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Cancer is a leading cause of death globally, and established therapeutic options have limits. Nanoparticles, which are distinguished by their versatility in size, shape, and surface charge, have shown great promise in tumor diagnostics and therapy. Nanoparticles increase therapeutic efficacy while decreasing toxicity by delivering drugs to target tumors. While multiple studies have revealed nanoparticles' great potential as anticancer drug carriers, their therapeutic efficiency remains limited, partly due to the poor understanding of the penetration behavior of nanoparticles within tumors. Understanding the nanoparticle penetration behavior and the factors that control this process is crucial for improving the in vivo delivery efficiency of nanoparticles. The 2D cell culture models are unable to simulate the complexities of the tumor microenvironment accurately, such as the cell-to-cell interactions and the structure of the extracellular matrix (ECM). To address these drawbacks, the 3D multicellular spheroid model was created providing an inexpensive, labor-saving, and time-saving substitute for 2D and animal models. This thesis begins by describing the penetration of tumor tissues and provides an overview of the critical factors influencing penetration into tumor tissues, including tumor-specific features and nanoparticle properties. Chapter 3 introduces a new label- free quantitative analytical technique that combines two-photon microscopy, synchrotron X-ray fluorescence microscopy (XFM), and inductively coupled plasma mass spectrometry (ICP-MS) to investigate the distribution and penetration pathways of gold nanoparticles (AuNPs) of different sizes inside a tumor cell spheroid model. In Chapter 4, a hybrid approach is adopted, integrating computational and experimental techniques to create new 3D microscale Computational Fluid Dynamics-Discrete Element Method (CFD-DEM) models. This model accurately replicates nanoparticle penetration in the extracellular tumor environment, making it a cost-effective and powerful tool for forecasting nanoparticle absorption in tumor spheroids and designing nanomedicines.

Aminoglycosides are broad-spectrum antibiotics widely used as chemotherapeutic agents for the treatment of serious bacterial infections. Aminoglycosides were first established as antibiotics in the 1940s with the discovery of the first treatment for tuberculosis, streptomycin. Aminoglycosides target the prokaryotic ribosome by binding the decoding A-site of the 16S rRNA, inhibiting protein translation and ultimately leading to cell death. One major problem with this class of drugs is that decades of intensive clinical use has selected for bacterial resistance. The most common mechanism of bacterial resistance arises from their structural modifications by aminoglycoside-modifying enzymes (AMEs). This dissertation focuses on the aminoglycoside acetyltransferase (AAC) family of AMEs which uses AcCoA to regio-specifically acetylate amino groups on aminoglycosides. We reported the development of a chemoenzymatic methodology that utilizes AACs for the generation of N-acylated aminoglycoside analogs. The studied AACs showed diverse substrate promiscuity towards a variety of aminoglycosides as well as acyl-CoA derivatives. Some acylated aminoglycosides retained antibacterial properties against Bacillus subtilus. Our chemoenzymatic approach offers access to regioselectively N-acylated aminoglycosides in quantities that allow testing of antibacterial potential, making it possible to identify molecules worth synthesizing on a larger scale. This is a demonstration of utilizing the cosubstrate promiscuity of enzymes to re-purpose their use for scaffold diversification towards the development of new drugs. We also demonstrated that aminoglycosides can be doubly modified by the sequential actions of AMEs in some cases. These observations will help anticipate the effect of a modification on the subsequent activity of AMEs and guide the design of novel aminoglycoside antibiotics. Next, we focused on studying the the unusually regioversatile acetyltransferase, Eis, which is responsible for resistance to kanamycin in a significant fraction of kanamycin-resistant Mycobacterium tuberculosis clinical isolates. We found that mycobacterial Eis has an unprecedented ability to acetylate multiple amines of many aminoglycosides. We also found that Eis, in contrast to its broad substrate profile, has limited cosubstrate promiscuity. In addition, several inhibitors of the Eis enzyme were identified and characterized. We hope that understanding the mechanism of this resistance conferring enzyme, will enable us to design better drugs/regimens to fight Mycobacterium tuberculosis infection.