Marcelo F. Masman

Penetratin and derivatives acting as antifungal agents

The synthesis, in vitro evaluation, and conformational study of RQIKIWFQNRRMKWKK-NH(2) (penetratin) and related derivatives acting as antifungal agents are reported. Penetratin and some of its derivatives displayed antifungal activity against the human opportunistic pathogenic standardized ATCC strains Candida albicans and Cryptococcus neoformans as well as clinical isolates of C. neoformans. Among the compounds tested, penetratin along with the nonapeptide RKWRRKWKK-NH(2) and the tetrapeptide RQKK-NH(2) exhibited significant antifungal activities against the Cryptococcus species. A comprehensive conformational analysis on the peptides reported here using three different approaches, molecular mechanics, simulated annealing and molecular dynamics simulations, was carried out. The experimental and theoretical results allow us to identify a topographical template which may provide a guide for the design of new compounds with antifungal characteristics against C. neoformans.

Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool.

Background: Aβ peptide, implicated in Alzheimer disease, occurs in various lengths. Results: Non-abundant Aβ1–38 and Aβ1–43 affect oligomerization, cytotoxicity, and aggregation of Aβ1–40 and Aβ1–42. Conclusion: Small amounts of Aβ lengths other than Aβ1–40 or Aβ1–42 significantly alter the behavior of the total Aβ pool. Significance: Drug strategies targeting APP processing to affect Aβ1–38 levels need careful consideration. Current therapeutic approaches under development for Alzheimer disease, including γ-secretase modulating therapy, aim at increasing the production of Aβ1–38 and Aβ1–40 at the cost of longer Aβ peptides. Here, we consider the aggregation of Aβ1–38 and Aβ1–43 in addition to Aβ1–40 and Aβ1–42, in particular their behavior in mixtures representing the complex in vivo Aβ pool. We demonstrate that Aβ1–38 and Aβ1–43 aggregate similar to Aβ1–40 and Aβ1–42, respectively, but display a variation in the kinetics of assembly and toxicity due to differences in short timescale conformational plasticity. In biologically relevant mixtures of Aβ, Aβ1–38 and Aβ1–43 significantly affect the behaviors of Aβ1–40 and Aβ1–42. The short timescale conformational flexibility of Aβ1–38 is suggested to be responsible for enhancing toxicity of Aβ1–40 while exerting a cyto-protective effect on Aβ1–42. Our results indicate that the complex in vivo Aβ peptide array and variations thereof is critical in Alzheimer disease, which can influence the selection of current and new therapeutic strategies.

LPYFDa Neutralizes Amyloid-beta-Induced Memory Impairment and Toxicity

Misfolding, oligomerization, and aggregation of the amyloid-beta (Abeta) peptide is widely recognized as a central event in the pathogenesis of Alzheimers disease (AD). Recent studies have identified soluble Abeta oligomers as the main pathogenic agents and provided evidence that such oligomeric Abeta aggregates are neurotoxic, disrupt synaptic plasticity, and inhibit long-term potentiation. A promising therapeutic strategy in the battle against AD is the application of short synthetic peptides which are designed to bind to specific Abeta-regions thereby neutralizing or interfering with the devastating properties of oligomeric Abeta species. In the present study, we investigated the neuroprotective properties of the amyloid sequence derived pentapeptide LPYFDa in vitro as well as its memory preserving capacity against Abeta(42)-induced learning deficits in vivo. In vitro we showed that neurons in culture treated with LPYFDa are protected against Abeta (42) -induced cell death. Moreover, in vivo LPYFDa prevented memory impairment tested in a contextual fear conditioning paradigm in mice after bilateral intrahippocampal Abeta (42) injections. We thus showed for the first time that an anti-amyloid peptide like LPYFDa can preserve memory by reverting Abeta (42) oligomer-induced learning deficits.

New mimetic peptides inhibitors of Αβ aggregation. Molecular guidance for rational drug design

A new series of mimetic peptides possessing a significant Aβ aggregation modulating effect was reported here. These compounds were obtained based on a molecular modelling study which allowed us to perform a structural-based virtual selection. Monitoring Aβ aggregation by thioflavin T fluorescence and transmission electron microscopy revealed that fibril formation was significantly decreased upon prolonged incubation in presence of the active compounds. Dot blot analysis suggested a decrease of soluble oligomers strongly associated with cognitive decline in Alzheimers disease. For the molecular dynamics simulations, we used an Aβ42 pentameric model where the compounds were docked using a blind docking technique. To analyze the dynamic behaviour of the complexes, extensive molecular dynamics simulations were carried out in explicit water. We also measured parameters or descriptors that allowed us to quantify the effect of these compounds as potential inhibitors of Aβ aggregation. Thus, significant alterations in the structure of our Aβ42 protofibril model were identified. Among others we observed the destruction of the regular helical twist, the loss of a stabilizing salt bridge and the loss of a stabilizing hydrophobic interaction in the β1 region. Our results may be helpful in the structural identification and understanding of the minimum structural requirements for these molecules and might provide a guide in the design of new aggregation modulating ligands.

Comprehensive conformational analysis of N-acetyl-l-isoleucine-N-methylamide: an ab initio study

Abstract A conformational study on N -acetyl- l -isoleucine- N -methylamide was carried out using ab initio (RHF/3-21G and RHF/6-31G(d)) calculations. All backbone and side-chain conformations in this compound were explored. N -acethyl- l -isoleucine- N -methylamide displayed a significant molecular flexibility. Also a different conformational behaviour was obtained for this amino acid residue in comparison with other amino acids possessing shorter apolar side-chains. These results can be attributed, at least in part, to the side-chain/backbone interactions, which are stabilizing the low-energy conformations in this molecule.

A Comprehensive Conformational Analysis of Bullacin B, a Potent Inhibitor of Complex I. Molecular Dynamics Simulations and Ab Initio Calculations

Using a conformational systematic search combined with semiempirical and ab initio (RHF/3-21G and RHF/6-31G(d)) calculations, the conformational space of bullacin B was examined for the first time. In addition, molecular dynamics simulations were carried out to better evaluate the conformational behavior of this acetogenin. Our results indicate that bullacin B possesses a significant molecular flexibility. Although many different conformations were identified, at ab initio level, the L forms were energetically mostly preferred. Our results support the use of molecular dynamics simulations for this compound suggesting that a combined decane/water system is a good solvent system to simulate the biological environment of this molecule acting as inhibitor of complex I.

Ironing out Their Differences: Dissecting the Structural Determinants of a Phenylalanine Aminomutase and Ammonia Lyase

Deciphering the structural features that functionally separate ammonia lyases from aminomutases is of interest because it may allow for the engineering of more efficient aminomutases for the synthesis of unnatural amino acids (e.g., β-amino acids). However, this has proved to be a major challenge that involves understanding the factors that influence their activity and regioselectivity differences. Herein, we report evidence of a structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL) and aminomutase (PAM). An inner loop region that closes the active sites of both PAM and PAL was mutated within PAM (PAM residues 77-97) in a stepwise approach to study the effects when the equivalent residue(s) found in the PAL loop were introduced into the PAM loop. Almost all of the single loop mutations triggered a lyase phenotype in PAM. Experimental and computational evidence suggest that the induced lyase features result from inner loop mobility enhancements, which are possibly caused by a 310-helix cluster, flanking α-helices, and hydrophobic interactions. These findings pinpoint the inner loop as a structural determinant of the lyase and mutase activities of PAM.

Braak Staging in Mouse Models of Alzheimer's Disease

In the present paper by David E. Hurtado and colleagues report on a new mouse model for AD bearing Aβ and MAPT pathology by crossing PS19 and PDAPP Tg mice. Here, we tried to highlight the importance and necessity of the critical and systematic analysis of models such as the Braak like staging in AD mouse models.

Zoledronate derivatives as potential inhibitors of uridine diphosphate-galactose ceramide galactosyltransferase 8: A combined molecular docking and dynamic study

Krabbes disease is a neurodegenerative disorder caused by deficiency of galactocerebrosidase activity that affects the myelin sheath of the nervous system, involving dysfunctional metabolism of sphingolipids. It has no cure. Because substrate inhibition therapy has been shown to be effective in some human lysosomal storage diseases, we hypothesize that a substrate inhibition therapeutic approach might be appropriate to allow correction of the imbalance between formation and breakdown of glycosphingolipids and to prevent pathological storage of psychosine. The enzyme responsible for the biosynthesis of galactosylceramide and psychosine is uridine diphosphate‐galactose ceramide galactosyltransferase (2‐hydroxyacylsphingosine 1‐β‐galactosyltransferase; UGT8; EC 2.4.1.45), which catalyzes the transferring of galactose from uridine diphosphate‐galactose to ceramide or sphingosine, an important step of the biosynthesis of galactosphingolipids. Because some bisphosphonates have been identified as selective galactosyltransferase inhibitors, we verify the binding affinity to a generated model of the enzyme UGT8 and investigate the molecular mechanisms of UGT8–ligand interactions of the bisphosphonate zoledronate by a multistep framework combining homology modeling, molecular docking, and molecular dynamics simulations. From structural information on UGTs’ active site stereochemistry, charge density, and access through the hydrophobic environment, the molecular docking procedure allowed us to identify zoledronate as a potential inhibitor of human ceramide galactosyltransferase. More importantly, zoledronate derivates were designed through computational modeling as putative new inhibitors. Experiments in vivo and in vitro have been planned to verify the possibility of using zoledronate and/or the newly identified inhibitors of UGT8 for a substrate inhibition therapy useful for treatment of Krabbes disease and/or other lysosomal disorders.

Aromatization within the putative bio-medical action mechanism of berberine and related cationic alkaloids with double iso-quinolinoid skeleton. A theoretical study

In the putative mechanism of action for berberin, to prevent DNA replication the first step is aromatization. The aromatization process, via dehydrogenation has been studied for a series of compounds related to berberine. In contrast to the covalent dehydrogenation, which is endothermic, the aromatization under ionic conditions was found to be exothermic. The availability of the hydride for ionic aromatization was indicated by the effective HOMO of berberine and related compounds. The results indicate that in the aromatization process the ease of hydride ion removal parallels the stabilizations energy of the aromatic compounds to be formed. Comparing the nucleophilic additions to the π-system, the LUMO energy values suggested a greater accessibility of the N(+) heterocycles in comparison to the polycycle aromatic hydrocarbons.