The Molecular Mechanism Of The Interactions Between Gold Clusters And Cancer Related Cysteine Proteases

Cysteine proteases(EC 3.4.22),also known as thiol proteases are named for their catalytically active sites contain a cysteine residue(Cys).Among them,the largest family is the papain-like cysteine proteases superfamily including papain,cathepsin B,H,K and so on.Cathepsin B(CB)activity is up-regulated and over-expressed in cancer making it an ideal marker for cancer.Overexpression of CB activity accelerates the degradation of extracellular matrix and basement membrane components which contribute to the invasion and metastasis of cancer cells.Thus CB is an important indicator of cancer diagnosis,treatment and prognosis assessment.Inhibiting protease activity is helpful to cancer treatment.Recent studies have found that peptide-coated gold clusters(AuPCs)can inhibit cysteine proteases activities targeted and induce tumor cell apoptosis.However,detailed interaction mechanism and binding sites between gold clusters and these proteases are still lacking.It's difficult to determine the specific binding sites information experimentally.The binding sites and interaction mechanism play major roles in the process of ligand binding to protein receptor.Therefore,determining the binding sites and interaction mechanism are critical to drug design and have become the bottleneck of targeted nano drug design.In this thesis,molecular docking and molecular dynamics simulations were used to study the interaction mechanism between gold cluster and papain-like cysteine proteases.The work of this dissertation mainly consists of two aspects.Firstly,gold cluster model targeted cysteine proteases was constructed.The molecular docking software AutoDock Vina and ZDOCK and the molecular dynamics simulation software NAMD2 were used to study the relationship between AuPC and target protein CB.The binding sites and interaction mechanism were used to verify the binding stability.Then,the binding sites of the surrogate enzyme papain and AuPC were studied using replica exchange molecular dynamics(REMD)accelerated sampling method.Gold cluster mainly bind to the target protein through electrostatic interactions and hydrophobic interactions.The charged amino acid and hydrophobic amino acid play key roles in the binding process.Through the analysis of binding energy and binding sites,we found that AuPC could bind to the papain-like cysteine protease and inhibit proteases activities.Due to the presence of an occluding loop of cathepsin B,its binding stability was weaker than papain.Further analysis revealed that gold cluster bind to proteases mainly through hydrogen bonds,salt bridges and hydrophobic interactions.Electrostatic effects played a crucial role in binding process.AuPC has the potential to become a new type of cancer targeted therapeutic drug providing guidance for the formulation of therapeutic protocols.The simulation results can not only provide theoretical basis and guidance for experiments,but also can break through the limits of microscopic characterization of experiments and provide new ideas for the design of new cancer therapeutic drugs.Through further study of the essential laws of life phenomena promotes the development of science and technology and medical care.It has important biological research significances.