Humans are tightly linked to their thermal microclimatic environments, yet few studies have evaluated the outdoor thermal comfort of users performing physical activity. The purpose of this research was to critically review, assess, and apply findings using the COMFA ('COMfort FormulA') human energy budget for users performing physical activity outdoors. Research objectives were: to apply an improved multi-segmented skin temperature approach to the COMFA model; to evaluate its accuracy in predicting actual thermal sensation (ATS); to implement techniques to account for human behaviours associated with clothing and metabolic variations; to spatially assess human energy budget moderating effects of urban parks; and to investigate extreme heat stress situations. To evaluate modelled mean skin temperature (T_sk), field tests were conducted on subjects performing 30 minute outdoor sessions of steady-state moderately intense activity (cycling and running). The model accurately predicted T_sk, showing significantly strong agreement (r = 0.859, p<0.01). ATS votes displayed significantly strong rank correlation with budget scores calculated using both measured and predicted T_sk (r_s = 0.507 and 0.517, respectively, p<0.01). A further improvement of Incorporating conditioning level of an individual gave more realistic estimations of metabolism for budget estimation. Adopting a new relative wind velocity (v_r) equation, which incorporates wind to body angle, revealed errors of the original v_r equation in the modelling of convective heat loss and T_sk. Application of the COMFA model in urban spaces showed that energy budgets were more closely correlated to incoming solar radiation (r = 0.941) than air temperature (r = 0.490), with a significantly strong linear regression found with radiation absorbed by a human (R^2=0.858). Treed greenspace was shown to strongly enhance thermal comfort the greatest, decreasing budgets on average by 25.5 Wm^2. Budget values were found to be a strong predictor of emergency dispatch calls received in Toronto during the July 2010 heat wave (R^2 = 0.86). This study has displayed the potential of the COMFA outdoor model as a new tool to make heat forecasting more meaningful to the public, emergency responders, and urban planners. / OGS; NSERC

Salvinorin A is a non-nitrogenous, selective kappa opioid receptor agonist with potent hallucinogenic properties. Because Salvinorin A has no basic nitrogen, it does not readily adhere to the “message-address” concept of selectivity for the opioid receptors. Therefore, a better understanding of how salvinorin A and its analogs interact with the kappa opioid receptor may shed some light on how salvinorin A obtains its potency and selectivity. The structure-affinity relationships (SAFIR) of salvinorin A and its analogs along with a discussion of the selectivity of the opioid receptors, is presented. A fragment of salvinorin A, methyl-3-acetoxy-4-oxocyclohexanecarboxylate, was synthesized to determine if the B, C and D rings are or are not necessary for binding to the opioid receptors. The fragment was found not to bind to the kappa, delta or mu receptor which reinforces the importance of the B, C and D rings in the binding of salvinorin A to the kappa opioid receptor. Homology models of the kappa, delta and mu opioid receptors were constructed based on inactive bovine rhodopsin, light-activated bovine rhodopsin and the human beta-2 adrenergic receptors. The program MODELLER was also used to construct the kappa opioid receptor. Two comparative molecular field analysis (CoMFA) studies are then presented which compared three different types of alignment methods. The alignment methods employed included a receptor-docked alignment in which the salvinorin A analogs were docked into a model of the kappa opioid receptor using the program GOLD. The docked poses for this alignment were chosen based on their similarity to our postulated model of salvinorin A in the kappa opioid receptor. In our model the furan oxygen forms hydrogen bonds with Q115(2.60) and Y320(7.43), the methoxy oxygen of the C-4 position ester group may form a hydrogen bond with Y312(7.35) and the methyl group of the C-2 position acetoxy moiety forms a hydrophobic interaction with Y313(7.36). These interactions are consistent with mutagenesis studies. The other alignment methods employed were a FlexS alignment and a realignment of the receptor-docked poses using the Fit Atoms function within SYBYL. Only the receptor-docked alignment method resulted in robust and predictive CoMFA models which indicates that the analogs may bind to the kappa opioid receptor in a similar but non-identical way. In addition, information from the CoMFA models based on the receptor-docked alignment led to a postulated binding mode for a set of amine analogs of salvinorin A which were not part of the original data set. Docking studies have the positively charged C-2 position amine group interacting with E209(XL2.49) while the furan oxygen and C-4 position ester group interacts with the same residues as in our model of salvinorin A in the kappa opioid receptor. The studies presented here not only support our postulated model of salvinorin A binding to the kappa opioid receptor but may also explain the trend of the beta epimers of the amine analogs to have a higher affinity than the corresponding alpha epimers. Site-directed mutagenesis studies could provide data to support or refute the postulated models of the amines docked in the kappa opioid receptor presented here.

<p>Ten years ago, the first protease inhibitor targeting the human immunodeficiency virus (HIV) was approved for clinical use. Highly active antiretroviral therapy (HAART), which combined protease and reverse transcriptase inhibitors, quickly became the standard therapy for treating patients infected with HIV and Acquired Immune Deficiency Syndrome (AIDS). Nevertheless, last year the AIDS pandemic reached its highest level ever. Many infected patients, mainly in the developing countries, are still without treatment. Among those patients who receive treatment, an increase in drug resistance and new-infection with drug-resistant strains are seen. To come to terms with these problems, new drugs that are efficient against resistant strains and can be produced at low cost are needed.</p><p>In this study, we have focused our research efforts on cyclic sulfamides active as HIV-1 protease inhibitors. Distinctive to this compound class, as compared to the inhibitors so far approved for clinical use, was the incorporation of a water mimic that displaces the structural water (W301) observed in the X-ray crystal co-complexes. The first part of the study was aimed at understanding the rationale behind the nonsymmetric binding mode that the inhibitor adopted when bound to the enzyme. Symmetric and nonsymmetric inhibitors were synthesized and the structure-activity relationships and preferable binding modes were rationalized with the help of Comparative Molecular Field Analysis (CoMFA).</p><p>In the second part of the study, an attempt was made to reduce the size of these inhibitors. As a result, the traditional P1/P1' substituents were removed, while the P2/P2' substituents were elongated in an attempt to reach between the binding sites. The design hypothesis was shown to be successful and inhibitors possessing nanomolar activity were identified.</p>

<p>Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT₂ receptor.</p><p>The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT₂ receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan.</p><p>To further examine ligand binding, a 3D model of the AT₂ receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT₂ receptor.</p><p>By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT₂ receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT₁ and AT₂ receptor affinity as well as selectivity were derived. </p>

Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT2 receptor. The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT2 receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan. To further examine ligand binding, a 3D model of the AT2 receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT2 receptor. By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT2 receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT1 and AT2 receptor affinity as well as selectivity were derived.

Ten years ago, the first protease inhibitor targeting the human immunodeficiency virus (HIV) was approved for clinical use. Highly active antiretroviral therapy (HAART), which combined protease and reverse transcriptase inhibitors, quickly became the standard therapy for treating patients infected with HIV and Acquired Immune Deficiency Syndrome (AIDS). Nevertheless, last year the AIDS pandemic reached its highest level ever. Many infected patients, mainly in the developing countries, are still without treatment. Among those patients who receive treatment, an increase in drug resistance and new-infection with drug-resistant strains are seen. To come to terms with these problems, new drugs that are efficient against resistant strains and can be produced at low cost are needed. In this study, we have focused our research efforts on cyclic sulfamides active as HIV-1 protease inhibitors. Distinctive to this compound class, as compared to the inhibitors so far approved for clinical use, was the incorporation of a water mimic that displaces the structural water (W301) observed in the X-ray crystal co-complexes. The first part of the study was aimed at understanding the rationale behind the nonsymmetric binding mode that the inhibitor adopted when bound to the enzyme. Symmetric and nonsymmetric inhibitors were synthesized and the structure-activity relationships and preferable binding modes were rationalized with the help of Comparative Molecular Field Analysis (CoMFA). In the second part of the study, an attempt was made to reduce the size of these inhibitors. As a result, the traditional P1/P1' substituents were removed, while the P2/P2' substituents were elongated in an attempt to reach between the binding sites. The design hypothesis was shown to be successful and inhibitors possessing nanomolar activity were identified.

The hepatitis C virus (HCV), with a global prevalence of roughly 2%, is among the most serious diseases today. Among the more promising HCV targets is the NS3 protease, for which several drug candidates have entered clinical trials. In this work, computational methods have been developed and applied to the design of inhibitors of the HCV NS3 protease. Comparative molecular field analysis (CoMFA) modeling and molecular docking are the two main computational tools used in this work. CoMFA is currently the most widely used 3D-QSAR method. Methodology for improving its predictive performance by evaluating 6120 combinations of non-default parameters has been developed. This methodology was tested on 9 data sets for various targets and found to consistently provide models of enhanced predictive accuracy. Validation was performed using q2, r2pred and response variable randomization. Molecular docking was used to develop SARs in two series of inhibitors of the HCV NS3 protease. In the first series, preliminary investigations indicated that replacement of P2 proline with phenylglycine would improve potency. Docking suggested that phenylglycine-based inhibitors may participate in two additional interactions but that the larger, more flexible phenylglycine group may result in worse ligand fit, explaining the loss in potency. In the second series, β-amino acids were explored as α-amino acid substitutes. Although β-amino acid substitution may reduce the negative attributes of peptide-like compounds, this study showed that β-amino acid substitution resulted in reduced potency. The P3 position was least sensitive to substitution and the study highlighted the importance of interactions in the oxyanion hole. Finally, docking was used to provide the conformations and alignment necessary for a CoMFA model. This CoMFA model, derived using default settings, had q2 = 0.31 and r2pred = 0.56. Application of the optimization methodology provided a more predictive model with q2 = 0.48 and r2pred = 0.68.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2014-11-13T17:53:26Z No. of bitstreams: 2 dissertacao - Cleber Camilo de Melo Filho - 2014.pdf: 4135177 bytes, checksum: 8cda88d9da11bbe2de5d43dbb24799a9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-11-17T15:09:35Z (GMT) No. of bitstreams: 2 dissertacao - Cleber Camilo de Melo Filho - 2014.pdf: 4135177 bytes, checksum: 8cda88d9da11bbe2de5d43dbb24799a9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-11-17T15:09:35Z (GMT). No. of bitstreams: 2 dissertacao - Cleber Camilo de Melo Filho - 2014.pdf: 4135177 bytes, checksum: 8cda88d9da11bbe2de5d43dbb24799a9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-10 / Schistosomiasis is a neglected tropical disease (NTD) that affects many individuals, mainly in tropical areas. This disease is caused by blood flukes of the genus Schistosoma, which have the snails of the genus Biomphalaria as their intermediate hosts. The most used drug in schistosomiasis treatment is praziquantel, which because of its widespread use, brings concerns about the development of resistance. The enzyme Thioredoxin Glutathione Reductase of Schistosoma mansoni (SmTGR) has an important function in reactive oxygen species (ROS) detoxification, allowing the survival of parasites for a very long time in blood stream, protecting them against the host immune system. The dependence of the parasite on a single system for ROS detoxification, makes the SmTGR a promissing target in the development of new schistosomicidal drugs. Facing the need for development of new drugs against schistosomiasis, quantitative structure activity relationships (QSAR) studies were carried out for a series of oxadiazoles-2-oxides reported in literature as SmTGR inhibitors. Hologram-QSAR (HQSAR) analysis, a two-dimensional QSAR method (2D-QSAR), was performed. Furthermore comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA), that are three-dimensional QSAR (3D-QSAR), were also carried out. In 3D-QSAR methods, two partial charge calculation methods were used: the empirical method Gasteiger-Hückel and the semiempirical method AM1-BCC. Two alignment strategies were also tested, one based on molecular volume superposition and the other based on a morphological similarity function. The QSAR models generated showed great robustness and external predictivity and can be used to predict the biological activity of new compounds inhibitors of SmTGR. The contribution and contour maps showed important structural information about oxadiazoles-2-oxides that was used for the design of new SmTGR inhibitors. / A esquistossomose é uma doença tropical negligenciada (DTN) que afeta grande número de indivíduos, principalmente em áreas tropicais. Esta doença é causada por vermes platelmintos do gênero Schistosoma, que possuem como hospedeiros intermediários os caramujos do gênero Biomphalaria. O fármaco mais utilizado no tratamento atualmente é o praziquantel, que devido à grande disseminação do seu uso, traz preocupações quanto ao desenvolvimento de resistência. A enzima tioredoxina glutationa redutase de Schistosoma mansoni (SmTGR) desempenha um papel importante na detoxificação de espécies reativas de oxigênio (ROS), permitindo a sobrevivência dos parasitos por muito tempo na circulação sanguínea, protegendo-os do sistema imune do hospedeiro. A dependência do parasito de um único sistema para detoxificação de ROS, torna a SmTGR um alvo promissor no desenvolvimento de novos fármacos esquistossomicidas. Frente à necessidade de se desenvolver novos fármacos contra esquistossomose, foram realizados estudos quantitativos da relação entre estrutura e atividade (QSAR) para uma série de oxadiazóis-2-óxidos reportados na literatura como inibidores de SmTGR. Foi realizada análise de holograma-QSAR (HQSAR), que é um método de QSAR bidimensional (QSAR-2D). Além disso, foram utilizadas a análise comparativa de campos moleculares (CoMFA) e a análise comparativa dos índices de similaridade molecular (CoMSIA), que são métodos de QSAR tridimensional (QSAR-3D). Nos métodos de QSAR-3D foram utilizados dois métodos de cálculo de cargas parciais: o método empírico Gasteiger-Hückel e o semi-empírico AM1-BCC. Foram também testadas duas estratégias de alinhamento, uma baseada na sobreposição de volumes moleculares e outra baseada em uma função de similaridade morfológica. Os modelos de QSAR gerados demonstraram boa robustez e preditividade externa e foram usados para predição da atividade biológica de novos compostos inibidores de SmTGR. Os mapas de contribuição e de contorno obtidos forneceram informações estruturais importantes a respeito dos oxadizóis-2-óxidos, que foram utilizadas no planejamento de novos inibidores da SmTGR.

<p>Human Immunodeficiency Virus (HIV) is the causative agent of the pandemic disease Acquired Immune Deficiency Syndrome (AIDS). HIV acts to disrupt the immune system which makes the body susceptible to opportunistic infections. Untreated, AIDS is generally fatal. Twenty years of research by countless scientists around the world has led to the discovery and exploitation of several targets in the replication cycle of HIV. Many lives have been saved, prolonged and improved as a result of this massive effort. One particularly successful target has been the inhibition of HIV protease. In combination with the inhibition of HIV reverse transcriptase, protease inhibitors have helped to reduce viral loads and partially restore the immune system. Unfortunately, viral mutations leading to drug resistance and harmful side-effects of the current medicines have identified the need for new drugs to combat HIV.</p><p>This study presents computational efforts to understand the interaction of inhibitors to HIV protease. The first part of this study has used molecular modelling and Comparative Molecular Field Analysis (CoMFA) to help explain the structure-active relationship of a novel series of protease inhibitors. The inhibitors are sulfamide derivatives structurally similar to the cyclic urea candidate drug mozenavir (DMP-450). The central ring of the sulfamides twists to adopt a nonsymmetrical binding mode distinct from that of the cyclic ureas. The energetics of this twist has been studied with <i>ab initio</i> calculations to develop improved empirical force field parameters for use in molecular modelling.</p><p>The second part of this study has focused on an analysis of the association and dissociation kinetics of a broad collection of HIV protease inhibitors. Quantitative models have been derived using CoMFA which relate the dissociation rate back to the chemical structures. Efforts have also been made to improve the models by systematically varying the parameters used to generate them.</p>

Human Immunodeficiency Virus (HIV) is the causative agent of the pandemic disease Acquired Immune Deficiency Syndrome (AIDS). HIV acts to disrupt the immune system which makes the body susceptible to opportunistic infections. Untreated, AIDS is generally fatal. Twenty years of research by countless scientists around the world has led to the discovery and exploitation of several targets in the replication cycle of HIV. Many lives have been saved, prolonged and improved as a result of this massive effort. One particularly successful target has been the inhibition of HIV protease. In combination with the inhibition of HIV reverse transcriptase, protease inhibitors have helped to reduce viral loads and partially restore the immune system. Unfortunately, viral mutations leading to drug resistance and harmful side-effects of the current medicines have identified the need for new drugs to combat HIV. This study presents computational efforts to understand the interaction of inhibitors to HIV protease. The first part of this study has used molecular modelling and Comparative Molecular Field Analysis (CoMFA) to help explain the structure-active relationship of a novel series of protease inhibitors. The inhibitors are sulfamide derivatives structurally similar to the cyclic urea candidate drug mozenavir (DMP-450). The central ring of the sulfamides twists to adopt a nonsymmetrical binding mode distinct from that of the cyclic ureas. The energetics of this twist has been studied with ab initio calculations to develop improved empirical force field parameters for use in molecular modelling. The second part of this study has focused on an analysis of the association and dissociation kinetics of a broad collection of HIV protease inhibitors. Quantitative models have been derived using CoMFA which relate the dissociation rate back to the chemical structures. Efforts have also been made to improve the models by systematically varying the parameters used to generate them.