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opencc-by-4.0Nov 2024View details →

The Ketogenic Diet Alters Microbiome-Metabolome Profiles and Enhances Therapeutic Efficacy in West Syndrome

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dryad28/100

Data from: An investigation of the therapeutic effects of statins with metformin on polycystic ovary syndrome: a meta-analysis of randomized controlled trials

Objectives: To investigate the therapeutic effects of statins with metformin on polycystic ovary syndrome (PCOS). Settings: Endocrinology department. Participants: MEDLINE, EMBASE and Cochrane Central Register of Controlled Trials were searched until October 2014. Studies comparing statins and placebo, as well as the combination of statins and metformin and metformin alone, were included in the analysis. Interventions: Data were independently extracted by two researchers; any convergence was resolved by a third reviewer. Primary and secondary outcome measures: The following properties were extracted from the qualified trials to identify the effects of statins: clinical variables, metabolic characteristics, hormone outcomes, sign of inflammation, glucose parameters and insulin outcomes. Results: Data from four trials comparing statin and metformin with metformin alone were analysed. The combination of statins and metformin decreases the levels of C reactive protein (standardised mean difference (SMD) −0.91; 95% CI −1.81 to −0.02; p=0.046), triglyceride (SMD −1.37; 95% CI −2.46 to −0.28; p=0.014), total cholesterol (SMD −1.28; 95% CI −1.59 to −0.97; p=0.000) and low-density lipoprotein (LDL) cholesterol (SMD −0.74; 95% CI −1.03 to −0.44; p=0.000). However, the combined therapy fails to reduce fasting insulin (SMD −0.92; 95% CI −2.07 to 0.24; p=0.120), homeostasis model assessment of insulin resistance (SMD −1.15; 95% CI −3.36 to 1.06; p=0.309) and total testosterone (SMD −1.12; 95% CI −2.29 to 0.05; p=0.061). Analysis of the five trials comparing statin with placebo shows that statin monotherapy reduces LDL-cholesterol, triglyceride and total cholesterol. Conclusions: Combined statin and metformin therapy can improve lipid and inflammation parameters, but cannot effectively improve insulin sensitivity and reduce hyperandrogenism in women with PCOS. A large-scale randomised controlled study must be conducted to ascertain the long-term effects of the therapy.

opencc-zeroDec 2014View details →

opencc-by-4.0Jul 2021View details →

Segregated Nanocompartments Containing Therapeutic Enzymes and Imaging Compounds within DNA-Zipped Polymersome Clusters for Advanced Nanotheranostic Platform

Data underlying the figures in the publication “Segregated Nanocompartments Containing Therapeutic Enzymes and Imaging Compounds within DNA-Zipped Polymersome Clusters for Advanced Nanotheranostic Platform”, published in Small, 2020, 16, 1906492. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201906492">https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201906492</a> Table of contents: 1. Figure 2; Zip file containing the numerical data for the graphs of Figure 2 (2c, 2e, 2g & 2i). 2. Figure 3; Zip file containing the numerical data for the graphs of Figure 3 (3a-d). 3. Figure 4; Zip file containing the numerical data for the graphs of Figure 4 (4a-d). 4. Figure 5; Zip file containing the CLSM microscopic images from four different locations of 488-633-Ncomp clusters attached to the surface (Figure 5a) and images of the merged DY-633 and Atto-488 channels of the four locations with colocalized regions appearing in white (Figure 5b). The dataset also includes the numerical data/images for the Figures S2, S3, S5, S7, S9, S10, S11, S13, S14 and S16-S22.

dryad28/100

Therapeutic genome screen in AsPC1

Pancreatic adenocarcinoma generally does not respond to our current therapeutic approaches of surgical resection, radiation and chemotherapy with an overall five-year survival of only 8%. In an effort to identify potential new therapeutic approaches for pancreatic cancer, we carried out a targeted synthetic lethal CRISPR screens in the pancreatic cell line AsPC1. A custom CRISPR knockout library, termed the Therapeutic Genome (RxG) Library, which targets genes for which a current drug already exists was utilized in the screens. We used the RxG library to identify genes and corresponding gene products which modulate the sensititive and resistance to three chemotherapeutics, Gemcitabine, 5-fluorouracil, and Niraparib in the AsPC1 cell line. This screen identified multiple gene products which potentiate sensitivity to these three chemotherapeutics, and in particular, BCL2L1 which encodes BCL-xL, was identified as a common genetic factor that when mutant, enhances sensitivity to all three drugs. A novel drug, DT2216, in Phase I clinical trials which targets BCL-xL for degradation was shown to enhance the effectiveness of Gemcitabine in additional pancreatic cancer cell lines as well as patient-derived xenograft models without enhanced systemic toxicity. This work supports a possible utility of combined Gemcitabine/DT2216 as a novel therapy for pancreatic cancer.

opencc-zeroOct 2021View details →

opencc-by-4.0May 2023View details →

BRD8 is a therapeutic vulnerability for overcoming resistance to dual ER/HER2 blockade therapy in HR+/HER2+ breast cancer

.rda file for Seurat object of scRNA-seq data from BT474 breast cancer cell lines treated with DMSO, Neratinib, Fulvestrant, and a combination of Neratinib and Fulvestrant.

opencc-by-4.0Mar 2023View details →

dataset for paper Toxicity Test of Propolis Product as Protective and Therapeutic Substance for Embryo of Chicken

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opencc-by-4.0Sep 2023View details →

data for the article In-Silico Exploration of Acyclovir Derivatives: Potential Therapeutic Candidates Against COVID-19 Through Molecular Docking Studies

Docking and Binding result as picture

opencc-by-4.0Nov 2024View details →

Therapeutic Potential of the Laminin-1-Derived Peptide C16 in Interactions with αvβ3 and α5β1 Integrins: In Silico Analysis and Implications for Angiogenesis, Cancer, and Tissue Regeneration

Molecular Dynamics Molecular Docking there has also been performed molecular dynamics simulation studies by GROMACS 2023 to study the relationship between structure and function and properties by the analysis of molecular conformation sampling (cluster analysis, dominant conformation identification), interaction analysis (hydrogen bonding network, Contact-Map, Binding free energy calculations (MM-PBSA), backbone fluctuation analysis (RMSD, RMSF), Conformational transition analysis (simple normal mode analysis, dominant conformation identification), and physicochemical property analysis (energy, volume, pressure, temperature, density monitoring) (Luzik et al., 2019; Zhang et al., 2003). For simulation purposes, a simulation system was set up for the protein-ligand complex with solvent using GPU-enabled GROMACS 2024.2 package (Abraham et al., 2024). The αvβ3 and α5β1 in water simulation were performed with GROMACS standard protocols also, αvβ3_S1@C16, αvβ3_S2@C16, α5β1@C16 complex, and αvβ3, αvβ3 proteins MD simulation was carried out in triplicate. All necessary topology files were generated using CHARMM-GUI (Lee et al., 2016; Park et al., 2023).  CHARMM-GUI was used to build the simulation system (Allouche, 2012). And provided scripts compatible with GROMACS  (Lee et al., 2016), provideding TIP3P water model to solvate the system. The dimensions of the box were defined by ensuring at least a 10 Å distance between the protein and the box edges to avoid boundary effects. Proper neutralization of the system was achieved by adding counterions (Na+ and Cl−) based on the protein’s charge automatically calculated by CHARMM-GUI. CHARMM36 force field was chosen, which provides parameters for proteins and peptides. Before the production MD simulation, energy minimization was performed to remove any unfavorable contacts or steric clashes in the system. CHARMM-GUI The system was equilibrated in two stages. First, the system was equilibrated under an NVT ensemble (constant number of particles, volume, and temperature) with restraints applied to the heavy atoms of the protein to allow the water and ions to relax around the solute. This phase runs for 100 ps. Second, the restraints were removed, and the system was equilibrated under an NPT ensemble (constant number of particles, pressure, and temperature) for an additional 1 ns to stabilize the density of the system (Galmozzi et al., 2014; K. W. Wang et al., 2022). The minimization, equilibration, and production steps were performed using the GROMACS 2024.2 The steepest-descent energy minimization was used, and the maximum force was set to 100 kJ/(mol∙nm) on any atom. The solvated system was equilibrated with two steps. First, the system was equilibrated for 1 ns under a constant volume ensemble (NVT) without restraints applied. Second, the system was equilibrated for another 1 ns under a constant pressure ensemble (NPT) without any restraint. Production simulation was conducted for 100 ns under the NPT ensemble. All bonds containing hydrogen atoms were constrained using the default LINCS constraint algorithm. The coupling algorithm of Nose-Hoover was used to maintain temperature (310 K) and Parrinello-Rahman algorithm to maintain temperature pressure (1 atm, 101 325 Pa) with a constant of 1.0 ps. The electrostatic interactions were treated with the particle mesh-Ewald (PME) method. The integration time step was set to 2 fs and periodic boundary conditions were applied in all directions (Bansal et al., 2021; H. Yu et al., 2015).  2.4.1. MMPBSA analyses  GROMACS modules gmx rms for root mean square deviation (RMSD), gmx rmsf for root mean square fluctuation (RMSF), gmx hbond for numbers of hydrogen-bond (Hbond), gmx gyrate for the radius of gyration (Rg), gmx sasa for solvent accessible surface area (SASA) were used to analyze each complex system. The xmgrace module was employed to generate plots and graphs to represent binding energies, interaction frequencies, and structural changes. The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) binding free energies like van der Waals and electrostatic interactions, potential energy, polar, and non-polar solvation energies were calculated by gmx_MMPBSA a tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files (Valdés-Tresanco et al., 2021). It has employed the visualization tools VMD and PyMOL to examine the trajectory and interaction details. References: Allouche, A. (2012). Software News and Updates Gabedit — A Graphical User Interface for Computational Chemistry Softwares. Journal of Computational Chemistry, 32, 174–182. https://doi.org/10.1002/jcc. Galmozzi, A., Dominguez, E., Cravatt, B. F., & Saez, E. (2014). CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. Methods Enzymol., 538(1), 151–169. Bansal, R., Mohagaonkar, S., Sen, A., Khanam, U., & Rathi, B. (2021). In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein. In Silico Pharmacology, 9(1), 1–14. https://doi.org/10.1007/s40203-021-00103-z. Park, S. J., Kern, N., Brown, T., Lee, J., & Im, W. (2023). CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation. Journal of Molecular Biology, 435(14), 167995. https://doi.org/10.1016/j.jmb.2023.167995. Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935.  Luzik, D. A., Rogacheva, O. N., Izmailov, S. A., Indeykina, M. I., Kononikhin, A. S., & Skrynnikov, N. R. (2019). Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Scientific Reports, 9(1), 1–18. https://doi.org/10.1038/s41598-019-56078-7. Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx\_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645. Wang, K. W., Lee, J., Zhang, H., Suh, D., & Im, W. (2022). CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. Journal of Physical Chemistry B, 126(38), 7354–7364. https://doi.org/10.1021/acs.jpcb.2c05294.  Yu, H., Wang, M. jun, Xuan, N. xia, Shang, Z. cai, & Wu, J. (2015). Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides. Journal of Zhejiang University: Science B, 16(10), 883–896. https://doi.org/10.1631/jzus.B1500106.  Zhang, Z., Shi, Y., & Liu, H. (2003). Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophysical Journal, 84(6), 3583–3593. https://doi.org/10.1016/S0006-3495(03)75090-5.

Home-based Therapeutic Drug Monitoring in Kidney Transplantation

ClinicalTrials.gov study NCT05005221. IPD Sharing: NO. Countries: 1. Publications: 0.

Observational Non-Interventional Study Of Febrile Neutropenia Patients To Evaluate Antibacterial Therapeutical Options

ClinicalTrials.gov study NCT00945555. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Evaluation of Therapeutic Adherence Among Patients Followed in the Department of Hereditary Metabolic Diseases at Necker Hospital

ClinicalTrials.gov study NCT07356557. IPD Sharing: NO. Countries: 1. Publications: 0.

Thrombo-inflammation in Acute Neurovascular Diseases: Definition of New Therapeutic Targets (TARGETS)

ClinicalTrials.gov study NCT07354321. IPD Sharing: UNDECIDED. Countries: 0. Publications: 15.

Study of the Safety of Therapeutic Treatment With an Immunomodulatory Agent (N-803) in Adults With COVID-19

ClinicalTrials.gov study NCT04385849. IPD Sharing: NO. Countries: 1. Publications: 0.

Brown Adipose Tissue as a Therapeutic for the Metabolic and Cardiac Dysfunction With Senescence (BATSR)

ClinicalTrials.gov study NCT04168580. IPD Sharing: NO. Countries: 1. Publications: 0.

Tolerability Study of a Novel Microbiome Therapeutic in Subjects With Gastroesophageal Reflux Disease

ClinicalTrials.gov study NCT04491734. IPD Sharing: NO. Countries: 1. Publications: 0.

Ginger's Therapeutic Potential in Asthma

ClinicalTrials.gov study NCT03705832. IPD Sharing: NO. Countries: 1. Publications: 0.

A Pilot Study of the Therapeutic Potential of Stem Cell Educator Therapy in Type 1 Diabetes

ClinicalTrials.gov study NCT02624804. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Therapeutic Hepatitis B Vaccine (Mimogen-based) Joint Entecavir in Treating Chronic Hepatitis B Patients

ClinicalTrials.gov study NCT01326546. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.

Innovative Digital Therapeutic for Smoking Cessation

ClinicalTrials.gov study NCT03694327. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Evaluation of Therapeutic Efficacy in Use of Chamomilla Gel, Chamomilla Infuse and Urea in Radiodermatitis

ClinicalTrials.gov study NCT02251392. IPD Sharing: Not stated. Countries: 0. Publications: 1.