DDI-CPI, a server that predicts drug–drug interactions through implementing the chemical–protein interactome

Drug–drug interactions (DDIs) may cause serious side-effects that draw great attention from both academia and industry. Since some DDIs are mediated by unexpected drug–human protein interactions, it is reasonable to analyze the chemical–protein interactome (CPI) profiles of the drugs to predict their DDIs. Here we introduce the DDI-CPI server, which can make real-time DDI predictions based only on molecular structure. When the user submits a molecule, the server will dock user's molecule across 611 human proteins, generating a CPI profile that can be used as a feature vector for the pre-constructed prediction model. It can suggest potential DDIs between the user's molecule and our library of 2515 drug molecules. In cross-validation and independent validation, the server achieved an AUC greater than 0.85. Additionally, by investigating the CPI profiles of predicted DDI, users can explore the PK/PD proteins that might be involved in a particular DDI. A 3D visualization of the drug-protein interaction will be provided as well. The DDI-CPI is freely accessible at http://cpi.bio-x.cn/ddi/

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

New Reactions in Metal-based and Enzymatic Catalysis

Aquesta tesi doctoral es proposa investigar noves funcions catalítiques a partir d'estratègies ben establertes en catàlisi asimètrica, amb l'objectiu de desenvolupar processos enantioselectius no convencionals des del punt de vista del mecanisme. En el primer projecte, es va mostrar com la irradiació de llum visible podria desviar la reactivitat d'un complex quiral d'iridi (III)--allil amb la funció ben establerta d'electròfil a l'estat fonamental per convertir-se en un oxidant d'un sol electró a l'estat excitat. La fotoexcitació d'aquest complex d'organoiridi quiral va permetre la implementació d'un acoblament creuat C-C enantioselectiu basat en un mecanisme radical inassolible en el domini tèrmic. El mètode ens va permetre acoblar alcohols allílics de bencil racèmics i 4-alquil-dihidropiridines (DHP), que van generar radicals α-amino després de l'oxidació per l'estat excitat del complex d'iridi(III). La reacció va transcórrer sota irradiació de 460 nm a temperatura ambient i va proporcionar els productes allílics desitjats amb alts rendiments i excés enantiomèric. En el segon projecte, es va mostrar com la modificació genètica d'un enzim ben establert la va convertir en un biocatalitzador multifuncional, que podria impulsar una reacció en biocascada nova des del punt de vista del mecanisme ja que l'enzim catalitzava tots els passos de la seqüència en cascada amb un alt control estereoscòpic. Aquests biocatalitzadors multifuncionals pertanyien a la família d'enzims 4-oxalocrotonat tautomerasa (4-OT) i podien fer tant l'activació amb enamina d'aldehids com l'activació amb ions imini d'enals de forma seqüencial. Això ens va permetre implementar les versions enzimàtiques de les dues reaccions en cascada clàssiques en organocatàlisi descrites per Enders per a la síntesi de carbaldehids de ciclohexens altament enriquits i complexos. El nostre protocol biocatalític va coincidir, i de vegades va superar, el mètode organocatalític en termes d'eficiència i estereoselectivitat.La presente tesis doctoral se propone de investigar nuevas funciones catalíticas a partir de estrategias bien establecidas en catálisis asimétrica, con el objetivo de desarrollar procesos enantioselectivos no convencionales desde el punto de vista del mecanismo. En el primer proyecto, se mostró cómo la irradiación de luz visible podría desviar la reactividad de un complejo quiral de iridio (III)--alilo con la función bien establecida de electrófilo en el estado fundamental para convertirse en un oxidante de un solo electrón en el estado excitado. La fotoexcitación de este complejo de organoiridio quiral permitió la implementación de un acoplamiento cruzado C-C enantioselectivo basado en un mecanismo radical inalcanzable en el dominio térmico. El método nos permitió acoplar alcoholes alílicos de bencilo racémicos y 4-alquil-dihidropiridinas (DHP), que generaron radicales α-amino tras la oxidación por el estado excitado del complejo de iridio(III). La reacción transcurrió bajo irradiación de 460 nm a temperatura ambiente y proporcionó los productos alílicos deseados con altos rendimientos y exceso enantiomérico. En el segundo proyecto, se mostró cómo la modificación genética de una enzima bien establecida la convirtió en un biocatalizador multifuncional, que podría impulsar una reacción en biocascada novedosa desde el pnto de vista del mecanismo ya que la enzima catalizaba todos los pasos de la secuencia en cascada con un alto control estereoscópico. Estos biocatalizadores multifuncionales pertenecían a la familia de enzimas 4-oxalocrotonato tautomerasa (4-OT) y podían realizar tanto la activación con enamina de aldehídos como la activación con iones iminio de enales de forma secuencial. Esto nos permitió implementar las versiones enzimáticas de las dos reacciones en cascada clásicas en organocatálisis descritas por Enders para la síntesis de carbaldehídos de ciclohexenos altamente enriquecidos y complejos. Nuestro protocolo biocatalítico coincidió, y en ocasiones superó, el método organocatalítico en términos de eficiencia y estereoselectividad.The objective of this research thesis was to upgrade established strategies of asymmetric catalysis by disclosing novel catalytic functions, useful to develop mechanistically-divergent enantioselective processes. In the first project, visible light irradiation was used to divert the well-established reactivity of a chiral iridium(III)--allyl complex that functioned as a general electrophile in the ground state. Upon excitation it became instead a single electron transfer (SET) oxidant in the excited state. The photoexcitation of this chiral organoiridium complex enabled a mechanistically-novel enantioselective radical C-C cross coupling that was unattainable in the thermal domain. The method allowed us to couple racemic benzyl allylic alcohols and 4-alkyl-dihydropyridines (DHPs), which delivered α-amino radicals upon SET oxidation by the excited state of the iridium(III) complex. The reaction proceeded under 460 nm irradiation at room temperature and afforded the desired allylic products in high yields and enantiomeric excess. In the second project, we used the genetic modification of a well-established enzyme to turn it into a multifunctional biocatalyst, which could drive a mechanistically-novel biocascade reaction by catalyzing all the steps of the cascade sequence with high stereocontrol. Our new multifunctional biocatalysts belonged to the 4-oxalocrotonate tautomerase (4-OT) family of enzymes and they could perform both the enamine activation of linear aldehydes and the iminium ion activation of enals in a sequential way. This allowed us to implement the enzymatic versions of the two classic organocascade reactions reported by Enders for the synthesis of complex and highly enantioenriched cyclohexene carbaldehyde scaffolds. Our biocatalytic protocol matched, and sometimes surpassed, the organocatalytic approach in terms of efficiency and stereoselectivity

Separação de enantiómeros de ácido mandélico usando sistemas aquosos bifásicos contendo seletores quirais bifásicos

Mestrado em Bioquímica - Métodos BiomolecularesA quiralidade é a uma propriedade importante na indústria farmacêutica, uma vez que um enantiómero de um fármaco pode exercer o efeito terapêutico desejado enquanto o outro pode ser inerte ou mesmo nefasto. Embora vários fármacos sejam comercializados na sua forma racémica, as entidades regulatórias aconselham o desenvolvimento de fármacos enantiomericamente puros e mais seguros. Neste contexto, a indústria farmacêutica procura formas baratas e eficientes de produzir fármacos enantiomericamente puros, sendo este o objetivo da presente tese. A separação enantiomérica do ácido mandélico (AM), aqui utilizado como um fármaco racémico modelo, será tentada recorrendo a sistemas aquosos bifásicos (SABs) constituídos por seletores quirais de origem natural (proteínas e açúcares). Serão usadas duas abordagens: (i) a introdução de proteínas como seletores quirais em diferentes tipos de SABs; e (ii) o uso de (D)-sacarose simultaneamente como seletor quiral e componente de fase em SABs. Na primeira abordagem, foram utilizados diferentes tipos de SABs (polímero+polímero, polímero+sal, sal+líquido iónico (LI), polímero+LI e polímero+açúcar) e duas proteínas (albumina de soro bovino – BSA – e citocromo C – Cit c). A escolha das proteínas assentou em resultados de molecular docking que indicaram interações distintas entre diferentes proteínas e os enantiómeros do AM. Nestas fases, os sistemas constituídos por PPG400+(D)-Sacarose+BSA (excesso enantiómerico de -5.9± 0.5%) e PPG400+dihidrogeno fosfato de colínio+Cit c (excesso enantiomérico de -9.0 ± 1.2%) revelaram-se os mais eficientes. As proteínas e os constituintes de fase dos SABs afetaram a separação enantiomérica de ácido mandélico. Uma vez que a docagem molecular não considera as interações com os componentes de fase, esta abordagem revelou ser incapaz de prever o desempenho das proteínas como seletores quirais em SABs. Com o objetivo de ultrapassar as limitações de seletividade enantiomérica e melhorar a simplicidade operacional da tecnologia proposta, a (D)-sacarose foi usada simultaneamente como formador de fase e seletor quiral em SABs. Depois de uma otimização cuidada, foi possível obter um excesso enantiomérico máximo de -12.3 ± 0.5% com um SAB constituído por polímero e (D)-sacarose.Chirality is an important property for the pharmaceutical industry, since one enantiomer of a drug can exert a therapeutic action, while the other may be inert or even nefarious. While several drugs are commercialized as racemates, regulatory bodies strongly encourage the development of safer enantiopure drugs. In this context, pharmaceutical industry seeks for cheap and efficient ways of obtaining enantiopure pharmaceuticals and this is the main objective of this thesis. The enantiomeric separation of mandelic acid (MA), here used as a model racemic drug, using aqueous biphasic systems (ABS) composed of natural chiral selectors (proteins and sugars) will be proposed. Two different approaches were used: (i) the introduction of proteins as chiral selectors in several types of ABS; and (ii) ABS formed by D-Sucrose as both phase former and chiral selector. Within the first approach, different types of systems (polymer+polymer, polymer+salt, polymer+sugar, and ionic liquids (ILs)+salt, ILs+polymer) and of proteins (bovine serum albumin –BSA - and cytochrome C – Cyt C) were used. These two proteins were chosen based on molecular docking results that shown distinctive interactions with the two MA enantiomers among eleven screened proteins. PPG400+(D)-sucrose+BSA system (enantiomeric excess of -5.9 ± 0.5%) and PPG+cholinium dihydrogenphosphate+Cyt C (enantiomeric excess of -9.0 ± 1.2% were the most efficient ABS developed up to this stage. Both the protein and ABS phase formers affected the enantioseparation of MA. Since molecular docking does not encompass the interactions with the ABS phase formers, it was limited at predicting the proteins’ performance as chiral selectors in ABS. In order to surpass the limited enantioselectivity displayed and to improve the operational simplicity of the proposed technology, (D)-sucrose was employed as both chiral selector and phase former in ABS. After a proper optimization, it was possible to achieve a maximum enantiomeric excess of -12.3 ± 0.5% with an ABS composed of polymer and (D)-sucrose

Organocatalytic access to a cis-Cyclopentyl-gamma-amino acid: an intriguing model of selectivity and formation of a stable 10/12-helix from the corresponding gamma/alpha-peptide

In this study, we have developed a highly enantioselective organocatalytic route to the (1S,2R)-2-(aminomethyl)cyclopentane-1-carboxylic acid monomer precursor, which has a cis-configuration between the C- and N-termini around the cyclopentane core. Kinetic measurements show that the product distribution changes over time due to epimerization of the C1 center. Computations suggest the cis-selectivity is a result of selective C-C bond formation, whilst subsequent steps appear to infuence the selectivity at higher temperature. The resulting gamma-amino acid residue was incorporated into a novel gamma/alpha-peptide which forms a well-ordered 10/12-helix with alternate H-bond directionality in spite of the smallest value of the zeta-angle yet observed for a helix of this type. This highly dened structure is a result of the narrow range of potential zeta-angles in our monomer. In contrast, the larger range of potential zeta-values observed for the corresponding trans-system can be fulfilled by several competing helical structures

Automated in Silico Design of Homogeneous Catalysts

Catalyst discovery is increasingly relying on computational chemistry, and many of the computational tools are currently being automated. The state of this automation and the degree to which it may contribute to speeding up development of catalysts are the subject of this Perspective. We also consider the main challenges associated with automated catalyst design, in particular the generation of promising and chemically realistic candidates, the tradeoff between accuracy and cost in estimating the catalytic performance, the opportunities associated with automated generation and use of large amounts of data, and even how to define the objectives of catalyst design. Throughout the Perspective, we take a cross-disciplinary approach and evaluate the potential of methods and experiences from fields other than homogeneous catalysis. Finally, we provide an overview of software packages available for automated in silico design of homogeneous catalysts.publishedVersio