Recent Advances on the Structure, Genomic Arrangement, Life Cycle, and Virus-Host Proteins Interactome of SARS CoV-2

Novel coronavirus disease of 2019 (COVID-19) is a highly contagious disease that has been recorded as a third global pandemic caused by the coronavirus (CoV) family in the past twenty years in the aftermath of severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). COVID 19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is transmitted by person-to-person transmission and it remains asymptomatic or presented with mild flu-like symptoms in most occasions, while in some instances, it may progress to severe life threatening and potentially fatal illnesses. This disease is now imposing immense negative influences across the world due to the highly contagious nature of the disease as well as due to the absence of effective treatment targeting the disease. This review addresses the recent advances on the structure and genomic arrangement of SARS-CoV-2 as well as the viral entry, replication and virus-host protein interactome that potentially contribute to cell infectivity, immune evasion, and viral spread. Unveiling the details of such aspects of SARS-CoV-2, therefore, possibly has paramount importance for discovering therapeutic targets.

Mass spectrometry-based protein‒protein interaction techniques and their applications in studies of DNA damage repair / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein‒protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein‒protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein‒protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein‒protein interaction. In addition, we discuss the application of these tools in the investigation of protein‒protein interaction networks involved in DNA damage response and DNA repair.

Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair

GAGA associated factor (GAF) is a sequence-specific DNA binding transcription factor that is evolutionarilyconserved from flies to humans. Emerging evidence shows a context-dependent function of vertebrate GAF(vGAF, a.k.a. ThPOK) in multiple processes like gene activation, repression, and enhancer-blocking. Wehypothesize that context-dependent interaction of vGAF with a diverse set of proteins forms the basis for themultifunctional nature of vGAF. To this end, we deciphered the protein–protein interactome of vGAF andshow that vGAF interacts with chromatin remodelers, RNA metabolic machinery, transcriptional activators/repressors, and components of DNA repair machinery. We further validated the biological significance of ourprotein–protein interaction data with functional studies and established a novel role of vGAF in DNA repairand cell-survival after UV-induced DNA damage. One of the major risk factors for skin cutaneous melanoma isprolonged exposure of UV and subsequent DNA damage. vGAF is highly expressed in normal skin tissue.Interestingly, our analysis of high-throughput RNA-sequencing data shows that vGAF is heavily downregulated across all major stages of skin cutaneous melanoma suggesting its potential as a diagnostic biomarker.Taken together, our study provides a plausible explanation for the diverse gene regulatory functions of vGAFand unravels its novel role in DNA repair.

Meta-analysis of genomic variants and gene expression data in schizophrenia suggests the potential need for adjunctive therapeutic interventions for neuropsychiatric disorders

Schizophrenia (SZ) is a debilitating mental illness with a multigenic aetiology and significant heritability. Despite extensive genetic studies, the molecular aetiology has remained enigmatic. A recent systems biology study suggested a protein–protein interaction network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominant during adolescence, often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan Atlas data allowed us to re-examine the genes present in the SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and nonpsychiatric Exome Aggregation Consortium database allowed us to identify the variants of criticality. The expression of the SZ candidate genes responsible for cognition and disease onset was studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by theprevious interactome study to 10 proteins. These proteins belonging to 81 biological pathways are targeted by 34 known Food and Drug Administration-approved drugs that have distinct potential for the treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to celecoxib pharmacodynamics, Gα signalling and cGMP-PKG signalling pathwaysthat are not known to be specific to SZ aetiology.

Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis / 中国结合医学杂志

OBJECTIVE@#To explore the molecular-level mechanism on the hematopoiesis effect of Angelicae sinensis Radix (ASR) with systems-based interactome analysis.@*METHODS@#This systems-based interactome analysis was designed to enforce the workflow of "ASR (herb)→compound→target protein→internal protein actions→ending regulated protein for hematopoiesis". This workflow was deployed with restrictions on regulated proteins expresses in bone marrow and anemia disease and futher validated with experiments.@*RESULTS@#The hematopoiesis mechanism of ASR might be accomplished through regulating pathways of cell proliferation towards hemopoiesis with cross-talking agents of spleen tyrosine kinase (SYK), Janus kinase 2 (JAK2), and interleukin-2-inducible T-cell kinase (ITK). The hematopoietic function of ASR was also validated by colony-forming assay performed on mice bone marrow cells. As a result, SYK, JAK2 and ITK were activated.@*CONCLUSION@#This study provides a new approach to systematically study and predict the therapeutic mechanism for ASR based on interactome analysis towards biological process with experimental validations.

Identification of neprilysin as a potential target of arteannuin using computational drug repositioning

ABSTRACT The discovery of arteannuin (qinghaosu) in the 20th Century was a major advance for medicine. Besides functioning as a malaria therapy, arteannuin is a pharmacological agent in a range of other diseases, but its mechanism of action remains obscure. In this study, the reverse docking server PharmMapper was used to identify potential targets of arteannuin. The results were checked using the chemical-protein interactome servers DRAR-CPI and DDI-CPI, and verified by AutoDock Vina. The results showed that neprilysin (also known as CD10), a common acute lymphoblastic leukaemia antigen, was the top disease-related target of arteannuin. The chemical-protein interactome and docking results agreed with those of PharmMapper, further implicating neprilysin as a potential target. Although experimental verification is required, this study provides guidance for future pharmacological investigations into novel clinical applications for arteannuin.

Techniques for molecular network construction in network pharmacology study / 国际药学研究杂志

Network construction technology is the basis for network pharmacology research. Data originated from experiment, database and computational prediction can be used to construct drugome network, diseaseome network and molecular interactome network. The molecular network construction for the complex diseases represented by Alzheimer′s disease (AD) could be used to identify the important targets, pathogenesis and drug action mechanism, and guide drug development and drug reposition. This paper reviews techniques for molecular network construction in network pharmacology study.

Techniques for molecular network construction in network pharmacology study / 国际药学研究杂志

Network construction technology is the basis for network pharmacology research. Data originated from experiment, database and computational prediction can be used to construct drugome network,diseaseome network and molecular interactome net?work. The molecular network construction for the complex diseases represented by Alzheimer′s disease(AD)could be used to identify the important targets,pathogenesis and drug action mechanism,and guide drug development and drug reposition. This paper reviews techniques for molecular network construction in network pharmacology study.

Análisis topológico del interactoma de Helicobacter pylori revela proteínas topológicamente esenciales: identificación de blancos terapéuticos / Topological analysis of the interactome of Helicobacter pylori reveals topologically essential proteins: identification of therapeutic targets

La Helicobacter pylori ha colonizado la mitad de la población mundial; su infección presenta una prevalencia del 70% al 90% en países en vía de desarrollo y del 25% al 50% en países industrializados. Está establecido que la infección se asocia con el desarrollo de gastritis crónica, úlcera gástrica y duodenal y con cáncer de estómago en el humano. Helicobacter pylori fue la primera bacteria patógena para la cual se dedujo el interactoma y por análisis topológicos se identificaron 702 proteínas involucradas en 1359 interacciones con una cobertura del 97,7% con escala libre; es decir, que el interactoma contiene proteínas topológicamente esenciales. Sin embargo, dichas proteínas y sus asociaciones fisiológicas no han sido descritas, perdiendo de esta manera la posibilidad de identificar posibles blancos terapéuticos. Con el objetivo de identificar proteínas topológicamente esenciales se realizó una reconstrucción del interactoma de la cepa H. pylori ATCC 26695 empleando los complementos BioNetBuilder y NetworkAnalyzer de Cytoscape y la aplicación web cytoHubba. La reconstrucción presentó 896 proteínas y 2416 interacciones con una cobertura del 96% del proteoma ajustada a la distribución de ley de potencias, es decir, presentó escala libre. Usando NetworkAnalyzer y la aplicación Hubba se identificaron proteínas esenciales según los parámetros K y BC; con las que se construyó una subred. El análisis de esta subred mostró que el sistema de secreción tipo IV interactúa con subsistemas metabólicos de lípidos, aminoácidos y ácidos nucleicos por medio de proteínas, para las cuales esta interacción no había sido sugerida. Además, estas interacciones son explicables por perfiles de expresión dependientes del pH, adhesión y homeostasis del hierro; lo cual permite complementar tanto la biología básica de la cepa como postular nuevos blancos terapéuticos putativos.

Isolamento e cultivo de neurônios e neuroesferas de córtex cerebral aviar / Isolation and culture of neurons and neurospheres from chicken brain cortex

Métodos de cultivo celular são convenientes na realização de análises funcionais de alterações/interações protéicas das células neuronais, auxiliando a decifrar o interactoma de proteínas chaves na neurogênese de doenças do Sistema Nervoso Central. Por esse motivo, culturas de neurônios e neuroesferas isolados do córtex cerebral aviar representam um modelo acessível para o estudo de diversas doenças neurológicas, tal como a epilepsia. A espécie aviar apresenta peculiaridades em seu proteoma neuronal, visto a presença de uma expressão diferenciada de proteínas chaves no metabolismo energético cerebral, algumas destas (VDAC1 e VDAC2) desempenham papel importante na compreensão do mecanismo da epilepsia refratária. A metodologia estabelecida no presente estudo obteve cultivo de neuroeferas, onde as células cresceram tipicamente em aglomerados atingindo, dentro de 7 dias, o diâmetro ideal de 100-200 µm. A diferenciação celular das neuroesferas foi obtida após a aderência destas às placas tratadas com poli-D-lisina, evidenciada pela migração de fibras do interior da neuroesfera. Ao contrário das neuroesferas, os neurônios em cultivo extenderam seus neuritos após 11 dias de isolamento. Tal modelo in vitro pode ser utilizado com sucesso na identificação das variáveis neuroproteômicas, propiciando uma avaliação global das alterações dinâmicas e suas interações protéicas. Tal modelo pode ter aplicações em estudos dos efeitos de indutores da morte celular e bloqueadores de canais de membrana mitocondriais em proteínas chaves do metabolismo energético cerebral.

Cell culture methods are used for studies of protein interactions in neural cells, helping to detect the interactome of proteins linked to generation of central nervous system diseases. For this reason, neural cells and neurospheres isolated from cortical chicken brain are a current model for studies of neurological diseases, such as epilepsy. Chicken brain has key characteristics on its proteome, with a differential expression of proteins linked to energy metabolism, some of them (VDAC 1 and VDAC 2) play an important role in understanding mechanism of refractory epilepsy. Using the methods described, we found neurospheres, in which cells grow in structures with the ideal diameter of 100-200µm within seven days after isolation. Neurospheres differentiation was obtained after adhesion of these cells to surfaces coated with poly-D-Lysine, detected by migration of fibers inside them. Unlike neurospheres, neurons extended neurites after 11 days of isolation. Here we describe a method to isolate and culture neurons and neurospheres from chicken cerebral cortex. Such "in vitro" model can be utilized on studies of neuronal protein differential expression and interaction. Cultures of isolated neurons represent an accessible model on studies of apoptosis and channel blockers of key proteins linked to brain metabolism.

Probing the evolutionary conserved regions within functional site of drug-resistant target proteins of Staphylococcus aureus: In silico phylogenetic motif profiling approach.

Staphylococcus aureus is one of the major causes of clinical infections and increasing mortality due to multi-drug resistance. In this study, eight drug-resistant genes, beta-lactamase, metallo-beta-lactamase, vanB, mecA, norA, qacA, qacB and qacC of S. aureus strain Mu50 (vancomycin resistant) were studied to predict the evolutionary conserved functional site residues in their protein sequences. It was found that in beta-lactamase, Tyr, Gly, Thr, Asn and in metallo-beta-lactamase, Thr, His, Gly, Leu, Arg and Asp residues were highly conserved. In vanB, Gly, His and Asp residues were highly conserved. Whereas in mecA, His, Val, Phe, Gln, Lys and in norA, Ser, Leu and Ala residues showed conservedness at moderate level. In the multi-drug efflux pump (corresponding to qacA, qacB and qacC), Gly residue was found to be highly conserved. The homology clustering of target proteins through SCI-PHY algorithm and homologues identified through PSI-BLAST were compared to identify the degree of conservation of functional residues. The phylogenetic motifs identified using homologues of target proteins were validated through domain search to locate their site and functionality in the protein sequences. Interactome analysis was performed to understand the possible mode of interaction of target proteins with their functional partners.

Purificação e caracterização da VDAC de mitocôndrias corticais aviares: identificação de modificações pós-traducionais nas porinas neuronais murinas e aviares / Purification and characterization of avian cortical mitochondrial VDAC: identification of post-translational modifications of rat and avian neuronal porins

A VDAC é uma porina presente na MME cuja função é crucial no metabolismo energético, sobrevivência e morte celular. A caracterização da VDAC torna-se importante para a compreensão das inter-relações da mitocôndria com os diferentes componentes citosólicos, tais como a HK. A ligação HK-VDAC favorece a utilização do ATP intramitocondrial em células neuronais, a HK cerebral pode interagir de formas diferentes com a VDAC, o que resulta em diferentes sítios de ligação (sítios A e B). Os variados papéis metabólicos das isoformas da VDAC podem ser explicados pela presença de alterações pós-traducionais. No presente trabalho purificamos a VDAC1 mitocondrial neuronal proveniente de cérebro aviar. Paralelamente, comprovamos que a presença de múltiplas formas das VDACs 1 e 2 em cérebros murino e aviar, seja devida à presença de modificações pós-traducionais, nomeadamente a fosforilação. A proteína isolada apresentou peso molecular de 30KDa. Quando submetida à eletroforese e posteriormente à coloração para a identificação de fosfoproteínas, a mesma mostrou-se desfosforilada. O conhecimento da presença, ou ausência de fosforilação das VDACs, reside na importância de estabelecer-se as bases moleculares ligadas à existência de sítios A e B nas mitocôndrias neuronais.

VDAC (voltage-dependent anion channel) is a pore forming protein from outer mitochondrial membrane. It has key functions on energetic metabolism, and cell death and survival. VDAC characterization is important for understanding mitochondrial interactions with cytosolic proteins, such as hexokinase (HK). HK-VDAC interaction supports preferential access to intramitochondrial ATP in neural cells. Brain HK interacts in different ways with VDAC. It results in two HK binding sites (A and B). VDAC isoforms differential metabolic roles may be explained by the presence of post-translational modifications. In this study we purified avian neuronal mitochondrial VDAC1. At same time we showed that VDACs 1 and 2 pI heterogeneity in rat and avian brains is due to phosphorylation. Purified VDAC had a molecular weight of 30 KDa. The purified VDAC submitted to phosphorylated protein staining on gel, was dephosphorylated. The knowledge of presence or absence of VDAC phosphorylation is important for understanding the molecular nature basis of A and B HK binding sites in brain mitochondria.

Análise interactômica da VDAC (voltage-dependent anion selective channel) nos cérebros aviar, bovino e murino / Interactomic analysis of VDAC (voltage-dependent anion selective channel) in rat, bovine and chicken brain

A VDAC é a proteína mais abundante na membrana mitocondrial externa. Exerce o controle da atividade desta organela através da regulação da troca de metabólitos e tem função crucial no mecanismo de apoptose. Em nosso caso, os estudos dos complexos protéicos, das interações entre a VDAC e outras proteínas presentes no interior do neurônio que auxiliam na manutenção das funções das organelas e da célula, fazem parte da chamada interactômica. O presente estudo determinou o interactoma do complexo protéico He-xoquinase-VDAC-ANT presente em cérebros murino, bovino e aviar. Nosso objetivo foi identificar se as expressões diferenciadas da VDAC1 e VDAC2 verificadas nos cérebros murino, aviar e bovino, estão associadas a diferenças nos interactomas dessas proteínas. Este estudo revelou que as espécies aviar e bovina apresentaram o maior número de complexos protéicos contendo VDACs (5) quando comparadas com os neurônios de rato (1), o que é indicativo de uma cinética diferencial de montagem ou desmontagem do complexo. Além disso, a VDAC mitocondrial neuronal aviar também interage com mais proteínas em relação à VDAC mitocondrial neuronal bovina, o que é resultado de uma composição de subunidades diferenciada. Tais resultados indicam diferenças significativas quanto ao metabolismo energético e apoptótico no cérebro aviar, bovino e murino, existindo interações diferenciais da VDAC no cérebro aviar.

The voltage dependent anion channel (VDAC) is the most abundant protein of outer mitochondrial membrane. VDAC controls metabolite exchange through this membrane and the apoptosis machinery. Interactomics is the study of protein complexes, their interactions and the consequences of these interactions. In our case we studied the interactome of the hexokinase-VDAC-ANT (adenine nucleotide transporter) complex in mitochondria of neuronal cells from rat, bovine and chicken brain. We wished to understand if the differential expression of VDAC1 and VDAC2 verified in these cells was linked to differences in the interactions between proteins in these complexes. Our results showed that avian and bovine neurons had more protein complexes (5) containing VDAC than rat cells (1), which indicates a differential kinetics of assembly or disassembly. Moreover, mitochondrial neuronal chicken VDAC interacts with more proteins in comparison with bovine neuronal VDAC, which is indicative of a differential subunit composition. These results supported evidences of differential apoptotic and energetic mechanisms between these brains.

Biotecnologia translacional: hemopressina e outros peptídeos intracelulares / Translational biotechnology: hemopressin and other intracellular peptides

A biotecnologia é uma prática antiga, sendo utilizada desde o antigo Egito para a produção de pão e cerveja. No mundo contemporâneo, a biotecnologia tem sido utilizada de diversas formas, incluindo o tratamento de doenças. No universo acadêmico, a biotecnologia tem permitido um avanço rápido do conhecimento. Neste artigo, fazemos um breve resumo sobre o que é biotecnologia, sua relação com o processo de inovação e produção de biofármacos. No universo acadêmico, a biotecnologia tem contribuído de forma decisiva para a descoberta de novas moléculas bioativas, como no caso da hemopressina e de diversos outros peptídeos intracelulares.

Biotechnology has been used since ancient Egypt for the production of bread and beer. In the modern world, biotechnology has been used in several ways, including for the treatment of diseases. In academia, biotechnology has allowed a rapid advance of knowledge. In this article, we make a brief summary of what is biotechnology and its relation to the process of innovation and production of biopharmaceuticals. In academia, biotechnology has contributed decisively to the discovery of new bioactive molecules, such as in hemopressin and several other intracellular peptides.

Biological Network Evolution Hypothesis Applied to Protein Structural Interactome

The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.

LARGE-SCALE YEAST TWO-HYBRID SYSTEM IN THE APPLICATION ON MAP OF PROTEOME INTERACTOME / 微生物学通报

Protein fulfilling the their roles, one of important ways is through protein-protein interaction. In functional genomic era, identifying all of protein-protein interaction in proteome and mapping the protein interactions that have been attracting many scientists' attention , of which large-scale yeast two-hybrid system is one strategy of most widely used. In recent two years, ambitious projects have launched to examine all of the protein-protein interaction in Saccharomyces cer-evisiae using large-scale yeast two-hybrid system. Nevertheless, huge protein network is larger than that we predict and single yeast two-hybrid system cannot solve all the problems, which need be complemented by other wags.