Computer-aided design of fragment mixtures for NMR-based screening

Fragment-based drug discovery is widely applied both in industrial and in academic screening programs. Several screening techniques rely on NMR to detect binding of a fragment to a target. NMR-based methods are among the most sensitive techniques and have the further advantage of yielding a low rate of false positives and negatives. However, NMR is intrinsically slower than other screening techniques; thus, to increase throughput in NMR-based screening, researchers often assay mixtures of fragments, rather than single fragments. Herein we present a fast and straightforward computer-aided method to design mixtures of fragments taken from a library that have minimized NMR signal overlap. This approach enables direct identification of one or several active fragments without the need for deconvolution. Our approach entails encoding of NMR spectra into a computer-readable format that we call a fingerprint, and minimizing the global signal overlap through a Monte Carlo algorithm. The scoring function used favors a homogenous distribution of the global signal overlap. The method does not require additional experimental work: the only data required are NMR spectra, which are generally recorded for each compound as a quality control measure before its insertion into the library

Model for quantitative tip-enhanced spectroscopy and the extraction of nanoscale-resolved optical constants

Near-field infrared spectroscopy by elastic scattering of light from a probe tip resolves optical contrasts in materials at dramatically sub-wavelength scales across a broad energy range, with the demonstrated capacity for chemical identification at the nanoscale. However, current models of probe-sample near-field interactions still cannot provide a sufficiently quantitatively interpretation of measured near-field contrasts, especially in the case of materials supporting strong surface phonons. We present a model of near-field spectroscopy derived from basic principles and verified by finite-element simulations, demonstrating superb predictive agreement both with tunable quantum cascade laser near-field spectroscopy of SiO$_2$ thin films and with newly presented nanoscale Fourier transform infrared (nanoFTIR) spectroscopy of crystalline SiC. We discuss the role of probe geometry, field retardation, and surface mode dispersion in shaping the measured near-field response. This treatment enables a route to quantitatively determine nano-resolved optical constants, as we demonstrate by inverting newly presented nanoFTIR spectra of an SiO$_2$ thin film into the frequency dependent dielectric function of its mid-infrared optical phonon. Our formalism further enables tip-enhanced spectroscopy as a potent diagnostic tool for quantitative nano-scale spectroscopy.Comment: 19 pages, 9 figure

Detection of High Energy Ionizing Radiation using Deeply Depleted Graphene-Oxide-Semiconductor Junctions

Graphene's linear bandstructure and two-dimensional density of states provide an implicit advantage for sensing charge. Here, these advantages are leveraged in a deeply depleted graphene-oxide-semiconductor (D2GOS) junction detector architecture to sense carriers created by ionizing radiation. Specifically, the room temperature response of the silicon-based D2GOS junction is analyzed during irradiation with 20 MeV Si4+ ions. Detection was demonstrated for doses ranging from 12-1200 ions with device functionality maintained with no substantive degradation. To understand the device response, D2GOS pixels were characterized post-irradiation via a combination of electrical characterization, Raman spectroscopy, and photocurrent mapping. This combined characterization methodology underscores the lack of discernible damage caused by irradiation to the graphene while highlighting the nature of interactions between the incident ions and the silicon absorber.Comment: 15 pages, 4 figure

Relative efficiency of polariton emission in two-dimensional materials

We investigated emission and propagation of polaritons in a two dimensional van der Waals material hexagonal boron nitride (hBN). Our specific emphasis in this work is on hyperbolic phonon polariton emission that we investigated by means of scattering-type scanning near-field optical microscopy. Real-space nano-images detail how the polaritons are launched in several common arrangements including: light scattering by the edges of the crystal, metallic nanostructures deposited on the surface of hBN crystals, as well as random defects and impurities. Notably, the scanned tip of the near-field microscope is itself an efficient polariton launcher. Our analysis reveals that the scanning tips are superior to other types of emitters we have investigated. Furthermore, the study of polariton emission and emission efficiency may provide insights for development of polaritonic devices and for fundamental studies of collective modes in other van der Waals materials.Comment: 19 pages, 3 figure

Phase transition in bulk single crystals and thin films of VO2 by nanoscale infrared spectroscopy and imaging

We have systematically studied a variety of vanadium dioxide (VO2) crystalline forms, including bulk single crystals and oriented thin films, using infrared (IR) near-field spectroscopic imaging techniques. By measuring the IR spectroscopic responses of electrons and phonons in VO2 with sub-grain-size spatial resolution (∼20nm), we show that epitaxial strain in VO2 thin films not only triggers spontaneous local phase separations, but also leads to intermediate electronic and lattice states that are intrinsically different from those found in bulk. Generalized rules of strain- and symmetry-dependent mesoscopic phase inhomogeneity are also discussed. These results set the stage for a comprehensive understanding of complex energy landscapes that may not be readily determined by macroscopic approaches

Combined use of NMR and computational tools for fragment based drug discovery targeting protein-protein interactions VEGF protein surface recognition as a case study

[spa] En el contexto de la presente tesis hemos abordado los siguientes objetivos: 1. El uso de métodos de RMN, basados tanto en la observación del ligando como en la observación de proteína, para estudiar la unión de los compuestos de una quimioteca a la zona de VEGF involucrada en la unión a sus receptores. La interacción VEGF/VEGFR puede ser considerada como un caso de estudio para la evaluación de las interfaces proteína-proteína mediante cribado de fragmentos. 2. Desarrollar herramientas basadas en la combinación de RMN y métodos computacionales para abordar: i) un sistema automático de diseño de mezclas de fragmentos; ii) el análisis automático de datos procedentes de cribados basados en RMN; iii) la evolución de fragmentos con muy baja afinidad. 3. Explorar el uso de técnicas de “mRNA display” para el descubrimiento de nuevos ligandos peptídicos para VEGF.[eng] The capacity of proteins to interact with each other rests at the core of biology. Given the ubiquitous nature of these interactions they have attracted the attention of scientists for the development of inhibitors or biochemical tools.The use of biologics to target protein-protein interfaces is relatively advanced; suffer although from some intrinsic drawbacks as the danger of immunogenicity, the inability to cross biological barriers efficiently and high production costs. Small molecule inhibitors do not necessarily share these drawbacks. Unfortunately the druggability of protein-protein interfaces and strategies to target them with small molecules is under open debate. In this work we explore the druggability and methods to target the protein-protein interface of VEGF, a model system with therapeutic relevance in the fields of tumor biology and macular degeneration. We focus mainly on a fragment based approach for the following reasons: i.) proved to be successful at least for some particular protein-protein interfaces, ii.) offers a good coverage of the chemical space with small libraries, iii.) may lead to compounds with improved physicochemical properties compared to HTS. NMR, which is an omnipresent method in the field of fragment based drug discovery since the pioneering work of Fesik, was our tool of choice with a strong focus on combination with novel computational approaches. In the first part of our work we express the required amounts of recombinant VEGF. Then we design and prepared a fragment library after the “SAR by catalog” principle. We developed a new methodology that allowed the preparation of fragment mixtures for NMR based screening with minimized signal overlap. This allowed the direct assessment of nearly all fragment mixtures without the need of mixture deconvolution. Further we developed a program that allowed the automatic evaluation of NMR derived fragment screening data. While being faster than tedious manual interpretation of NMR data it offered a degree of quantitative analysis that would otherwise not be possible in a reasonable amount of time. Our library consistent of over 500 fragments was screened using STD- and CPMG filtered NMR experiments. The analysis of the NMR data resulted in high hit rates but apparent very weak affinity of identified ligands. We successfully developed a competitive 19F NMR based screening assay to identify ligands that bind to the protein-protein interface of VEGF, however none clear competitors could be identified. A second library of over 350 19F containing molecules was screened which led to low hit rates and identification of ligands with apparent very weak affinity. Finally a computational analysis of VEGF surface predicted a low druggability of the protein-protein interface which was in accordance to our experimental observations. The characterization of weak binding fragments and their structural evolution was elaboration was achieved by a combined approach based on NMR and computational experiments. Ligand binding was assessed by the NMR chemical shift perturbation methodology using as probes both amide backbone N-H groups of the protein and its side chain methionine methyl groups. Binding poses were predicted by induced fit docking with the PELE algorithm under strong guidance by NMR derived restrains. Predicted binding modes were used to select fragment analogs with improved binding parameters. This was performed for three cycles and led finally to the discovery of several scaffold families that bind to or in proximity to the protein-protein interface of VEGF. Finally, we present a preliminary exploration of mRNA display for the selection of novel peptide based VEGF ligands

Tuning the Optical Response of Graphene and Metamaterials

The following dissertation examines the tunability of two types of proof-of-concept devices centering around post-fabrication modification of the infrared optical response. The first device, created through the hybridization of the metamaterials and the phase-transition oxide vanadium dioxide (VO2), is probed using Fourier transform infrared spectroscopy. We demonstrate that, through application of voltage pulses to this initially uniform device, a gradient in the optical properties can be obtained. This macroscopic control mechanism enables persistent modification of the device, though the hysteretic nature of the VO2 insulator to metal transition (IMT), on spatial scales on the order of a few wavelengths of the probing light. In addition to effects from current-induced heating, we show that the optical response can also be modified through the use of an ionic gel to oxidize or reduce the vanadium ions in VO2, thereby driving its IMT. These measurements also demonstrate the potential for metamaterials as a means of probing metal-to-insulator transitions, allowing for enhanced optical probing of changes in VO2 properties due to electric fields from the ion gel. The second device we explored is a graphene based device used for examining the modification of graphene’s plasmonic response in conjunction with the ferroelectric high-κ dielectric lead zirconium titanate (PZT) employed as a gate dielectric. By using PZT, the carrier concentration, and therefore the optical properties of graphene, can be heavily modified with small back-gate voltages. Additionally, the use of a ferroelectric dielectric enables a form of memory in the device where transient voltage application leads to persistent changes in graphene properties. Examination of this device using scanning near-field optical microscopy allows us to determine the usefulness of similar devices in future plasmonic device

Tuning the Optical Response of Graphene and Metamaterials

The following dissertation examines the tunability of two types of proof-of-concept devices centering around post-fabrication modification of the infrared optical response. The first device, created through the hybridization of the metamaterials and the phase-transition oxide vanadium dioxide (VO2), is probed using Fourier transform infrared spectroscopy. We demonstrate that, through application of voltage pulses to this initially uniform device, a gradient in the optical properties can be obtained. This macroscopic control mechanism enables persistent modification of the device, though the hysteretic nature of the VO2 insulator to metal transition (IMT), on spatial scales on the order of a few wavelengths of the probing light. In addition to effects from current-induced heating, we show that the optical response can also be modified through the use of an ionic gel to oxidize or reduce the vanadium ions in VO2, thereby driving its IMT. These measurements also demonstrate the potential for metamaterials as a means of probing metal-to-insulator transitions, allowing for enhanced optical probing of changes in VO2 properties due to electric fields from the ion gel. The second device we explored is a graphene based device used for examining the modification of graphene’s plasmonic response in conjunction with the ferroelectric high-κ dielectric lead zirconium titanate (PZT) employed as a gate dielectric. By using PZT, the carrier concentration, and therefore the optical properties of graphene, can be heavily modified with small back-gate voltages. Additionally, the use of a ferroelectric dielectric enables a form of memory in the device where transient voltage application leads to persistent changes in graphene properties. Examination of this device using scanning near-field optical microscopy allows us to determine the usefulness of similar devices in future plasmonic device