926 endothelial cell line. In vitro, the accumulation of the pro-angiogenic factors EMMRPIN, VEGF and MMP-9 in the supernatants was increased by co-culturing the HT1080 fibroblasts and the U937 monocytes, while the accumulation of the anti-angiogenic factor thrombospondin-1 (Tsp-1) and the expression levels of miR-146a-5p were reduced. Transfection of HT1080 cells with the miR-146a-5p mimic, decreased the accumulation of EMMPRIN, VEGF and MMP-9. When EMMPRIN was neutralized with a blocking antibody, supernatants derived from these co-cultures exhibited reduced migration, proliferation and tube formation in functional assays. ConclusionsOur findings implicate miR-146a-5p in the regulation of EMMPRIN and propose that TCZ affects angiogenesis through its effects on EMMRPIN and miR-146a-5p.

Sign in / Sign up

Export Citation Format

Share Document