Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro. A library of 288 flavonoids extracted from Brazilian biodiversity was screened to select potential Mpro inhibitors. An initial filter based on Lipinski's rule of five was applied, and 204 compounds that did not violate any of the Lipinski rules were selected. The compounds were then docked into the active site of Mpro using the GOLD program, and the poses were subsequently re-scored using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) binding free energy calculations performed by AmberTools23. The top five flavonoids with the best MM-GBSA binding free energy values were selected for analysis of their interactions with the active site residues of the protein. Next, we conducted a toxicity and drug-likeness analysis, and non-toxic compounds were subjected to molecular dynamics simulation and free energy calculation using the MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. It was observed that the five selected flavonoids had lower MM-GBSA binding free energy with Mpro than the co-crystal ligand. Furthermore, these compounds also formed hydrogen bonds with two important residues, Cys145 and Glu166, in the active site of Mpro. Two compounds that passed the drug-likeness filter showed stable conformations during the molecular dynamics simulations. Among these, NuBBE_867 exhibited the best MM-PBSA binding free energy value compared to the crystallographic inhibitor. Therefore, this study suggests that NuBBE_867 could be a potential inhibitor against the main protease of SARS-CoV-2 and may be further examined to confirm our results.

Exploring the Potentiality of Natural Products from Essential Oils as Inhibitors of Odorant-Binding Proteins: A Structure- and Ligand-Based Virtual Screening Approach To Find Novel Mosquito Repellents

Odorant-binding proteins (OBPs) are the main olfactory proteins of mosquitoes, and their structures have been widely explored to develop new repellents. In the present study, we combined ligand- and structure-based virtual screening approaches using as a starting point 1633 compounds from 71 botanical families obtained from the Essential Oil Database (EssOilDB). Using as reference the crystallographic structure of N,N-diethyl-meta-toluamide interacting with the OBP1 homodimer of Anopheles gambiae (AgamOBP1), we performed a structural and pharmacophoric similarity search to select potential natural products from the library. Thymol acetate, 4-(4-methyl phenyl)-pentanal, thymyl isovalerate, and p-cymen-8-yl demonstrated a favorable chemical correlation with DEET and also had high-affinity interactions with the OBP binding pocket that molecular dynamics simulations showed to be stable. To the best of our knowledge, this is the first study to evaluate on a large scale the potentiality of NPs from essential oils as inhibitors of the mosquito OBP1 using in silico approaches. Our results could facilitate the design of novel repellents with improved selectivity and affinity to the protein binding pocket and can shed light on the mechanism of action of these compounds against insect olfactory recognition.

Compostagem de resíduos sólidos orgânicos como tema incentivador de educação ambiental

O presente trabalho diz respeito a uma prática ambiental promovida com a cooperação de alunos do ensino fundamental de uma escola localizada no município de São Miguel do Guamá - PA. Diante das constantes transformações que a sociedade passa ao longo dos anos, a poluição ambiental torna-se por vezes resultado de práticas inconscientes. Para tanto, torna-se necessária a aplicação de atividades sustentáveis também no âmbito escolar, pois nele encontram-se alunos em processo de formação. Neste sentido, o aproveitamento de resíduos sólidos orgânicos provenientes de merenda escolar foi utilizado na produção de adubo orgânico a partir de processo de compostagem e mostrou-se uma alternativa viável para o incentivo da Educação Ambiental no espaço escolar, levando os participantes, professores e alunos a serem agentes de boas ações no ambiente em que trabalham e estudam, colaborando durante o processo que culminou no reaproveitamento dos resíduos sólidos orgânicos gerados na instituição de ensino, onde o adubo ecologicamente formado pôde ser aplicado na horta feita a partir de materiais reciclados para benefício de todos. É importante ressaltar, que os trabalhos nesta área também auxiliam na construção de conhecimentos importantes no ensino fundamental. 

Métodos semiempíricos de química quântica no ensino da entalpia das reações químicas

A carência de métodos para auxiliar o ensino Química torna o assunto desafiador diante das didáticas de ensino. No entanto, pesquisas têm sido feitas para propor novas metodologias que visam contribuir neste sentido. Dentre as propostas, o uso do computador no auxílio ao aprendizado se destaca como sendo uma das mais promissoras. Essa metodologia pode ser bem-vinda no tratamento didático da entalpia, pois, entender esse significado requer conhecer o problema que lhe deu origem e o encaminhamento da sua solução. Neste sentido, foram realizadas simulações em um software de análise química teórica, a fim de obter a entalpia de algumas reações e compará-las com as suas entalpias experimentais. Além disso, fez-se a aplicação desse método junto a graduandos em química para verificar a viabilidade em aplicar esta atividade. Assim, este trabalho apresenta a Química computacional através de métodos quânticos semiempíricos como complemento ao ensino de entalpia das reações Químicas na graduação.

Structural analysis of viral infectivity factor of HIV type 1 and its interaction with A3G, EloC and EloB

BACKGROUND

The virion infectivity factor (Vif) is an accessory protein, which is essential for HIV replication in host cells. Vif neutralizes the antiviral host protein APOBEC3 through recruitment of the E3 ubiquitin ligase complex.

METHODOLOGY

Fifty thousand Vif models were generated using the ab initio relax protocol of the Rosetta algorithm from sets of three- and nine-residue fragments using the fragment Monte Carlo insertion-simulated annealing strategy, which favors protein-like features, followed by an all-atom refinement. In the protocol, a constraints archive was used to define the spatial relationship between the side chains from Cys/His residues and zinc ions that formed the zinc-finger motif that is essential for Vif function. We also performed centroids analysis and structural analysis with respect to the formation of the zinc-finger, and the residue disposal in the protein binding domains. Additionally, molecular docking was used to explore details of Vif-A3G and Vif-EloBC interactions. Furthermore, molecular dynamics simulation was used to evaluate the stability of the complexes Vif-EloBC-A3G and Vif-EloC.

PRINCIPAL FINDINGS

The zinc in the HCCH domain significantly alters the folding of Vif and changes the structural dynamics of the HCCH region. Ab initio modeling indicated that the Vif zinc-finger possibly displays tetrahedral geometry as suggested by Mehle et al. (2006). Our model also showed that the residues L146 and L149 of the BC-box motif bind to EloC by hydrophobic interactions, and the residue P162 of the PPLP motif is important to EloB binding.

CONCLUSIONS/SIGNIFICANCE

The model presented here is the first complete three-dimensional structure of the Vif. The interaction of Vif with the A3G protein and the EloBC complex is in agreement with empirical data that is currently available in the literature and could therefore provide valuable structural information for advances in rational drug design.