Conventional screening of potential drug candidates through wet lab affinity experiments using libraries of thousands of modified molecules is time and resource consuming, along with the fact that it contributes to the widening time gap between the discovery of disease-causing mutations and the implementation of resulting novel treatments. It is necessary to explore whether the preliminary use of high-throughput virtual screening (HTVS) software such as PyRx will curb both the time and money spent in discovering novel treatments for diseases such as congenital heart defects (CHDs). For example, AXIN2, a protein involved in a negative feedback loop inhibiting the Wnt/β-catenin signaling pathway important for cardiogenesis, has recently been associated with CHD. The loss-of-function mutation L10F on the tankyrase-binding domain of AXIN2 has been shown to upregulate the pathway by loss of inhibition ability, leading to the accumulation of intracellular β-catenin. In a different paper, however, AXIN2 has been shown to be stabilized using XAV-939, a small-molecule drug which targets tankyrase. PyRx and VMD will be used to modify the drug in order to increase its binding affinity to AXIN2, stabilizing the protein and reinstating its inhibitory property to treat CHDs. When used in adjunction to wet lab experiments, HTVS software may decrease costs and the time required to bring a potentially life-saving treatment into use.

Over the past few decades, amorphous solid dispersions (ASDs) have been of great interest to pharmaceutical scientists to address bioavailability issues associated with poorly water-soluble drugs. ASDs consist of an active pharmaceutical ingredient (API) that is typically dispersed in an inert polymeric matrix. Despite promising advantages, a major concern that has resulted in limited marketed formulations is the physical instability of these complex formulations. Physical instability is often manifested as phase heterogeneity, where the drug and carrier migrate and generate distinct phases, which can be a prelude to recrystallization. One important factor that dictates the physical stability of ASDs is the spatial distribution of API in the polymeric matrix. It is generally agreed that intimate mixing of the drug and polymer is necessary to achieve maximum stabilization, and thus understanding the factors controlling phase mixing and nano-domain structure of ASDs is crucial to rational formulation design. The focus of this thesis work is to better understand the factors involved in phase mixing on the nanometric level and get insights on the role of excipients on overall stabilization of these systems. The central hypothesis of this research is that an intimately mixed ASD will have better physical stability as compared to a partially homogeneous or a non-homogeneous system. Our approach is to probe and correlate phase homogeneity and intermolecular drug-excipient interactions to better understand the physical stability of ASDs primarily using solid-state nuclear magnetic resonance (SSNMR) spectroscopy and other solid-state characterization tools. A detailed investigation was carried out to understand the role of hydrogen bonding on compositional homogeneity on different model systems. A comprehensive characterization of ternary ASDs in terms of molecular interactions and physical stability was studied. Finally, long-term physical stability studies were conducted in order to understand the impact of different grades of a cellulosic polymer on phase homogeneity for two sets of samples prepared via different methods. Overall, through this research an attempt has been made to address some relevant questions pertaining to nano-phase heterogeneity in ASDs and provide a molecular level understanding of these complex systems to enable rational formulation design.

In order to reduce the time associated with and the costs of drug discovery, machine learning is being used to automate much of the work in this process. However the size and complex nature of molecular data makes the application of machine learning especially challenging. Much work must go into the process of engineering features that are then used to train machine learning models, costing considerable amounts of time and requiring the knowledge of domain experts to be most effective. The purpose of this work is to demonstrate data driven approaches to perform the feature selection and extraction steps in order to decrease the amount of expert knowledge required to model interactions between proteins and drug molecules.

The overall aim of this research project was to develop surfactant dry powder formulations and devices for efficient delivery of aerosol formulations to infants using the excipient enhanced growth (EEG) approach. Use of novel formulations and inline delivery devices would allow for more efficient treatment of infants suffering from neonatal respiratory distress syndrome and bronchiolitis. A dry powder aerosol formulation has been developed using the commercial product, Survanta ® (beractant) and EEG technology to produce micrometer-sized hygroscopic particles. Spray drying and formulation parameters were initially determined with dipalmitoylphosphatidylcholine (DPPC, the dominant phospholipid in pulmonary surfactant), which produced primary particles 1 um in size with a mass median aerodynamic diameter of 1-2 um. Investigation of dry powder dispersion enhancers and alcohol concentration on the effect of powder aerosol characteristics were performed with the Survanta-EEG formulation. The optimal formulation consisted of Survanta ® , mannitol and sodium chloride as hygroscopic excipients, and leucine as the dry powder dispersion enhancer, prepared in 20% v/v ethanol/water. The powders produced primary particles of 1 um with >50% of the particles less than 1 um. The presence of surfactant proteins and surface activity were demonstrated with the Survanta-EEG formulation following processing. A novel containment unit dry powder inhaler (DPI) was designed for delivery of the surfactant-EEG formulation using a low volume of dispersion air. Studies explored optimization of air entrainment pathway, inlet hole pattern, delivery tube internal diameter and length. With 3- 10 mg fill masses of spray dried surfactant powder, the DPI enabled delivery of >2 mg using one 3-mL actuation of dispersion air. Overall, it was possible to deliver >85% of the loaded fill mass using three actuations. Nebulized aerosol formulations are characterized with low delivered doses. Using a novel mixer-heater delivery system, the highest estimated percent lung dose achieved during realistic in vitro testing of a Survanta-EEG formulation aerosolized with a commercial mesh nebulizer was when nebulization was synchronized with inhalation of the breathing profile. Design changes to the mixer-heater system eliminated the need for synchronization, achieving an estimated percent lung dose of 31% of the nominal, an improvement compared with existing systems that achieve approximately <2% lung dose.

The aim of the present study is to develop a statistical algorithm and model associ- ated with breast and lung cancer patients. In this study, we developed several statistical softwares, R packages, and models using our new statistical approach. In the present study, we used the five parameters logistic model for determining the optimal doses of a pharmaceutical drugs, including dynamic initial points, an automatic process for outlier detection and an algorithm that develops a graphic user interface(GUI) program. The developed statistical procedure assists medical scientists by reducing their time in determining the optimal dose of new drugs, and can also easily identify which drugs need more experimentation. Secondly, in the present study, we developed a new classification method that is very useful in the health sciences. We used a new decision tree algorithm and a random forest method to rank our variables and to build a final decision tree model. The decision tree can identify and communicate complex data systems to scientists with minimal knowledge in statistics. Thirdly, we developed statistical packages using the Johnson SB probability distribu- tion which is important in parametrically studying a variety of health, environmental, and engineering problems. Scientists are experiencing difficulties in obtaining estimates for the four parameters of the subject probability distribution. The developed algorithm com- bines several statistical procedures, such as, the Newtwon Raphson, the Bisection, the Least Square Estimation, and the regression method to develop our R package. This R package has functions that generate random numbers, calculate probabilities, inverse probabilities, and estimate the four parameters of the SB Johnson probability distribution. Researchers can use the developed R package to build their own statistical models or perform desirable statistical simulations. The final aspect of the study involves building a statistical model for lung cancer sur- vival time. In developing the subject statistical model, we have taken into consideration the number of cigarettes the patient smoked per day, duration of smoking, and the age at diagnosis of lung cancer. The response variables the survival time. The significant factors include interaction. the probability density function of the survival times has been obtained and the survival function is determined. The analysis is have on your groups the involve gender and with factors. A companies with the ordinary survival function is given.

Nasal administration has potential for the treatment of indications requiring a fast onset of effect or for drugs with low oral bioavailability. Liquid nasal sprays are relatively common, but can be associated with suboptimal absorption from the nasal cavity; this thesis shows that nasal absorption can be significantly enhanced with a dry powder formulation. It was shown that interactive mixtures, consisting of fine drug particles adhered to the surface of mucoadhesive carrier particles, could be created in a particle size suitable for nasal administration. Sodium starch glycolate (SSG), a common tablet excipient, was used as carrier material. In vitro evaluation of the formulation indicated that the mucoadhesion of the carrier was unlikely to be affected by the addition of a drug. The powder formulation did not improve the in vitro transfer of dihydroergotamine across porcine nasal mucosa compared with a liquid formulation; however, the results were associated with methodological shortcomings. The binding of model substances to SSG and three other excipients was evaluated. Ion exchange interactions were for example detected between SSG and cationic drugs, but these interactions were most extensive at low salt concentrations and should unlikely affect in vivo bioavailability at physiological salt concentrations. Absorption of the peptide drug desmopressin from the SSG nasal formulation, from a novel sublingual tablet formulation and from a commercial nasal liquid spray was evaluated in a clinical trial. While no improvement over the liquid spray was seen with the sublingual tablet, plasma concentrations after the nasal powder formulation were three times higher than those after the liquid spray. All formulations were well accepted by the volunteers. The use of currently available mucoadhesive carrier particles in interactive mixtures offers potential for a new method of producing nasal powder formulations that should also be applicable to large scale production.

Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

1-Aza-2-azoniaallene salts are reactive intermediates that undergo [3+2] cycloaddition with many different types of multiple bonds. For the past several years, the Brewer group has studied the reactivity of these intermediates in intramolecular reactions, and have discovered that these cationic heteroallenes can react through a variety of other, mechanistically distinct, pathways to give different classes of nitrogen heterocycles. For example, prior work in the Brewer group revealed that 1-aza-2-azoniaallene salts could react in an intramolecular [4+2] cycloaddition reaction to give protonated azomethine imine salts containing a 1,2,3,4-tetrahydrocinnoline scaffold. Further study of the scope and limitations of this Diels-Alder-like reaction are described herein. These studies primarily focused on how varying the N-aryl ring and alkene substituents affected the reaction. We discovered that in several instances, the metal mediated reaction did not facilitate the cycloaddition very well, so we searched for alternative ways to facilitate the reaction. We discovered that a non-metallic Lewis acid (TMSOTf) provided very clean products with α-chloroazo compounds. I hypothesized that changing the leaving group adjacent to the azo might further improve the reaction. With this in mind, I developed a technique to prepare α-trifluoroacetoxyazo compounds by treating aryl hydrazones with trifluoroacetoxy dimethylsulfonium trifluoroacetate. This technique is compatible with all types of functional groups including nitro aryl compounds, which gave low yields of the corresponding chloroazo derivatives. Importantly, these α-trifluoroacetoxyazo compounds gave even better cycloaddition results when treated with TMSOTf, and this method is more practical, more environmentally friendly, and greener than the metal mediated technique. This process even returned sterically hindered products in high yield, and provide a dearomatized non-protonated azomethine imine salt, which further verified the proposed mechanism of the [4+2] cycloaddition. Azomethine imines are well known to undergo 1,3-dipolar cycloadditions with alkenes. We wondered if the protonated azomethine imine salts generated by the [4+2] cycloaddition could be used in a subsequent base-mediated [3+2] cycloaddition to generate structurally complex tetra- or pentacyclic products. We were pleased to find that the protonated azomethine imines indeed reacted smoothly with a variety of π-system in the presence of triethylamine to give the corresponding cycloadducts in high yields with moderate to high diastereoselectivities. In an attempt to understand the diastereoselectivity of these [3+2] cycloadditions better, I modeled them computationally.

The Electrospray (ES) technique is a promising particle generation method for drug delivery due to its capabilities of producing monodisperse PLGA composite particles with unique configurations and high drug encapsulation efficiency. In the dissertation work, the coaxial dual capillary ES was used to generate drug-loaded core-shell PLGA particles to study the effects of particle filling materials, drug loading locations and particle shell thicknesses on the resultant in vitro release behaviors of the hydrophilic and/ or hydrophobic model drugs. Through release profile characterization of drug-loaded PLGA particles (particle size: 400 nm and 1 μm), it was confirmed that the co-encapsulation of Budesonide (BUD, the hydrophobic small-molecule model drug) and Theophylline (THY, the hydrophilic small-molecule model drug) in the particle cores is the most effective drug loading strategy for extended release of the fixed combined BUD and THY. Particles composed of PLGA fillers with lower molecular weights and with greater shell layer thicknesses could release THY in a well controlled fashion. On the other hand, a slower release rate of Bovine Serum Albumin (BSA, the protein model drug) from PLGA particles with greater shell thickness was also observed. Sequential release of BSA and Paclitaxel (PTX, the hydrophobic small-molecule anti-cancer model drug) was achieved by the 400-nm PLGA (Mw: 7,000-17,000 g/mol, LA/GA: 50/50) particles with potential biopharmaceutical applications in cancer therapy.

Theranostics is an emerging treatment approach that combines diagnostics with therapy in order to personalize treatment regimens for individual patients and decrease cancer mortality. Previously, nanoparticles entrapping conventional fluorescent dyes were developed for cancer theranostics, but fluorescent nanoparticles did not allow clinicians to significantly improve cancer treatments. The use of fluorescent dyes that are sensitive to solvent acidity (halo-fluorochromism) and polarity (solvato-fluorochromism) may overcome the limitations of fluorescent nanoparticles and improve cancer therapy by enabling researchers to detect chemical properties within the nanoparticle core environment. The model halo- and solvato-fluorochromic dye Nile blue was attached to the core of nanoscale drug delivery systems called polymer nanoassemblies (PNAs), which were created by tethering hydrophilic polymers and hydrophobic groups to a cationic polymer scaffold. The fluorescence of empty PNAs increased by 100% at pH 5.0 compared to pH 7.4, and the fluorescence of drug-loaded PNAs increased up to 300% compared to empty PNAs. A comparison of the fluorochromic properties between PNAs with various core properties indicated that both hydrophobic pendant groups and scaffold amines contributed to the fluorochromism of PNAs. The halo-fluorochromism of PNAs allowed investigators to minimize the detection of fluorescence signals in healthy organs such as the liver. Fluorescence imaging of halo-fluorochromic PNAs diffused into tissue mimics indicated that fluorescence of PNAs in tissues increased by 100% at pH 7.0 compared to pH 7.4. In addition, halo-fluorochromic PNAs identified the acidic perimeter surrounding metastatic tumors in orthotopic metastatic tumor models. Computational simulations of metastatic lesions verified that some halo-fluorochromic PNAs accumulate in the hypoxic/acidic regions of metastatic tumors following intravenous administration. These simulations also indicated that the accumulation of PNAs in the hypoxic regions of tumors doubles at 12 hours post-treatment compared to 1.8 hours post-treatment. The solvato-fluorochromism of PNAs enabled the fluorescence-based measurement of drug release from the nanoassembly core during dialysis-based drug release measurements. Solvato-fluorochromic methods indicated faster drug release rates than HPLC-based methods. Mechanistic modeling of drug release indicated that solvato-fluorochromic methods were unaffected by released drugs that interfered with HPLC-based methods. However, mechanistic modeling also indicated that drug rebinding and diffusion did not account for all of the differences between drug release rates determined by solvato-fluorochromic- and HPLC-based methods. Based on this evidence, it was hypothesized that solvato-fluorochromic drug release methods measure drug diffusion from near the scaffold of PNAs in a small region of the nanoassembly core, and that this process contributes to overall drug release but does not indicate apparent drug release rates for PNAs. In order to develop PNAs for potential clinical applications, ionizable amines were removed from the polymer scaffold to increase drug loading and sustain the release of model drugs carfilzomib and docetaxel. The removal of primary amines decreased drug diffusivity in the core of PNAs (D from 3.9*10-18 cm2/s to 0.1*10-19 cm2/s) and increased the drug release half-life (t1/2 from 4 to 26 hours). The controlled release of carfilzomib from PNAs reduced drug metabolism by 60% for up to one hour and sustained proteasome inhibition in cancer cells at 72 h post-treatment compared to free drug. Overall, this work provides insight into the design of theranostic nanoparticles with beneficial properties for improving cancer treatment.