Patricia Saenz-Méndez

• PhD
• Professor (Associate) at Karlstads Universitet

Exotoxin A (ETA) is an extracellular secreted toxin and a single-chain polypeptide with A and B fragments that is produced by Pseudomonas aeruginosa. It catalyzes the ADP-ribosylation of a post-translationally modified histidine (diphthamide) on eukaryotic elongation factor 2 (eEF2), which results in the inactivation of the latter and the inhibitio...

Due to the steric effects imposed by bulky polymers, the formation of catalytically competent enzyme and substrate conformations is critical in the biodegradation of plastics. In poly(ethylene terephthalate) (PET), the backbone adopts different conformations, gauche and trans, coexisting to different extents in amorphous and crystalline regions. Ho...

Galectins, soluble lectins widely expressed intra- and extracellularly in different cell types, play major roles in deciphering the cellular glycocode. Galectin-1 (Gal-1), a prototype member of this family, presents a carbohydrate recognition domain (CRD) with specific affinity for β-galactosides such as N-acetyllactosamine (β-D-Galp-(1→4)-D-GlcpNA...

The chapter on protein engineering has introduced and discussed an overview of the available methods for the modification of enzymes. Starting with the classical directed evolution (DE) technique, which has been applied extensively throughout several different biocatalytic processes, the reader moves toward the semi‐rational, rational, and de novo...

Structural information is crucial for understanding catalytic mechanisms and to guide enzyme engineering efforts of biocatalysts, such as terpene cyclases. However, low sequence similarity can impede homology modeling, and inherent protein instability presents challenges for structural studies. We hypothesized that X-ray crystallography of engineer...

This chapter discusses the change in the paradigm of drug discovery, shifting from the “magic bullet” concept to the “magic shotgun” or “silver bullet” approach, i.e., one-compound—multiple-target model. The concept of polypharmacology and its aspects related to drug discovery and development, such as drug attrition and drug repurposing are present...

Galectins are a family of carbohydrate-recognizing proteins that by interacting with specific glycoepitopes can mediate important biological processes, including immune cell homeostasis and activation of tolerogenic circuits. Among the different members of this family, Galectin 1 and 3 have shown pro-tumorigenic effects, being overexpressed in nume...

span>El primer curso de Química Orgánica (Química Orgánica 101) de la Facultad de Química, Universidad de la República (Montevideo, Uruguay) se dicta para las carreras de Química Farmacéutica, Ingeniería Química, Química, Bioquímica Clínica e Ingeniería en Alimentos, y tiene como objetivo dar una visión general de química orgánica, poniendo énfasis...

Nowadays it is widely accepted that one compound can be able to hit several targets at once. This “magic shotgun” approach for drug development properly describes the mechanism of biomolecular recognition. The need to take into account the polypharmacology in structure-based drug design has led to the development of several computational tools. Her...

Eukaryotic Diphthine Synthase, Dph5, is a promiscuous methyltransferase that catalyzes an extraordinary N,O-tetramethylation of 2-(3-carboxy-3-aminopropyl)-L-histidine (ACP) to yield diphthine methyl ester (DTM). These are intermediates in the biosynthesis of the post-translationally modified histidine residue diphthamide, a unique and essential re...

Initiation of celiac disease is triggered in the gastrointestinal tract by transglutaminase 2 (TG2) assisted deamidation of gluten peptides. Deamidation is a side-reaction to transamidation and occurs if primary amines are absent. In contrast to deamidation, transamidation does not trigger an immune response. The aim of the study was to identify a...

The rapid development of efficient computational tools has allowed researchers to tackle biological problems and to predict, analyse and monitor, at an atomic level, molecular recognition processes. This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research. Chapters from i...

RtcB is an essential human tRNA ligase required for ligating the 2',3'-cyclic phosphate and 5'-hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology mo...

A first principles simulation of the crystal structure of potassium peroxocarbonate is presented, using density functional methods (both local and semilocal) for the calculations. An experimental crystal structure with a seemingly inconsistent disposition of the peroxide bonds was used as initial input. Both geometry optimizations of the molecular...

Bacterial adenosine 5’-diphosphate-ribosylating toxins are encoded by several human pathogens, such as Pseudomonas aeruginosa (exotoxin A (ETA)), Corynebacterium diphtheriae (diphtheria toxin (DT)), and Vibrio cholerae (cholix toxin (CT)). The toxins modify eukaryotic elongation factor 2, an essential human enzyme in protein synthesis, thereby caus...

A new homology model of human microsomal epoxide hydrolase (mEH) was derived based on multiple templates. The model obtained was fully evaluated, including MD simulations and ensemble-based docking, showing that the quality of the structure is better than that of only previously known model. Particularly, a catalytic triad was clearly identified, i...

The Eukaryotic translation Elongation Factor 2 (eEF2) is an essential enzyme in protein synthesis. eEF2 contains a unique modification of a histidine (His699 in yeast; HIS) into diphthamide (DTA), obtained via 3-amino-3-carboxypropyl (ACP) and diphthine (DTI) intermediates in the biosynthetic pathway. This essential and unique modification is also...

A new CYP26A1 homology model was built based on the crystal structure of cyanobacterial CYP120A1. The model quality was examined for stereochemical accuracy, folding reliability, and absolute quality using a variety of different bioinformatics tools. Furthermore, the docking capabilities of the model were assessed by docking of the natural substrat...

Dehalopeoxidase A (DHP A) is a detoxifying enzyme found in the marine worm Amphitrite ornata. This enzyme converts halophenols found in the environment where the worm lives, into quinones by dehalogenation. The enzyme has globin structure and function, but works also as a peroxidase in the presence of H2O2 which binds to the iron present in the hem...

Protein tyrosine phosphorylation is a post-translational modification mechanism, crucial for the regulation of nearly all aspects of cell life. This dynamic, reversible process is regulated by the balanced opposing activity of protein tyrosine kinases and protein tyrosine phosphatases. In particular, the protein tyrosine phosphatase 1B (PTP1B) is i...

Lipase-catalyzed transesterification was used as an efficient tool for the interconversion of β-ketoesters. Catalytic activity of commercial lipase B from Candida antarctica (Novozym 435) was evaluated in systems involving non activated acyl donors, and enhanced using microwave irradiation. Interestingly, the combination of CAL B in microwave irrad...

Paves the way for new industrial applications using redox biocatalysis Increasingly, researchers rely on the use of enzymes to perform redox processes as they search for novel industrial synthetic routes. In order to support and advance their investigations, this book provides a comprehensive and current overview of the use of redox enzymes and enz...

Homology models of CYP26B1 (cytochrome P450RAI2) and CYP26B1 spliced variant were derived using the crystal structure of cyanobacterial CYP120A1 as template for the model building. The quality of the homology models generated were carefully evaluated, and the natural substrate all-trans-retinoic acid (atRA), several tetralone-derived retinoic acid...

Paves the way for new industrial applications using redox biocatalysis Increasingly, researchers rely on the use of enzymes to perform redox processes as they search for novel industrial synthetic routes. In order to support and advance their investigations, this book provides a comprehensive and current overview of the use of redox enzymes and enz...

All-trans retinoic acid (atRA) plays an essential role in the regulation of gene expression, cell growth and differentiation and is also important for normal cardiovascular development but may in turn be involved in cardiovascular diseases, i.e. atherosclerosis and restenosis. The cellular atRA levels are under strict control involving several cyto...

Synthesis and cytotoxicity of imidazo[5,4-f]benzimidazolequinones and iminoquinone derivatives is described, enabling structure-activity relationships to be obtained. The most promising compound (an iminoquinone derivative) has undergone National Cancer Institute (NCI) 60 cell line (single and five dose) screening, and using the NCI COMPARE program...

Density functional and MP2 calculations with extended basis sets were performed on the species participating in both the previously suggested and a newly proposed mechanisms of partial dechlorination of chloropicrin by simple sulfur species, both in gas phase and in a simulated water environment. Thermochemistry of both mechanisms in the gas phase...

Allopsoralens are angular psoralen derivatives presenting advantages over the parent compound because of monofunctional DNA-photobinding and consequent lower toxicity. Allopsoralen molecules with three different substituents and different protonation states were studied using the molecular dynamics technique. The location of these molecules when in...

Lyase catalyzed C-C bond formation is reviewed and an overview of the latest developments in the field of synthetic applications of enzymatic aldol, acyloin condensation, and cyanohydrin reactions, is presented. New insights on enzymatic mechanism and structure, added to an increasing number of synthetic applications has made possible the developme...

The mechanism and the final outcome of the Knoevenagel-Doebner reaction are discussed. The condensation reaction between different hydroxy-substituted aromatic aldehydes and malonic acid is performed using piperidine as organocatalyst. The key role of the catalyst is clearly pointed out during the decarboxylation of ferulic acid, without the use of...

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct form...

We have investigated important intermediates and key transition states of the organocatalyzed Knoevenagel condensation using density functional theory and two different basis sets (6-31 G(d,p) and 6-311++G(2df,2pd)), both in gas phase and simulating the bulk solvent (pyridine) using the PCM method. Calculated structures for reactants, intermediates...

Bicarbonate ion reacts with aqueous hydrogen peroxide, yielding monoperoxocarbonate (HCO4-, PCA-). This species is a better oxidizing agent than hydrogen peroxide itself and has been shown to lead to double bond epoxidation of alkenes under mild conditions. The structure of this anion as well as that of the parent monoperoxocarbonic acid (H2CO4, HP...

HCO3- reacts with H2O2 yielding monoperoxocarbonate (HCO4-), an oxidizing agent able to epoxidize alkenes. The structures of HCO4- and of parent monoperoxocarbonic acid (HPCA) are not known. However, the structure of the related peroxyformic acid (PFA) has been determined using microwave spectroscopy. We used in this work experimental and theoretic...

Ring-opening of epoxides with boron trifluoride yielding syn-fluorohydrins was investigated using density functional methods (PBE) and two different basis sets (6-31G(d) and 6-311++G(2df,2pd), both in gas phase and simulating the bulk solvent using the PCM method. The only mechanism previously suggested for the formation of fluorohydrins from epoxi...

Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove bi...

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct for...

Several 1:1, 1:2, and 2:2 complexes between BF3 and CH3OH (Met), CH3COOH (AcA), (CH3)2O (DME), (CH3CH2)2O (DEE), and (CH2)2O (EOX) have been studied using ab initio (MP2) and density functional theory (DFT) (PBE, B3LYP) methods and the 6-311++G(3df,2pd) basis set. Geometrical structures and vibrational frequencies are reported, in most cases, for t...

For Abstract see ChemInform Abstract in Full Text.

For Abstract see ChemInform Abstract in Full Text.

New 5-(2-arylethenyl)-1, 2, 4-triazine N-oxide and N, N'-dioxide derivatives were synthesized in order to obtain compounds as selective hypoxic cell cytotoxins. The desired products were obtained when the 5-methyl heterocycle reacted with the corresponding iminium electrophiles. The new compounds were tested for their cytotoxicity in oxia and hypox...

New 1, 2, 4-Triazine N-oxide and N, N'-dioxide derivatives were synthesized in order to obtain compounds as selective hypoxic cell cytotoxins. The starting heterocycles have been prepared using a standard microwave oven in a clean and good-yielded process. The reactivity of methyl-1, 2, 4-triazine N(4)-oxide and N(1), N(4)-dioxide with different el...

span>El primer curso de Química Orgánica (Química Orgánica 101) de la Facultad de Química, Universidad de la República (Montevideo, Uruguay) se dicta para las carreras de Química Farmacéutica, Ingeniería Química, Química, Bioquímica Clínica e Ingeniería en Alimentos, y tiene como objetivo dar una visión general de química orgánica, poniendo énfasis...

A receptor-based pharmacophore, previously derived using de novo ligand design technique, has been employed to design dual binding site acetylcholinesterase (AChE) inhibitors. The synthesis of the resultant substituted imidazoles followed by the corresponding enzymatic inhibition measurement yielded dual cholinergic inhibitors with modest activity...

12,4-Triazine N-oxide and N,N'-dioxide derivatives were synthesized in order to obtain compounds as potential selective hypoxic cell cytotoxins. All the compounds were tested for their cytotoxicity in oxia and hypoxia and some of them for their capacity to DNA-interaction in oxia. They proved to be less active in hypoxic conditions than the parent...

As part of an ongoing program on the chemistry and biological activity of N-oxide-containing molecules, a number of novel 1,2, 5-oxadiazole N-oxide, benzo[1,2-c]1,2,5-oxadiazole N-oxide, and quinoxaline N,N'-dioxide derivatives were synthesized and evaluated for their herbicidal activity. Many of these compounds exhibited moderate to good herbicida...

The syntheses of a new series of derivatives of 1,2,5-oxadiazole N-oxide, benzo[1,2-c]1,2,5-oxadiazole N-oxide, and quinoxaline di-N-oxide are described. In vitro antitrypanosomal activity of these compounds was tested against epimastigote forms of Trypanosoma cruzi. For the most effective drugs, derivatives IIIe and IIIf, the 50% inhibitory dose (...