Academic literature on the topic 'Computer-Aided Drug Discovery and Design (CADD)'

The continuous enhancements of computational tools for drug discovery, have greatly improved the pre-clinical stages of pharmaceutical research, to a higher level of efficiency and greater speed. The combination between homology modelling methods in structure-based drug design, and the chemoinformatics techniques in lead optimization, has allowed successful development of small molecule inhibitors with 30 folds higher potency of best known ASCT2 inhibitors. Three dimensional model of ASCT2 protein was constructed via fold recognition technique, the preferred method in absence of highly similar protein sequences. This model was used in virtual screening against commercial SPECs database comprised of approximately 300 000 compounds of drug-like molecules to identify potential inhibitors and characterize active site interactions through different docking procedures. Visual analysis of the docking poses with correlation to the biological results has allowed verification of the ASCT2 active site and determine the important residues for strong ligand binding. Furthermore, the ASCT2 model has been used to validate the biological results of the lead development stage through further docking analysis. AMACR homology model was built using the three dimensional X-ray crystal structure of MCR with high sequence similarity and shared protein family. The Maestro modelling software platform offered highly accurate model predictions and further docking calculations in the virtual screening stage. The biological testing was highly reliant on general cell viability results rather than specific AMACR inhibition due to the high cost and difficulties associated with AMACR activity assays. To conclude, computer-aided drug discovery in partnership with complementary in vitro techniques have made major contributions in this thesis, to develop biologically active molecules, demonstrating the high efficiency, great speed and cost-effective advantages of molecular modelling.

Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.<br>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.

Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug development to provide a rational basis of drug synthesis, rather than a trial and error approach. Molecular dynamics (MD) studies focus on investigating the details of drug-target interactions to elucidate various biophysical characteristics of interest. Infectious diseases like Trypanosoma brucei rhodesiense (TBR) and P. falciparum (malaria) are responsible for millions of deaths annually around the globe. This necessitates an immediate need to design and develop new drugs that efficiently battle these diseases. As a part of the initiatives to improve drug efficacy QSAR studies accomplished the formulation of chemical hypothesis to assist development of drugs against TBR. Results show that CoMSIA 3D QSAR models, with a Pearson’s correlation coefficient of 0.95, predict a compound with meta nitrogens on the phenyl groups, in the combinatorial space based on a biphenyl-furan diamidine design template, to have higher activity against TBR relative to the existing compound set within the same space. Molecular dynamics study, conducted on a linear benzimidazole-biphenyl diamidine that has non-classical structural similarity to earlier known paradigms of minor groove binders, gave insights into the unique water mediated interactions between the DNA minor groove and this ligand. Earlier experiments suggested the interfacial water molecules near the terminal ends of the ligand to be responsible for the exceptianlly high binding constant of the ligand. Results from MD studies show two other modes of binding. The first conformation has a single water molecule with a residency time of 6ns (average) that is closer to the central part of the ligand, which stabilizes the structure in addition to the terminal water. The second conformation that was detected had the ligand completely away from the floor of the minor groove, and hydrogen bonded to the sugar oxygens.

Virtual screening is a fast, low cost method to identify potential small molecule therapeutics from large chemical databases for the vast amount of target proteins emerging from the life sciences and bioinformatics. In this work, we applied several conventional and newly developed virtual screening approaches to identify novel non-steroidal ligands for the human and zebrafish sex hormone binding globulin (SHBG). The ‘benchmark set of steroids’ is a set of steroids with known affinities for human SHBG that has been widely used for validation in the development of different virtual screening methods. We have updated this data set by including additional steroidal SHBG ligands and by modifying the predicted binding orientations of several benchmark steroids in the SHBG binding site based on the use of an improved docking protocol and information from recent crystallographic data. The new steroid binding orientations and the expanded version of the benchmark set was then used to create new in silico models which were applied in virtual screening to identify high-affinity non-steroidal human SHBG ligands from a large chemical database. Anthropogenic compounds with the capacity to interact with the steroid-binding site of SHBG pose health risks to humans and other vertebrates including fish. We constructed a homology model of SHBG from zebrafish and applied virtual screening to identify ligands for zebrafish SHBG from a set of 80 000 existing commercial substances, many of which can be exposed to the aquatic environment. Six hits from this in silico screen were tested experimentally for zebrafish SHBG binding and three of them, hexestrol, 4-tert-octylcatechol, dihydrobenzo(a)pyren-7(8H)-one demonstrated micromolar binding affinity for the zebrafish SHBG. These findings demonstrate the feasibility of using virtual screening to identify anthropogenic compounds that may disrupt or highjack functionally important protein:ligand interactions. Studies applying this new computational toxicology method could increase the awareness of hazards posed by existing commercial chemicals at relatively low cost.

A situação da tuberculose (TB) foi alterada de forma significativa pela síndrome de imunodeficiência adquirida (SIDA ou AIDS) e pelo aparecimento de novas cepas do Mycobacterium tuberculosis resistentes ao tratamento quimioterápico, que justificariam a pesquisa de novos agentes antimicobacterianos. Alvos interessantes têm emergido para o planejamento racional de novos fármacos contra a TB, particularmente, considerando processos metabólicos específicos que ocorrem durante a biossíntese da parede celular micobacteriana e que envolvem a síntese de ácidos graxos (FAS-II, fatty acid synthase). O sistema FAS-II constitui diferença bioquímica importante entre mamíferos e micobatérias. A enzima enoil-acp (acyl carrier protein, proteína acil-carregadora) redutase (ENR) é alvo determinante no sistema FAS-II, responsável pela etapa de alongamento dos ácidos micólicos, que são os principais componentes da parede celular do M. tuberculosis. O presente projeto tem como objetivo a aplicação de metodologias do planejamento de fármacos auxiliado por computador, CADD (Computer-Aided Drug Design), em um conjunto de derivados pirrolidina carboxamidas descritos como inibidores potenciais da ENR do M. tuberculosis (InhA) com intuito de mapear o farmacóforo, investigar a orientação dos ligantes no sítio ativo e os tipos de interações que se estabelecem com os resíduos de aminoácidos do sítio de interação. Inicialmente, investigaram-se as relações quantitativas entre estrutura química e atividade biológica (QSAR, quantitative structure-activity relationships) com aplicação de abordagem multivariada. O melhor modelo QSAR indicou que propriedades estruturais, termodinâmicas e eletrônicas devem ser consideradas no processo de planejamento e proposição de novos protótipos potencialmente tuberculostáticos.<br>The incidence of tuberculosis (TB) disease has significantly changed considering the acquired immunodeficiency syndrome (AIDS) co-infection as well as the emergence of new Mycobacterium tuberculosis strains resistant to the currently chemotherapy. These facts support the search for novel antimycobacterial agents. Interesting targets have been elucidated and could be used for the rational design of new drugs against TB, primarily those related to specific biochemical metabolic pathways that occur during the cell wall biosynthesis, specially involved in the fatty acid synthase (FAS) system. The FAS-II system is an important biochemical difference between mammals and mycobacteria. The enoyl-ACP reductase (ENR) is the key enzyme in the FAS-II system, responsible for the elongation step of mycolic acids, which are the major components in the M. tuberculosis cell wall. This research project aims the application of computer-aided drug design (CADD) methodologies to a set of pyrrolidine carboxamide derivatives, which were previously reported as potential M. tuberculosis ENR (InhA) inhibitors, for mapping the pharmacophore, investigating the ligands\' orientation at the active site and also the interaction types regarding the amino acid residues in the active site. Initially, the quantitative structure-activity relationships (QSAR) were performed applying a multivariate approach. The best QSAR model indicated the structural, thermodynamic, and electronic properties must be taken into account in the design of novel leads as potential antituberculosis agents.

The potential of natural products in general, and marine natural products in particular, as pharmacological entities has been widely demonstrated in recent years. Marine benthic ecosystems contain an extraordinary range of diverse organisms that possess bioactive natural compounds, which are commonly used as defensive or protective chemical mechanisms. These effective defensive strategies are based on secondary metabolites that are crucial for the species survival. The pharmacological properties of these unique chemical compounds constitute an interesting and emerging hot research line, based upon exploiting them for the development of new drugs. The evolution, biodiversity, and specific environmental conditions found in marine ecosystems, such as Antarctica and the Mediterranean Sea, make them an amazing source of potential therapeutic agents. Interestingly, some of these natural products are capable to modulate protein functions in pathogenesis-related pathways. The process of discovery and development of new drugs, for instance small molecules, with the aforementioned capacity to modulate protein functions, is a tedious procedure that requires economic resources and time. To reduce these drawbacks, computer-aided drug design (CADD) has emerged as one of the most effective methods. A rapid exploration of the chemical space can be done with computational methods, and they are very interesting and useful complementary approaches to experimental methods. CADD techniques can be applied in different steps of the drug discovery pipeline, and also, can cover several phases of this pipeline. To that end, several objectives have been set and reached in this thesis: 1. To find possible therapeutic activities and to establish the capability to modulate protein functions in pathogenesis-related pathways from marine molecules by using different CADD tools and techniques: I. Improve the drug discovery pipeline by the elucidation of the possible therapeutic potential of a set of marine molecules against a list of targets related to different pathologies. II. Elucidation of different pharmacophoric features of marine compounds and a precise in silico binding study, highlighting the power of CADD techniques, and reporting the inhibitory activity of different natural products and indole scaffold derivatives as GSK3β, CK1δ, DYRK1A, and CLK1 inhibitors. III. Computational study and an experimental validation of meridianins and lignarenones as possible ATP and/or substrate inhibitors of GSK3β. The main conclusions of this thesis are that marine molecules can be used as therapeutic agents against protein kinases related to the AD, and the exemplification of CADD potential applied to marine drug discovery.<br>El potencial dels productes naturals en general, i els productes naturals marins en particular, com a entitats farmacològiques ha quedat demostrat al llarg dels últims anys. Els ecosistemes bentònics marins contenen una extraordinària diversitat d'organismes que posseeixen compostos naturals bioactius, que utilitzen com mecanismes químics defensius i de protecció. Aquestes efectives estratègies defensives es basen en metabòlits secundaris, crucials per a la supervivència de les espècies. Tenint en compte les propietats farmacològiques d'aquests compostos químics únics, utilitzar-los per al desenvolupament de nous fàrmacs constitueix una línia interessant de recerca emergent. L'evolució, la biodiversitat i les condicions específiques que es troben en els ecosistemes marins, com ara l'Antàrtida i el mar Mediterrani, els converteixen en una font increïble de possibles agents terapèutics, capaços de modular funcions de proteïnes involucrades en determinades patologies. El procés de descobriment i desenvolupament de nous fàrmacs, per exemple, molècules petites, és un procediment tediós que requereix de recursos econòmics i de temps. Per reduir aquests inconvenients, el disseny de fàrmacs assistit per ordinador (DFAO) ha sorgit com un dels mètodes principals i més eficaços. Es pot fer una exploració ràpida de l'espai químic amb mètodes computacionals i a més, són aproximacions complementàries als mètodes experimentals molt interessants i útils. Les tècniques de DFAO es poden aplicar en diferents passos del procés de descobriment de fàrmacs, i també, poden cobrir diverses fases d'aquest pipeline. Amb aquesta finalitat, es varen establir diversos objectius en aquesta tesi: 1. Dilucidar la possible activitat terapèutica i la capacitat per modular les funcions de proteïnes que estan relacionades amb una determinada patologia de les molècules marines mitjançant l'ús de diferents eines i tècniques de DFAO: I. millorar el pipeline de descobriment de fàrmacs mitjançant l'elucidació del possible potencial terapèutic d'un conjunt de molècules marines enfront d'una llista de dianes relacionades amb diferents patologies. II. Dilucidació de les diferents característiques farmacofóriques dels compostos marins i en un precís estudi d’unió in silico, destacant el poder de les tècniques de DFAO, i avaluar l'activitat inhibidora de diferents productes naturals i derivats d’esquelets indòlics com inhibidors de GSK3β, CK1δ, DYRK1A i CLK1. III. Estudi computacional i validació experimental de meridianines i lignarenones com a possibles inhibidors de GSK3β mitjançant la unió a la cavitat de l'ATP i/o del substrat. En relació amb aquests objectius, les conclusions principals d'aquesta tesi són, que les molècules marines poden ser utilitzades com a agents terapèutics contra proteïnes quinases relacionades amb la malaltia d’Alzheimer, i l'exemplificació del potencial de les tècniques de DFAO aplicat al descobriment de fàrmacs marins.