Targeting protein dynamics in drug design
نویسنده
چکیده
The dynamic nature of protein structures provides challenges and opportunities for ligand design. I will first discuss some of the different ways in which protein dynamics can be targeted, giving examples from our experience in the design of inhibitors of thymidylate synthase [1-3]. I will then describe the development of a computational toolbox (TRAPP: TRAnsient Pockets in Proteins) to identify and visualize transient pockets in proteins that may be exploited in ligand design.
منابع مشابه
In Silico Design and Verification of LAMP-BDNF Chimeric Protein for Presentation of BDNF on the Surface of Exosomes for Drug Delivery Through Blood-Brain Barrier
Background and purpose: The mature form of brain-derived neurotrophic factor (BDNF) binds to BDNF/NT-3 growth factors receptor (Trk-B). This binding leads to activation of Ras–MAPK pathway which is integrated with cell growth and proliferation. The BDNF deficiency is correlated with various diseases and affects aging and miscellaneous. In the present study we aimed to design a chimeric LAMP-BDN...
متن کاملMolecular Docking Based on Virtual Screening, Molecular Dynamics and Atoms in Molecules Studies to Identify the Potential Human Epidermal Receptor 2 Intracellular Domain Inhibitors
Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...
متن کاملIn vitro study of drug-protein interaction using electronic absorption, fluorescence, and circular dichroism spectroscopy
In the near future, design of a new generation of drugs targeting proteins will be required. Considering the complex bond between the drug and protein, the structure and stability of the target protein should be considered. So far, a series of in vitro investigations have been conducted with the aim of predicting drug-biological medium interactions. In these studies, use of spectroscopic method...
متن کاملHow Do Palladium Complexes Affect on Coil Structure of Human Serum Albumin in the Presence of Carbon Nanotube? A Molecular Dynamics Study
To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin, three anti-cancer drugs ([Pd(phen)(R-gly)]NO3, R = methyl, propyl and amyl) with different hydrophobic tails and anticancer activities were selected. These drugs have better anti-tumor activity and less side effects than that known cis-platinum drug. Human serum albumin is also ...
متن کاملDopamine-conjugated apoferritin protein nanocage for the dual-targeting delivery of epirubicin
Objective(s): Nanocarriers are drug delivery vehicles, which have attracted the attention of researchers in recent years, particularly in cancer treatment. The encapsulation of anticancer drugs using protein nanocages is considered to be an optimal approach to reducing drug side-effects and increasing the bioavailability of anticancer drugs. Epirubicin (EPR) is an active chemotherapeutic medica...
متن کاملIsothermal Titration Calorimetry and Molecular Dynamics Simulation Studies on the Binding of Indometacin with Human Serum Albumin
Human serum albumin (HSA) is the most abundant protein in the blood plasma. Drug binding to HSA is crucial to study the absorption, distribution, metabolism, efficiency and bioavailability of drug molecules. In this study, isothermal titration calorimetry and molecular dynamics simulation of HSA and its complex with indometacin (IM) were performed to investigate thermodynamics parameters and th...
متن کامل