The principles are illustrated using fluorescence and circular dichroism measurements, and can be applied to other analytical techniques or be adapted with minor modifications for use with other proteins.This chapter contributes a short tutorial on the preparation of molecular dynamics (MD) simulations for a peptide in solution at the interface of an uncoated gold nanosurface. Specifically, the step-by-step procedure will give guidance to set up the simulation of a 16 amino acid long antimicrobial peptide on a gold layer using the program Gromacs for MD simulations.The performance of polymeric nanomaterials relies greatly upon their properties which are intimately related to the methods of fabrication of their materials. Among various synthetic polymers the polymers of 2-hydroxyethyl methacrylate (PHEMA) maintains a prime position in the biomedical field due to their useful physicochemical properties and suitability for controlled drug delivery applications. Furthermore, the addition of iron oxide to PHEMA nanoparticles imparts superparamagnetism to the nanoparticles and expands the range of their uses to include magnetic drug targeting applications. Here we focus on three methods for preparation of PHEMA nanoparticles, one by suspension polymerization, a second by emulsion polymerization without the use of any surfactants, and the final one with the incorporation of iron oxide into PHEMA nanoparticles.Preservation of cellular homeostasis requires constant synthesis of fresh proteins and cellular organelles and efficient degradation or removal of damaged proteins and cellular components. This involves two cellular degradation processes or molecular mechanisms the ubiquitin-proteasome and autophagy-lysosomal systems. Impairment of these catabolic processes has been linked to pathogenesis of a variety of chronic obstructive lung diseases such as COPD (chronic obstructive pulmonary disease) and CF (cystic fibrosis). Proteosomal and autophagic functions (proteostasis) are known to decline with advancing age leading to accumulation of cellular debris and proteins, initiating cellular senescence or death and accelerating lung aging. Obstructive lung diseases associated with airway hyperinflammation and mucus obstruction provide major challenges to the delivery and therapeutic efficacy of nanotherapeutics systems as they need to bypass the airway defense. Targeted autophagy augmentation has emerged, as a promising therapeutic utility for alleviating obstructive lung diseases, and promoting healthy aging. A targeted dendrimer-based approach has been designed to penetrate the airway obstruction and allow the selective correction of proteostasis/autophagy in the diseased cells while circumventing the side effects. This report describes methods for synthesis and therapeutic evaluation of autophagy augmenting dendrimers in the treatment of obstructive lung disease(s). The formulations and methods of autophagy augmentation described here are currently under clinical development in our laboratory for alleviating pathogenesis and progression of chronic obstructive lung diseases, and promoting healthy aging.Chronic airway inflammation is a hallmark of chronic obstructive airway diseases, including chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and asthma. Airway inflammation and mucus obstruction present major challenges to drug or gene delivery and therapeutic efficacy of nano-based carriers in these chronic obstructive airway conditions. To achieve targeted drug delivery of NPs to the diseased cells, NPs need to bypass the obstructive airway and circumvent the airway's defense mechanisms. Although there has been increasing interest and significant progress in development of NPs for targeting cancer, relatively little progress has been made towards designing novel systems for targeted treatment of chronic inflammatory and obstructive airway conditions. Hence, we describe here methods for preparing drug loaded multifunctional nanoparticles for targeted delivery to specific airway cell types in obstructive lung diseases. The formulations and methods for selective drug delivery in the treatment of chronic airway conditions such as COPD, CF, and asthma have been evaluated using a variety of preclinical models by our laboratory and currently ongoing further clinical development for translation from bench to bedside.The use of nanoparticulate systems for pulmonary drug delivery offers a number of advantages including significantly improved delivery efficiency to deep lung and the improved bioavailability. https://www.selleckchem.com/products/ots514.html The traditional nanoparticle manufacturing process such as ball/jet milling often yields large aggregates, which could detrimentally inhibit the effective delivery of drug particles to the lower respiratory tract. Here we report an alternative technique of spray-drying the microemulsions to produce nanoparticles ( less then 100 nm) that can be dispersed homogenously in the propellant to form an extremely stable pressurized metered-dose inhaler (pMDI) formulations. Such nanoparticulate formulations provide an ideal tool for pulmonary drug delivery.Organically modified silica (ORMOSIL) nanoparticles have found many biomedical applications and emerged as biocompatible and efficient carriers of diagnostic and therapeutic agents, such as fluorophores, drugs, and DNA. Herein, we describe two major in vivo studies exemplifying the use of these nanoparticles as carriers of active agents. The first part of this report details a systemic administration and biodistribution of radiolabeled and fluorophore-incorporated ORMOSIL nanoparticles in mice. The second part of this report focuses on the use of ORMOSIL nanoparticles as carriers of plasmid DNA for nonviral gene delivery to the mouse brain. We provide detailed protocols describing preparation and characterization of ORMOSIL nanoparticles, methods used for loading the particles with active agents (e.g., radioimaging agents, plasmid DNA), and in vivo administration of the particles.Thrombin, a major protein involved in the clotting cascade by the conversion of inactive fibrinogen to fibrin, plays a crucial role in the development of thrombosis. Antithrombin nanoparticles enable site-specific anticoagulation without increasing bleeding risk. Here we outline the process of making and the characterization of bivalirudin and D-phenylalanyl-L-prolyl-L-arginyl-chloromethyl ketone (PPACK) nanoparticles. Additionally, the characterization of these nanoparticles, including particle size, zeta potential, and quantification of PPACK/bivalirudin loading, is also described.