La present tesi, tot i que emmarcada dins de la teoria de les Mesures Semblança Molecular Quántica (MQSM), es deriva en tres àmbits clarament definits:- La creació de Contorns Moleculars de IsoDensitat Electrònica (MIDCOs, de l'anglès Molecular IsoDensity COntours) a partir de densitats electròniques ajustades.- El desenvolupament d'un mètode de sobreposició molecular, alternatiu a la regla de la màxima semblança.- Relacions Quantitatives Estructura-Activitat (QSAR, de l'anglès Quantitative Structure-Activity Relationships).L'objectiu en el camp dels MIDCOs és l'aplicació de funcions densitat ajustades, ideades inicialment per a abaratir els càlculs de MQSM, per a l'obtenció de MIDCOs. Així, es realitza un estudi gràfic comparatiu entre diferents funcions densitat ajustades a diferents bases amb densitats obtingudes de càlculs duts a terme a nivells ab initio. D'aquesta manera, l'analogia visual entre les funcions ajustades i les ab initio obtinguda en el ventall de representacions de densitat obtingudes, i juntament amb els valors de les mesures de semblança obtinguts prèviament, totalment comparables, fonamenta l'ús d'aquestes funcions ajustades. Més enllà del propòsit inicial, es van realitzar dos estudis complementaris a la simple representació de densitats, i són l'anàlisi de curvatura i l'extensió a macromolècules. La primera observació correspon a comprovar no només la semblança dels MIDCOs, sinó la coherència del seu comportament a nivell de curvatura, podent-se així observar punts d'inflexió en la representació de densitats i veure gràficament aquelles zones on la densitat és còncava o convexa. Aquest primer estudi revela que tant les densitats ajustades com les calculades a nivell ab initio es comporten de manera totalment anàloga. En la segona part d'aquest treball es va poder estendre el mètode a molècules més grans, de fins uns 2500 àtoms.Finalment, s'aplica part de la filosofia del MEDLA. Sabent que la densitat electrònica decau ràpidament al allunyar-se dels nuclis, el càlcul d'aquesta pot ser obviat a distàncies grans d'aquests. D'aquesta manera es va proposar particionar l'espai, i calcular tan sols les funcions ajustades de cada àtom tan sols en una regió petita, envoltant l'àtom en qüestió. Duent a terme aquest procés, es disminueix el temps de càlcul i el procés esdevé lineal amb nombre d'àtoms presents en la molècula tractada.En el tema dedicat a la sobreposició molecular es tracta la creació d'un algorisme, així com la seva implementació en forma de programa, batejat Topo-Geometrical Superposition Algorithm (TGSA), d'un mètode que proporcionés aquells alineaments que coincideixen amb la intuïció química. El resultat és un programa informàtic, codificat en Fortran 90, el qual alinea les molècules per parelles considerant tan sols nombres i distàncies atòmiques. La total absència de paràmetres teòrics permet desenvolupar un mètode de sobreposició molecular general, que proporcioni una sobreposició intuïtiva, i també de forma rellevant, de manera ràpida i amb poca intervenció de l'usuari. L'ús màxim del TGSA s'ha dedicat a calcular semblances per al seu ús posterior en QSAR, les quals majoritàriament no corresponen al valor que s'obtindria d'emprar la regla de la màxima semblança, sobretot si hi ha àtoms pesats en joc.Finalment, en l'últim tema, dedicat a la Semblança Quàntica en el marc del QSAR, es tracten tres aspectes diferents:- Ús de matrius de semblança. Aquí intervé l'anomenada matriu de semblança, calculada a partir de les semblances per parelles d'entre un conjunt de molècules. Aquesta matriu és emprada posteriorment, degudament tractada, com a font de descriptors moleculars per a estudis QSAR. Dins d'aquest àmbit s'han fet diversos estudis de correlació d'interès farmacològic, toxicològic, així com de diverses propietats físiques.- Aplicació de l'energia d'interacció electró-electró, assimilat com a una forma d'autosemblança. Aquesta modesta contribució consisteix breument en prendre el valor d'aquesta magnitud, i per analogia amb la notació de l'autosemblança molecular quàntica, assimilar-la com a cas particular de d'aquesta mesura. Aquesta energia d'interacció s'obté fàcilment a partir de programari mecanoquàntic, i esdevé ideal per a fer un primer estudi preliminar de correlació, on s'utilitza aquesta magnitud com a únic descriptor. - Càlcul d'autosemblances, on la densitat ha estat modificada per a augmentar el paper d'un substituent. Treballs previs amb densitats de fragments, tot i donar molt bons resultats, manquen de cert rigor conceptual en aïllar un fragment, suposadament responsable de l'activitat molecular, de la totalitat de l'estructura molecular, tot i que les densitats associades a aquest fragment ja difereixen degut a pertànyer a esquelets amb diferents substitucions. Un procediment per a omplir aquest buit que deixa la simple separació del fragment, considerant així la totalitat de la molècula (calcular-ne l'autosemblança), però evitant al mateix temps valors d'autosemblança no desitjats provocats per àtoms pesats, és l'ús de densitats de Forats de fermi, els quals es troben definits al voltant del fragment d'interès. Aquest procediment modifica la densitat de manera que es troba majoritàriament concentrada a la regió d'interès, però alhora permet obtenir una funció densitat, la qual es comporta matemàticament igual que la densitat electrònica regular, podent-se així incorporar dins del marc de la semblança molecular. Les autosemblances calculades amb aquesta metodologia han portat a bones correlacions amb àcids aromàtics substituïts, podent així donar una explicació al seu comportament.Des d'un altre punt de vista, també s'han fet contribucions conceptuals. S'ha implementat una nova mesura de semblança, la d'energia cinètica, la qual consisteix en prendre la recentment desenvolupada funció densitat d'energia cinètica, la qual al comportar-se matemàticament igual a les densitats electròniques regulars, s'ha incorporat en el marc de la semblança. A partir d'aquesta mesura s'han obtingut models QSAR satisfactoris per diferents conjunts moleculars. Dins de l'aspecte del tractament de les matrius de semblança s'ha implementat l'anomenada transformació estocàstica com a alternativa a l'ús de l'índex Carbó. Aquesta transformació de la matriu de semblança permet obtenir una nova matriu no simètrica, la qual pot ser posteriorment tractada per a construir models QSAR. / The present work, even embraced by the Molecular Quantum Similarity Measures (MQSM) theory, is divided into three clearly defined frameworks:- Creation of Molecular IsoDensity Contours (MIDCOs) from fitted electronic densities.- Development of an alternative superposition method to replace the maximal similarity rule.- Quantitative Structure-Activity Relationships (QSAR).The objective in field of MIDCOs is the application of fitted density functions, initially developed to reduce the computational costs of calculating MQSM, in order to obtain MIDCOs. So, a graphical comparison is carried out using different fittings to different basis sets, derived from calculations carried out at ab initio level. In this way, the visual analogy between the density representations, along with the values of previously calculated similarity measures, which in turn are fully comparable, reinforces the usage of such fitted densities.Apart from the initial idea, two further studies were done to complement the simple density representations, these are the curvature analysis and the extension to macromolecules. The first step corresponds not only to verify the visual similarity between MIDCOs, but to ensure their coherence in their behaviour at curvature level, allowing to observe inflexion points in the representations and those regions where the density itself presents a convex or concave shape. This first study reveals that both fitted and ab initio densities behave in the same way. In the second study, the method was extended to larger molecules, up to 2500 atoms.Finally, some of the MEDLA philosophy is applied. Knowing that electronic density rapidly decays as it is measured further from nuclei, its calculation at large distances from the nearest nucleus can be avoided. In this way, a partition of the space was proposed, and the fitted density basis set is only calculated for each atom only in its vicinity. Using this procedure, the calculation time is reduced and the whole process becomes linear with the number of atoms of the studied molecule.In the chapter devoted to molecular superposition, the creation of an algorithm, along with its practical implementation, called Topo-Geometrical Superposition Algorithm (TGSA), able to direct those alignments that coincide with chemical intuition. The result is an informatics program, codified in Fortran 90, which aligns the molecules by pairs, considering only atomic numbers and coordinates. The complete absence of theoretical parameters allows developing a general superposition method, which provides an intuitive superposition, and it is also relevant, in a fast way without much user-supplied information. Major usage of TGSA has been devoted to provide an alignment to later compute similarity measures, which in turn do not customarily coincide with those values obtained from the maximal similarity rule, most if heavy atoms are present.Finally, in the last studied subject, devoted to the Quantum Similarity in the QSAR field, three different scopes are treated:1) Usage of similarity matrices. Here, the so-called similarity matrix, calculated from pairwise similarities in a molecular set, is latterly, and properly manipulated, used a source of molecular descriptors for QSAR studies. With in this framework, several correlation studies have been carried out, involving relevant pharmacological properties, as well as toxicity and physical properties.2) Application of the electron-electron repulsion energy. This simple contribution consists briefly of taking the value of this magnitude, and by analogy with the self-similarity notation, it is assimilated as a particular case of this measure. This interaction energy is easily obtainable from mecanoquantic software and becomes ideal in order to make a preliminary correlation study, where this magnitude is used as a single descriptor.3) Calculation of self-similarities, where the density has been modified to account a particular substituent. Previous studies using density fragments, even they provide valuable results, lack of conceptual rigour when isolating a fragment, supposed to be responsible for a particular molecular response, even those densities associated to a particular fragment are already different due to they belong to a common skeleton with different substitutions. A procedure able to fill the gap between usage of density fragments , which avoid the heavy atom effect, and the whole molecular density, which allows to compute a self-similarity, is proposed. It consists of using Fermi Hole density functions, where the holes are defined and averaged around a particular fragment. This procedure medifies the density in a way that is basically collapsed in this molecular bay, but allowing at the same time obtaining a a density function that behaves mathematically in the same way as a regular electronic density; hence it is included in the similarity framework. Those self-similarities computed using this procedure provide good correlations with substituted aromatic acids, allowing to provide an explanation for their acidic behaviour.From another point of view, conceptual contributions have been developed. A new similarity measure, Kinetic Energy-based, has been implemented, which consists of taking the recently developed Kinetic Energy density function, which has been incorporated into the similarity framework due to it mathematically behaves like a regular density function. Satisfactory QSAR models, derived from this new measure, have been obtained for several molecular systems. Within the similarity matrices field, it has been implemented a new scaling, called stochastic transformation, as an alternative to Carbó Index. This transformation of the matrix allows obtaining a new non-symmetric matrix, which can be later used as a source of descriptors to build QSAR model.

Submitted by Pedro Silva Filho (pfsilva@ipen.br) on 2017-11-22T16:34:17Z No. of bitstreams: 0 / Made available in DSpace on 2017-11-22T16:34:17Z (GMT). No. of bitstreams: 0 / A cultura de segurança na área nuclear é definida como o conjunto de características e atitudes da organização e dos indivíduos que fazem que, com uma prioridade insuperável, as questões relacionadas à proteção e segurança nuclear recebam a atenção assegurada pelo seu significado. Até o momento, não existem instrumentos validados que permitam avaliar a cultura de segurança na área nuclear. Em vista disso, os resultados da definição de estratégias para o seu fortalecimento e o acompanhamento do desempenho das ações de melhorias tornam-se difíceis de serem avaliados. Este trabalho teve como objetivo principal desenvolver e validar um instrumento para a avaliação da cultura de segurança de organizações nucleares, utilizando o Instituto de Pesquisas Energéticas e Nucleares como unidade de pesquisa e coleta de dados. Os indicadores e variáveis latentes do instrumento foram definidos utilizando como referência modelos de avaliação de cultura de segurança da área da saúde e área nuclear. O instrumento de coleta de dados proposto inicialmente foi submetido à avaliação por especialistas da área nuclear e, posteriormente, ao pré-teste com indivíduos que pertenciam à população pesquisada. A validação do modelo foi feita por meio da modelagem por equações estruturais utilizando o método de mínimos quadrados parciais (Partial Least Square - Structural Equation Modeling PLS-SEM), no software SmartPLS. A versão final do instrumento foi composta por quarenta indicadores distribuídos em nove variáveis latentes. O modelo de mensuração apresentou validade convergente, validade discriminante e confiabilidade e, o modelo estrutural apresentou significância estatística, demonstrando que o instrumento cumpriu adequadamente todas as etapas de validação. / Tese (Doutorado em Tecnologia Nuclear) / IPEN/T / Instituto de Pesquisas Energéticas e Nucleares - IPEN-CNEN/SP

Les maladies tropicales négligées causées par les protozoaires kinétoplastidés du genre Leishmania et Trypanosoma représentent une menace pour près d’un demi-milliard de personnes en zone intertropicale, entrainant jusqu’à 50 000 décès par an. Parmi les molécules en développement clinique pour traiter ces pathologies, le fexinidazole est une prodrogue appartenant à la famille des 5-nitroimidazoles et qui exerce son action anti-infectieuse via une étape de bioactivation catalysée par des nitroréductases (NTR) parasitaires, enzymes dont le co-facteur est une flavine. Afin d’identifier de nouveaux nitrohétérocycles antiparasitaires substrats des NTR, une petite chimiothèque d’imidazo[1,2-a]pyridines synthétisées au laboratoire a subi un criblage in vitro ayant conduit à l’identification d’une molécule Hit, à la fois active sur Leishmania donovani et Trypanosoma brucei brucei. Ce composé a servi de point de départ à un travail de pharmacomodulation, dans un premier temps en position 8 du cycle imidazo[1,2-a]pyridine : l’introduction de groupements variés à l’aide de réactions de couplage pallado-catalysées de Suzuki-Miyaura, Sonogashira et Buchwald-Hartwig ou des réactions de SNAr, a permis de mettre en lumière plusieurs composés « tête de série » au profil biologique nettement amélioré. Dans un second temps, le travail de pharmacomodulation entrepris a été étendu aux positions 2, 3 et 6 du cycle imidazo[1,2-a]pyridine en vue de compléter les données de relations structure-activité, d’étudier en particulier l’impact du potentiel rédox et d’optimiser les paramètres physico-chimiques et pharmacocinétiques in vitro des meilleurs composés. / The kinetoplastids of the Leishmania and Trypanosoma genus are the causative agents of neglected tropical diseases that threaten nearly half a billion people in the intertropical zone, resulting in 50 000 deaths per year. Among the molecules in clinical development to treat these pathologies, fexinidazole is a prodrug belonging to the 5-nitroimidazoles family, which exerts its anti-infectious action via a bioactivation step catalyzed by parasitic nitroreductases (NTR), enzymes whose cofactor is a flavin. In order to identify novel nitroheterocycles as parasitic NTR substrates, a small chemical library of imidazo[1,2-a]pyridines synthesized by our laboratory was screened in vitro, leading to the identification of a Hit molecule active both on Leishmania donovani and Trypanosoma brucei brucei. This compound served as a starting point for a pharmacomodulation work, initially in position 8 of the imidazo[1,2-a]pyridine ring: the introduction of various chemical groups using the pallado-catalyzed coupling reactions of Suzuki-Miyaura, Sonogashira and Buchwald-Hartwig, or SNAr reactions, highlighted several "lead" compounds with a significantly improved biological profile. In a second step, the pharmacomodulation work was extended to positions 2, 3 and 6 of the imidazo[1,2-a]pyridine ring in order to complete the structure-activity relationship data, to study in particular the impact of the redox potential and to optimize the physicochemical and in vitro pharmacokinetic parameters of the best compounds in order to initiate the study of their in vivo activity on a trypanosomiasis mouse model.

Indiana University-Purdue University Indianapolis (IUPUI) / Proteins are nano-machines that work inside every living organism. Functional disruption of one or several proteins is the cause for many diseases. However, the functions for most proteins are yet to be annotated because inexpensive sequencing techniques dramatically speed up discovery of new protein sequences (265 million and counting) and experimental examinations of every protein in all its possible functional categories are simply impractical. Thus, it is necessary to develop computational function-prediction tools that complement and guide experimental studies. In this study, we developed a series of predictors for highly accurate prediction of proteins with DNA-binding, RNA-binding and carbohydrate-binding capability. These predictors are a template-based technique that combines sequence and structural information with predicted binding affinity. Both sequence and structure-based approaches were developed. Results indicate the importance of binding affinity prediction for improving sensitivity and precision of function prediction. Application of these methods to the human genome and structure genome targets demonstrated its usefulness in annotating proteins of unknown functions and discovering moon-lighting proteins with DNA,RNA, or carbohydrate binding function. In addition, we also investigated disruption of protein functions by naturally occurring genetic variations due to insertions and deletions (INDELS). We found that protein structures are the most critical features in recognising disease-causing non-frame shifting INDELs. The predictors for function predictions are available at http://sparks-lab.org/spot, and the predictor for classification of non-frame shifting INDELs is available at http://sparks-lab.org/ddig.

Indiana University-Purdue University Indianapolis (IUPUI) / Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in malignant tumors, and its activation is associated with high histological grade and advanced cancer stage. STAT3 has been shown to play important roles in multiple aspects of cancer aggressiveness including proliferation, survival, self-renewal, migration, invasion, angiogenesis and immune response by regulating the expression of diverse downstream target genes. Thus, inhibiting STAT3 promises to be an attractive strategy for treatment of advanced tumors with metastatic potential. We firstly identified a STAT3 inhibitor, inS3-54, by targeting the DNA-binding site of STAT3 using an in-silico screening approach; however, inS3-54 was finally found not to be appropriate for further studies because of low specificity on STAT3 and poor absorption in mice. To develop an effective and specific STAT3 inhibitor, we identified 89 analogues for the structure-activity relationship analysis. By using hematopoietic progenitor cells isolated from wild-type and STAT3 conditional knockout mice, further studies showed that three analogues (A18, A26 and A69) only inhibited STAT3-dependent colony formation of hematopoietic progenitor cells, indicating a higher selectivity for STAT3 than their parental compound, inS3-54. These compounds were found to (1) inhibit STAT3-specific DNA binding activity; (2) bind to STAT3 protein; (3) suppress proliferation of cancer cells harboring aberrant STAT3 signaling; (4) inhibit migration and invasion of cancer cells and (5) inhibit STAT3-dependent expression of downstream targets by blocking the binding of STAT3 to the promoter regions of responsive genes in cells. In addition, A18 can reduce tumor growth in a mouse xenograft model of lung cancer with little effect on body weight. Taken together, we conclude that it is feasible to inhibit STAT3 by targeting its DNA-binding domain for discovery of anticancer therapeutics.

Indiana University-Purdue University Indianapolis (IUPUI) / Fatty acid synthase (FASN) is over-expressed in many cancers, and novel inhibitors that target FASN may find use in the treatment of cancers. It has been shown that orlistat, an FDA approved drug for weight loss, inhibits the thioesterase (TE) of FASN, but can be hydrolyzed by TE. To understand the mechanisms of TE action and for designing better FASN inhibitors, I examined the mechanism of orlistat hydrolysis by TE using molecular dynamics simulations. I found that the hexyl tail of orlistat undergoes a conformational transition, destabilizing a hydrogen bond that forms between orlistat and the active site histidine. A water molecule can then hydrogen bond with histidine and become activated to hydrolyze orlistat. These findings suggest that rational design of inhibitors that block hexyl tail transition may lead to a more potent TE inhibitor. To search for novel inhibitors of TE, I performed virtual DOCK screening of FDA approved drugs followed by a fluorogenic assay using recombinant TE protein and found that proton pump inhibitors (PPIs) can competitively inhibit TE. PPIs, which are used for the treatment of gastroesophageal reflux and peptic ulcers, work to decrease gastric acid production by binding irreversibly with gastric hydrogen potassium ATPase in the stomach. Recently, PPIs have been reported to reduce drug resistance in cancer cells when used in combination with chemotherapeutics, although the mechanism of resistance reduction is unknown. Further investigation showed that PPIs are able to decrease FASN activity and cancer cell proliferation in a dose-dependent manner. These findings provide new evidence that FDA approved PPIs may synergistically suppress cancer cells by inhibiting TE of FASN and suggests that the use of PPIs in combinational therapies for the treatment of many types of cancer, including pancreatic cancer, warrants further investigation.

<p dir="ltr">The BRG1/BRM-associated factor (BAF) complexes, also called SWI/SNF, are multi-subunit chromatin remodelers that regulate chromatin compaction in an ATP-dependent manner. In the past decade, BAF complexes have been under the spotlight in cancer research, especially after proteomic analyses revealed the genes encoding the subunits are amongst the most frequently mutated genes in cancer. The present dissertation focuses on prostate cancer (PCa), a disease in which the role of the BAF subunits is increasingly being explored but is yet to be defined as a potential therapeutic target. According to the GLOBOCAN report, PCa is the second most frequent cancer in males worldwide. Since most of the variants of PCa rely on the androgen receptor (AR) axis, surgical or chemical castration and androgen deprivation therapy (ADT) are the main treatment strategies for PCa patients. Even though these therapeutic approaches prolong survival, reduce tumor burden, and relieve symptoms, PCa patients eventually relapse and develop castration resistant PCa (CRPC). At present, the mechanisms underlying ADT resistance are not fully understood, current efforts focus on finding new targets for PCa treatment.</p><p dir="ltr">In the projects included in this dissertation we explored the function of the PBAF complex, a BAF subtype, in a variety of models of PCa and its potential as a therapeutic target by inhibiting or depleting its different subunits. To do so we (i) developed the first inhibitors for BRD7 (a subunit unique to PBAF) and (ii) established cell-based assays in multiple PCa cell lines to study BRD7 and other PBAF unique subunits.</p><p dir="ltr">Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer. Bromodomain-containing protein 7 (BRD7) has been implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease. Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a binding pocket exclusive to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two inhibitors with increased selectivity towards BRD7, 1-78 and 2-77, which bind with submicromolar affinity to the BRD7 BD. Our binding mode analyses indicate that these ligands occupy a uniquely accessible binding cleft in BRD7 and maintain key interactions with the asparagine and tyrosine residues critical for acetylated lysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.</p><p dir="ltr">There are three BAF complexes that have been biochemically characterized up to date: canonical BAF (cBAF), polybromo-associated BAF (PBAF) and GLTSCR1/like-containing BAF (GBAF or ncBAF). All BAF complexes are characterized by containing an ATPase and accessory subunits that may be shared between them or unique to each subtype. PBAF, the BAF subtype of interest of this dissertation, contains four unique subunits: BRD7, PBRM1, ARID2 and BAF45A. We showed that knocking down BRD7 and ARID2 leads to reduction of cell viability in PCa cells with ligand-dependent and independent AR signaling, while knocking down PBRM1 leads to reduction in viability of cells with only ligand-dependent AR signaling. We also performed a chromatin immunoprecipitation assay with BAF45A and observed that it does not colocalize with AR binding sites, indicating that the mechanism by which PBAF regulates AR signaling is indirect. This observation was further supported by the fact that knocking down BRD7 prevents expression of genes related to adaptive processes, but not AR target genes, in response to androgen treatment. Further mechanistic studies will aid in understanding the function of PBAF in PCa. However, overall, our results indicate that PBAF is a promising therapeutic target in PCa models expressing AR, including CRPC systems.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / Intrinsically disordered proteins are proteins characterized by lack of stable tertiary structures under physiological conditions. Evidence shows that disordered proteins are not only highly involved in protein interactions, but also have the capability to associate with more than one partner. Short disordered protein fragments, called “molecular recognition features” (MoRFs), were hypothesized to facilitate the binding diversity of highly-connected proteins termed “hubs”. MoRFs often couple folding with binding while forming interaction complexes. Two protein disorder mechanisms were proposed to facilitate multiple partner binding and enable hub proteins to bind to multiple partners: 1. One region of disorder could bind to many different partners (one-to-many binding), so the hub protein itself uses disorder for multiple partner binding; and 2. Many different regions of disorder could bind to a single partner (many-to-one binding), so the hub protein is structured but binds to many disordered partners via interaction with disorder. Thousands of MoRF-partner protein complexes were collected from Protein Data Bank in this study, including 321 one-to-many binding examples and 514 many-to-one binding examples. The conformational flexibility of MoRFs was observed at atomic resolution to help the MoRFs to adapt themselves to various binding surfaces of partners or to enable different MoRFs with non-identical sequences to associate with one specific binding pocket. Strikingly, in one-to-many binding, post-translational modification, alternative splicing and partner topology were revealed to play key roles for partner selection of these fuzzy complexes. On the other hand, three distinct binding profiles were identified in the collected many-to-one dataset: similar, intersecting and independent. For the similar binding profile, the distinct MoRFs interact with almost identical binding sites on the same partner. The MoRFs can also interact with a partially the same but partially different binding site, giving the intersecting binding profile. Finally, the MoRFs can interact with completely different binding sites, thus giving the independent binding profile. In conclusion, we suggest that protein disorder with post-translational modifications and alternative splicing are all working together to rewire the protein interaction networks.