Leishmanicidal activity and 4D quantitative structure-activity relationship and molecular docking studies of vanillin-containing 1,2,3-triazole derivatives

Aim: The assessment of the antileishmanial potential of 22 vanillin-containing 1,2,3-triazole derivatives against Leishmania braziliensis is reported. Materials & methods: Initial screening was performed against the parasite promastigote form. The most active compound, 4b, targeted parasites within amastigotes (IC50 = 4.2 ± 1.0 μmol l-1), presenting low cytotoxicity and a selective index value of 39. 4D quantitative structure-activity relationship and molecular docking studies provided insights into structure-activity and biological effects. Conclusion: A vanillin derivative with significant antileishmanial activity was identified. Enhanced activity was linked to increased electrostatic and Van der Waals interactions near the benzyl ring of the derivatives. Molecular docking indicated the inhibition of the Leishmania amazonensis sterol 14α-demethylase, using Leishmania infantum sterol 14α-demethylase as a model, without affecting the human isoform. Inhibition was active site competition with lanosterol.

Synthesis and Fungicide Activity on Asperisporium caricae of Glycerol Derivatives Bearing 1,2,3-Triazole Fragments

In agriculture, the control of fungal infections is essential to improve crop quality and productivity. This study describes the preparation and fungicidal activity evaluation of 12 glycerol derivatives bearing 1,2,3-triazole fragments. The derivatives were prepared from glycerol in four steps. The key step corresponded to the Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction between the azide 4-(azidomethyl)-2,2-dimethyl-1,3-dioxolane (3) and different terminal alkynes (57-91% yield). The compounds were characterized by infrared spectroscopy, nuclear magnetic resonance (¹H and ¹³C), and high-resolution mass spectrometry. The in vitro assessment of the compounds on Asperisporium caricae, that is, the etiological agent of papaya black spot, at 750 mg L^-1 showed that the glycerol derivatives significantly inhibited conidial germination with different degrees of efficacy. The most active compound 4-(3-chlorophenyl)-1-((2,2-dimethyl-1,3-dioxolan-4-yl) methyl)-1H-1,2,3-triazole (4c) presented a 91.92% inhibition. In vivo assays revealed that 4c reduced the final severity (70.7%) and area under the disease severity progress curve of black spots on papaya fruits 10 days after inoculation. The glycerol-bearing 1,2,3-triazole derivatives also present agrochemical-likeness properties. Our in silico study using molecular docking calculations show that all triazole derivatives bind favorably to the sterol 14α-demethylase (CYP51) active site at the same region of the substrate lanosterol (LAN) and fungicide propiconazole (PRO). Thus, the mechanism of action of the compounds 4a-4l may be the same as the fungicide PRO, blocking the entrance/approximation of the LAN into the CYP51 active site by steric effects. The reported results point to the fact that the glycerol derivatives may represent a scaffold to be explored for the development of new chemical agents to control papaya black spot.

Traditional herbal compounds as candidates to inhibit the SARS-CoV-2 main protease: an in silico study

COVID-19, a disease caused by the SARS-CoV-2 virus, is responsible for a pandemic since March 2020 and it has no cure. Therefore, herein, different theoretical methods were used to obtain potential candidates from herbal compounds to inhibit the SARS-CoV-2 main protease (M^pro). Initially, the 16 best-scored compounds were selected from a library containing 4066 ligands using virtual screening by molecular docking. Among them, six molecules (physalin B 5,6-epoxide (PHY), methyl amentoflavone (MAM), withaphysalin C (WPC), daphnoline or trilobamine (TRI), cepharanoline (CEP) and tetrandrine (TET)) were selected based on Lipinski's rule and ADMET analysis as criteria. These compounds complexed with the M^pro were submitted to triplicate 100 ns molecular dynamics simulations. RMSD, RMSF, and radius of gyration results show that the overall protein structure is preserved along the simulation time. The average ΔG_binding values, calculated by the MM/PBSA method, were -41.7, -55.8, -45.2, -38.7, -49.3, and -57.9 kcal/mol for the PHY-M^pro, MAM-M^pro, WPC-M^pro, CEP-M^pro, TRI-M^pro, and TET-M^pro complexes, respectively. Pairwise decomposition analyses revealed that the binding pocket is formed by His41-Val42, Met165-Glu166-Leu167, Asp187, and Gln189. The PLS regression model generated by QSPR analysis indicated that non-polar and polar groups with the presence of hydrogen bond acceptors play an important role in the herbal compounds-M^pro interactions. Overall, we found six potential candidates to inhibit the SARS-CoV-2 M^pro and highlighted key residues from the binding pocket that can be used for future drug design. Communicated by Ramaswamy H. Sarma.

Comparative study of benznidazole encapsulation in boron nitride and carbon nanotubes: A quantum chemistry study

Quantum chemistry methods were used to study boron nitride and carbon nanotubes as possible carriers of antichagasic benznidazole to improve their water solubility and bioavailability. Structurally, no significant changes were observed in both nanotubes throughout the encapsulation process. For the BNZ@BNNT complex, it was possible to notice short interactions, at 0.215 nm, between the hydrogen atoms of the BNZ and the nitrogen atoms of the BNNT. The binding energy reveals that both nanotubes are capable of encapsulating BNZ in an aqueous medium, with values of �71.79 and �62.68 kcal/mol for the BNZ@BNNT and BNZ@CNT complexes. The enthalpy of solvation indicates that the complexes are soluble in water with values of �32.35 and �28.76 kcal mol�1 for the BNZ@BNNT and BNZ@CNT complexes. Regarding chemical stability, Eg and ? show that BNZ@BNNT has greater stability (Eg/? of 3.35/1.68 eV) than BNZ@CNT (0.16/0.08 eV). Overall, our results demonstrate that BNNT is a better candidate to be used as a carrier of BNZ than CNT due to its greater structural and chemical stability.

Single-walled silicon nanotube as an exceptional candidate to eliminate SARS-CoV-2: a theoretical study

In this work, computational chemistry methods were used to study a silicon nanotube (Si₁₉₂H₁₆) as possible virucidal activity against SARS-CoV-2. This virus is responsible for the COVID-19 disease. DFT calculations showed that the structural parameters of the Si₁₉₂H₁₆ nanotube are in agreement with the theoretical/experimental parameters reported in the literature. The low energy gap value (0.29 eV) shows that this nanotube is a semiconductor and exhibits high reactivity. For nanomaterials to be used as virucides, they need to have high reactivity and high inhibition constant values. Therefore, the adsorption of ³O₂ and H₂O on the surface of Si₁₉₂H₁₆ (Si₁₉₂H₁₆@O₂-H₂O) was performed. In this process, the formation and activation energies were -51.63 and 16.62 kcal/mol, respectively. Molecular docking calculations showed that the Si₁₉₂H₁₆ and Si₁₉₂H₁₆@O₂H-OH nanotubes bind favorably on the receptor-binding domain of the SARS-CoV-2 spike protein with binding energy of -11.83 (Ki = 2.13 nM) and -11.13 (Ki = 6.99 nM) kcal/mol, respectively. Overall, the results obtained herein indicate that the Si₁₉₂H₁₆ nanotube is a potential candidate to be used against COVID-19 from reactivity process and/or steric impediment in the S-protein.Communicated by Ramaswamy H. Sarma.

Insights into β-amyloid transition prevention by cucurbit[7]uril from molecular modeling

In this study, comparable molecular dynamic (MD) simulations of 1.2 microseconds were performed to clarify the prevention of the β-amyloid peptide (Aβ_1-42) aggregation by cucurbit[7]uril (CB[7]). The accumulation of this peptide in the brain is one of the most harmful in Alzheimer's disease. The inhibition mechanism of Aβ_1-42 aggregation by different molecules is attributed to preventing of Aβ_1-42 conformational transition from α-helix to the β-sheet structure. However, our structural analysis shows that the pure water and aqueous solution of the CB[7] denature the native Aβ_1-42 α-helix structure forming different compactness and unfolded conformations, not in β-sheet form. On the other hand, in the three CB[7]@Aβ_1-42 complexes, it was observed the encapsulation of N-terminal (Asp1), Lys16, and Val36 by CB[7] along the MD trajectory, and not with aromatic residues as suggested by the literature. Only in one CB[7]@Aβ_1-42 complex was observed stable Asp23-Lys28 salt bridge with an average distance of 0.36 nm. All CB[7]@Aβ_1-42 complexes are very stable with binding free energy lowest than ∼-50 kcal/mol between the CB[7] and Aβ_1-42 monomer from MM/PBSA calculation. Therefore, herein we show that the mechanism of the prevention of elongation protofibril by CB[7] is due to the disruption of the Asp23-Lys28 salt bridge and steric effects of CB[7]@Aβ_1-42 complex with the fibril lattice, and not due to the transition from α-helix to β-sheet following the dock-lock mechanism.Communicated by Ramaswamy H. Sarma.

Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening

Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from "up" to "down" conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below -8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak. [Formula: see text]Communicated by Ramaswamy H. Sarma.

Encapsulation of the Sulfur Compounds by Cucurbit[7]uril: A Quantum Chemistry Study

Benzothiophene (BT) and dibenzothiophene (DT) are the most important contaminants in the petroleum derivatives responsible for serious environmental and health problems. Therefore, we have investigated the absorption of these compounds for the first time by considering cucurbit[7]uril (CB[7]) as the host molecule and using the theoretical levels of density functional theory//B3LYP-D3/6-31G(d). BT and DT absorbed into CB[7] do not undergo a significant structural change in the CB[7] structure. The energy gap of the S-compounds@CB[7] in water and hexane solvents was approximately 5 eV, and this large value implies that the complexes have high chemical stability. Moreover, the absorption of the BT and DT into CB[7] in the water and hexane solvents is a favorable process, whereas the lowest binding energy was observed between the dibenzothiophene and CB[7] in the DT@CB[7] complex. The solvation enthalpy shows a preferential solvation of the complexes in water than in hexane solvent. This trend is confirmed by the AIM analysis that shows the highest stability for the DT@CB[7] system with the contribution of cooperative hydrogen bonding. The transfer free energy of S-compounds@CB[7] complexes from hexane to water are -66.12 and -59.56 kcal/mol for BT@CB[7] and DT@CB[7], respectively, implying the spontaneous transference of these complexes from hexane to water solvent. Overall, our results show that the cucurbiturils can be a new class of host molecules to be used in the removal of S-compounds from petroleum derivatives. Finally, a schematic flow diagram of the desulfurization process by cucurbiturils was proposed.

Encapsulation of the Sulfur Compounds by Cucurbit[7]uril: A Quantum Chemistry Study

Benzothiophene (BT) and dibenzothiophene (DT) are the most important contaminants in the petroleum derivatives responsible for serious environmental and health problems. Therefore, we have investigated the absorption of these compounds for the first time by considering cucurbit[7]uril (CB[7]) as the host molecule and using the theoretical levels of density functional theory//B3LYP-D3/6-31G(d). BT and DT absorbed into CB[7] do not undergo a significant structural change in the CB[7] structure. The energy gap of the S-compounds@CB[7] in water and hexane solvents was approximately 5 eV, and this large value implies that the complexes have high chemical stability. Moreover, the absorption of the BT and DT into CB[7] in the water and hexane solvents is a favorable process, whereas the lowest binding energy was observed between the dibenzothiophene and CB[7] in the DT@CB[7] complex. The solvation enthalpy shows a preferential solvation of the complexes in water than in hexane solvent. This trend is confirmed by the AIM analysis that shows the highest stability for the DT@CB[7] system with the contribution of cooperative hydrogen bonding. The transfer free energy of S-compounds@CB[7] complexes from hexane to water are -66.12 and -59.56 kcal/mol for BT@CB[7] and DT@CB[7], respectively, implying the spontaneous transference of these complexes from hexane to water solvent. Overall, our results show that the cucurbiturils can be a new class of host molecules to be used in the removal of S-compounds from petroleum derivatives. Finally, a schematic flow diagram of the desulfurization process by cucurbiturils was proposed.

Computational Studies on the Encapsulation of 1,4-Dihydropyridine Derivatives into CNT(10,10)

Semiempirical and density functional theory (DFT) methods were herein used to study the encapsulation process of 1,4-dihydropyridine (DHP) derivatives into (10,10) armchair carbon nanotube (CNT(10,10)). The encapsulated DHPs do not affect the overall structural and electronic properties of the CNT(10,10). The following binding energy was obtained from DFT-D3 calculations: DHP_Cl2@CNT(10,10) (–62.36 kcal mol–1) < DHP_Ph@CNT(10,10) (–54.71 kcal mol–1) < DHP_OH@CNT(10,10) (–43.92 kcal mol–1) < DHP_NO2@CNT(10,10) (–41.71 kcal mol–1) < DHP_H@CNT(10,10) (–32.74 kcal mol–1). The increase in the dipole moment for all DHPs@CNT(10,10) indicates their partial solubility in water. Our results play a promising role as a guide for future experiments using CNTs as a vehicle to transport DHP derivatives.

Computational studies of acetylcholinesterase complexed with fullerene derivatives: a new insight for Alzheimer disease treatment

Here, we propose five fullerene (C60) derivatives as new drugs against Alzheimer's disease (AD). These compounds were designed to act as new human acetylcholinesterase (HssAChE) inhibitors by blocking its fasciculin II (FASII) binding site. Docking and molecular dynamic results show that our proposals bind to the HssAChE tunnel entrance, forming stable complex, and further binding free energy calculations suggest that three of the derivatives proposed here could be potent HssAChE inhibitors. We found a region formed by a set of residues (Tyr72, Asp74, Trp286, Gln291, Tyr341, and Pro344) which can be further exploited in the drug design of new inhibitors of HssAChE based on C60 derivatives. Results presented here report for the first time by a new class of molecules that can become effective drugs against AD.

Quantum chemistry studies of meta-tetra(hydroxyphenyl)chlorin (mTHPC) and its isomers

Quantum chemistry methods were used to study the meta-tetra(hydroxyphenyl)chlorin (mTHPC) and its isomers. The mTHPC (Foscan®) is a commercial chlorin, used in photodynamic therapy (PDT) and is classified as a second-generation drug in PDT. The present work is to obtain quantum chemistry properties which can explain the high efficiency of the mTHPC compared with its isomers (ortho and para) and other chlorins. Based in the chemical hardness and ionization potential obtained from HOMO and LUMO orbitals energy, our results show that all chlorins have similar reactivity. Moreover, all chlorins have approximately the same capacity to storage energy in the triplet excited state, with energy differences between the ground state and the triplet excited state of 1.38, 1.39 and 1.36 eV for oTHPC, mTHPC and pTHPC, respectively. The calculated UV spectra (a very important quantity which can be correlated with the photosensitizer (PS) efficiency property), shows that the present chlorins all have a peak at 622 nm. Finally, after analysis of the dipole moment differences, between the three isomers, an explanation about the greater mTHPC efficiency in PDT, was possible. Due to its greater lipophilic character, mTHPC is absorbed by tumor cells to a greater degree than oTHPC and pTHPC. Our findings are consistent with literature and can be used to help new drug design for use in PDT.

Solvation of sodium octanoate micelles in concentrated urea solution studied by means of molecular dynamics simulations

The effects of urea on self-assembling remains a challenging topic on surface chemistry, and computational modeling may have a role on the unraveling of the molecular mechanisms underlying these effects. Bearing that in mind, we performed a set of molecular dynamics simulations to assess the effects of urea on the self-assembling properties of sodium octanoate, an anionic surfactant, as compared to the aggregation of the same surfactant in pure water as the solvent. The concentration of free monomers increased 3-fold in the presence of urea, in agreement with the accepted view that urea should increase monomer solubility. Regarding the size distribution of micellar aggregates, the urea solution favored smaller micelles and a narrower distribution. Preferential solvation by either water or urea changed along the surfactant molecules, from urea-rich shells around apolar atoms at the end of the hydrophobic tails to nearly no urea at the polar headgroups. This solvation profile is consistent with two different hypotheses from the literature: on one hand, urea molecules interact directly with apolar atoms from the hydrophobic tails, acting as a surfactant, and on the other hand the presence of urea molecules increases the hydration of polar sites. Another important observation regards the solvent structure, which exhibits a complex composition profile around both water and urea molecules. Although the solvent structure was appreciably different in each case, the free energy calculations for the dissociation of a pair of octanoate molecules pointed to a purely enthalpic free energy loss in urea solution, a finding that does not lend support to the third hypothesis that is often claimed as accounting for the urea effects, namely, that urea disrupts water structure and that this structural change decreases the hydrophobic effect due to an entropy change. The presence of urea had no significant effect on the molecular structure of the surfactant molecules, although it caused chain dynamics to become slower. The overall picture arising from the molecular-scale data extracted from our computational models is somewhat different from the traditional views about the structural and dynamical features of self-assembled surfactant systems, pointing out the need for more studies on other self-organized systems using a realistic model system as a way to achieve a more detailed picture.