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<p>Understanding and predicting chemical phenomena is the main goal of computational chemistry. In this thesis I present my work on applying computational approaches to study chemical processes in biological and supramolecular systems.</p> <p>pH-responsive molecular tweezers have been proposed as an approach for targeting drug-delivery to tumors, which tend to have a lower pH than normal cells. In chapter 2 I present a computational study I performed on a pH-responsive molecular tweezer using <em>ab initio</em> quantum chemistry in the gas phase and molecular dynamics simulations in solution. The binding free energy in solution was calculated using Steered Molecular Dynamics. We observe, in atomistic detail, the pH-induced conformational switch of the tweezer and the resulting release of the drug molecule. Even when the tweezer opens, the drug molecule remains near a hydrophobic arm of the molecular tweezer. Drug release cannot occur, it seems, unless the tweezer is a hydrophobic environment with low pH.</p> <p>The protonation state of amino acid residues in proteins depends on their respective pK_a values. Computational methods are particularly important for estimating the pK_a values of buried and active site residues, where experimental data is scarce. In chapter 3 I used the cluster model approach to predict the pK_a of some challenging protein residues and for which methods based on the numerical solution of the Poisson-Boltzmann equation and empirical approaches fail. The ionizable residue and its close environment were treated quantum mechanically, while the rest of the protein was replaced by a uniform dielectric continuum. The approach was found to overestimate the electrostatic interaction leading to predicting lower pK_a values.</p> / Master of Science (MSc)

The objective of this research is to explore the use of ionic liquds in crystal engineering and drug delivery. Ionic liquids have a wide range of applications in pharmaceutical field due to their unique physicochemical propertie ssuch as chemical, thermal stability, low melting point, nonvolatility, nonflamability, low toxicity and recyclability which offer unique and interesting potential for pharmaceuitcal applications. Currently, many research groups are working on the development of ionic liquids to use in this field but there is need to develop systematic understanding about new techniques for synthesis and applications of ionic liquids to obtain new crystal form and potential of drug ionic salts. The synthesis of fifteen phosphonium ionic liquids under microwave irradiation and their physicochemical properties was investigated. The reaction time was significantly reduced compared to conventional methods, and higher yields were reported. The crystallisation of pharmaceutical drugs such as sulfathiazole, chlorpropamide, phenobarbital and nifedipine were investigated using imidazolium ionic liquids. The supramolecular complex of sulfathiazole and phenobarbital with imidazolium ionic liquids and polymorphic change in chlorpropamide was achieved. The ionic liquids provides unique environment for the crystallisation. The imidazolium salts of ibuprofen and diclofenac were synthesised and evaluated for physicochemical properties and their pharmaceutical performances especially transdermal absorption. The investigation of physicochemcal properties and pharmaceutical performance of imidazolium drug salts indicated opportunity to optimise lipophilicity and other physicochemical properties such as molecular size, osmolality, viscosity to achieve desired skin deposition and permeation. This study will provide a new approach to design of new drug salts develop using the interdisciplinary knowledge of chemical synthesis and drug delivery. / Social Justice Department, Government of Maharashtra, India.

One of the major challenges faced by the pharmaceutical industry is to accelerate the product innovation process and reduce the time-to-market for new drug developments. This involves billions of dollars of investment due to the large amount of experimentation and validation processes involved. A computational modeling approach, which could explore the design space rapidly, reduce uncertainty and make better, faster and safer decisions, fits into the overall goal and complements the product development process. Our research focuses on the early preclinical stage of the drug development process involving lead selection, optimization and candidate identification steps. Our work helps in screening the most favorable candidates based on the biopharmaceutical and pharmacokinetic properties. This helps in precipitating early development failures in the early drug discovery and candidate selection processes and reduces the rate of late-stage failures, which is more expensive. In our research, we successfully integrated two well-known models, namely the drug release model (dissolution model) with a drug transport model (compartmental absorption and transit (CAT) model) to predict the release, distribution, absorption and elimination of an oral drug through the gastrointestinal (GI) tract of the human body. In the CAT model, the GI tract is envisioned as a series of compartments, where each compartment is assumed to be a continuous stirred tank reactor (CSTR). We coupled the drug release model in the form of partial differential equations (PDE's) with the CAT model in the form of ordinary differential equations (ODE's). The developed model can also be used to design the drug tablet for target pharmacokinetic characteristics. The advantage of the suggested approach is that it includes the mechanism of drug release and also the properties of the polymer carrier into the model. The model is flexible and can be adapted based on the requirements of the clients. Through this model, we were also able to avoid depending on commercially available software which are very expensive. In the drug discovery and development process, the tablet formulation (oral drug delivery) is an important step. The tablet consists of active pharmaceutical ingredient (API), excipients and polymer. A controlled release of drug from this tablet usually involves swelling of the polymer, forming a gel layer and diffusion of drug through the gel layer into the body. The polymer is mainly responsible for controlling the release rate (of the drug from the tablet), which would lead to a desired therapeutic effect on the body. In our research, we also developed a molecular design strategy for generating molecular structures of polymer candidates with desired properties. Structure-property relationships and group contributions are used to estimate the polymer properties based on the polymer molecular structure, along with a computer aided technique to generate molecular structures of polymers having desired properties. In greater detail, we utilized group contribution models to estimate several desired polymer properties such as grass transition temperature (Tg), density (ρ) and linear expansion coefficient (α). We subsequently solved an optimization model, which generated molecular structures of polymers with desired property values. Some examples of new polymer repeat units are - [CONHCH₂ - CH₂NHCO]n -, - [CHOH - COO]n -. These repeat-units could potentially lead to novel polymers with interesting characteristics; a polymer chemist could further investigate these. We recognize the need to develop group contribution models for other polymer properties such as porosity of the polymer and diffusion coefficients of water and drug in the polymer, which are not currently available in literature. The geometric characteristics and the make-up of the drug tablet have a large impact on the drug release profile in the GI tract. We are exploring the concept of tablet customization, namely designing the dosage form of the tablet based on a desired release profile. We proposed tablet configurations which could lead to desired release profiles such as constant or zero-order release, Gaussian release and pulsatile release. We expect our work to aid in the product innovation process. / Ph. D.

La presente tesis doctoral titulada “Materiales de sílice funcionales para la liberación controlada, detección y eliminación de moléculas de interés” se centra en el diseño y desarrollo de materiales híbridos orgánico-inorgánicos mediante la aplicación de los conceptos de Química Supramolecular. Durante el desarrollo de la presente tesis doctoral se han preparado y caracterizado diferentes materiales de base silícea para distintas aplicaciones. La primera parte de la tesis se centra en el desarrollo de materiales de base silícea capaces de variar su comportamiento fluorescente en función de la presencia o ausencia de un cierto analito en el medio. Estos materiales emplean como soporte nanopartículas de sílice que se funcionalizan superficialmente con dos unidades diferentes, una coordinante y una indicadora (un fluoróforo). La interacción del analito de interés (en nuestro caso aniones) con la unidad coordinante modificará las propiedades emisivas del fluoróforo. Así, se han preparado dos materiales en los cuales el grupo fluorescente es rodamina mientras que el grupo coordinante es un imidazolato o una sal de guanidinio respectivamente. Una vez caracterizados ambos materiales se estudió su comportamiento frente a diferentes especies aniónicas a diferentes concentraciones resultando selectivos a la presencia de benzoato (el material funcionalizado con imidazolatos), dihidrógeno fosfato e hidrógeno sulfato (el material funcionalizado con sales de guanidinio). El tercer capítulo de la tesis se centra en la aplicación de materiales híbridos orgánico-inorgánicos para la detección y eliminación de especies altamente tóxicas como son los agentes neurotóxicos. Estos son compuestos organofosforados capaces de causar graves lesiones en el sistema nervioso central. En una primera aproximación se emplea el concepto de puerta molecular para la detección de agentes neurotóxicos. Para ello, se utiliza como soporte inorgánico un material mesoporoso de sílice (MCM-41) cuyos poros se cargan con un colorante que actúa de indicador mientras que la superficie externa del mismo se funcionaliza con una molécula capaz de reaccionar con dichos agentes neurotóxicos. Dicha molécula es capaz de interaccionar entre sí (mediante enlaces de hidrógeno) formando una red que mantiene bloqueada la salida de los poros. En presencia de DCP (dietilclorofosfato, un simulante de agente neurotóxico), y después de que este reaccione con dicha molécula, se produce una reorganización espacial que permite la liberación del colorante. De este modo, la presencia de los agentes neurotóxicos está señalizada mediante un cambio de color. En una segunda aproximación se aborda el uso de soportes inorgánicos de tipo MCM-41 como materiales para la eliminación de agentes neurotóxicos. Para ello se modificaron químicamente las superficies de estos materiales silíceos mediante tratamiento con distintas bases. Como consecuencia de este tratamiento básico los silanoles de la superficie se desprotonan dando lugar a los correspondientes silanolatos (nucleófilos fuertes). Estos silanolatos son capaces de reaccionar con los agentes neurotóxicos descomponiéndolos y favoreciendo su eliminación de un medio contaminado. Por último, se estudia la aplicación de materiales híbridos orgánico-inorgánicos funcionalizados con puertas moleculares en aplicaciones de liberación controlada, concretamente, en liberación controlada intracelular de fármacos de interés. El material híbrido consta de un soporte de sílice mesoporosa cuyos poros se cargan con un compuesto citotóxico (camptotecina) y su superficie externa se funcionaliza con una gluconamida. La presencia de una monocapa densa de gluconamidas por el exterior del material inhibe la liberación del compuesto citotóxico. Al añadir enzimas con capacidad para hidrolizar enlaces amida (amidasa y pronasa) se produce la liberación de la camptotecina. El correcto funcionamiento del material se comprobó in vitro e in vivo (en células HeLa). / Candel Busquets, I. (2014). Functional silica materials for controlled release, sensing and elimination of target molecules [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/39101

Yes / Three dimensional printing (3DP) was used to engineer novel oral drug delivery devices, with specialised design configurations loaded with multiple actives, with applications in personalised medicine. A filament extruder was used to obtain drug-loaded - paracetamol (acetaminophen) or caffeine - filaments of polyvinyl alcohol with characteristics suitable for use in fused-deposition modelling 3D printing. A multi-nozzle 3D printer enabled fabrication of capsule-shaped solid devices, containing paracetamol and caffeine, with different internal structures. The design configurations included a multilayer device, with each layer containing drug, whose identity was different from the drug in the adjacent layers; and a two-compartment device comprising a caplet embedded within a larger caplet (DuoCaplet), with each compartment containing a different drug. Raman spectroscopy was used to collect 2-dimensional hyper spectral arrays across the entire surface of the devices. Processing of the arrays using direct classical least squares component matching to produce false colour representations of distribution of the drugs showed clearly the areas that contain paracetamol and caffeine, and that there is a definitive separation between the drug layers. Drug release tests in biorelevant media showed unique drug release profiles dependent on the macrostructure of the devices. In the case of the multilayer devices, release of both drugs was simultaneous and independent of drug solubility. With the DuoCaplet design it was possible to engineer either rapid drug release or delayed release by selecting the site of incorporation of the drug in the device, and the lag-time for release from the internal compartment was dependent on the characteristics of the external layer. The study confirms the potential of 3D printing to fabricate multiple-drug containing devices with specialized design configurations and unique drug release characteristics, which would not otherwise be possible using conventional manufacturing methods. / The full-text of this article will be released for public view at the end of the publisher embargo on 10 Oct 2016.