Study of the Rv1417 and Rv2617c Membrane Proteins and Their Interactions with Nicotine Derivatives as Potential Inhibitors of Erp Virulence-Associated Factor in Mycobacterium tuberculosis: An In Silico Approach.

The increasing emergence of Mycobacterium tuberculosis (Mtb) strains resistant to traditional anti-tuberculosis drugs has alarmed health services worldwide. The search for new therapeutic targets and effective drugs that counteract the virulence and multiplication of Mtb represents a challenge for the scientific community. Several studies have considered the erp gene a possible therapeutic target in the last two decades, since its disruption negatively impacts Mtb multiplication. This gene encodes the exported repetitive protein (Erp), which is located in the cell wall of Mtb. In vitro studies have shown that the Erp protein interacts with two putative membrane proteins, Rv1417 and Rv2617c, and the impairment of their interactions can decrease Mtb replication. In this study, we present five nicotine analogs that can inhibit the formation of heterodimers and trimers between these proteins. Through DFT calculations, molecular dynamics, docking, and other advanced in silico techniques, we have analyzed the molecular complexes, and show the effect these compounds have on protein interactions. The results show that four of these analogs can be possible candidates to counteract the pathogenicity of Mtb. This study aims to combine research on the Erp protein as a therapeutic target in the search for new drugs that serve to create new therapies against tuberculosis disease.

Theoretical Study at the Molecular Mechanics Level of the Interaction of Tetracycline and Chloramphenicol with the Antibiotic Receptors Present in Enterococcus faecalis (Q839F7) and Streptococcus mutans (Q8DS20).

When dental infections occur, various types of antibiotics are used to combat them. The most common antibiotics to be used are tetracycline and chloramphenicol; likewise, the most common bacteria in dental infections are Enterococcus faecalis and Streptococcus mutans. In the present work, we have studied by molecular mechanics methods the interactions of the ribosomal proteins L16 present in Enterococcus faecalis and Streptococcus mutans, identified with UNIPROT code Q839F7 and Q8DS20, respectively. We evaluated the interactions between Q839F7 and Q8DS20 with tetracycline and chloramphenicol antibiotics. We found that the interaction between Enterococcus faecalis (Q839F7) is much more favorable when treated with chloramphenicol. In contrast, the interaction with tetracycline is favored in the case of Q8DS20 present in Streptococcus mutans. This suggests that the treatment should be differentiated depending on the infection level and the presence of some of these bacteria.

Novel In Silico Insights into Rv1417 and Rv2617c as Potential Protein Targets: The Importance of the Medium on the Structural Interactions with Exported Repetitive Protein (Erp) of Mycobacterium tuberculosis.

Nowadays, tuberculosis is the second leading cause of death from a monopathogenic transmitted disease, only ahead of COVID-19. The role of exported repetitive protein (Erp) in the virulence of Mycobacterium tuberculosis has been extensively demonstrated. In vitro and in vivo assays have identified that Erp interacts with Rv1417 and Rv2617c proteins, forming putative transient molecular complexes prior to localization to the cell envelope. Although new insights into the interactions and functions of Erp have emerged over the years, knowledge about its structure and protein-protein interactions at the atomistic level has not been sufficiently explored. In this work, we have combined several in silico methodologies to gain new insights into the structural relationship between these proteins. Two system conditions were evaluated by MD simulations: Rv1417 and Rv2617c embedded in a lipid membrane and another with a semi-polar solvent to mimic the electrostatic conditions on the membrane surface. The Erp protein was simulated as an unanchored structure. Stabilized structures were docked, and complexes were evaluated to recognize the main residues involved in protein-protein interactions. Our results show the influence of the medium on the structural conformation of proteins. Globular conformations were favored under high polarity conditions and showed a higher energetic affinity in complex formation. Meanwhile, disordered conformations were favored under semi-polar conditions and an increase in the number of contacts between residues was observed. In addition, the electrostatic potential analysis showed remarkable changes in protein interactions due to the polarity of the medium, demonstrating the relevance of Erp protein in heterodimer formation. On the other hand, contact analysis showed that several C-terminal residues of Erp were involved in the protein interactions, which seems to contradict experimental observations; however, these complexes could be transient forms. The findings presented in this work are intended to open new perspectives in the studies of Erp protein molecular interactions and to improve the knowledge about its function and role in the virulence of Mycobacterium tuberculosis.

In Silico Analysis of the Antagonist Effect of Enoxaparin on the ApoE4-Amyloid-Beta (Aß) Complex at Different pH Conditions.

Apolipoprotein E4 (ApoE4) is thought to increase the risk of developing Alzheimer's disease. Several studies have shown that ApoE4-Amyloid ß (Aß) interactions can increment amyloid depositions in the brain and that this can be augmented at low pH values. On the other hand, experimental studies in transgenic mouse models have shown that treatment with enoxaparin significantly reduces cortical Aß levels, as well as decreases the number of activated astrocytes around Aß plaques. However, the interactions between enoxaparin and the ApoE4-Aß proteins have been poorly explored. In this work, we combine molecular dynamics simulations, molecular docking, and binding free energy calculations to elucidate the molecular properties of the ApoE4-Aß interactions and the competitive binding affinity of the enoxaparin on the ApoE4 binding sites. In addition, we investigated the effect of the environmental pH levels on those interactions. Our results showed that under different pH conditions, the closed form of the ApoE4 protein, in which the C-terminal domain folds into the protein, remains stabilized by a network of hydrogen bonds. This closed conformation allowed the generation of six different ApoE4-Aß interaction sites, which were energetically favorable. Systems at pH5 and 6 showed the highest energetic affinity. The enoxaparin molecule was found to have a strong energetic affinity for ApoE4-interacting sites and thus can neutralize or disrupt ApoE4-Aß complex formation.

Estudio teórico de la oxidación de CO con O2 usando catalizadores de Au-Pd y Au-Pt / Theoretical study of the CO Oxidation with O2 using Au-Pd and Au-Pt catalysts / Estudo teórico da oxidação de CO com O2 usando catalisadores de Au-Pd e Au-Pt

Resumen En el presente estudio se realizaron cálculos con base en la Teoría del Funcional de la Densidad Electrónica (DFT) con la aproximación B3PW91/LANL2DZ para optimizar los sistemas monometálicos y bimetálicos Au9, Au8Pd, Au8Pt, AuPd8, AuPt8, Pd9 y Pt9. Los materiales fueron teóricamente evaluados como catalizadores para la oxidación de monóxido de carbono (CO) y se determinó el sistema más favorable para la adsorción de esta molécula. La sustitución de átomos de Pt y Pd por átomos de Au en los nonámeros generó un cambio en la estructura tridimensional del sistema. El análisis de reactividad global mostró que el clúster más reactivo es PÍ9, seguido por AuPt s . Los índices de Fukui identificaron los sitios más susceptibles para un ataque nucleofílico de ambos clústeres. La adsorción de CO generó una cascada de oxidación que liberó ~4,5 eV, indicando que la reacción es altamente exotérmica y exergónica. Los clústeres AuPt s y Pt 9 mostraron los valores más bajos de energía de activación de la etapa determinante del mecanismo. En general, la sustitución de un átomo de platino (o paladio) por un átomo de oro no afecta la reactividad de los nonámeros y, por tanto, se infiere que el clúster AuPt s podría ser un catalizador promisorio en la oxidación de CO.

Abstract In the current study were development calculations based on Density Functional Theory (DFT) with the B3PW91/LANL2DZ approach for optimizing both monometallic and bimetallic systems: Au9, AusPd, Au8Pt, AuPds, AuPts, Pd9 y Pt9. Such materials were theoretically tested as catalyst for the oxidation of carbon monoxide (CO) and the most favorable system for its further adsorption was determined. The substitution of Pt and Pd by Au atoms in the nonamers generated a change in the tridimensional structure of the system. The global reactivity analysis showed that the most reactive cluster is Pt9 followed by AuPts. On the other hand, the Fukui indexes identified the most susceptible sites for a nucleophilic attack of both clusters. The CO adsorption generated an oxidation cascade which liberated ∼ 4.5 eV, indicating that the reaction is highly exothermic and exergonic. Both AuPt8 and Pt9 showed the lowest values of activation energy in the determining step of the mechanism. In general, the substitution of a Pt (Pd) atom by an Au atom does not affect the reactivity of the nonamers and then it is inferred that the AuPds cluster could be a promissory catalyst in the CO oxidation.

Resumo No presente estudo, cálculos baseados na Teoria do Funcional da Densidade Eletrônica (DFT) com a abordagem B3PW91/LANL2DZ foram realizados para otimizar sistemas monometálicos e bimetálicos Au9, Au8Pd, Au8Pt, AuPd8, AuPt8, Pd9 y Pt9. Tais materiais foram teoricamente avaliados como catalisadores para a oxidação do monóxido de carbono (CO) e foi determinado o sistema mais favorável para a adsorção desta molécula. A substituição dos átomos de Pt e Pd por átomos de Au nós não-nomes gerou uma mudança na estrutura tridimensional do sistema. A análise de reatividade global mostrou que o cluster mais reativo é Pt9, seguido por AuPt8. Os índices de Fukui identificaram os sítios mais suscetíveis ao ataque nucleofílico de ambos os clusters. A adsorção de CO gerou uma cascata de oxidação que liberou ~4,5 eV, indicando que a reação é altamente exotérmica e exergônica. Os aglomerados AuPt 8 y Pt 9 apresentaram os menores valores de energia de ativação do estágio determinante do mecanismo. Em geral, a substituição de um átomo de platina (ou paládio) por um átomo de ouro não afeta a reatividade dos não-nomes e, portanto, infere-se que o aglomerado AuPt 8 pode ser um catalisador promissor na oxidação do CO.

Structural and Functional Analysis of Female Sex Hormones against SARS-CoV-2 Cell Entry.

Emerging evidence suggests that males are more susceptible to severe infection by the SARS-CoV-2 virus than females. A variety of mechanisms may underlie the observed gender-related disparities including differences in sex hormones. However, the precise mechanisms by which female sex hormones may provide protection against SARS-CoV-2 infectivity remains unknown. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further report that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly, estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV-2 thereby blocking its entry into cells. In a mouse model of COVID-19, estrogens reduced ACE2 glycosylation and thereby alveolar uptake of the SARS-CoV-2 spike protein. These results shed light on a putative mechanism whereby female sex hormones may provide protection from developing severe infection and could inform the development of future therapies against COVID-19.

Structural and Energetic Affinity of Annocatacin B with ND1 Subunit of the Human Mitochondrial Respiratory Complex I as a Potential Inhibitor: An In Silico Comparison Study with the Known Inhibitor Rotenone.

ND1 subunit possesses the majority of the inhibitor binding domain of the human mitochondrial respiratory complex I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, that some metabolites from Annona muricata called acetogenins have important biological activities, such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine mitochondrial respiratory complex I by bis-tetrahydrofurans acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human mitochondrial respiratory complex I. In this work, we evaluate the in silico molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, quantum mechanical optimizations, molecular dynamics simulations and the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known mitochondrial respiratory complex I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger binding free energy compared to the rotenone complex. Detailed analysis of the binding free energy shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of the mitochondrial respiratory complex I.

Li8 Si8 , Li10 Si9 , and Li12 Si10 : Assemblies of Lithium-Silicon Aromatic Units.

We report the global minima structures of Li8 Si8 , Li10 Si9 , and Li12 Si10 systems, in which silicon moieties maintain structural and chemical bonding characteristics similar to those of their building blocks: the aromatic clusters Td -Li4 Si4 and C2v -Li6 Si5 . Electron counting rules, chemical bonding analysis, and magnetic response properties verify the silicon unit's aromaticity persistence. This study demonstrates the feasibility of assembling silicon-based nanostructures from aromatics clusters as building blocks.

Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations.

The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue's charge state depending on the assigned individual pKa obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four (αß)3 subunits of the global structure ((αß)3)4 of urease start to separate.

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis.

Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.

Amyloid beta oligomers: how pH influences over trimer and pentamer structures?

The aggregation of proteins in the brain is one of the main features of neurodegenerative diseases. In Alzheimer's disease, the abnormal aggregation of Aß-42 is due to intrinsic and extrinsic factors. The latter is due to variations in the environment, such as temperature, salt concentration, and pH. We evaluated the effect of protonation/deprotonation of residues that are part of trimeric and pentameric oligomers at pH 5, pH 6, and pH 7. Molecular dynamics simulation at 200 ns in the canonical ensemble was implemented. The results have revealed that histidine, glutamic acid, and aspartic acid residues showed a protonation/deprotonation effect in oligomers. The root mean square deviation analysis was used to analyze the structural stability at different pHs. We found an increase in hydrophobicity in the side chains of the trimer, while in the pentamer, the structural instability of a compact structure at pH 5 caused the hydrophobic core to open, revealing the hydrophobic region to the environment. At this point, we believe that conformational changes mediated by pH are essential in the aggregation of Aß-42 oligomers.

Theoretical study of the antioxidant capacity of the flavonoids present in the Annona muricata (Soursop) leaves.

A theoretical approach was used to evaluate the antioxidant capacity of 20 flavonoids reported in Annona muricata leaves. The theoretical study was at the GGA level using the wB97XD functional and the cc-pvtz basis set. The calculations were performed in gas phase and implicit solvent phase. The flavonol robinetin (03c) and the flavanol gallocatechin (01c) are species that exhibited the best antioxidant capacity in the HAT, SEPT, and SPLET mechanisms. On the other hand, in the SET I mechanism, flavonol quercetin (03b) was the best, and in the SET II mechanism, the most favored species is the flavanol catechin (01a). However, these species do not achieve to overcome the antioxidant capacity presented by the Trolox.

Nanoformulation for potential topical delivery of Vismodegib in skin cancer treatment.

Vismodegib (Erivedge®, Genentech) is a first-in-class inhibitor of the hedgehog signaling pathway for the treatment of basal cell carcinoma (BCC). The treatment currently consists of the oral administration of Erivedge® capsules. Although it has shown therapeutic efficacy in clinical trials, there are many side effects related to its systemic distribution. In this work, we have incorporated vismodegib to ultradeformable liposomes in order to obtain a nano-drug delivery system via topical route, which could be useful to reduce systemic distribution -and consequently side effects- while achieving a viable epidermis-specific target where neoplastic events of BCC develop. Vismodegib was loaded into liposomes composed of soy phosphatidylcholine and sodium cholate, and the obtained formulation was characterized by different techniques, both experimental and computational. Several analyses were performed,with a special focus on the interaction of the drug with the liposomal membrane. Additionally, the penetration of Vismodegib delivered by ultradeformable liposomes was assessed on human skin explants. This is one of the first works that propose the topical route for Vismodegib and the first, to our knowledge, in stabilizing this active into a nano-drug delivery system specifically designed for penetrating the stratum corneum impermeable barrier.

Quantum chemical study of the inhibitive properties of 2-pyridyl-azoles.

Four molecules that have been proven to act as corrosion inhibitors of mild steel in acidic media are studied. The inhibitive efficiency of these molecules is explained by means of electronic structure calculations of the protonated species that seem to represent better the actual situation of the experimental conditions. By assuming that the interaction between the inhibitor and the metallic surface occurs through donation and back-donation, it is shown, with a simple charge transfer model, that the interaction energy is favored when hardness increases, in agreement with the experimentally observed inhibition efficiencies. A local analysis with Hirshfeld condensed Fukui functions, and local Fukui functions, provides further support to the donation and back-donation mechanism.

Molecular fragments in density functional theory.

The second-order density functional approach to the partitioning of the molecular density of Cedillo, Chattaraj, and Parr (Int. J. Quantum Chem. 2000, 77, 403-407) is used, together with a local assumption for the function that projects the total density into its components, to show that the distribution function adopts a stockholders form, in terms of the local softness of the isolated fragments, and that the molecular Fukui function is distributed in the molecular fragments in the same proportion as the electronic density.