Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most basic and fundamental problems at the heart of bioinformatics. It is central to problems currently under intense investigation in protein structure prediction, phylogenetic analyses, and computational drug development. Currently discriminative methods for homology detection, which are not readily interpretable, are substantially more powerful than their more interpretable counterparts, particularly when sequence identity is very low. Here I present a computational graph-based framework for homology inference using physiochemical amino acid properties which aims to both reduce the gap in accuracy between discriminative and generative methods and provide a framework for easily identifying the physiochemical basis for the structural similarity between proteins. The accuracy of my method slightly improves on the accuracy of PSI-BLAST, the most popular generative approach, and underscores the potential of this methodology given a more robust statistical foundation.

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Analysis of genome sequences is enabling identification of numerous novel characteristics that provide valuable means for genetic and biochemical studies. Of these characteristics, Conserved Signature Indels (CSIs) in proteins which are specific for a given group of organisms have proven particularly useful for evolutionary and biochemical studies. My research work focused on using comparative genomics techniques to identify a large number of CSIs which are distinctive characteristics of fungi and other important groups of organisms. These CSIs were utilized to understand the evolutionary relationships among different proteins (species), and also regarding their structural features and functional significance. Based on multiple CSIs that I have identified for the PIP4K/PIP5K family of proteins, different isozymes of these proteins and also their subfamilies can now be reliably distinguished in molecular terms. Further, the species distribution of CSIs in the PIP4K/PIP5K proteins and phylogenetic analyses of these protein sequences, my work provides important insights into the evolutionary history of this protein family. The functional significance of one of the CSI in the PIP5K proteins, specific for the Saccharomycetaceae family of fungi, was also investigated. The results from structural analysis and molecular dynamics (MD) simulation studies show that this 8 aa CSI plays an important role in facilitating the binding of fungal PIP5K protein to the membrane surface. In other work, we identified multiple highly-specific CSIs in the phosphoketolase (PK) proteins, which clearly distinguish the bifunctional form of PK found in bifidobacteria from its homologs (monofunctional) found in other organisms. Structural analyses and docking studies with these proteins indicate that the CSIs in bifidobacterial PK, which are located on the subunit interface, play a role in the formation/stabilization of the protein dimer. We have also identified 2 large CSIs in SecA proteins that are uniquely found in thermophilic species from two different phyla of bacteria. Detailed bioinformatics analyses on one of these CSIs show that a number of residues from this CSI, through their interaction with a conserved network of water molecules, play a role in stabilizing the binding of ADP/ATP to the SecA protein at high temperature. My work also involved developing an integrated software pipeline for homology modeling of proteins and analyzing the location of CSIs in protein structures. Overall, my thesis work establishes the usefulness of CSIs in protein sequences as valuable means for genetic, biochemical, structural and evolutionary studies. / Dissertation / Doctor of Philosophy (PhD)

Schizophrenia is a chronic psychotic illness affecting ~21 million people globally. Currently available antipsychotic agents act through a dopamine D2 receptor mechanism, and produce extrapyramidal or metabolic side effects. Hence, there is a need for novel targets and agents. The mGlu2/5-HT2A receptor heteromer has been implicated in the action of antipsychotic agents, and represents a novel and attractive therapeutic target for the treatment of schizophrenia. A long-term goal of this project is to synthesize bivalent ligands where a 5-HT2A receptor antagonist is tethered to an mGlu2 PAM via a linker. The goals of the investigation were to study the SAR of risperidone (an atypical antipsychotic agent) at 5-HT2A receptors using a “deconstruction-reconstruction-elaboration” approach to determine the minimal structural features of risperidone that contribute to its 5-HT2A receptor affinity and antagonism, and to determine where on the “minimized risperidone” structure an mGlu2 PAM can be introduced. Additional goals included studying the binding modes of various mGlu2 PAMs and identifying where on an mGlu2 PAM a risperidone “partial” structure could be introduced. Biological studies of deconstructed/elaborated analogs of risperidone suggest that the entire structure of risperidone is not necessary for 5-HT2A receptor affinity and antagonism, and that a fluoro group contributes to 5-HT2A binding. 6-Fluoro-3-(4-piperidinyl)-1,2-benz[d]isoxazole that has only half the structural features of risperidone retains 5-HT2A receptor affinity and antagonist activity, and represents the “minimized risperidone” structure with the piperidine nitrogen atom representing a potential linker site for eventual construction of bivalent ligands. Molecular modeling studies at 5-HT2A receptors suggest that risperidone and its analogs have more than one binding mode. Modeling studies to evaluate binding modes of various PAMs at mGlu2 receptors, coupled with known SAR information, were used to identify a PAM (JNJ-40411813), and the pyridone nitrogen atom of JNJ-40411813 as a potential linker site. Additionally, potential synthetic routes for JNJ-40411813 were explored that might be of value in the synthesis of bivalent ligands. Based on the structural features of 6-fluoro-3-(4-piperidinyl)-1,2-benz[d]isoxazole, a new pharmacophore for 5-HT2A receptor antagonists, consisting of one aromatic region, a basic protonated amine and hydrogen bond acceptors, has been proposed.

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.

The Dukat laboratory developed 2-amino-6-chloro-3,4-dihydroquinazoline (A6CDQ) as a 5-HT3 receptor ligand. A6CDQ and one of its positional isomers, the 7-chloro analog A7CDQ, produced antidepressant-like effects in the mouse tail suspension test (TST). We investigated and systematically ruled out a solely 5-HT3 receptor or hSERT mediated mechanism of antidepressant-like effect for both A6CDQ and A7CDQ. The role of organic cation transporter 3 (OCT3) as an alternative mechanism in the regulation of neurotransmitters including serotonin (5-HT) and the therapeutic potential of targeting hOCT3 to achieve antidepressant effects has been established. By virtue of possessing protonatable nitrogen atoms, 2-aminodihyroquinazolines could potentially exhibit activity at OCT3. A major goal of our present study was to explore the non-serotonergic mechanism of antidepressant-like effects and to study the as yet unexplored structure-activity-relationships (SARs) at OCT3. We examined the role of i) the chloro group, ii) the methylene bridge and iii) electronic/lipophilic effects at the 6-position. We developed the first 3-D homology models of both the human and mouse orthologs of OCT3, conducted docking studies and HINT analysis, and identified critical amino acid residues interacting with 2-aminodihydroquinazoline analogs at hOCT3 and mOCT3. Retention of antidepressant-like activity in the mouse and potential locomotor stimulant effects for TST-active doses were thoroughly investigated. We have successfully investigated initial SAR of 2-aminodihydroquinazolines at hOCT3 and generated the first 3-D homology models of hOCT3 and mOCT3. Highly potent and selective compounds could potentially be developed as radioligands to probe the binding site of OCT3 and as a mechanistically novel class of antidepressants.

Marihuana (Cannabis sativa) é uma planta amplamente usada pelo ser humano há séculos e suas várias aplicações têm benefícios importantes. A planta Cannabis sativa tem sido usada pelo homem como comida, em práticas medicinais e rituais religiosos. Seus efeitos incluem analgesia, alteração na percepção, cognição, memória e atividade psicomotora. Os compostos canabinoides têm sido usados na quimioterapia do câncer e AIDS. No entanto, o uso da marijuana é um problema devido aos seus efeitos indesejados, nesse caso, a atividade psicotrópica apresentada pelos compostos canabinoides. Devido ao grande interesse nos efeitos causados pelos compostos extraídos da Cannabis, vários estudos têm sido realizados com o objetivo de melhor entender a relação entre a estrutura química e a atividade biológica de compostos canabinoides, bem como as suas interações com os receptores canabinoides, CB1 e CB2. Ambos são receptores de sete transmembranas (TM) que pertencem à família classe A, como a da rodopsina bovina, dos receptores acoplados à proteína-G (GPCRs). Esta Tese representa um estudo da modelagem molecular do receptor CB1 baseado na estrutura da rodopsina bovina já publicada, uma vez que a maioria dos efeitos terapêuticos dos canabinoides tem sido mostrado serem mediados pelo receptor canabinoide CB1. Esse trabalho fornece, também, uma investigação da interação ligante-receptor e um estudo da ativação do receptor CB1. Ao final, foi feito um estudo de docking a fim de entender as principais interações que ocorrem entre o ∆9 -THC, a principal molécula psicoativa presente na Cannabis, e seu receptor CB1. / Marijuana (Cannabis sativa) is a widely used plant and its various applications have important benefits. The plant Cannabis sativa has been used by man for centuries for eating, medicinal practices and religious rituals. In human subjects, its effects include analgesia, alterations in perceptions, cognition, memory and psychomotor activity. The cannabinoid compounds have been used in the cancer chemotherapy and AIDS, but the use of marijuana is a problem due to its unwanted effects (the psychotropic activity presented by the cannabinoid compounds). Due to the great interest in the effects caused by the compounds extracted from the Cannabis, several studies have been carried out with the aim to better understand the relationship between the chemical structure and the biological activity of cannabinoid compounds, as well as their interaction with the cannabinoid receptors (CB1 and CB2). Both are seven-transmembrane (TM) receptors that belong to the rhodopsin-like family Class A of G protein coupled receptors (GPCRs). This work represents a study of molecular modeling of the CB1 receptor based upon the published bovine rhodopsin structure, once the most of the therapeutic effects of cannabinoids compounds have been shown to be mediated through the CB1 cannabinoid receptor. This work also provides an investigation of the CB1 receptor-ligand interaction and a study of the CB1 receptor activation. A docking study was also performed in order to understand the main interactions that occur between ∆9 -THC, the principal psychoactive molecule present in cannabis, and its receptor CB1.

Os hormônios tireoidianos estão envolvidos em vários efeitos regulatórios, em órgãos diversos. Suas variações no organismo estão relacionadas a quadros clínicos de grande relevância. A presente dissertação trata do estudo de duas proteínas diretamente relacionadas ao complexo sistema regulatório associado a tais hormônios. A primeira delas é a globulina de ligação à tiroxina (TBG), responsável pelo transporte da grande maioria dos hormônios tireoidianos circulantes, e cujas alterações estão relacionadas a falhas na interpretação de testes de avaliação da função tireoidiana, podendo levar a tratamentos desnecessários. A segunda proteína é o receptor tireoidiano (TR), responsável pela mediação dos efeitos regulatórios do hormônio tireoidiano, tendo sua estimulação de atividade transcricional relacionada à ligação do hormônio em um de seus domínios. A TBG foi estudada através da técnica computacional conhecida como modelagem molecular por homologia, aplicada à proteína em sua forma selvagem e a mutantes observados no Brasil, com o intuito de relacionar a inviabilidade de tais mutantes a aspectos estruturais. Foi proposto que, para dois dos mutantes estudados, a formação das estruturas secundárias como na forma nativa da proteína seria inviável, enquanto que para o terceiro mutante a inviabilidade poderia ser causada por enovelamento incorreto causado por uma possível interação entre um resíduo de cisteína adveniente da mutação e outros resíduos do mesmo aminoácido em posição fisicamente próxima. O estudo do TR teve como base as estruturas cristalográficas das duas isoformas humanas do receptor (hTR α e hTR β) quando ligadas ao tiromimético GC-1. Esse composto tem a propriedade de ligar-se preferencialmente à isoforma β, o que pode ter interessantes aplicações farmacológicas. A análise comparativa da ligação do GC-1 às duas isoformas mostrou que, para tal composto, a seletividade se deve a mudanças consideráveis no modo de ligação ao hTR α e hTR β. Para a isoforma , há dois modos de ligação, envolvendo conformações alternativas de ligante e proteína, onde em uma delas a ligação é mais favorável e semelhante à ligação do composto à isoforma , enquanto no outro modo de ligação há a perda de uma interação direta entre composto e proteína, explicando a mais baixa afinidade do GC-1 à isoforma quando comparado à isoforma . O mecanismo de -seletividade para esse composto está relacionado a um átomo de oxigênio específico que não existe no ligante natural do receptor, o que fornece úteis informações para a criação de novos compostos. / The thyroid hormones are involved in various regulatory effects, on diverse organs. Their fluctuations on the body are related to clinical scenarios of great relevance. This work deals with the study of two proteins which are directly related to the regulatory system associated to these hormones. The first one is the thyroxine-binding globulin (TBG), responsible for the transport of a large part of the thyroid hormones in serum, and whose variations are related to misinterpretation of thyroid function tests. The second protein is the thyroid receptor (TR), responsible for the mediation of the thyroid hormone regulatory effects . the transcriptional activity being related to ligand binding to one of the protein domains. The wild-type TBG and three mutants discovered in Brazil were studied by the computational technique known as homology modeling. The purpose of this investigation was to relate protein unviability to structural aspects. It was proposed that, for two mutants, the unviability was related to the impossibility of secondary structure formation as needed to form the native folding, while the third mutant the cause could be the formation of an incorrect folding due to possible interactions involving a cysteine residue created by the mutation and other nearby cysteine residues. The thyroid receptor was studied in the light of the x-ray structures of the two isoforms of the protein (hTR α and hTRβ) bound to GC-1, a synthesized compound which resembles the thyroid hormones. This ligand binds preferably the isoform, a feature that may have interesting pharmacological applications. The comparative analysis of GC-1 binding to the two isoforms allowed the construction of a structural basis of its -selectivity property, which is due to considerable differences in the binding modes for the two isoforms. This involves two different configurations of ligand and protein conformations for the isoform - on one of them, the ligand docks to the molecule the same way it docks to hTRβ, while on the second configuration it loses one direct interaction to the protein, explaining its lower affinity to hTR α when compared to hTRβ. The -selectivity mechanism for this compound is related to a specific oxygen atom which doesn?t exist on the receptor endogenous ligand, providing useful information for the development of new compounds.