Protein Network Level Research Articles

Uncovering the efficacy and mechanisms of Genkwa flos and bioactive ingredient genkwanin against L. monocytogenes infection

Ethnopharmacological relevanceGenkwa flos (yuanhua in Chinese), the dried flower buds of the plant Daphne genkwa Siebold & Zucc., as a traditional herb widely used for the treatment of inflammation-related symptoms and diseases, with the efficacies of diuretic, phlegm-resolving and cough suppressant. Aim of the studyTraditional Chinese Medicine (TCM) is presumed to be of immense potential against pathogens infection. Whereas, the potential efficacy and mechanisms of Genkwa flos against L. monocytogenes infection has not been extensively explored. The present study aimed to identify the bioactive ingredients of Genkwa flos against L. monocytogenes infection and to delineate the underlying mechanisms of action. Materials and methodsBioinformatics approach at protein network level was employed to investigate the therapeutic mechanisms of Genkwa flos against L. monocytogenes infection. And hemolysis inhibition assay, cytoprotection test, western blotting, oligomerization assay and molecular docking analysis were applied to substantiate the multiple efficacies of Genkwa flos and the bioactive ingredient genkwanin. Histopathological analysis and biochemistry detection were conducted to evaluate the in vivo protective effect of genkwanin. ResultsNetwork pharmacology and experimental validation revealed that Traditional Chinese Medicine (TCM) Genkwa flos exhibited anti-L. monocytogenes potency and was found to inhibit the hemolytic activity of LLO. Bioactive ingredient genkwanin interfered with the pore-forming activity of LLO by engaging the active residues Tyr414, Tyr98, Asn473, Val100, Tyr440 and Val438, and thereby attenuated LLO-mediated cytotoxicity. Consistent with the bioinformatics prediction, exposed to genkwanin could upregulate the Nrf2 level and promote the translocation of Nrf2. In vivo, genkwanin oral administration (80 mg/kg) significantly protected against systemic L. monocytogenes infection, as evidenced by reduced myeloperoxidase (MPO) and malondialdehyde (MDA) levels, increased mice survival rate by 30% and decreased pathogen colonization. ConclusionOur study demonstrated that Genkwa flos is a potential anti-L. monocytogenes TCM, highlighted the therapeutic potential of Genkwa flos active ingredient genkwanin by targeting the pore-forming cytolysin LLO and acting as a promising antioxidative candidate against L. monocytogenes infection.

Abstract IA22: Systems approach to rational combination therapy

Abstract Tumors evolve under therapeutic pressure both through rapid epigenomic mechanisms primarily at the protein network level and long-term genomic evolution. The realization of the promise of personalized molecular medicine will require efficient development and implementation of effective combination therapies able to capitalize on or interdict tumor evolution under therapeutic pressure. While we are beginning to develop a series of biomarkers able to predict which patients will benefit from monotherapy, our ability to predict which combination therapies will be active in particular patients is in its infancy. Integration of spatially oriented DNA, RNA, and protein information content as they change under therapeutic pressure has the potential to help identify patients likely to respond to combination therapy. Therapy resistance can be pre-existing, adaptive, or acquired. Resistance can also occur through a heterogeneity of molecular changes within the tumor and metastases. Adaptive resistance, which is the consequence of activation of homeostatic loops and phylogenetically conserved stress responses, provides a potential therapeutic liability that can be leveraged for rational combinatorial therapy. Thus, a comprehensive analysis of patient tumors before, during, and after treatment should become the standard of practice to enable identification of mechanisms of resistance as well as to allow rapid evolution of patient therapy. Testing these precepts will require the development and implementation of novel biopsy-driven trial designs and CLIA-compliant analytics that can be deployed in real time to allow rapid evolution of therapeutic approaches. We have implemented a suite of biopsy-driven trials linked to deep molecular analysis with the goal of rapid identification of tumor evolution to enable change in therapy to counter tumor evolution as it arises. We have implemented a series of studies based on PARP inhibitors as a backbone with the goal of increasing the depth and duration of response while at the same time extending the population of patients who benefit beyond those with homologous recombination defects. Concurrently, we have a series of n-of-one studies with combinations of FDA-approved drugs. Early data suggest that these approaches have the potential to greatly improve patient outcomes. Citation Format: Gordon B. Mills. Systems approach to rational combination therapy [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr IA22.

Diverse patterns of molecular changes in the mechano-responsiveness of focal adhesions

Focal adhesions anchor contractile actin fibers with the extracellular matrix, sense the generated tension and respond to it by changing their morphology and composition. Here we ask how this mechanosensing is enabled at the protein-network level, given the modular assembly and multitasking of focal adhesions. To address this, we applied a sensitive 4-color live cell imaging approach, enabling monitoring patterns of molecular changes in single focal adhesions. Co-imaging zyxin, FAK, vinculin and paxillin revealed heterogeneities in their responses to Rho-associated kinase (ROCK)-mediated perturbations of actomyosin contractility. These responses were rather weakly correlated between the proteins, reflecting diverse compositional changes in different focal adhesions. This diversity is partially attributable to the location of focal adhesions, their area, molecular content and previous contractility perturbations, suggesting that integration of multiple local cues shapes differentially focal adhesion mechano-responsiveness. Importantly, the compositional changes upon ROCK perturbations exhibited distinct paths in different focal adhesions. Moreover, the protein exhibiting the strongest response to ROCK perturbations varied among different focal adhesions. The diversity in response patterns is plausibly enabled by the modular mode of focal adhesions assembly and can provide them the needed flexibility to perform multiple tasks by combining optimally a common set of multifunctional components.

Analysis of Cynandione A's Anti-Ischemic Stroke Effects from Pathways and Protein-Protein Interactome.

Ischemic stroke is the third leading cause of death in the world. Our previous study found that cynandione A (CYNA), the main component from the root of Cynanchum bungei, exhibits anti-ischemic stroke activity. In this work, we investigated the therapeutic mechanisms of CYNA to ischemic stroke at protein network level. First, PC12 cells and cerebellar granule neurons were prepared to validate the effects of CYNA against glutamate injury. Our experiments suggested that CYNA could dose-dependently mitigate glutamate-induced neurons neurotoxicity and inhibit glutamate-induced upregulation of KHSRP and HMGB1, further confirming the neuroprotective effects of CYNA in vivo. Then, on the pathway sub-networks, which present biological processes that can be impacted directly or in periphery nodes by drugs via their targets, we found that CYNA regulates 11 pathways associated with the biological process of thrombotic or embolic occlusion of a cerebral artery. Meanwhile, by defining a network-based anti-ischemic stroke effect score, we showed that CYNA has a significantly higher effect score than random counterparts, which suggests a synergistic effect of CYNA to ischemic stroke. This study may shed new lights on the study of network based pharmacology.

Bioinformatics Analysis for the Antirheumatic Effects of Huang-Lian-Jie-Du-Tang from a Network Perspective

Huang-Lian-Jie-Du-Tang (HLJDT) is a classic TCM formula to clear “heat” and “poison” that exhibits antirheumatic activity. Here we investigated the therapeutic mechanisms of HLJDT at protein network level using bioinformatics approach. It was found that HLJDT shares 5 target proteins with 3 types of anti-RA drugs, and several pathways in immune system and bone formation are significantly regulated by HLJDT's components, suggesting the therapeutic effect of HLJDT on RA. By defining an antirheumatic effect score to quantitatively measure the therapeutic effect, we found that the score of each HLJDT's component is very low, while the whole HLJDT achieves a much higher effect score, suggesting a synergistic effect of HLJDT achieved by its multiple components acting on multiple targets. At last, topological analysis on the RA-associated PPI network was conducted to illustrate key roles of HLJDT's target proteins on this network. Integrating our findings with TCM theory suggests that HLJDT targets on hub nodes and main pathway in the Hot ZENG network, and thus it could be applied as adjuvant treatment for Hot-ZENG-related RA. This study may facilitate our understanding of antirheumatic effect of HLJDT and it may suggest new approach for the study of TCM pharmacology.

Protein co-evolution, co-adaptation and interactions

Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.

Alternative splicing and protein structure evolution

Alternative splicing is thought to be one of the major sources for functional diversity in higher eukaryotes. Interestingly, when mapping splicing events onto protein structures, about half of the events affect structured and even highly conserved regions i.e. are non-trivial on the structure level. This has led to the controversial hypothesis that such splice variants result in nonsense-mediated mRNA decay or non-functional, unstructured proteins, which do not contribute to the functional diversity of an organism. Here we show in a comprehensive study on alternative splicing that proteins appear to be much more tolerant to structural deletions, insertions and replacements than previously thought. We find literature evidence that such non-trivial splicing isoforms exhibit different functional properties compared to their native counterparts and allow for interesting regulatory patterns on the protein network level. We provide examples that splicing events may represent transitions between different folds in the protein sequence–structure space and explain these links by a common genetic mechanism. Taken together, those findings hint to a more prominent role of splicing in protein structure evolution and to a different view of phenotypic plasticity of protein structures.