Rational drug design is a powerful method in which new and innovative therapeutics can be designed based on knowledge of the biological target aiming to provide more efficacious and responsible therapeutics. Understanding aspects of the targeted biological agent is important to optimize drug design and preemptively design to slow or avoid drug resistance. Chagas disease, an endemic disease for South and Central America and Mexico is caused by Trypanosoma cruzi, a protozoan parasite known to consist of six separate genetic clusters or DTUs (discrete typing units). Chagas disease therapeutics are problematic and a call for new therapeutics is widespread. Many researchers are working to use rational drug design for developing Chagas drugs and one potential target that receives a lot of attention is the T. cruzi trans-sialidase protein. Trans-sialidase is a nuclear gene that has been shown to be associated with virulence. In T. cruzi, trans-sialidase (TcTS) codes for a protein that catalyzes the transfer of sialic acid from a mammalian host coating the parasitic surface membrane to avoid immuno-detection. Variance in disease pathology depends somewhat on T. cruzi DTU, as well, there is considerable genetic variation within DTUs. However, the role of TcTS in pathology variance among and within DTU’s is not well understood despite numerous studies of TcTS. These previous studies include determining the crystalline structure of TcTS as well as the TS protein structure in other trypanosomes where the enzyme is often inactive. However, no study has examined the role of natural selection in genetic variation in TcTS. In order to understand the role of natural selection in TcTS DNA sequence and protein variation, we sequenced 540 bp of the TcTS gene from 48 insect vectors. Because all 48 sequences had multiple polymorphic bases, we examined cloned sequences from two of the insect vectors. The data are analyzed to understand the role of natural selection in shaping genetic variation in TcTS and interpreted in light of the possible role of TcTS as a drug target.

O Mal de Alzheimer é o maior causador de demência em idosos: acomete 10% da população mundial com idade em torno dos 65 anos e atinge cerca de 50% dos indivíduos com mais de 85 anos. A progressão dos sintomas da doença está associada a modificações estruturais nas sinapses colinérgicas em determinadas regiões cerebrais. A maior característica fisiopatológica do AD é a deposição de placas neuríticas extracelulares em áreas cerebrais relacionadas à memória, placas constituídas pelo peptídeo ?-amiloide 40/42, que é formado pela clivagem da Proteína Precursora Amiloide, durante seu metabolismo pela via amiloidogênica, que começa com a enzima ?-secretase. O objetivo do trabalho foi o planejamento e avaliação de novos inibidores de ?-secretase. Para isso, foram utilizadas diferentes técnicas de modelagem molecular e planejamento de moléculas, tendo como base os inibidores da ?-secretase descritos na literatura cujas estruturas estão depositadas no PDB. Posteriormente, foi realizada a avaliação in vitro da atividade inibitória de algumas destas moléculas, onde observou-se que três são capazes de satisfatoriamente inibir a atividade da ?-secretase na concentração de 1 µM. / The Alzheimer\'s disease is the major cause of elderly dementia: it affects 10% of global population with 65 years old and about 50% of individuals with 85 years old or more. The evolution of the disease symptoms is associated with structural changes in cholinergic synapses at certain brain regions. The major pathophysiological feature of AD is the deposition of extracellular neuritic plaques in areas of the brain related to memory. The ?-amyloid peptide 40/42 constitutes the plaques. It\'s formed by cleavage of the amyloid precursor protein during its metabolism by the amyloidogenic pathway, which starts with the ?-secretase enzyme. The goal of this project was the planning and evaluation of new ?-secretase inhibitors activity. For this, we used different molecular modeling and drug design techniques, based on the ?-secretase inhibitors described in the literature, whose structures are deposited in the PDB, with subsequent in vitro evaluation of this molecules activity. The in vitro assays showed three molecules able to inhibit ?-secretase at 1 µM.

The main topic of this thesis is the development of computational search methods that are useful in drug design applications. The emphasis is on exhaustiveness of the search method such that it can guarantee a certain level of geometric accuracy. In particular, the following two problems are addressed: (i) Prediction of binding mode of a drug molecule to a receptor and (ii) prediction of crystal structures of drug molecules. Predicting the binding mode(s) of a drug molecule to a target receptor is pivotal in structure-based rational drug design. In contrast to most approaches to solve this problem, the idea in this work is to analyze the search problem from a computational perspective. By building on top of an existing docking tool, new methods are proposed and relevant computational results are proven. These methods and results are applicable for other place-and-join frameworks as well. A fast approximation scheme for the docking of rigid fragments is described that guarantees certain geometric approximation factors. It is also demonstrated that this can be translated into an energy approximation for simple scoring functions. A polynomial time algorithm is developed for the matching phase of the docked rigid fragments. It is demonstrated that the generic matching problem is NP-hard. At the same time the optimality of the proposed algorithm is proven under certain scoring function conditions. The matching results are also applicable for some of the fragment-based de novo design methods. On the practical side, the proposed method is tested on 829 complexes from the PDB. The results show that the closest predicted pose to the native structure has the average RMS deviation of 1.06 °A. The prediction of crystal structures of small organic molecules has significantly improved over the last two decades. Most of the new developments, since the first blind test held in 1999, have occurred in the lattice energy estimation subproblem. In this work, a new efficient systematic search method that avoids random moves is proposed. It systematically searches through the space of possible crystal structures and conducts search space cuts based on statistics collected from the structural databases. It is demonstrated that the fast search method for rigid molecules can be extended to include flexible molecules as well. Also, the results of some prediction experiments are provided showing that in most cases the systematic search generates a structure with less than 1.0°A RMSD from the experimental crystal structure. The scoring function that has been developed for these experiments is described briefly. It is also demonstrated that with a more accurate lattice energy estimation function, better results can be achieved with the proposed robust search method.

The main topic of this thesis is the development of computational search methods that are useful in drug design applications. The emphasis is on exhaustiveness of the search method such that it can guarantee a certain level of geometric accuracy. In particular, the following two problems are addressed: (i) Prediction of binding mode of a drug molecule to a receptor and (ii) prediction of crystal structures of drug molecules. Predicting the binding mode(s) of a drug molecule to a target receptor is pivotal in structure-based rational drug design. In contrast to most approaches to solve this problem, the idea in this work is to analyze the search problem from a computational perspective. By building on top of an existing docking tool, new methods are proposed and relevant computational results are proven. These methods and results are applicable for other place-and-join frameworks as well. A fast approximation scheme for the docking of rigid fragments is described that guarantees certain geometric approximation factors. It is also demonstrated that this can be translated into an energy approximation for simple scoring functions. A polynomial time algorithm is developed for the matching phase of the docked rigid fragments. It is demonstrated that the generic matching problem is NP-hard. At the same time the optimality of the proposed algorithm is proven under certain scoring function conditions. The matching results are also applicable for some of the fragment-based de novo design methods. On the practical side, the proposed method is tested on 829 complexes from the PDB. The results show that the closest predicted pose to the native structure has the average RMS deviation of 1.06 °A. The prediction of crystal structures of small organic molecules has significantly improved over the last two decades. Most of the new developments, since the first blind test held in 1999, have occurred in the lattice energy estimation subproblem. In this work, a new efficient systematic search method that avoids random moves is proposed. It systematically searches through the space of possible crystal structures and conducts search space cuts based on statistics collected from the structural databases. It is demonstrated that the fast search method for rigid molecules can be extended to include flexible molecules as well. Also, the results of some prediction experiments are provided showing that in most cases the systematic search generates a structure with less than 1.0°A RMSD from the experimental crystal structure. The scoring function that has been developed for these experiments is described briefly. It is also demonstrated that with a more accurate lattice energy estimation function, better results can be achieved with the proposed robust search method.

Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated. A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems. A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs.  In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted. The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.

O Mal de Alzheimer é o maior causador de demência em idosos: acomete 10% da população mundial com idade em torno dos 65 anos e atinge cerca de 50% dos indivíduos com mais de 85 anos. A progressão dos sintomas da doença está associada a modificações estruturais nas sinapses colinérgicas em determinadas regiões cerebrais. A maior característica fisiopatológica do AD é a deposição de placas neuríticas extracelulares em áreas cerebrais relacionadas à memória, placas constituídas pelo peptídeo ?-amiloide 40/42, que é formado pela clivagem da Proteína Precursora Amiloide, durante seu metabolismo pela via amiloidogênica, que começa com a enzima ?-secretase. O objetivo do trabalho foi o planejamento e avaliação de novos inibidores de ?-secretase. Para isso, foram utilizadas diferentes técnicas de modelagem molecular e planejamento de moléculas, tendo como base os inibidores da ?-secretase descritos na literatura cujas estruturas estão depositadas no PDB. Posteriormente, foi realizada a avaliação in vitro da atividade inibitória de algumas destas moléculas, onde observou-se que três são capazes de satisfatoriamente inibir a atividade da ?-secretase na concentração de 1 µM. / The Alzheimer\'s disease is the major cause of elderly dementia: it affects 10% of global population with 65 years old and about 50% of individuals with 85 years old or more. The evolution of the disease symptoms is associated with structural changes in cholinergic synapses at certain brain regions. The major pathophysiological feature of AD is the deposition of extracellular neuritic plaques in areas of the brain related to memory. The ?-amyloid peptide 40/42 constitutes the plaques. It\'s formed by cleavage of the amyloid precursor protein during its metabolism by the amyloidogenic pathway, which starts with the ?-secretase enzyme. The goal of this project was the planning and evaluation of new ?-secretase inhibitors activity. For this, we used different molecular modeling and drug design techniques, based on the ?-secretase inhibitors described in the literature, whose structures are deposited in the PDB, with subsequent in vitro evaluation of this molecules activity. The in vitro assays showed three molecules able to inhibit ?-secretase at 1 µM.

1. SUMMARYMyeloperoxidase (MPO) which belongs to the peroxidase family, is found in mammalian neutrophils. This heme enzyme contributes to the production of (pseudo)halogenous acid such as HOCl which oxidizes proteins, cell membrane, DNA and RNA causing death for the pathogens. It has an antimicrobial effect due to HOCl secreting inside the phagosomes of the neutrophils, whereas it will be released outside neutrophils causing oxidative damages for the host tissues. Proteins, lipids, lipoproteins, DNA and RNA are potential targets of the MPO resulting in several chronic syndromes. Many researchers have discovered the harmful effects of MPO and its products demonstrating its role in many inflammatory chronic diseases such as: Cardiovascular diseases as in atherosclerosis. MPO contribution in atherosclerosis development has been demonstrated. Neurodegenerative diseases also was related to MPO: such as Alzheimer’s disease (AD), multiple sclerosis (MSc) and Parkinson’s disease The enzyme has been also pointed out in other diseases such as renal disease and cancer.For these reasons, MPO as a target of drug discovery has attracted the attention of many researchers. X-ray 3D structures were resolved for this enzyme, biological activity and mechanism of action were investigated in depth, and many medicinal chemists have investigated and screened for new MPO inhibitors. Indeed, this cumulative work including X-ray data, the role of MPO in different pathologies, MPO inhibitory mechanism of action, screening and various chemical entities that inhibit MPO, provided sufficient elements to start a new drug design and drug discovery process on MPO.The aim of the present study was to apply a rational drug design approach to the myeloperoxidase inhibition: from in silico to pharmacological activity. This includes:─ Conducting high throughput virtual screening in order to find new potential hits to inhibit MPO followed by mechanism of inhibition determination. ─ Selecting one hit and then implementing a whole pharmacomodulation process in order to increase the potency of the inhibition greater than the starting hit and to improve the selectivity.Firstly, a rational drug design process was launched to find new hits using high throughput virtual screening. The chosen database for the screening was ASINEX database published in ZINC.X-ray structure of human peroxidase complexed to cyanide and thiocyanate (PDB 1DNW) was selected to conduct High-Throughput Virtual Screening (HTVS). Three successive protocols with different levels of accuracy in the docking and scoring processes were used starting with HTVS, followed by Standard Precision (SP) and finally with Xtra Precision (XP). The quality of the docking process performed was validated by docking a set of 60 chosen molecules of varying chemical structure and known as MPO inhibitors. From the result of the HTVS conducted on 1,350,000 compounds, the 100 best compounds were selected. Among them, 81 molecules were available for purchase from ASINEX, those compounds were tested with a MPO inhibition assay. Thirty-two compounds (39 %) were active, but only 8 compounds were selected, featuring different chemical structures with IC50 values ranging between 0.46 ± 0.07 and 12 ± 3 μM. Among these molecules, two compounds were the best and considered as hits. One has purinedione structure which is similar with the structure of thioxanthine derivatives (F9, IC50=0.46±0.07μM). The second compound has a hexahydropyrimidine structure (A1, IC50 = 0.5 ± 0.1 μM) The most common interactions found among all 8 docked ligands are the ionic bond with Glu102 and a stacking (shifted or not) with pyrrole ring D of the prosthetic group. Hydrogen bonds with Glu102, Thr100, Gln91, Arg239, or the propionate groups of the heme are also found in several docked geometries of the complexes. Interestingly, interactions with Glu102 and pyrrole ring D of the heme were also seen with fluorotryptamine derivatives and also salicylhydroxamic acid (SHA).For measuring MPO-dependent LDL oxidation, the two best compounds were tested. Compounds A1 and F9 showed good inhibition on MPO-dependent LDL oxidation (62 ± 6, 4.5 ± 0.9, 11 ± 2% and 11 ± 2, 2.6 ± 0.8, 6 ± 4%, respectively).Consequently, in order to determine the mechanism of inhibition transient-state kinetics were further investigated of all the 8 selected compounds.Both new lead compounds (A1 and F9) act as electron donors of both Compound I and Compound II of MPO. The reaction with Compound I was significantly faster (k2 ≫ k3). As a consequence, the enzyme is trapped in the Compound II state. They reversibly inactivated the enzyme blocking the harmful halogenation activity of MPO by transferring it to the MPO peroxidase cycle. In the present study, 8 active and reversible MPO inhibitors were selected. They act as electron donors of the oxidoreductase and efficiently block the halogenation activity with reversible inactivation. Two of the selected compounds have a submicromolar activity and inhibit MPO-dependent LDL oxidation. The high-throughput virtual screening was proved to be a successful tool to find new leads of MPO inhibitors. Conducting HTVS on a large-scale database enabled selection of novel scaffolds of MPO inhibitors never explored before in less time and at less expenses.Finding 8 new different chemical scaffolds through the first step of this drug discovery process led us to choose a new hit, compound A1, which has a hexahydropyrimidine structure, compound F9 was not chosen despite being more active due to its similarity to compounds discovered by AstraZeneca. To conduct pharmacomodulation, a validation of the docking procedure was conducted by comparing the X-ray structures of MPO with 2-(3,5-bistrifluoromethylbenzylamino)-6-oxo-1H-pyrimidine-5- carbohydroxamic acid, HX1, and SHA in the X-ray structures of human MPO in complex with cyanide and thiocyanate (PDB code 1DNW) as well as in complex with HX1 (PDB code 4C1M). Compound A1 was docked into both target structures 1DNW and 4C1M. In both cases, A1 showed almost the same poses.Based on the binding modes of A1, different strategies were developed for the design of derivatives which were mainly focused on the substitution of the aromatic rings A and B, the 2 amino groups and the side chain bridges.Pharmacomodulation was carried out on the hit A1 with different strategies:─ Investigating the role of hydroxyl groups on both aromatic rings─ Shifting the position of the amino groups in the hexahydropyrimidine ring to obtain piperazine derivatives and introduction of fluorine ─ Eliminating of one ring and of an amino group in the hexahydropyrimidine ring leading to piperidine derivatives ─ Opening the hexahydropyrimidine ring while keeping amine function and changing the length of the bridge between this amino group and aromatic ring as well as the impact of substitutions on aromatic rings.─ Hybridization of fluorotryptamine derivatives (effective MPO inhibitors) with hit A1.Based on of the docking experiments, 37 designed compounds were synthesized. The assessment of inhibition of the chlorination activity of MPO was undertaken over the 37 compounds. The hit A1 IC50 = 500 nM. The best compounds inhibiting MPO exhibited the following characteristics:─ One amino group on the bridge between aromatic rings was sufficient for the establishment of binding to Glu102 ─ The presence of three methylene groups between the secondary amine and an aromatic ring improved the inhibition of chlorination and thus decreased the IC50 values. These results showed that the position of the hydroxyl group is important. The distance between the hydrogen bond acceptor (HBA) group of one aromatic ring and the amino group is very important. The docking experiments of bisarylpropylamine derivatives showed ionic and hydrogen bonding interactions between Glu102 and hydroxyl group on aromatic ring linked to the longer side chain.─ Hybridized compounds which carry a fluorotryptamine instead of the phenol ring obtained by hybridization of hit A1 and the potent MPO inhibitors fluorotryptamine derivatives. Actually, compound 38 (which had one aromatic ring and a propyl bridge attached to indole ring) had an IC50 = 54 nM which was 10 times more powerful than the starting hit.The 3 best compounds were tested to examine the transient kinetics. They act as electron donors of the oxidoreductase and efficiently shift MPO from the chlorination cycle to the peroxidase cycle. Due to the similarity of the best compound 38 to serotonin it was tested with the two other best compounds on serotonin transporter (SERT) to examine the selectivity between MPO and SERT.Compound 38 had higher selectivity over MPO but the best selective compound was 28 that contains two aromatic rings carrying one hydroxyl and one fluorine.Electron density maps were conducted to predict the site of oxidation. Results suggested it occurs preferentially at the benzene ring or the indole ring in the best compounds.Determination of redox potentials for the synthesized compounds were tested. Best compounds act as electron donors allowing a one-electron reduction of Compound I.In conclusion, the present study succeeded through rational drug design including structure-based drug design and HTVS to identify new chemical entities for MPO inhibition. Eight compounds were more active than the starting hit A1 with submicromolar inhibition potency. Hybridization and structure based design also gave improvement of selectivity of inhibitors against MPO such as compound 38. Bis-arylalkylamine derivatives are a new group of MPO inhibitors with higher selectivity which could be a new hit for future development. / Doctorat en Sciences biomédicales et pharmaceutiques (Pharmacie) / info:eu-repo/semantics/nonPublished

Lactate Dehydrogenase-A (LDH-A) is up-regulated in a broad array of cancers and is associated with poor prognosis. Involved in the hypoxic response, LDH-A is a HIF-1 target and is responsible for the enzymatic reduction of pyruvate to lactate. This is important for several reasons, chiefly (1) the regeneration of NAD+ which feeds back into earlier glycolytic stages and (2) the depletion of intracellular pyruvate concentrations. High intracellular pyruvate is known to inhibit HDACs and is associated with increased apoptosis. LDH-A is also known to be controlled by oncogenes such as c-Myc suggesting an oncogenic role. Studies have shown that the knock-out of LDH-A reduces proliferation and tumourgenicity, and stimulates the mitochondria. This thesis therefore had three aims: firstly, to validate LDH-A inhibition and elucidate its full nature in terms of the implications for tumour survival; secondly, to ascertain the role of LDH-B in order to determine whether selectivity towards LDH-A would be a necessary feature of any small molecule; lastly, to recapitulate siRNA mediated LDH-A inhibition with small molecule inhibitors that had the potential for clinical application. The thesis examined both clinical data and a broad panel of cultured cancer cell types in order to select appropriate model in which to validate siRNA mediated inhibition of LDH-A and LDH-B. After it was demonstrated that LDH-A inhibition reduced the growth of cultured cells, a range of techniques were used to quantify this reduced growth in terms of cell death and changes in metabolism. Further to this, literature studies had proposed a role for LDH-B in maintaining lactate fuelled tumour growth; however, this thesis shows that in the cell lines studied, lactate-fuelled tumour growth was an LDH-A dependent phenomenon. Finally, a high throughput assay system was designed and validated and a library of small molecules was selected, synthesized, and screened in order to identify selective inhibitors of LDH-A.

Nucleic acids have proven to be viable targets for small molecule drugs. While many examples of such drugs are detailed in the literature, only a select few have found practical use in a clinical setting. These currently employed nucleic acid targeting therapies suffer from either debilitating off-target side effects or succumb to a resistance mechanism of the target. The need for new small molecules that target nucleic acids is evident. However, designing a novel drug to bind to DNA or RNA requires a detailed understanding of exactly what binding environments each nucleic acid presents. In an effort to broaden this knowledge, the work presented in this thesis details the binding location and affinity of known and novel nucleic acid binding small molecules with targets ranging from simple RNA secondary structure all the way to the complex structure of ribosomal RNA. Specifically, it is shown that the anthracycline class of antineoplastics prefer to bind at or near mismatch base pairs in both physiologically relevant iron responsive element RNA hairpin constructs as well as DNA hairpin constructs presenting mismatched base pairs. Also characterized in this thesis is a novel class of topoisomerase II / histone deacetylase inhibitor conjugates that display a unique affinity for DNA over RNA. Finally, the novel class of macrolide-peptide conjugates, known as peptolides, are shown to retain potent translation inhibition of the prokaryotic ribosome. The binding pocket of the peptolides, including a crevice previously unreachable by macrolides that extends away from the peptidyl transferase center toward the subunit interface, is confirmed in detail via chemical footprinting of the 70S ribosome. Overall, the identification of a novel binding site for the anthracycline class of drugs and the characterization of the two novel drug designs presented in this thesis will undoubtedly aid in the effort to design and discover new molecules that aim for nucleic acid targets. For example, the anthracycline derivative topoisomerase II / histone deacetylase inhibitor conjugates, with their differential mode of nucleic acid binding, may prove to have a unique side effect profile in a therapeutic application. The peptolide compounds also have the potential to be applied as novel antibiotics as they bind to an area of the prokaryotic ribosome unrelated to known macrolide resistance mutations. Furthermore, as a result of the observation of this thesis work that some peptolides also posses eukaryotic translation inhibition capabilities, they could prove to be useful in preventing the growth of rapidly proliferating eukaryotic cells such as plasmodium, leishmania, or tumor cells. Additionally, different head groups could be utilized in creating new peptolides; for example, an oxazolidinone antibiotic could be employed to sample a different binding area of the ribosome.

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No. of bitstreams: 2 Dissertação - Ricardo Lemes Gonçalves - 2017.pdf: 6297486 bytes, checksum: 3393a7cb0ffe26eafd0acd04f1198ab0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-10-05 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Flavivirus-induced pathogens are considered a serious public health problem in the world, because they affect primarily the poor populations of underdeveloped tropical countries. This family of viruses has an enveloped positive RNA genome encoding tree structural proteins and seven non-structural proteins. In particular, non-structural protein 1 (NS1) is associated mainly with the viral replication process and immune system leakage, and can be found in different glycosylated oligomeric forms, but only "mature" after its dimerization, or when in the hexamer form. In this context, inhibition of the dimerization process of NS1 has been pointed as a great target for the rational design of drugs. However, for this type of rationalized approach to be successful, it is necessary to understand the molecular mechanisms involved in the process of dimerization, as well as characterize its functional regions. In this study, through Molecular Dynamics (DM) simulations, the structural behavior of the NS1's of the Dengue and Zika were evaluated and compared in the monomeric and dimeric forms, from structures crystallized with glycosylations. For the structure of the Dengue (PDB: 5k6k), there was a need to previously model the regions of missing residues, then making necessary to replace the sugars in the structures. All of the N-glycosylations and intercysteine bonds of each monomer and dimer were performed in the Amber14 software. Specific histidine protonation was predicted by the H++ assay before proceeding with DM. All structures were submitted to DM by 100ns using the GROMACS 5.1.2 software. The stability and flexibility of the structures observed in the trajectories were used to elucidate the mechanisms responsible for the monomer-monomer interaction, as well as to understand the singularities between the regions that stood out. In the monomeric form of the two species, large conformational fluctuations were observed in their N-terminal loops involved in the β-roll composition, which in the dimeric form were stabilized by the triad Ile/Val19 - Phe20 - Ile21 for creating a framework favorable to the interlacing of the N-terminal loops between the A and B chains. Concomitantly, Lysines-189 of the β-ladder domain acted as a key residue (staple) to stabilize the central portion of β-roll. The stability mechanisms of NS1 revealed in this work for the Zika and Dengue species, contribute to make the possibility of pharmacological intervention more accessible, in a rationalized way, whose approach could be directed at specific structural points responsible for its biological role. / As patogenias causadas pelos Flavivírus são consideradas um sério problema de saúde pública no mundo, pois afetam principalmente populações pobres de países tropicais subdesenvolvidos. Esta família de vírus apresenta um genoma de RNA positivo envelopado que codifica três proteínas estruturais e sete proteínas não estruturais. Em particular, a proteína não estrutural 1 (NS1) está associada principalmente aos processos de replicação viral e escape do sistema imune, sendo encontrada em diferentes formas oligoméricas glicosiladas, mas na sua forma “madura” somente após sua dimerização, ou quando na forma de hexâmero. Neste contexto, a inibição do processo de dimerização da NS1 tem sido apontada como um ótimo alvo para o design racional de fármacos. Contudo, para que este tipo de abordagem racional seja bem sucedida, é necessário compreender os mecanismos moleculares que estão envolvidos no seu processo de dimerização, bem como caracterizar suas regiões funcionais. Neste estudo, através de simulações de Dinâmica Molecular (DM), o comportamento estrutural das NS1’s do Zika e Dengue foram analisados e comparados nas formas monoméricas e diméricas, partindo de estruturas cristalizadas nas formas glicosiladas. No caso da estrutura do Dengue (PDB: 5k6k) houve a necessidade de modelar previamente as regiões dos resíduos faltantes, tornando em seguida necessária a recolocação dos açucares nas estruturas. Todas as N-glicosilações e ligações entre cisteínas de cada monômero e dímero, foram efetuadas a partir do software Amber 14. A protonação especifica das histidinas foi predita pelo servirdor H++ antes de proceder com a DM. Todas as estruturas foram submetidas à DM por 100ns usando o software GROMACS 5.1.2. A estabilidade e flexibilidade das estruturas observadas nas trajetórias foram usadas para elucidar os mecanismos responsáveis pela interação monômero-monômero, bem como compreender as singularidades entre as regiões que se destacaram. Na forma monomérica das duas espécies, observou-se grandes flutuações conformacionais nas suas alças N-terminais envolvidas na composição do β-roll, que na forma dimérica foram estabilizadas pela tríade Ile/Val19 - Phe20 - Ile21 por criar um arcabouço favorável ao entrelaço das alças N-terminais entre as cadeias A e B. Concomitantemente, as Lisinas-189 do domínio β-leadder atuaram como um resíduo chave (grampo) para estabilizar a porção central do β-roll. Os mecanismos de estabilidade da NS1 revelados neste trabalho para as espécies Zika e Dengue, contribuem para tornar mais acessível a possibilidade de uma intervenção farmacológica de forma racionalizada, cuja abordagem poderia ser dirigida em pontos estruturais específicos responsáveis por seu papel biológico.