Database development and machine learning prediction of pharmaceutical agents

Ph.DDOCTOR OF PHILOSOPH

Prioritizing Small Molecules for Drug Discovery or Chemical Safety Assessments using Ligand- and Structure-based Cheminformatics Approaches

Recent growth in the experimental data describing the effects of chemicals at the molecular, cellular, and organism level has triggered the development of novel computational approaches for the prediction of a chemical's effect on an organism. The studies described in this dissertation research predict chemical activity at three levels of biological complexity: binding of drugs to a single protein target, selective binding to a family of protein targets, and systemic toxicity. Optimizing cheminformatics methods that examine diverse sources of experimental data can lead to novel insight into the therapeutic use and toxicity of chemicals. In the first study, a combinatorial Quantitative Structure-Activity Relationship (QSAR) modeling workflow was successfully applied to the discovery of novel bioactive compound against one specific protein target: histone deacetylase inhibitors (HDACIs). Four candidate molecules were selected from the virtual screening hits to be tested experimentally, and three of them were confirmed active against HDAC. Next, a receptor-based protocol was established and applied to discover target-selective ligands within a family of proteins. This protocol extended the concept of protein/ligand interaction-guided pose selection by employing a binary classifier to discriminate poses of interest from a calibration set. The resulting virtual screening tools were applied for enriching beta2-adrenergic receptor (β2AR) ligands that are selective against other subtypes in the βAR family (i.e. β1AR and β3AR). Moreover, some computational 3D protein structures used in this study have exhibited comparative or even better performance in virtual screening than X-ray crystal structures of β2AR, and therefore computational tools that use these computational structures could complement tools utilizing experimental structures. Finally, a two-step hierarchical QSAR modeling approach was developed to estimate in vivo toxicity effects of small molecules. Besides the chemical structural descriptors, the developed models utilized additional biological information from in vitro bioassays. The derived models were more accurate than traditional QSAR models utilizing chemical descriptors only. Moreover, retrospective analysis of the developed models helped to identify the most informative bioassays, suggesting potential applicability of this methodology in guiding future toxicity experiments. These studies contribute to the development of computational strategies for comprehensive analysis of small molecules' biological properties, and have the potential to be integrated into existing methods for modern rational drug design and discovery.Doctor of Philosoph

Design, virtual screening and structural studies of new molecules with potential antitumor and antiinflammatory activity

2010 - 2011Computational methodologies in combination with experimental techniques as Nuclear Magnetic Resonance (NMR) have become a crucial component in drug discovery process, from hit identification to lead optimization. The study of ligand-macromolecule interactions, in fact, has a crucial role for the design and the development of new and more powerful drugs. In this project, different aspects of interaction and recognition processes between ligand and macromolecule, and streostructure assignment has been studied through this kind of combined approach with the aim to identify novel potential antitumor and/or antiinflammatory molecules. In particular, because the strong interconnection between the tumoral and inflammatory pathology has led to the identification of new target utilizable for the therapy, in this project will be described proteins (Histone deacetilase, HDAC; Nicotinamide Phosphoribosyltransferase, NMPRTase or Nampt; microsomal prostaglandin E2 synthase, mPGES-1; human synovial Phospholipases A2, hsPLA2; human Farnesoid-X-Receptor, FXR; human Pregnane-X-Receptor, PXR; Bile Acid Receptor GPBAR-1, TGR5) involved in essential cellular processes and acting at diverse levels and phases of the tumor and inflammation diseases. The results obtained can be summarized in three main areas of activity, whose relative weight was varied according to the development of the overall project: a) Support in the design of original scaffolds for the generation of libraries potentially utilizable in therapy. This work was exclusively conducted in silico by a molecular docking technique in order to direct the design of the new molecules basing on the analysis of ligand-target interactions and the synthetic possibilities. This kind of approach was successfully applied leading to the identification of new potential inhibitors for HDAC enzymes with ciclic (mono and bis amides, paragraph 2.2; conformationally locked calixarenes, paragraph 2.4), and linear (hydroxamic tertiary amines, paragraph 2.3) structures, and isoform selective (paragraph 2.6), and of ligands for microsomal prostaglandin E2 synthase (mPGES)-1 (two series of triazole-based compounds; paragraphs 4.2 and 4.3). For each of this described studied, the good qualitative accordance between the calculated and experimental data has made possible the identifications of new lead compounds, rationalizing in this way the key features to the target inhibition. b) Rationalization of the biological activity of compounds by the study of the drug-receptor interactions. Molecular docking was used for the detailed study of antiinflammatory and antitumoral compounds whose activities are known a priori. In fact, thanks to this procedure, in this thesis several rationalizations of binding modes were reported related to Ugi products derivatives of CHAP 1 (HDAC inhibitors, paragraph 2.5), new and potent inhibitor of NMPRTAse analogs of FK866 and CHS 828 (chapter 3), marine natural products as inhibitors of hsPLA2 (BLQ and CLDA, chapter 5), 4-methylen sterols extracted from Theonella swinhoei as ligands of FXR and PXR (chapter 6), and known compounds as taurolitholic acid and ciprofloxacin (chapter 7), agonists of TGR5. Through the in silico methodology the putative binding modes for the reported molecules was described offering a complete rationalization of docking results, evaluating the influence of the ligand target interactions (e.g. hydrophobic, hydrophilic, electrostatic contacts) on the biological activity. c) Determination of relative configuration of natural products. The complete comprehension of the three dimensional structure of synthetic or isolated molecules is fundamental to design and characterize new platform potentially utilizable in therapy. On this basis, the combined approach between the quantum mechanical (QM) calculation of NMR parameters and NMR spectroscopy was revealed a very useful mean to lead the total synthesis of natural product toward the right isomer avoiding waste of time and resources (paragraph 8.1). Moreover, the stereostructure assignment of marine natural products conicasterol F and its analog thonellasterol I was reported in the paragraph 8.2. by a novel combined approach between the quantitative interproton distance determinations by ROE and quantum mechanical calculations of chemical shifts. (edited by author)X n.s

Quantitative approaches to probe the acetylproteome

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (p. 173-175).Lysine acetylation is a prevalent post-translational modification whose multi-varied biological roles have recently emerged. While having all the necessary components of a signaling network, lysine acetylation studies have been limited to a small subset of proteins and pathways. Using a quantitative unbiased mass spectrometry approach, we explored the role of growth factor stimulation on lysine acetylation. Although the growth factors bind receptor tyrosine kinases, growth factor stimulation resulted in rapid and dynamic changes in lysine acetylation. Furthermore, we demonstrated that short-term HDAC inhibition alters phosphotyrosine-signaling networks. To better understand this behavior, a suite of biochemical and computational methods were developed. Bromodomains were engineered to explore binding preferences using degenerate peptide arrays as well as develop acetyllysine affinity reagents as an alternative to anti-acetyllysine antibodies. Additionally, bioorthogonal proteomics were employed to identify acetyltransferase substrates. Taken together, the knowledge generated and the methods developed provide a toolkit for the analysis of lysine acetylation networks in the context of many biological processes as well as diseases.by Bryan David Bryson.Ph.D

Drug Repurposing

This book focuses on various aspects and applications of drug repurposing, the understanding of which is important for treating diseases. Due to the high costs and time associated with the new drug discovery process, the inclination toward drug repurposing is increasing for common as well as rare diseases. A major focus of this book is understanding the role of drug repurposing to develop drugs for infectious diseases, including antivirals, antibacterial and anticancer drugs, as well as immunotherapeutics

Personalized Medicine in the Field of Inflammatory Skin Disorders

Skin inflammation is associated with a wide range of conditions which represent major health issues worldwide. Skin and mucosal surfaces represent the primary interface between the human body and the environment, susceptible to numerous factors whose action results in diseases produced by chemical substances, mechanical trauma, microbial agents, radiation, etc. Inflammation, a complex network of interactions between soluble molecules and cells, represents the main modality of the skin’s response to injuries. Numerous studies have revealed close links between chronic inflammation, oxidative stress, and carcinogenesis. Chronic inflammation induces the activation of various cell types and an increase in the production of reactive oxygen species, promoting the initiation of a malignant process. Identifying specific biomarkers is essential for understanding molecular mechanisms and developing therapies appropriate to the patient’s characteristics.Personalized medicine is an emerging field of medicine that has the potential to predict which therapy will be safe and efficacious for specific patients using an individual’s genetic profile to guide decisions regarding the diagnosis, treatment, as well as prevention of disease. This book gathers articles that present recent advancements in research involving the mechanisms that underlie the development of inflammatory skin disorders, skin and mucosal inflammation in general

Advanced Classical Hodgkin Lymphoma: new insights in prognostic factors using gene and microRNA expression signatures

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 24-10-201