Determination of prognostic markers for COVID-19 disease severity using routine blood tests and machine learning.

The need for the identification of risk factors associated to COVID-19 disease severity remains urgent. Patients' care and resource allocation can be potentially different and are defined based on the current classification of disease severity. This classification is based on the analysis of clinical parameters and routine blood tests, which are not standardized across the globe. Some laboratory test alterations have been associated to COVID-19 severity, although these data are conflicting partly due to the different methodologies used across different studies. This study aimed to construct and validate a disease severity prediction model using machine learning (ML). Seventy-two patients admitted to a Brazilian hospital and diagnosed with COVID-19 through RT-PCR and/or ELISA, and with varying degrees of disease severity, were included in the study. Their electronic medical records and the results from daily blood tests were used to develop a ML model to predict disease severity. Using the above data set, a combination of five laboratorial biomarkers was identified as accurate predictors of COVID-19 severe disease with a ROC-AUC of 0.80 ​±â€‹ 0.13. Those biomarkers included prothrombin activity, ferritin, serum iron, ATTP and monocytes. The application of the devised ML model may help rationalize clinical decision and care.

Advances in the phytochemical screening and biological potential of propolis.

Propolis is a natural resinous product collected from different parts of plants by bees and mixed with their salivary secretions. The occurrence of more than 180 different chemotypes has flavonoids, phenolic acids, esters, and phenolic aldehydes, as well as balsamic resins, beeswax, pollen, and essential and aromatic oils, among others. Its biological potential documented throughout the world justifies the need, from time to time, to organize reviews on the subject, with the intention of gathering and informing about the update on propolis. In this review (CRD42020212971), phytochemical advances, in vitro, in vivo, and clinical biological assays of pharmacological interest are showcased. The focus of this work is to present propolis clinical safety assays, antitumor, analgesic, antioxidant, anti-inflammatory, and antimicrobial activities. This literature review highlights propolis' promising biological activity, as it also suggests that studies associating propolis with nanotechnology should be further explored for enhanced bioprocessing applications.

Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses.

Arboviral infections such as Zika, chikungunya, dengue, and yellow fever pose significant health problems globally. The population at risk is expanding with the geographical distribution of the main transmission vector of these viruses, the Aedes aegypti mosquito. The global spreading of this mosquito is driven by human migration, urbanization, climate change, and the ecological plasticity of the species. Currently, there are no specific treatments for Aedes-borne infections. One strategy to combat different mosquito-borne arboviruses is to design molecules that can specifically inhibit a critical host protein. We obtained the crystal structure of 3-hydroxykynurenine transaminase (AeHKT) from A. aegypti, an essential detoxification enzyme of the tryptophan metabolism pathway. Since AeHKT is found exclusively in mosquitoes, it provides the ideal molecular target for the development of inhibitors. Therefore, we determined and compared the free binding energy of the inhibitors 4-(2-aminophenyl)-4-oxobutyric acid (4OB) and sodium 4-(3-phenyl-1,2,4-oxadiazol-5-yl)butanoate (OXA) to AeHKT and AgHKT from Anopheles gambiae, the only crystal structure of this enzyme previously known. The cocrystallized inhibitor 4OB binds to AgHKT with K i of 300 µM. We showed that OXA binds to both AeHKT and AgHKT enzymes with binding energies 2-fold more favorable than the crystallographic inhibitor 4OB and displayed a 2-fold greater residence time τ upon binding to AeHKT than 4OB. These findings indicate that the 1,2,4-oxadiazole derivatives are inhibitors of the HKT enzyme not only from A. aegypti but also from A. gambiae.

An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties.

The prediction of the free energy (ΔG) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its centrality in understanding protein association phenomena and protein engineering, the ΔG of binding is a daunting quantity to obtain theoretically. In this work, we devise a novel Artificial Neural Network (ANN) model to predict the ΔG of binding for a given three-dimensional structure of a protein-protein complex with Rosetta-calculated properties. Our model was tested using two data sets, and it presented a root-mean-square error ranging from 1.67 kcal mol-1 to 2.45 kcal mol-1, showing a better performance compared to the available state-of-the-art tools. Validation of the model for a variety of protein-protein complexes is showcased.

Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation.

Herein we describe the use of molecular docking simulations, quantitative structure-activity relationships studies and ADMETox predictions to analyse the molecular recognition of a series of 7-aryl-2,4-diaminoquinazoline derivatives on the inhibition of Staphylococcus aureus dihydrofolate reductase and conducted a virtual screening to discover new potential inhibitors. A quantitative structure-activity relationship model was developed using 40 compounds and two selected descriptors. These descriptors indicated the importance of pKa and molar refractivity for the inhibitory activity against SaDHFR. The values of R2train, CVLOO and R2test generated by the model were 0.808, 0.766, and 0.785, respectively. The integration between QSAR, molecular docking, ADMETox analysis and molecular dynamics simulations with binding free energies calculation, yielded the compounds PC-124127620, PC-124127795 and PC-124127805 as promising candidates to SaDHFR inhibitors. These compounds presented high potency, good pharmacokinetics and toxicological profile. Thus, these molecules are good potential antimicrobial agent to treatment of infect disease caused by S. aureus.Communicated by Ramaswamy H. Sarma.

Association strength of E6 to E6AP/p53 complex correlates with HPV-mediated oncogenesis risk.

Human papillomavirus (HPV) is recognized as the causative agent of cervical cancer in women, and it is associated with other anogenital and head/neck cancers. More than 120 types of HPV have been identified and many classified as high- or low-risk according to their oncogenic potential. One of its proteins, E6, has evolved to overcome the oncosuppressor functions of p53 by targeting this protein for degradation via interaction with the human ubiquitin-ligase E6AP. This study evaluates the correlation between the association strength of 40 HPV E6 types to the E6AP/p53 complex and the HPV oncogenesis risk using molecular simulations and machine and deep learning (ML/DL). In addition, a ML/DL-driven prediction is proposed for the HPV unclassified oncogenic risk type. The results indicate that thermodynamics play a pivotal role in the establishment of HPV-associated cancer and highlight the need to include some viral types in the HPV-related cancer surveillance and prevention strategies.

Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil.

The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly Δ144 or Δ141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we did not find an increased incidence of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sublineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting more infectious variants or antibody evasion mutations is expected to increase. IMPORTANCE The continuous evolution of SARS-CoV-2 is an expected phenomenon that will continue to happen due to the high number of cases worldwide. The present study analyzed how a Variant of Concern (VOC) could still circulate in a population hardly affected by two COVID-19 waves and with vaccination in progress. Our results showed that the answer behind that was a new generation of Gamma-like viruses, which emerged locally carrying mutations that made it more transmissible and more capable of spreading, partially evading prior immunity triggered by natural infections or vaccines. With thousands of new cases daily, the current pandemics scenario suggests that SARS-CoV-2 will continue to evolve and efforts to reduce the number of infected subjects, including global equitable access to COVID-19 vaccines, are mandatory. Thus, until the end of pandemics, the SARS-CoV-2 genomic surveillance will be an essential tool to better understand the drivers of the viral evolutionary process.

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein.

Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. Importantly, we detected the community transmission of different P.1 lineages bearing NTD indels ∆69-70 (which can impact several SARS-CoV-2 diagnostic protocols), ∆144 and ins214ANRN, and a new VOI N.10 derived from the B.1.1.33 lineage carrying three NTD deletions (∆141-144, ∆211, and ∆256-258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil generates new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.

Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies.

SARS-CoV-2 VOC immune evasion is mainly due to lower cross-reactivity from previously elicited class I/II neutralizing antibodies, while increased affinity to hACE2 plays a minor role. The affinity between antibodies and VOCs is impacted by remodeling of the electrostatic surface potential of the Spike RBDs. The P.3 variant is a putative VOC.

SARS-CoV-2 VOCs immune evasion from previously elicited neutralizing antibodies is mainly driven by lower cross-reactivity due to spike RBD electrostatic surface changes.

O rápido espalhamento das novas variantes do novo coronavírus SARS-CoV-2, como exemplificado pela alta prevalência da variante P.1 ainda nos dois primeiros meses após seu surgimento, junto a relatos de reinfecção causada por estas variantes, levanta para a ciência a questão de quais seriam os mecanismos por trás deste cenário. É de especial interesse para estas pesquisas o estudo das mutações no genoma das variantes ­ em particular, no gene da glicoproteína Spike (proteína S), que promove a entrada nas células humanas a partir da interação com a Enzima Conversora de Angiotensina 2 (hACE2), molécula que atua como receptor do vírus. A capacidade de se ligar à hACE2 pode tornar-se maior ou menor de acordo com as alterações na estrutura da proteína S, que variam entre linhagens do SARS-CoV-2 e cada uma de suas variantes. Essas alterações na estrutura da proteína S podem também resultar em uma menor capacidade de anticorpos gerados em resposta a uma infecção ­ ou, possivelmente, mesmo após a vacinação ­ de se ligarem à proteína S e neutralizar a capacidade do vírus de causar infecção. A presente publicação ­ agora também disponível em sua versão revisada por pares ­ investiga estes dois possíveis efeitos das mutações da proteína S detectadas em variantes como a P.1, variantes da linhagem B.1.351 e a B.1.1.7: a de uma interação "mais forte" com o receptor hACE2 ou a de uma interação "mais fraca" com os anticorpos anti-proteína-S. No link do ChemRxiv ainda em estágio pre-print, antes da revisão por pesquisadores independentes, o artigo descreve uma série de experimentos feitos com modelagem computacional das moléculas envolvidas (hACE2, anticorpos e as diversas "versões" da proteína S, referentes a cada uma das variantes estudadas). Com base na simulação computacional da interação entre as moléculas, foi possível verificar que a alteração da estrutura da proteína S não teve efeitos marcantes na interação com o receptor hACE2. Por outro lado, ao simular a interação dos anticorpos gerados em resposta a linhagens iniciais do SARS-CoV-2 com a proteína S das novas variantes, foi possível ver que há uma diminuição na ligação entre as moléculas, um achado que aponta para um potencial de "escape" da resposta imune. Segundo essa hipótese, as novas variantes seriam mais eficazes em fugir da neutralização proporcionada por anticorpos, e este seria um mecanismo mais relevante para explicar seu rápido espalhamento pela população. É importante ressaltar que, baseados em algumas medidas de afinidade entre variações da proteína S e o receptor hACE2, outros grupos de pesquisa previamente sugeriram que o aumento da transmissibilidade estaria relacionado com uma maior afinidade entre a proteína viral e o receptor humano, em contraste com os resultados do presente estudo. Contudo, estes estudos não exploraram a interação das diferentes proteínas S com os anticorpos neutralizantes. O artigo aponta ainda a nova variante denominada P.3 como uma potencial Variante de Preocupação (VOC), tendo em vista que a maioria dos anticorpos analisados no estudo não foram capazes de se ligar eficientemente à proteína S desta linhagem nas simulações realizadas.

Cooperative UAV-UGV Autonomous Power Pylon Inspection: An Investigation of Cooperative Outdoor Vehicle Positioning Architecture.

Realizing autonomous inspection, such as that of power distribution lines, through unmanned aerial vehicle (UAV) systems is a key research domain in robotics. In particular, the use of autonomous and semi-autonomous vehicles to execute the tasks of an inspection process can enhance the efficacy and safety of the operation; however, many technical problems, such as those pertaining to the precise positioning and path following of the vehicles, robust obstacle detection, and intelligent control, must be addressed. In this study, an innovative architecture involving an unmanned aircraft vehicle (UAV) and an unmanned ground vehicle (UGV) was examined for detailed inspections of power lines. In the proposed strategy, each vehicle provides its position information to the other, which ensures a safe inspection process. The results of real-world experiments indicate a satisfactory performance, thereby demonstrating the feasibility of the proposed approach.

Coordination among Bond Formation/Cleavage in a Bifunctional-Catalyzed Fast Amide Hydrolysis: Evidence for an Optimized Intramolecular N-Protonation Event.

A density functional theory (DFT) computational analysis, using the ωB97X-D functional, of a rapid amide cleavage in 2-carboxyphthalanilic acid (2CPA), where the amide group is flanked by two catalytic carboxyls, reveals key mechanistic information: (a) General base catalysis by a carboxylate coupled to general acid catalysis by a carboxyl is not operative. (b) Nucleophilic attack by a carboxylate on the amide carbonyl coupled to general acid catalysis at the amide oxygen can also be ruled out. (c) A mechanistic pathway that remains viable involves general acid proton delivery to the amide nitrogen by a carboxyl, while the other carboxylate engages in nucleophilic attack upon the amide carbonyl; a substantially unchanged amide carbonyl in the transition state; two concurrent bond-forming events; and a spatiotemporal-base rate acceleration. This mechanism is supported by molecular dynamic simulations which confirm a persistent key intramolecular hydrogen bonding. These theoretical conclusions, although not easily verified by experiment, are consistent with a bell-shaped pH/rate profile but are at odds with hydrolysis mechanisms in the classic literature.

The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-HIV-1 2F5 antibodies.

Antibodies against the HIV-1 2F5 epitope are known as one of the most powerful and broadly protective anti-HIV antibodies. Therefore, vaccine strategies that include the 2F5 epitope in their formulation require a robust method to detect specific anti-2F5 antibody production by B cells. Towards this goal, we have biotinylated a previously reported computer-designed protein carrying the HIV-1 2F5 epitope aiming the further development of a platform to detect human B-cells expressing anti-2F5 antibodies through flow cytometry. Biophysical and immunological properties of our devised protein were characterized by computer simulation and experimental methods. Biotinylation did not affect folding and improved protein stability and solubility. The biotinylated protein exhibited similar binding affinity trends compared to its unbiotinylated counterpart and was recognized by anti-HIV-1 2F5 antibodies expressed on the surface of patient-derived peripheral blood mononuclear cells. Moreover, we present a high affinity marker for the identification of epitope-specific B cells that can be used to measure the efficacy of vaccine strategies based on the HIV-1 envelope protein.

Molecular basis of Tityus stigmurus alpha toxin and potassium channel kV1.2 interactions.

The Tityus stigmurus scorpion is widely distributed in the Northeast of Brazil and is the main causal agent of human envenoming. The venom produced by this scorpion includes neurotoxins, which are peptides belonging to Family 2 toxins and are able to interact with ion channels. The KTx subfamily displays selectivity and affinity for Kv channel subtypes and the result of this interaction is the blockade of potassium channels, impairing vital functions. We report the optimized structural model of a transcript encoding a potassium channel blocker toxin from T. stigmurus. LC-MS analysis confirmed the presence of the toxin in the venom and the three-dimensional structure was obtained by computational homology modeling and refined by molecular dynamic simulations. Furthermore, docking simulations were performed using a Shaker kV-1.2 potassium channel from rats as receptor model and the contacts were identified revealing which amino acid residues and interactions could be involved in its blockade. These residues were mapped and their contact and electrostatic interactions were evaluated revealing the influence of positive lysine residues and the additional contribution of an asparagine to the stabilization of the complex, bringing new insights into the mechanism of action of this toxin.