Examinando por Autor "Tiznado, William"
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Ítem Alterations of mitochondrial biology in the oral mucosa of chilean children with autism spectrum disorder (ASD)(Cells, 2019-04-23) Carrasco, Manuel; Salazar, Celia; Tiznado, William; Ruiz, Lina MaríaAutistic Spectrum Disorder (ASD) is characterized by the impairment of socio-communicative skills and the presence of restricted and stereotyped behavior patterns. Recent researches have revealed the influence of mitochondrial physiology on the development of ASD. Several research groups have identified defects in respiratory complexes, coenzyme-Q10 deficiency, increased oxidative damage, decreased of superoxide dismutase (SOD2). A study on the influence of mitochondrial physiology on the development of ASD can provide new alternatives and challenges. That is why we set ourselves the general objective to initiate studies of mitochondrial physiology in Chilean children with ASD. A sample of oral mucosa was collected in a group of 12 children diagnosed with ASD and 12 children without ASD. In children with ASD, we found a significant increase in mitochondrial DNA levels. Likewise, in these children, an increase in the protein oxidation was observed. Finally, a downward trend in the expression of the HIGD2A and SOD2 genes was observed, while DRP1, FIS1, MFN1, MFN2, and OPA1 gene expression show an upward trend. The increment of mitochondrial DNA, high oxidative stress, and high expression of the MFN2 gene could help as a scanner of the mitochondrial function in children with ASD.Ítem Antioxidant activity and enzymatic of lichen substances: A study based on cyclic voltammetry and theoretical(2023-02) Yanez, Osvaldo; I.Osorio, Manuel; Osorio, Edison; Ruíz, Lina; Tiznado, William; García, Camilo; Orlando, Nagles,; Mario J, Simirgiotis,; Grover, Castañeta,; Olimpo, García-Beltrán,The antioxidant activity of nine lichen substances, including methylatrarate (1), methyl haematommate (2), lobaric acid (3), fumarprotocetraric acid (4), sphaerophorin (5), subsphaeric acid (6), diffractaic acid (7), barbatolic acid (8) and salazinic acid (9) has been determined through cyclic voltammetry. The compounds 1–4 presented slopes close to the Nernst constant of 0.059 V, indicating a 2H+/2e− relation between protons and electrons, as long as the compounds 5, 6, 7, 8, and 9 present slopes between 0.037 V and 0.032 V, indicating a 1H+/2e− relation between protons and electrons. These results show a high free radical scavenging activity by means of the release of H+, suggesting an important antioxidant capacity of these molecules. Theoretical calculations of hydrogen bond dissociation enthalpies (BDE), proton affinities (PA), and Proton Transfer (PT) mechanisms, at M06-2x/6-311+G(d,p) level complement the experimental results. Computations support that the best antioxidant activity is obtained for the molecules (3, 4, 5, 6, 7 and 8), that have a carboxylic acid group close to a phenolic hydroxyl group, through hydrogen atomic transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanisms. Additional computations were performed for modelling binding affinity of the lichen substances with CYPs enzymes, mainly CYP1A2, CYP51, and CYP2C9*2 isoforms, showing strong affinity for all the compounds described in this study. © 2023 The AuthorsÍtem Biosystem analysis of the hypoxia inducible domain family member 2A: Implications in cancer biology(MDPI AG, 2020-02) Salazar, Celia; Yañez, Osvaldo; Elorza, Alvaro A.; Cortes, Natalie; García-Beltrán, Olimpo; Tiznado, William; Ruiz, Lina MaríaThe expression of HIGD2A is dependent on oxygen levels, glucose concentration, and cell cycle progression. This gene encodes for protein HIG2A, found in mitochondria and the nucleus, promoting cell survival in hypoxic conditions. The genomic location of HIGD2A is in chromosome 5q35.2, where several chromosomal abnormalities are related to numerous cancers. The analysis of high definition expression profiles of HIGD2A suggests a role for HIG2A in cancer biology. Accordingly, the research objective was to perform a molecular biosystem analysis of HIGD2A aiming to discover HIG2A implications in cancer biology. For this purpose, public databases such as SWISS-MODEL protein structure homology-modelling server, Catalogue of Somatic Mutations in Cancer (COSMIC), Gene Expression Omnibus (GEO), MethHC: a database of DNA methylation and gene expression in human cancer, and microRNA-target interactions database (miRTarBase) were accessed. We also evaluated, by using Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR), the expression of Higd2a gene in healthy bone marrow-liver-spleen tissues of mice after quercetin (50 mg/kg) treatment. Thus, among the structural features of HIG2A protein that may participate in HIG2A translocation to the nucleus are an importin α-dependent nuclear localization signal (NLS), a motif of DNA binding residues and a probable SUMOylating residue. HIGD2A gene is not implicated in cancer via mutation. In addition, DNA methylation and mRNA expression of HIGD2A gene present significant alterations in several cancers; HIGD2A gene showed significant higher expression in Diffuse Large B-cell Lymphoma (DLBCL). Hypoxic tissues characterize the “bone marrow-liver-spleen” DLBCL type. The relative quantification, by using RT-qPCR, showed that Higd2a expression is higher in bone marrow than in the liver or spleen. In addition, it was observed that quercetin modulated the expression of Higd2a gene in mice. As an assembly factor of mitochondrial respirasomes, HIG2A might be unexpectedly involved in the change of cellular energetics happening in cancer. As a result, it is worth continuing to explore the role of HIGD2A in cancer biology. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.Ítem Chemical bonding analysis in boron clusters by means of localized orbitals according to the electron localization function topology(Springer Science and Business Media, LLC, 2015-03) Oña, Ofelia B.; Torres-Vega, Juan J.; Torre, Alicia; Lain, Luis; Alcoba, Diego R.; Vásquez-Espinal, Alejandro; Tiznado, WilliamA series of small planar boron clusters has extensively been studied in the past using different theoretical approximations, and their chemical bonding has been rationalized in terms of aromaticity, antiaromaticity and conflicting aromaticity. Here, we study these systems by means of our recently proposed orbital localization procedure based on the partitioning of the space according to the electron localization function (ELF) topology. The results are compared with those obtained from the adaptive natural density partitioning (AdNDP) method, which is a most extensively tested orbital localization procedure. Minor discrepancies have been found, especially in large clusters. In those cases, an alternative set of localized AdNDP orbitals recovered the representation obtained by ELF localization procedure. These results support the need for multicenter bonding incorporation into the localization models for rationalizing chemical bonding in atomic clusters. Additionally, the aromatic character of the clusters, when it is present, is adequately supported by the more classical treatment based on the ELF topological analysis. © 2015, Springer-Verlag Berlin Heidelberg.Ítem Cluster Assembled Silicon-Lithium Nanostructures: A Nanowire Confined Inside a Carbon Nanotube(Frontiers Media S.A., 2021-11) Orellana, Walter; Pino-Rios, Ricardo; Yañez, Osvaldo; Vásquez Espinal, Alejandro; Peccati, Francesca; Contreras García, Julia; Cardenas, Carlos; Tiznado, WilliamWe computationally explore an alternative to stabilize one-dimensional (1D) silicon-lithium nanowires (NWs). The Li12Si9 Zintl phase exhibits the NW (Formula presented.), combined with Y-shaped Si4 structures. Interestingly, this NW could be assembled from the stacking of the Li6Si5 aromatic cluster. The (Formula presented.) @CNT nanocomposite has been investigated with density functional theory (DFT), including molecular dynamics simulations and electronic structure calculations. We found that van der Waals interaction between Li’s and CNT’s walls is relevant for stabilizing this hybrid nanocomposite. This work suggests that nanostructured confinement (within CNTs) may be an alternative to stabilize this free NW, cleaning its properties regarding Li12Si9 solid phase, i.e., metallic character, concerning the perturbation provided by their environment in the Li12Si7 compound. Copyright © 2021 Orellana, Pino-Rios, Yañez, Vásquez-Espinal, Peccati, Contreras-García, Cardenas and Tiznado.Ítem Desarrollo e implementación de algoritmos híbridos para la exploración de la superficie de energía potencial en clusters atómicos y moleculares(Universidad Andrés Bello, 2018) Yáñez Osses, Osvaldo Andrés; Tiznado, William; Garza Olguín, Jorge; Facultad de Ciencias Exactaslos cúmulos atómicos (clusters en este escrito) son entidades químicas con propiedades, físicas y químicas, particulares y dependientes de su tamaño. la química teórica, enmarcada en la mecánica cuántica y clásica, cumple un rol fundamental en el estudio de estos sistemas, ya que éstos se sintetizan mediante la atomización del material (a altas temperaturas) y las propiedades que se logran medir son en estado gaseoso. Por este motivo la forma práctica de asignación estructural se basa en medir la propiedad experimental con su contraparte teórica. Por ejemplo, se utilizan los espectros fotoelectrónicos para estas asignaciones, siendo éstos característicos de cada isómero (la estructura electrónica es muy dependiente de la estructura geométrica). la predicción conformacional de clusters atómicos tiene implicaciones relevantes en campos tan variados como el diseño de nanomateriales, nanobiomedicina, catálisis, entre otros, por lo tanto es necesario contar con un método confiable o una combinación de varios métodos para la exploración de las superficie de energía potencial (SEP) de clusters atómicos y moleculares. En consecuencia, la determinación de la estructura y de las propiedades físicas de un sistema molecular está íntimamente relacionada con el mínimo global en su SEP.Ítem Evaluación de la participación de Mg2+ en el mecanismo de catálisis de la dnazima 8-17(Universidad Andrés Bello, 2020) Rojas Hernández, Francisca Catalina; Cepeda Plaza, Marjorie; Millán, Daniela; Tiznado, William; Facultad de Ciencias ExactasLas DNAzimas son hebras monocaternarias de ADN obtenidas en laboratorio a través de un proceso llamado selección in vitro, las cuales son capaces de catalizar diversas reacciones químicas, entre ellas la ruptura de ARN. En esta reacción, la DNAzima acelera la transferencia interna del fosfodiéster, utilizando un ion metálico como cofactor. Entre la gran variedad de enzimas de ADN seleccionadas hasta la fecha, la DNAzima 8-17 ha sido, sin duda, la más estudiada en términos catalíticos. Esta es una metaloenzima que tiene la particularidad de ser activa con una serie de metales divalentes, pero que muestra su mayor actividad en presencia de Pb 2+ . Sin embargo, la participación específica del cofactor metálico en la catálisis no ha sido aún del todo dilucidada, aunque en base a la evidencia colectada, una de las posibilidades podría ser la existencia de un evento de transferencia de protones que involucra al ion metálico hidratado. Por esta razón, este trabajo propone evaluar la influencia del pH en el mecanismo de reacción de la DNAzima 8-17, a través del estudio de perfiles de actividad (log (kobs) vs pH). Para ello es necesario estudiar la actividad de la enzima en un amplio rango de pH. No obstante, a altos valores de pH, la DNAzima tiene la particularidad de tener constantes de velocidad elevadas que dificultan su determinación por las técnicas disponibles. Para superar esta limitación, se plantea estudiar los perfiles de actividad de un análogo menos activo de la DNAzima 8-17. De esta manera, se compararán los perfiles de actividad de la DNAzima nativa y la análoga en presencia del ion metálico divalente. Para esto se realizarán ensayos de actividad a diferentes pHs con la DNAzima y un sustrato marcado con la sonda fluorescente FAM en la terminación-5Ꞌ, bajo condiciones de single-turnover. Las hebras correspondientes al sustrato y a los productos de reacción serán separados mediante electroforesis, en un gel denaturante de poliacrilamida al 20% (PAGE), la imagen obtenida será visualizada en un G:box Syngene Imager System, y la cuantificación se realizará por medio del software GeneTools Syngene. A partir de los datos de formación de producto en el tiempo, se calcularán las kobs para cada reacción, a cada uno de los pH bajo estudio. Estos datos cinéticos, permitirán evaluar la influencia del pH sobre la actividad de la DNAzima 8-17.Ítem Exploring the Potential Energy Surface of Medium-Sized Aromatic Polycyclic Systems with Embedded Planar Tetracoordinate Carbons: A Guided Approach(Multidisciplinary Digital Publishing Institute (MDPI), 2023-09) Inostroza, Diego; Leyva-Parra, Luis; Yañez, Osvaldo; Cooksy, Andrew L.; Thimmakondu, Venkatesan S.; Tiznado, WilliamThis study scrutinizes the complexities of designing and exploring the potential energy surfaces of systems containing more than twenty atoms with planar tetracoordinate carbons (ptCs). To tackle this issue, we utilized an established design rule to design a Naphtho [1,2-b:3,4-b′:5,6-b″:7,8-b′′′]tetrathiophene derivative computationally. This process began with substituting S atoms with CH− units, then replacing three sequential protons with two Si2+ units in the resultant polycyclic aromatic hydrocarbon polyanion. Despite not representing the global minimum, the newly designed Si8C22 system with four ptCs provided valuable insights into strategic design and potential energy surface exploration. Our results underscore the importance of employing adequate methodologies to confirm the stability of newly designed molecular structures containing planar hypercoordinate carbons. © 2023 by the authors.Ítem In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease(Frontiers Media S.A., 2021-02) Yañez, Osvaldo; Osorio, Manuel Isaías; Uriarte, Eugenio; Areche, Carlos; Tiznado, William; Pérez Donoso, José M.; García Beltrán, Olimpo; González Nilo, FernandoThe 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-CoV-2 Mpro, low toxicity is expected considering the Lipinski, Veber and Pfizer rules. Therefore, this novel study provides candidate inhibitors that would allow experimental studies which can lead to the development of new treatments for SARS-CoV-2. © Copyright © 2021 Yañez, Osorio, Uriarte, Areche, Tiznado, Perez-Donoso, García-Beltrán and González-Nilo.Ítem Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR(Public Library of Science, 2014-07) Quesada-Romero, Luisa; Mena-Ulecia, Karel; Tiznado, William; Caballero, JulioMany protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3b) using docking experiments. We found that the orientations that these compounds adopt inside GSK3b binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3b inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors.Ítem Interpreting Aromaticity and Antiaromaticity through Bifurcation Analysis of the Induced Magnetic Field(ChemistryOpen, 2019-03) Pino-Rios, Ricardo; Cárdenas-Jirón, Gloria; Ruiz, Lina; Tiznado, WilliamIn all molecules, a current density is induced when the molecule is subjected to an external magnetic field. In turn, this current density creates a particular magnetic field. In this work, the bifurcation value of the induced magnetic field is analyzed in a representative set of aromatic, non-aromatic and antiaromatic monocycles, as well as a set of polycyclic hydrocarbons. The results show that the bifurcation value of the ring-shaped domain adequately classifies the studied molecules according to their aromatic character. For aromatic and nonaromatic molecules, it is possible to analyze two ring-shaped domains, one diatropic (inside the molecular ring) and one paratropic (outside the molecular ring). Meanwhile, for antiaromatic rings, only a diatropic ring-shaped domain (outside the molecular ring) is possible to analyze, since the paratropic domain (inside the molecular ring) is irreducible with the maximum value (attractor) at the center of the molecular ring. In some of the studied cases, i. e., in heteroatomic species, bifurcation values do not follow aromaticity trends and present some inconsistencies in comparison to ring currents strengths, showing that this approximation provides only a qualitative estimation about (anti)aromaticity.Ítem Planar Elongated B12 Structure in M3B12 Clusters (M = Cu-Au)(MDPI, 2023-01) Solar-Encinas, José; Vásquez-Espinal, Alejandro; Leyva-Parra, Luis; Yañez, Osvaldo; Inostroza, Diego; Valenzuela, Maria Luisa; Orellana, Walter; Tiznado, WilliamHere, it is shown that the M3B12 (M = Cu-Au) clusters’ global minima consist of an elongated planar B12 fragment connected by an in-plane linear M3 fragment. This result is striking since this B12 planar structure is not favored in the bare cluster, nor when one or two metals are added. The minimum energy structures were revealed by screening the potential energy surface using genetic algorithms and density functional theory calculations. Chemical bonding analysis shows that the strong electrostatic interactions with the metal compensate for the high energy spent in the M3 and B12 fragment distortion. Furthermore, metals participate in the delocalized π-bonds, which infers an aromatic character to these species. © 2022 by the authors.Ítem Quercetin Affects Erythropoiesis and Heart Mitochondrial Function in Mice(Hindawi Publishing Corporation, 2015) Ruiz, Lina M.; Salazar, Celia; Jensen, Erik; Ruiz, Paula A.; Tiznado, William; Quintanilla, Rodrigo A.; Barreto, Marlen; Elorza, Alvaro A.Quercetin, a dietary flavonoid used as a food supplement, showed powerful antioxidant effects in different cellular models. However, recent in vitro and in vivo studies in mammals have suggested a prooxidant effect of quercetin and described an interaction with mitochondria causing an increase in O2- production, a decrease in ATP levels, and impairment of respiratory chain in liver tissue. Therefore, because of its dual actions, we studied the effect of quercetin in vivo to analyze heart mitochondrial function and erythropoiesis. Mice were injected with 50 mg/kg of quercetin for 15 days. Treatment with quercetin decreased body weight, serum insulin, and ceruloplasmin levels as compared with untreated mice. Along with an impaired antioxidant capacity in plasma, quercetin-treated mice showed a significant delay on erythropoiesis progression. Heart mitochondrial function was also impaired displaying more protein oxidation and less activity for IV, respectively, than no-treated mice. In addition, a significant reduction in the protein expression levels of Mitofusin 2 and Voltage-Dependent Anion Carrier was observed. All these results suggest that quercetin affects erythropoiesis and mitochondrial function and then its potential use as a dietary supplement should be reexamined. © 2015 Lina M. Ruiz et al.Ítem Quest for the Most Aromatic Pathway in Charged Expanded Porphyrins(John Wiley and Sons Inc, 2023-01) Casademont-Reig, Irene; Woller, Tatiana; García, Victor; Contreras-García, Julia; Tiznado, William; Torrent-Sucarrat, Miquel; Matito, Eduard; Alonso, MercedesDespite the central role of aromaticity in the chemistry of expanded porphyrins, the evaluation of aromaticity remains difficult for these extended macrocycles. The presence of multiple conjugation pathways and different planar and nonplanar π-conjugation topologies makes the quantification of global and local aromaticity even more challenging. In neutral expanded porphyrins, the predominance of the aromatic conjugation pathway passing through the imine-type nitrogens and circumventing the amino NH groups is established. However, for charged macrocycles, the question about the main conjugation circuit remains open. Accordingly, different conjugation pathways in a set of neutral, anionic, and cationic expanded porphyrins were investigated by means of several aromaticity indices rooted in the structural, magnetic, and electronic criteria. Overall, our results reveal the predominance of the conjugation pathway that passes through all nitrogen atoms to describe the aromaticity of deprotonated expanded porphyrins, while the outer pathway through the perimeter carbon atoms becomes the most aromatic in protonated macrocycles. In nonplanar and charged macrocycles, a discrepancy between electronic and magnetic descriptors is observed. Nevertheless, our work demonstrates AVmin remains the best tool to determine the main conjugation pathway of expanded porphyrins. © 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.Ítem Revisiting Aromaticity and Chemical Bonding of Fluorinated Benzene Derivatives(Wiley-VCH Verlag, 2015-06) Torres-Vega, Juan J.; Vásquez-Espinal, Alejandro; Ruiz, Lina; Fernández-Herrera, María A.; Alvarez-Thon, Luis; Merino, Gabriel; Tiznado, WilliamThe electron delocalization of benzene (C6H6) and hexafluorobenzene (C6F6) was analyzed in terms of the induced magnetic field, nucleus-independent chemical shift (NICS), and ring current strength (RCS). The computed out-of-plane component of the induced magnetic field at a distance (r) greater than or equal to 1.0 Å above the ring center correlates well (R2>0.99) with the RCS value. According to these criteria, fluorination has two effects on the C6 skeleton; concomitantly, the resonant effects diminish the π electron delocalization and the inductive effects decrease the charge density at the ring center and therefore reduce the magnitude of the paratropic current generated in this region. The equilibrium between both effects decreases aromaticity in the fluorinated benzene derivatives. These results can be extrapolated to determine the aromaticity of any derivative within the series of fluorinated benzene derivatives (C6H(6-n)Fn, where n=1-5). © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.Ítem Searching for double σ- And π-aromaticity in borazine derivatives(Royal Society of Chemistry, 2020-08) Pino-Rios, Ricardo; Vásquez-Espinal, Alejandro; Yañez, Osvaldo; Tiznado, WilliamInspired by the double-aromatic (σ and π) C6H3+, C6I62+, and C6(SePh)62+ ring-shaped compounds, herein we theoretically study their borazine derivative analogues. The systems studied are the cation and dications with formulas B3N3H3+, B3N3Br62+, B3N3I62+, B3N3(SeH)62+, and B3N3(TeH)62+. Our DFT calculations indicate that the ring-shaped planar structures of B3N3H3+, B3N3I62+, and B3N3(TeH)62+ are more stable in the singlet state, while those of B3N3Br62+ and B3N3(SeH)62+ prefer the triplet state. Besides, exploration of the potential energy surface shows that the ring-shaped structure is the putative global minimum only for B3N3I62+. According to chemical bonding analysis, B3N3H3+, B3N3I62+, and B3N3(TeH)62+ have σ and π delocalized bonds. The number of delocalized σ/π electrons is 2/6 for the first, and 10/6 for the second and third, similar to what their carbon analogs exhibit. Finally, the analysis of the magnetically induced current density allows B3N3H3+, B3N3I62+, and B3N3(TeH)62+ to be classified as strongly σ aromatic, and poorly π aromatic compounds. © The Royal Society of Chemistry.Ítem Searching for Systems with Planar Hexacoordinate Carbons(MDPI, 2023-03) Inostroza, Diego; Leyva-Parra, Luis; Yañez, Osvaldo; Solar-Encinas, José; Vásquez-Espinal, Alejandro; Valenzuela, Maria Luisa; Tiznado, WilliamHere, we present evidence that the D2h M2C50/2+ (M = Li-K, Be-Ca, Al-In, and Zn) species comprises planar hexacoordinate carbon (phC) structures that exhibit four covalent and two electrostatic interactions. These findings have been made possible using evolutionary methods for exploring the potential energy surface (AUTOMATON program) and the Interacting Quantum Atoms (IQA) methodology, which support the observed bonding interactions. It is worth noting, however, that these structures are not the global minimum. Nonetheless, incorporating two cyclopentadienyl anion ligands (Cp) into the CaC52+ system has enhanced the relative stability of the phC isomer. Moreover, cycloparaphenylene ([8]CPP) provides system protection and kinetic stability. These results indicate that using appropriate ligands presents a promising approach for expanding the chemistry of phC species. © 2023 by the authors.Ítem Steady State Kinetics for Enzymes with Multiple Binding Sites Upstream of the Catalytic Site(MDPI, 2024-12-12) Osorio, Manuel I.; Petrache, Mircea; Salinas, Dino G.; Valenzuela-Ibaceta, Felipe; González-Nilo, Fernando; Tiznado, William; Pérez-Donoso, José M.; Bravo, Denisse; Yáñez, OsvaldoThe Michaelis–Menten mechanism, which describes the binding of a substrate to an enzyme, is a simplification of the process on a molecular scale. A more detailed model should include the binding of the substrate to precatalytic binding sites (PCBSs) prior to the transition to the catalytic site. Our work shows that the incorporation of PCBSs, in steady-state conditions, generates a Michaelis–Menten-type expression, in which the kinetic parameters KM and Vmax adopt more complex expressions than in the model without PCBSs. The equations governing reaction kinetics can be seen as generalized symmetries, relative to time translation actions over the state space of the underlying chemical system. The study of their structure and defining parameters can be interpreted as looking for invariants associated with these time evolution actions. The expression of (Formula presented.) decreases as the number of PCBSs increases, while (Formula presented.) reaches a minimum when the first PCBSs are incorporated into the model. To evaluate the trend of the dynamic behavior of the system, numerical simulations were performed based on schemes with different numbers of PCBSs and six conditions of kinetic constants. From these simulations, with equal kinetic constants for the formation of the Substrate/PCBS complex, it is observed that (Formula presented.) and (Formula presented.) are lower than those obtained with the Michaelis–Menten model. For the model with PCBSs, the (Formula presented.) reaches a minimum at one PCBS and that value is maintained for all of the systems evaluated. Since (Formula presented.) decreases with the number of PCBSs, the catalytic efficiency increases for enzymes fitting this model. All of these observations are consistent with the general equation obtained. This study allows us to explain, on the basis of the PCBS to (Formula presented.) and (Formula presented.) ratios, the effect on enzyme parameters due to mutations far from the catalytic site, at sites involved in the first enzyme/substrate interaction. In addition, it incorporates a new mechanism of enzyme activity regulation that could be fundamental to search for new activity-modulating sites or for the design of mutants with modified enzyme parameters.Ítem Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA(Public Library of Science, 2014) Mena-Ulecia, Karel; Vergara-Jaque, Ariela; Poblete, Horacio; Tiznado, William; Caballero, JulioWe have carried out a protocol in computational biochemistry including molecular dynamics (MD) simulations and MM/GBSA free energy calculations on the complex between the protein kinase A (PKA) and the specific peptide substrate Kemptide (LRRASLG). We made the same calculations on other PKA complexes that contain Kemptide derivatives (with mutations of the arginines, and with deletions of N and C-terminal amino acids). We predicted shifts in the free energy changes from the free PKA to PKA-substrate complex (δδGE→ES) when Kemptide structure is modified (we consider that the calculated shifts correlate with the experimental shifts of the free energy changes from the free PKA to the transition states (δδGE→TS) determined by the catalytic efficiency (kcat/KM) changes). Our results demonstrate that it is possible to predict the kinetic properties of protein kinases using simple computational biochemistry methods. As an additional benefit, these methods give detailed molecular information that permit the analysis of the atomic forces that contribute to the affinity between protein kinases and their substrates. © 2014 Mena-Ulecia et al.Ítem Testing the effectiveness of the isoelectronic substitution principle through the transformation of aromatic osmathiophene derivatives into their inorganic analogues(Royal Society of Chemistry, 2017) Vásquez-Espinal, Alejandro; Poater, Jordi; Solà, Miquel; Tiznado, William; Islas, RafaelThe objective of the current work is to evaluate the effectiveness of the isoelectronic substitution (IS) principle on a series of complexes with the general formula OsCl2(SX3H3)(PH3)2, where X3 represents the moieties CCC, CCB, CCN, CBN, CNB or NCB, formed by substitution of the carbon atoms in CCC by either the isoelectronic B- or N+ separately, or by both. The SX3H3 moiety forms, together with Os, an aromatic five-membered ring (5-MR) called osmathiophene. The preservation of stability and aromaticity in the resulting systems is used to indicate the effectiveness of the IS principle. The aromaticity of the proposed molecules is analyzed according to the magnetic (induced magnetic field (Bind)) and electronic (through the multicenter index (MCI)) criteria. In addition a chemical bonding analysis on selected species is performed by the adaptive natural density partitioning (AdNDP) method. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.