The peptide bond rupture mechanism in the serine proteases: an in silico study based on sequential scale models.

Given the importance of serine proteases for biochemical processes, we have studied the peptide bond rupture mechanism using three sequential scale models as representations of the KLK5 enzyme (a protein overexpressed in ovarian cancer). The first model contains the basic functional groups of the residues that conform to the catalytic triad present in serine proteases; the second model contains some additional residues and, finally, the last representation includes all atoms of the KLK5 protein together with 10.000 explicit water molecules. This separation into three scale models allows us to separate the intrinsic reactivity of the catalytic triad from the process taking place in the enzyme. The methodologies employed in this work include full DFT calculations with a dielectric continuum in the first two models and a multi-level setup with a Quantum Mechanics/Molecular Mechanics (QM/MM) partition in the whole protein system. Our results show that the peptide-bond rupture mechanism is a stepwise process involving two proton transfer reactions. The rate-determining step is the second proton transfer from the imidazole group to the amidic nitrogen of the substrate. In addition, we find that the simplest model does not provide accurate results compared to the full protein system. This can be attributed to the electronic stabilization conferred by the residues around the reaction site. Interestingly, the energy profile obtained with the second scale model with additional residues shows the same trends as the full system and could therefore be considered an appropriate model system. It could be used for studying the peptide bond rupture mechanism in case full QM/MM calculations cannot be performed, or as a rapid tool for screening purposes.

Synthesis of bis-furyl-pyrrolo[3,4-b]pyridin-5-ones via Ugi-Zhu reaction and in vitro activity assays against human SARS-CoV-2 and in silico studies on its main proteins.

An Ugi-Zhu three-component reaction (UZ-3CR) coupled in one pot manner to a cascade process (N-acylation/aza Diels-Alder cycloaddition/decarboxylation/dehydration) was performed to synthesize a series of bis-furyl-pyrrolo[3,4-b]pyridin-5-ones in 45 to 82% overall yields using ytterbium triflate as a catalyst, toluene as a solvent, and microwaves as a heat source. The synthesized molecules were evaluated in vitro against human SARS-CoV-2 through a time-of-addition approach, finding that compound 1e, at a concentration of 10.0 µM, exhibited a significant reduction at the initial infection stages, thus showing prophylactic potential. On the other hand, it was found that compound 1d, at the same concentration, was significantly active when applied post-infection, thus exhibiting a therapeutic profile. Moreover, compound 1f showed both, prophylactic and therapeutic activity. Then, to understand interactions between synthesized compounds and the main proteins related to the virus, docking studies were performed on spike-glycoprotein, main-protease, and Nsp3 protein, finding moderate to strong binding energies, matching accurately with the in vitro results. Additionally, a pharmacophore model was computed behind further rational drug design.

Grammatical evolution-based design of SARS-CoV-2 main protease inhibitors.

A series of SARS-CoV-2 main protease (SARS-CoV-2-Mpro) inhibitors were modeled using evolutive grammar algorithms. We have generated an automated program that finds the best candidate to inhibit the main protease, Mpro, of SARS-CoV-2. The candidates were constructed based on a pharmacophore model of the above-mentioned target; relevant moieties of such molecules were modified using data-basis sets with similar chemical behavior to the reference moieties. Additionally, we used the SMILES language to translate 3D chemical structures to 1D words; then, an evolutive grammar algorithm was used to explore the chemical space and obtain new candidates, which were evaluated via the binding energy of molecular coupling assays as an evaluation function. Finally, sixteen molecules were obtained in 3 runs of our program, three of which show promising binding properties as SARS-CoV-2-Mpro inhibitors. One of them, TTO, maintained its relevant binding properties during 100 ns molecular dynamics experiments. For this reason, TTO is the best candidate to inhibit SARS-CoV-2-Mpro. The software we developed for this contribution is available at the following URL: https://github.com/masotelof/GEMolecularDesign.

Binding Analysis of Functionalized Multimode Optical-Fiber Sandwich-like Structure with Organic Polymer and Its Sensing Application for Humidity and Breath Monitoring.

In recent years, the chemical modification of optical fibers (OFs) has facilitated the manufacture of sensors because OFs can identify several analytes present in aqueous solutions or gas phases. Nevertheless, it is imperative better to understand the chemical interactions in this molecular system to generate low-cost and efficient sensors. This work presents a theoretical and experimental study of organic polymeric functionalized OF structures and proposes a cost-effective alternative to monitor breathing and humidity. The device is based on silicon optical fibers functionalized with (3-Aminopropyl) triethoxysilane (APTES) and alginate. The theoretical analysis is carried out to validate the activation of the silicon dioxide fiber surface; moreover, the APTES-alginate layer is discussed. The computational simulation suggests that water can be absorbed by alginate, specifically by the calcium atom linked to the carboxylic acid group of the alginate. The analysis also demonstrates a higher electrostatic interaction between the water and the OF-APTES-alginate system; this interaction alters the optical fiber activated surface's refractive index, resulting in transmission power variation. The humidity analysis shows a sensitivity of 3.1288 mV/RH, a time response close to 25 s, and a recovery time around 8 s. These results were achieved in the range of 50 to 95% RH. Moreover, the recovery and response time allow the human breath to be studied. The proposed mechanism or device is competitive with prior works, and the components involved made this sensor a cost-effective alternative for medical applications.

Search for Non-Protein Protease Inhibitors Constituted with an Indole and Acetylene Core.

A possible inhibitor of proteases, which contains an indole core and an aromatic polar acetylene, was designed and synthesized. This indole derivative has a molecular architecture kindred to biologically relevant species and was obtained through five synthetic steps with an overall yield of 37% from the 2,2'-(phenylazanediyl)di(ethan-1-ol). The indole derivative was evaluated through docking assays using the main protease (SARS-CoV-2-Mpro) as a molecular target, which plays a key role in the replication process of this virus. Additionally, the indole derivative was evaluated as an inhibitor of the enzyme kallikrein 5 (KLK5), which is a serine protease that can be considered as an anticancer drug target.

Molecular docking and pharmacophoric modelling of 1,5-disubstituted tetrazoles as inhibitors of two proteins present in cancer, the ABL and the mutated T315I kinase.

A docking study of a set of several 1,5-disubstituted tetrazoles compounds has been performed to predict the poses of some potential inhibitors of the Abelson tyrosine-protein kinase and the mutated Abelson tyrosine-protein kinase T315I. The study was conducted through Lamarckian genetic algorithms in Autodock4 package. Bayesian calculations were performed; specificity and sensitivity values as well as positive predicted values, and negative predicted values were calculated using a set of 99 known experimentally active ligands and 385 decoys for the Abelson tyrosine-protein kinase from the Directory of Useful Decoys database. Root mean square deviation values were calculated though the X-ray crystallographic data of the bioactive pose of imatinib as reference, and the pose obtained with the above methods. The obtained results show the importance of the protein interactions with the halogens present in some of these 1,5-disubstituted tetrazoles ligands, as well as the presence of some hydrophobic fragments, obtained via the pharmacophoric model, concluding that the eight novels 1,5-disubstituted tetrazoles compounds herein identified, could be effective inhibitors of Abelson tyrosine-protein kinase, using a docking calculations.

A Turn-On Luminescence Method for Phosphate Determination Based on Fast Green-Functionalized ZrO2:Yb,Er@ZrO2 Core@Shell Upconversion Nanoparticles.

The development of practical and sensitive tools for detecting phosphate deficiency could facilitate engineering approaches to enhance crop yield and quality in phosphate-stressed environments, reducing the misuse of nonrenewable fertilizers and their consequent ecological impact. Herein, a 975 nm-activated method based on ZrO2:Yb,Er@ZrO2 core@shell upconversion nanoparticles is presented for rapid visualization and determination of the phosphate ions in aqueous solutions and extracts. At optimized thickness, the nondoped ZrO2 shell not only enhances the emission of the ZrO2:Yb,Er but also provides an active surface for the intense interaction with the phosphate group, allowing a "label-free" determination that avoids the use of additional phosphate-recognizing elements like ligands or antibodies. According to the experimental evidence, the optical output of the ZrO2:Yb,Er@ZrO2 nanoparticles specifically matches with the absorption spectrum of the fast green alimentary dye (FG) electrostatically attached to the nanoparticle surface, activating the Förster resonance energy transfer (FRET) and thereby the upconversion luminescence quenching. Upon addition of the phosphate ions and the covalent interaction with the ZrO2:Yb,Er@ZrO2-FG nanocomplex, the FG is gradually removed, displaying a fast and reproducible "turn-on" luminescence which allows measurements in a few minutes. This rapid response is due to the stronger coordination between the ZrO2 shell and the phosphate compared to the FG molecules (-31.97 and -5.99 eV, respectively). The detection method was then effectively modulated in a 20-1000 nM linear response range without interfering effects of commonly coexisting ions, achieving a detection limit up to 15 times lower than that obtained with the conventionally used colorimetric methods.

Synthesis of Pyrrolo[3,4-b]pyridin-5-ones via Multicomponent Reactions and In Vitro-In Silico Studies Against SiHa, HeLa, and CaSki Human Cervical Carcinoma Cell Lines.

A series of 12 polysubstituted pyrrolo[3,4-b]pyridin-5-ones were synthesized via a one-pot cascade process (Ugi-3CR/aza Diels-Alder/N-acylation/decarboxylation/dehydration) and studied in vitro using human epithelial cervical carcinoma SiHa, HeLa, and CaSki cell line cultures. Three compounds of the series exhibited significative cytotoxicity against the three cell lines, with HeLa being the most sensitive one. Then, based on these results, in silico studies by docking techniques were performed using Paclitaxel as a reference and αß-tubulin as the selected biological target. Worth highlighting is that strong hydrophobic interactions were observed between the three active molecules and the reference drug Paclitaxel, to the αß-tubulin. In consequence, it was determined that hydrophobic-aromatic moieties of bioactive compounds and Paclitaxel play a key role in making stronger interactions to the ligand-target complex. A quantitative structure activity relationship (QSAR) study revealed that the six membered rings are the most significant molecular frameworks, being present in all proposed models for the in vitro-studied cell lines. Finally, also from the docking interpretation, a ligand-based pharmacophore model is proposed in order to find further potential polyheterocyclic candidates to bind stronger to the αß-tubulin.

Binding of Pb-Melatonin and Pb-(Melatonin-metabolites) complexes with DMT1 and ZIP8: implications for lead detoxification.

We have applied the docking methodology to characterize the binding modes of the divalent metal transporter 1 (DMT1) and the zinc transporter 8 (ZIP8) protein channels with: melatonin, some melatonin metabolites, and a few lead complexes of melatonin and its metabolites, in three different coordination modes (mono-coordinated, bi-coordinated and tri-coordinated). Our results show that bi-coordinated and tri-coordinated lead complexes prefer to bind inside the central region of ZIP8. Moreover, the interaction strength is larger compared with that of the free melatonin and melatonin metabolites. On the other hand, the binding modes with DMT1 of such complexes display lower binding energies, compared with the free melatonin and melatonin metabolites. Our results suggest that ZIP8 plays a major role in the translocation of Pb, bi or tri coordinated, when melatonin metabolites are present. Finally, we have characterized the binding modes responsible for the ZIP8 large affinities, found in bi-coordinated and tri-coordinated lead complexes. Our results show that such interactions are greater, because of an increase of the number of hydrogen bonds, the number and intensity of electrostatic interactions, and the interaction overlay degree in each binding mode. Our results give insight into the importance of the ZIP8 channel on lead transport and a possible elimination mechanism in lead detoxification processes. Graphical abstract .

Computational study of metal complexes formed with EDTA, melatonin, and its main metabolites: implications in lead intoxication and clues to a plausible alternative treatment.

Melatonin has been proposed as an alternative treatment to the usage of EDTA for lead intoxication. In this computational paper, since previous work has not systematically studied the complexes that may be formed in the existing and proposed treatments, we study 45 possible complexes that we suggest may be formed between Pb and some essential metals with melatonin, melatonin metabolites, and EDTA, analyzing the stability and viability of these through the Gibbs free energy of complexation (ΔΔG), molecular orbitals, and energy decomposition analysis at the DFT level of theory PBE/TZ2P. Our findings show that most complexes present exergonic energies of reaction, and thus spontaneous complex formation. In addition, we show that the AMK and 3OHM melatonin metabolites possess electronic and thermodynamic properties adequate to act as lead trapping molecules due to the lower Pauli repulsion energies involved in the complexes they form and their large negative values of ΔΔG. Therefore, it is shown that both melatonin and some of its metabolites may be employed in a viable treatment for lead intoxication through formation of stable Pb-complexes. Graphical abstract Metal complexes formed with EDTA, melatonin, and its main metabolites.

Effects of lead and lead-melatonin exposure on protein and gene expression of metal transporters, proteins and the copper/zinc ratio in rats.

Human lead (Pb) exposure induces many adverse health effects, including some related to lead accumulation in organs. Although lead bio-distribution in the body has been described, the molecular mechanism underlying distribution and excretion is not well understood. The transport of essential and toxic metals is principally mediated by proteins. How lead affects the expression of metal transporter proteins in the principal metal excretory organs, i.e., the liver and kidney, is unknown. Considering that co-administration of melatonin and lead reduces the toxic effects of lead and lead levels in the blood in vivo, we examined how lead and co-administration of lead and melatonin affect the gene and protein expression of metal transporter proteins (ZIP8, ZIP14, CTR1 and DMT1) in these organs. Rats were exposed intraperitoneally to lead or lead-melatonin. Our results show that Pb exposure induces changes in the protein and gene expression of ZIP8, ZIP14 and CTR1. Alterations in the copper/zinc ratio found in the blood, liver and kidney were likely related to these changes. With DMT1 expression (gene and protein), a positive correlation was found with lead levels in the kidney. Co-administration of melatonin and lead reduced lead-induced DMT1 expression through an unknown mechanism. This effect of melatonin relates to reduced lead levels in the blood and kidney. The metal transport protein function and our results suggest that DMT1 likely contributes to lead accumulation in organs. These data further elucidate the effects of lead on Cu and Zn and the molecular mechanism underlying lead bio-distribution in animals.

Synthesis of azepino[4,5-b]indol-4-ones via MCR/free radical cyclization and in vitro-in silico studies as 5-Ht6R ligands.

A series of nine new 3-acetamide-azepino[4,5-b]indol-4-ones were synthesized in two steps: (i) multicomponent reaction (Ugi-4CR/SN2) and (ii) free radical-mediated cyclization. These compounds, along with their tetrazole-based analogs, were studied in vitro to assess their binding with the 5-hydroxytryptamine type 6 receptor (5-Ht6R). The 3-acetamide-azepino[4,5-b]indol-4-ones displayed moderate affinity, whereas the 3-tetrazolylmethyl-azepino[4,5-b]indol-4-ones affinity values are lower. However, one of the 3-acetamide-azepino[4,5-b]indol-4-ones exhibited a hit value of Ki (211.2nM) to the 5-Ht6R. Minimal-energy structures of one cis-amide and its tetrazole-based analog (calculated by means of the Density Functional Theory) were analyzed to assess some interesting bioisosterism aspects. Interactions and binding energies between all products and the 5-Ht6R were calculated through in silico molecular couplings. Finally, a QSAR model was proposed using the results of the in vitro assays.

In vitro and in silico evaluation of twelve newly-synthesized 1-acetamide-5-methoxy-2-oxindoles as 5-Ht7 receptor ligands.

Based on in vitro studies of twelve newly-synthesized 1-acetamide-5-methoxy-2-oxindoles as 5-Ht7 receptor ligands, Structure Affinity Relationship (SAR) and Quantitative Structure Affinity Relationship model (QSAR) are provided. Also, a ligand-based pharmacophore model is proposed through molecular docking techniques and Nucleus Independent Chemical Shift DFT calculations (NICS).

Unraveling the origin of the relative stabilities of group 14 M2N2(2+) (M, N = C, Si, Ge, Sn, and Pb) isomer clusters.

We analyze the molecular structure, relative stability, and aromaticity of the lowest-lying isomers of group 14 M2N2(2+) (M and N = C, Si, and Ge) clusters. We use the gradient embedded genetic algorithm to make an exhaustive search for all possible isomers. Group 14 M2N2(2+) clusters are isoelectronic with the previously studied group 13 M2N2(2-) (M and N = B, Al, and Ga) clusters that includes Al4(2-), the archetypal all-metal aromatic molecule. In the two groups of clusters, the cyclic isomers present both σ- and π-aromaticity. However, at variance with group 13 M2N2(2-) clusters, the linear isomer of group 14 M2N2(2+) is the most stable for two of the clusters (C2Si2(2+) and C2Ge2(2+)) , and it is isoenergetic with the cyclic D(4h) isomer in the case of C4(2+). Energy decomposition analyses of the lowest-lying isomers and the calculated magnetic- and electronic-based aromaticity criteria of the cyclic isomers help to understand the nature of the bonding and the origin of the stability of the global minima. Finally, for completeness, we have also analyzed the structure and stability of the heavier Sn and Pb group 14 M2N2(2+) analogues.

Synthesis of 3-tetrazolylmethyl-azepino[4,5-b]indol-4-ones in two reaction steps: (Ugi-azide/N-acylation/SN2)/free radical cyclization and docking studies to a 5-Ht(6) model.

A series of nine novel 3-tetrazolylmethyl-azepino[4,5-b]indol-4-ones were prepared in moderate to good overall yields in only two reaction steps. The first step consisted of a one-pot sequential process of an Ugi-azide multicomponent reaction, N-acylation and SN2 to give the xanthates. The second step was an intramolecular cyclization under free radical conditions. Also, their binding modes have been modelled using docking techniques.