Structure-activity relationships of novel substituted naphthalene diimides as anticancer agents

Novel 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) derivatives were synthesized and evaluated for their antiproliferative activity on a wide number of different tumor cell lines. The prototypes of the present series were derivatives 1 and 2 characterized by interesting biological profiles as anticancer agents. The present investigation expands on the study of structure-activity relationships of prototypes 1 and 2, namely, the influence of the different substituents of the phenyl rings on the biological activity. Derivatives 3-22, characterized by a different substituent on the aromatic rings and/or a different chain length varying from two to three carbon units, were synthesized and evaluated for their cytostatic and cytotoxic activities. The most interesting compound was 20, characterized by a linker of three methylene units and a 2,3,4-trimethoxy substituent on the two aromatic rings. It displayed antiproliferative activity in the submicromolar range, especially against some different cell lines, the ability to inhibit Taq polymerase and telomerase, to trigger caspase activation by a possible oxidative mechanism, to downregulate ERK 2 protein and to inhibit ERKs phosphorylation, without acting directly on microtubules and tubuline. Its theoretical recognition against duplex and quadruplex DNA structures have been compared to experimental thermodynamic measurements and by molecular modeling investigation leading to putative binding modes. Taken together these findings contribute to define this compound as potential Multitarget-Directed Ligands interacting simultaneously with different biological targets. \ua9 2012 Elsevier Masson SAS. All rights reserved

Molecular recognition of the HPLC Whelk-O1 selector towards the conformational enantiomers of nevirapine and oxcarbazepine

The presence of stereogenic elements is a common feature in pharmaceutical compounds, and affording optically pure stereoisomers is a frequent issue in drug design. In this context, the study of the chiral molecular recognition mechanism fundamentally supports the understanding and optimization of chromatographic separations with chiral stationary phases. We investigated, with molecular docking, the interactions between the chiral HPLC selector Whelk-O1 and the stereoisomers of two bioactive compounds, the antiviral Nevirapine and the anticonvulsant Oxcarbazepine, both characterized by two stereolabile conformational enantiomers. The presence of fast-exchange enantiomers and the rate of the interconversion process were studied using low temperature enantioselective HPLC and VT-NMR with Whelk-O1 applied as chiral solvating agent. The values of the energetic barriers of interconversion indicate, for the single enantiomers of both compounds, half-lives sufficiently long enough to allow their separation only at critically sub-ambient temperatures. The chiral selector Whelk-O1 performed as a strongly selective discriminating agent both when applied as a chiral stationary phase (CSP) in HPLC and as CSA in NMR spectroscopy

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in BiochemistryEnzyme evolution is often constrained by aspects of catalysis. Mechanistically diverse enzymes evolved from a common ancestor still preserve those structural signatures essential to the core chemistry retained by all members of the superfamily. Indeed, these shared features allow superfamilies to be accurately classified, while derived features allow nested families and subfamilies to be identified in a hierarchical fashion. Accurate classification has helped elucidate mechanisms promoting functional diversification, for example catalytic promiscuity, and protein engineering by rational design. Nowadays, a holistic view of enzymes` regulatory mechanisms and catalytic proficiency is provided by the identification of conserved features of molecular architecture in combination with aspects of reaction dynamics. My work focused on the structural elucidation and analysis of three enzymes: a glycosyltransferase; a phosphatase and an oxidorreductase. “Snapshots” along the reaction coordinate of each enzyme were obtained by combining X-ray diffraction with “cryo-trapping” ligand-binding methods. These were used to characterize the molecular mechanisms involved in substrate recognition and binding. They were also used to distinguish between models proposed for the catalytic mechanisms of each enzyme, and provide insights into enzyme dynamics essential for catalysis and the stereo and regio-selective strategies at work.(...)Apoio financeiro da FCT e do POPH/FSE no âmbito do Quadro Comunitário de Apoio, Bolsa Nº SFRH/BD/23222/2005

Effect of the human immunodeficiency virus type 1 reverse transcriptase polymorphism Leu-214 on replication capacity and drug susceptibility

A negative association between polymorphism Leu-214 and type-1 thymidine analogue mutations (TAM1) and a positive association with a clinically favorable virological response to thymidine analogue-based combination antiretroviral therapy have been described. In this study, the impact of Leu-214 on replication capacity and resistance to zidovudine (ZDV) of viruses containing TAM1 or TAM2 was determined. Leu-214 decreased the growth rate of viruses bearing Tyr-215, as well as their resistance to ZDV. This observation was confirmed by structural and molecular modeling data, suggesting a regulatory role for Leu-214 in the emergence and phenotypic resistance of TAM1

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Los receptores para el reconocimiento de patrones moleculares: aportaciones de la química computacional para el diseño de fármacos y la modulación de la inmunidad innata

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Farmacia, Departamento de Química Orgánica y Farmacéutica, leída el 18/11/2019In this Thesis we have aimed the study of the molecular recognition processes of receptors involved in the innate immunity. More concretely, we have focused in two different types of lectins, Galectins and DC-SIGN, and in Toll-like receptor 4. We have made use of computational techniques, including docking and virtual screening, molecular dynamics simulations, conformational analysis and quantum mechanics calculations. The work has been organized into several chapters that are summarized as follows: Chapter 1 corresponds to the current knowledge and perspectives about receptors related to immunity, in particular: galectins, DC-SIGN, and Toll-like receptor 4, corresponding to the molecular recognition events and modulation by small molecules. Chapter 2 describes the state-of-the-art methods in molecular modeling and computational chemistry applied to the study of molecular recognition processes and drug design...En esta tesis hemos estudiado los procesos reconocimiento molecular de receptores involucrados en la inmunidad innata. Más concretamente, nos hemos centrado en dos tipos diferentes de lectinas, Galectinas y DC-SIGN, y en el receptor Toll-like 4 (TLR4). Hemos utilizado técnicas computacionales, incluyendo docking y cribado virtual, simulaciones de dinámica molecular, análisis conformacional y cálculos de mecánica cuántica. El trabajo se ha organizado en diferentes capítulos que se resumen como sigue: El capítulo 1 corresponde al estado del arte y las perspectivas relacionadas con los estudios de reconocimiento molecular proteína-carbohidrato y diseño de nuevos moduladores con actividad biológica en receptores de la inmunidad, en particular galectinas, DC-SIGN y el receptor Toll-like 4. El capítulo 2 describe el estado actual de los métodos en modelado molecular y química computacional aplicados al estudio de los procesos de reconocimiento molecular y diseño de fármacos...Fac. de FarmaciaTRUEunpu

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 378)

This bibliography lists 185 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during Aug. 1993. Subject coverage includes: aerospace medicine and physiology, life support systems and man/system technology, protective clothing, exobiology and extraterrestrial life, planetary biology, and flight crew behavior and performance

Computational studies of mutations associated to resistance in HIV-1 macromolecular targets and implications in rational design of novel antiviral agents

Al fine di identificare nuovi farmaci anti-HIV capaci di superare i problemi legati alla resistenza, è stato condotto uno studio teorico combinando l’analisi strutturale sui modelli cristallografici della trascrittasi inversa (RT), i dati clinici relativi ai residui conservati dell’RT ed un’innovativa metodica computazionale basata sulle mappe di GRID. Tale analisi ha permesso di riprodurre i risultati clinici e di evidenziare le conseguenze delle mutazioni nella fase di ricognizione. Inoltre l’approccio computazionale ha portato all’identificazione di un modello farmacoforico utile per la progettazione di nuovi inibitori dell’RT. E’ stato riscontrato che la presenza del polimorfismo I135T nei pazienti NNRTI-naïve correlasse in modo significativo con la mutazione K103N nei casi di fallimento agli NNRTI, suggerendo così che la sostituzione I135T rappresenti un punto cruciale per l’evoluzione della resistenza agli NNRTI. Le simulazioni di dinamica molecolare (MD) hanno mostrato che la mutazione I135T contribuisce alla stabilizzazione della chiusura della tasca di legame degli NNRTI indotta dalla K103N in seguito alla riduzione della distanza ed all’aumento del numero di legami idrogeno tra l’Asn103 e la Tyr188. Inoltre è stata valutata l’influenza di due mutazioni associate a resistenza, L33F e L76V, presenti a livello della proteasi (PR) di HIV-1 rispetto alla ricognizione molecolare del Lopinavir (LPV) e dell’Atazanavir (ATV). L’analisi delle energie di interazione ottenute in seguito alla MD ha rivelato che la mutazione L33F determina una riduzione delle interazioni tra il ligando ed il recettore, dell’affinità di legame e della stabilità del dimero per entrambi gli inibitori della PR. In presenza della mutazione L76V, il LPV ha mostrato una minore affinità di legame ed un ridotto network di legami idrogeno, mentre i complessi con l’ATV hanno rivelato una migliore affinità, un effetto stabilizzante a livello dell’interfaccia del dimero e più efficaci interazioni ligando-recettore, in accordo con i dati di ipersuscettibilità. Al fine di valutare la stabilità del 6-helix bundle, sono state studiate le proprietà conformazionali della glicoproteina gp41 in presenza delle mutazioni associate a resistenza all’enfuvirtide V38A ed N140I. Le simulazioni di MD hanno mostrato che la copresenza delle mutazioni V38A+N140I è in grado di abolire l’interazione stabilita tra i residui 38 e 145, che risulta fondamentale per la stabilizzazione del 6-helix bundle.In order to discover novel selective anti-HIV resistance-evading drugs, a theoretical study was carried out combining structural analysis of RT crystallographic models, clinical data about RT conserved residues and an innovative computational method based on GRID maps. Such analysis allowed to reproduce clinical results and to highlight the consequences of the mutations in the recognition step. Moreover the computational approach generated a pharmacophore model useful for the design of novel RT inhibitors. The presence of the I135T polymorphism in NNRTI-naive patients significantly correlated with the appearance of K103N in cases of NNRTI failure, suggesting that I135T may represent a crucial determinant of NNRTI resistance evolution. Molecular Dynamics simulations (MD) showed that I135T can contribute to the stabilization of the K103N-induced closure of the NNRTI binding pocket by reducing the distance and increasing the number of hydrogen bonds between 103N and 188Y. In addition the influence of two drug resistance-associated mutations, L33F and L76V, of HIV-1 PR has been evaluated with respect to lopinavir (LPV) and atazanavir (ATV) molecular recognition. The evaluation of the interaction energies after the MD revealed that L33F substitution is related to reduced host/guest interactions, decreased affinity and to a dimer destabilizing effect for both PR inhibitors. In presence of L76V mutation, LPV showed a lowered binding affinity and a reduced hydrogen bonding network, while ATV complexes revealed a more productive binding affinity, increased host/guest interactions and dimer stabilizing effects, in agreement with hyper susceptibility data. With the aim to estimate the stability of its 6-helix bundle, the gp41 conformational properties were investigated in presence of V38A and N140I, known enfuvirtide resistance-associated mutations. MD showed that the co-presence of V38A+N140I abolished the interaction between residue 38 and 145 important for the 6-helix-bundle stabilization