Fernando González-nilo | Universidad Andrés Bello (original) (raw)

Papers by Fernando González-nilo

International Journal of Molecular Sciences, 2022

Endoxylanases belonging to family 10 of the glycoside hydrolases (GH10) are versatile in the use ... more Endoxylanases belonging to family 10 of the glycoside hydrolases (GH10) are versatile in the use of different substrates. Thus, an understanding of the molecular mechanisms underlying substrate specificities could be very useful in the engineering of GH10 endoxylanases for biotechnological purposes. Herein, we analyzed XynA, an endoxylanase that contains a (β/α)8-barrel domain and an intrinsically disordered region (IDR) of 29 amino acids at its amino end. Enzyme activity assays revealed that the elimination of the IDR resulted in a mutant enzyme (XynAΔ29) in which two new activities emerged: the ability to release xylose from xylan, and the ability to hydrolyze p-nitrophenyl-β-d-xylopyranoside (pNPXyl), a substrate that wild-type enzyme cannot hydrolyze. Circular dichroism and tryptophan fluorescence quenching by acrylamide showed changes in secondary structure and increased flexibility of XynAΔ29. Molecular dynamics simulations revealed that the emergence of the pNPXyl-hydrolyzing...

Additional file 3: Figure S3. Radial distribution functions of a) water at 298 K (liquid water) a... more Additional file 3: Figure S3. Radial distribution functions of a) water at 298 K (liquid water) and b) 220 K (ice) determined experimentally from X-ray and neutron diffraction by Soper [47]. Images were obtained and adapted from http://rkt.chem.ox.ac.uk/lectures/liqsolns/liquids.html .

Additional file 2: Figure S2. Ramachandran plot analysis of the dihedral angles PSI (ψ) and PHI (... more Additional file 2: Figure S2. Ramachandran plot analysis of the dihedral angles PSI (ψ) and PHI (ɸ) of the generated models for (a) afp5A, (b) gu3A and (c) gu3B obtained by RAMPAGE. The three plots show favorable positioning of amino acids for the different models generated.

Additional file 1: Figure S1. Multiple sequence alignment between the DUF3494 domains of the iden... more Additional file 1: Figure S1. Multiple sequence alignment between the DUF3494 domains of the identified antifreeze proteins gu3A, gu3B and afp5A. Asterisks (*) indicate positions with fully conserved residues; colons (:) indicate conservation of residues with strong similar properties; periods (.) indicate conservation of weakly similar residues. Alignment was performed using ClustalW.

Bioorganic & medicinal chemistry letters, 2005

Relationships between the structural characteristics of flavonoids isolated from the resinous exu... more Relationships between the structural characteristics of flavonoids isolated from the resinous exudate of Heliotropium sinuatum and their antioxidant activity were studied. Radical formation energies, DeltaH of dehydrogenation and spin densities were calculated using DFT methods (B3LYP/6-31G*). Results show that studied flavonoids can be divided into two sets according to their activity. It has been found that antioxidant activity depends both on substitution pattern of hydroxyl groups of the flavonoid skeleton and the presence of an unsaturation at the C2-C3 bond. A good tendency between DeltaH of dehydrogenation and antioxidant activity was established.

Several antidepressants inhibit nicotinic acetylcholine receptors (nAChRs) in a non-competitive a... more Several antidepressants inhibit nicotinic acetylcholine receptors (nAChRs) in a non-competitive and voltage-dependent fashion. Here, we asked whether antidepressants with a different structure and pharmacological profile modulate the rat α7 nAChR through a similar mechanism by interacting within the ion-channel. We applied electrophysiological (recording of the ion current elicited by choline, ICh, which activates α7 nAChRs from rat CA1 hippocampal interneurons) and in silico approaches (homology modeling of the rat α7 nAChR, molecular docking, molecular dynamics simulations, and binding free energy calculations). The antidepressants inhibited ICh with the order: norfluoxetine ~ mirtazapine ~ imipramine < bupropion ~ fluoxetine ~ venlafaxine ~ escitalopram. The constructed homology model of the rat α7 nAChR resulted in the extracellular vestibule and the channel pore is highly negatively charged, which facilitates the permeation of cations and the entrance of the protonated form ...

Journal of Cellular Physiology, 2021

Large-pore channels, including those formed by connexin, pannexin, innexin proteins, are part of ... more Large-pore channels, including those formed by connexin, pannexin, innexin proteins, are part of a broad family of plasma membrane channels found in vertebrates and invertebrates, which share topology features. Despite their relevance in parasitic diseases such as Chagas and malaria, it was unknown whether these large-pore channels are present in unicellular organisms. We identified 14 putative proteins in Trypanosomatidae parasites as presumptive homologs of innexin proteins. All proteins possess the canonical motif of the innexin family, a pentapeptide YYQWV, and 10 of them share a classical membrane topology of large-pore channels. A sequence similarity network analysis confirmed their closeness to innexin proteins. A bioinformatic model showed that a homolog of Trypanosoma cruzi (T. cruzi) could presumptively form a stable octamer channel with a highly positive electrostatic potential in the internal cavities and extracellular entrance due to the notable predominance of residues such as Arg or Lys. In vitro dye uptake assays showed that divalent cations-free solution increases YO-PRO-1 uptake and hyperosmotic stress increases DAPI uptake in epimastigotes of T. cruzi. Those effects were sensitive to probenecid. Furthermore, probenecid reduced the proliferation and transformation of T. cruzi. Moreover, probenecid or carbenoxolone increased the parasite sensitivity to antiparasitic drugs commonly used in therapy against Chagas. Our study suggests the existence of innexin homologs in unicellular organisms, which could be protein subunits of new large-pore channels in unicellular organisms.

Biomedicine & Pharmacotherapy, 2021

Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-... more Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-CoV-2), which causes a severe acute respiratory syndrome (COVID-19). In particular, protease. Therefore, using in silico tests, 30 molecules obtained from cocoa were evaluated. Using molecular docking and quantum mechanics calculations, the chemical properties and binding efficiency of each ligand was evaluated, which allowed the selection of 5 compounds of this series. The ability of amentoflavone, isorhoifolin, nicotiflorin, naringin and rutin to bind to the main viral protease was studied by means of free energy calculations and structural analysis performed from molecular dynamics simulations of the enzyme/inhibitor complex. Isorhoifolin and rutin stand out, presenting a more negative binding ΔG than the reference inhibitor N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-L-valyl-N~1~-((1R,2Z)− 4-(benzyloxy)− 4-oxo-1-{[(3R)− 2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide (N3). These results are consistent with high affinities of these molecules for the major SARS-CoV-2. The results presented in this paper are a solid starting point for future in vitro and in vivo experiments aiming to validate these molecules and /or test similar substances as inhibitors of SARS-CoV-2 protease.

Frontiers in Chemistry, 2021

The pandemic that started in Wuhan (China) in 2019 has caused a large number of deaths, and infec... more The pandemic that started in Wuhan (China) in 2019 has caused a large number of deaths, and infected people around the world due to the absence of effective therapy against coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2). Viral maturation requires the activity of the main viral protease (Mpro), so its inhibition stops the progress of the disease. To evaluate possible inhibitors, a computational model of the SARS-CoV-2 enzyme Mpro was constructed in complex with 26 synthetic ligands derived from coumarins and quinolines. Analysis of simulations of molecular dynamics and molecular docking of the models show a high affinity for the enzyme (∆Ebinding between −5.1 and 7.1 kcal mol−1). The six compounds with the highest affinity show Kd between 6.26 × 10–6 and 17.2 × 10–6, with binding affinity between −20 and −25 kcal mol−1, with ligand efficiency less than 0.3 associated with possible inhibitory candidates. In addition to the high affinity of these compounds for SARS...

Scientific Reports, 2020

High order oligomers are crucial for normal cell physiology, and protein function perturbed by mi... more High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. Dynamin-2 is one of such protein forming helical oligomers that catalyze membrane fission. Mutations in this protein, where R465W is the most frequent, cause dominant centronuclear myopathy, but the molecular mechanisms underpinning the functional modifications remain to be investigated. To unveil the structural impact of this mutation in dynamin-2, we used full-atom molecular dynamics simulations and coarse-grained models and built dimers and helices of wild-type (WT) monomers, mutant monomers, or both WT and mutant monomers combined. Our results show that the mutation R465W causes changes in the interactions with neighbor amino acids that propagate through the oligomer. These new interactions perturb the contact between monomers and favor an extended conformation of the bundle signaling element (BSE), a dynamin region that...

Frontiers in Pharmacology, 2020

Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 2019

Scientific Reports, 2019

the accessory β1 subunit modulates the Ca 2+-and voltage-activated K + (BK) channel gating proper... more the accessory β1 subunit modulates the Ca 2+-and voltage-activated K + (BK) channel gating properties mainly by increasing its apparent Ca 2+ sensitivity. β1 plays an important role in the modulation of arterial tone and blood pressure by vascular smooth muscle cells (SMCs). 17β-estradiol (E2) increases the BK channel open probability (P o) in SMCs, through a β1 subunit-dependent modulatory effect. Here, using molecular modeling, bioinformatics, mutagenesis, and electrophysiology, we identify a cluster of hydrophobic residues in the second transmembrane domain of the β1 subunit, including the residues W163 and F166, as the binding site for E2. We further show that the increase in P o induced by E2 is associated with a stabilization of the voltage sensor in its active configuration and an increase in the coupling between the voltage sensor activation and pore opening. Since β1 is a key molecular player in vasoregulation, the findings reported here are of importance in the design of novel drugs able to modulate BK channels. The large conductance, Ca 2+-and voltage-activated K + (BK) channel is a tetrameric transmembrane protein composed of α subunits that form the K + selective pore 1,2. The α subunit is broadly expressed in mammalian tissues 3 , where it is co-expressed with an accessory β subunits in a tissue-specific manner 4,5. The α subunit comprises seven transmembrane segments (S0-S6), leaving the amino terminus exposed to the external medium. The large intracellular carboxyl terminus domain consisting of two RCK domains contains the Ca 2+ binding sites. The different β subunits (β1-β4) are formed by two transmembrane segments linked by a large extracellular loop and are responsible for the modulation of the biophysical and pharmacological characteristics of the α subunit 4,6. The β1 subunit is abundantly expressed in smooth muscle cells and acts to increase the apparent sensitivity to Ca 2+ and dramatically slows down the activation and deactivation channel-gating kinetics 7-12. The presence of the BK α/β1 channel lowers the risk of pathologies associated with the vascular tone by causing a membrane hyperpolarization, decreasing vasoconstriction, and inducing a faster relaxation of the blood vessels 13,14. β subunits appear to regulate the BK channel activity by targeting specific gating mechanisms 11,14,15. In particular, by biasing the equilibrium resting-active of the voltage sensor towards its active configuration, β1 increases the apparent BK Ca 2+ sensitivity 14,16 Co-expression of BK α and β subunits can dramatically modify pharmacological responses of the channel 17-19 as potential targets for channel modulators such as alcohol 20 , estrogens 19 , hormones 21 and fatty acids 22,23. 17β-Estradiol (E2) is the main circulating oestrogen in women and reaches a plasma concentration of 30-400 pg/mL before menopause. E2 regulates growth and the development of the reproductive system, also, helps to maintain the osseous tissue, the central nervous system and the vasodilatation in the vascular tissue 24. The protective effect of E2 in the vasculature and against cardiovascular disease (CVD) has been demonstrated in several hormone replacement studies 25,26. E2 activates BK channels 19,27-30 via a process that requires the presence

Journal of Sensory Studies, 2018

Bioconjugate chemistry, Jan 30, 2018

Cell-to-cell transmission is the most effective pathway for the spread of human immunodeficiency ... more Cell-to-cell transmission is the most effective pathway for the spread of human immunodeficiency virus (HIV-1). Infected cells expose virus-encoded fusion proteins on their surface as a consequence of HIV-1 replicative cycle that interacts with noninfected cells through CD4 receptor and CXCR4 coreceptor leading to the formation of giant multinucleated cells known as syncytia. Our group previously described the potent activity of dendrimers against CCR5-tropic viruses. Nevertheless, the study of G1-S4, G2-S16, and G3-S16 dendrimers in the context of X4-HIV-1 tropic cell-cell fusion referred to syncytium formation remains still unknown. These dendrimers showed a suitable biocompatibility in all cell lines studied and our results demonstrated that anionic carbosilane dendrimers G1-S4, G2-S16, and G3-S16 significantly inhibit the X4-HIV-1 infection, as well as syncytia formation, in a dose dependent manner. We also demonstrated that G2-S16 and G1-S4 significantly reduced syncytia format...

Microbial cell factories, Jan 7, 2017

Antifreeze proteins (AFPs) production is a survival strategy of psychrophiles in ice. These prote... more Antifreeze proteins (AFPs) production is a survival strategy of psychrophiles in ice. These proteins have potential in frozen food industry avoiding the damage in the structure of animal or vegetal foods. Moreover, there is not much information regarding the interaction of Antarctic bacterial AFPs with ice, and new determinations are needed to understand the behaviour of these proteins at the water/ice interface. Different Antarctic places were screened for antifreeze activity and microorganisms were selected for the presence of thermal hysteresis in their crude extracts. Isolates GU1.7.1, GU3.1.1, and AFP5.1 showed higher thermal hysteresis and were characterized using a polyphasic approach. Studies using cucumber and zucchini samples showed cellular protection when samples were treated with partially purified AFPs or a commercial AFP as was determined using toluidine blue O and neutral red staining. Additionally, genome analysis of these isolates revealed the presence of genes tha...