In this work, QM/MM calculations were employed to examine the catalytic mechanism of the retaining glucosyltransferase GTF-SI enzyme, which participates in the process of caries formation. Our goal was to characterize, with atomistic details, the mechanism of sucrose hydrolysis and the catalytic factors that modulate this reaction. Our results suggest a concerted mechanism for sucrose hydrolysis in which the first event corresponds to the glycosidic bond breakage assisted by Glu515, followed by the nucleophilic attack of Asp477, leading to the formation of the Covalent Glycosyl Enzyme (CGE) intermediate. A novel conformational itinerary of the glucosyl moiety along the reaction mechanism was identified: 2H3 → 2H3-E3 → 4C1, and the calculated energy barrier is 16.4 kcal mol-1, which is in good agreement with experimental evidence showing a major contribution coming from the glycosidic bond breakage. Our calculations also revealed that Arg475 and Asp588 play a critical role as TS-stabilizers by electrostatic and charge transfer mechanisms, respectively. This is the first report dealing with the specific features of the mechanism and catalytic residues involved in GTF-SI hydrolysis of sucrose, which is a matter of relevance in enzyme catalysis and could be valuable to aid the design of novel and specific inhibitors targeting GTF-SI.

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-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.

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Glucansucrase GTF‐SI from Streptococcus mutans is a multidomain enzyme that catalyzes the synthesis of glucan polymers. Domain V locates 100 Å from the catalytic site and is required for an optimal activity. Nevertheless, the mechanism governing its functional role remains elusive. In this work, homology modeling and molecular dynamics simulations were employed to examine the effect of domain V in the structure and glucan‐binding ability of GTF‐SI in full and truncated enzyme models. Our results showed that domain V increases the flexibility of the α4′‐loop‐α4″ motif near the catalytic site resulting in a higher surface for glucan association, and modulates the orientation of a growing oligosaccharide (N=8‐23) in glucan‐enzyme complexes towards engaging in favorable contacts throughout the protein, whereas in the truncated model the glucan protrudes randomly from domain B towards the solvent. These results are valuable to increase understanding about the functional role of domain V in GH70 glucansucrases.

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~-((1 R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3 R)-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.

The Mapuche and their ancestors have used D. winteri in traditional medicine. In the present study, the essential oil extract of D. winteri leaves (DW_EO) were characterized chemically and biologically to evaluate its pharmacological activity. In vitro antioxidant activity was assayed, and antitumor activity was evaluated in non-tumor and tumor-cell culture lines. Caenorhabditis elegans was used as a model to evaluate toxicity, and the chemical composition of the essential oil was analyzed by gas chromatography-mass spectrometry. The chemical oil composition was characterized principally of five major terpenes: 4 sesquiterpenes γ-Eudesmol (39.7%), β-Caryophyllene (33.7%), Elemol (25.9%), α-Eudesmol (0.3%) and 1 diterpene Kaunene (0.4%). By quantum calculations, it was determined that all oils have the ability to capture and yield electrons, which is consistent with the moderate antioxidant activity of DW_EO detected in vitro. Furthermore, by molecular docking is estimated that these oils can bind to proteins involved in the production of oxygen radicals. Of these proteins, CYP2C9 could bind energetically, reaching binding energy between −6.8 and −9.2 kCal/mol for the 5 terpenes studied, highlighting among these β-Caryophyllen and γ-Eudesmol. DW_EO has effect against H. pylori (MIC 32 μg/ml), S. aureus (MIC 8 μg/ml), E. coli (MIC 32 μg/ml) and C. albicans (MIC 64 μg/ml), β-Caryophyllen and γ -Eudesmol (MIC 64 μg/ml) and could selectively inhibit the proliferation of epithelial tumor cell lines but showed low against C. elegans (0.39–1.56 μg mL−1). Therefore, DW_EO may be used as a source of bioactive compounds in novel pharmacological treatments for medical application, agronomics, sanitation, and food.

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