Yongyan Wang

Modular pharmacology: the next paradigm in drug discovery

Introduction: Effective regulation of abnormal targets of disease requires the alteration of either the topological structure or dynamic characteristics of modules in a given target network. In order to disturb the complex direct and indirect target hubs, new approaches in adaptive pharmacology should be developed to regulate target loops using module-based designs. Areas covered: This review discusses the formation in disease-associated structural networks with multiple drug targets and the optimization of a multi-objective system of modules. Expert opinion: On the basis of these concepts, modular pharmacology (MP) has emerged as a method that can balance multiple outcomes by regulating the response of property modules on the basis of the benefits and risks of diversified modules and drugs, thereby allowing novel approaches for drug discovery. Further research of pharmacological mechanisms underlying diversity interactions between multiple modules is necessary for a better understanding of the basic therapeutic processes.

Convergent and divergent pathways decoding hierarchical additive mechanisms in treating cerebral ischemia-reperfusion injury.

Cerebral ischemia is considered to be a highly complex disease resulting from the complicated interplay of multiple pathways. Disappointedly, most of the previous studies were limited to a single gene or a single pathway. The extent to which all involved pathways are translated into fusing mechanisms of a combination therapy is of fundamental importance.

Variations in target gene expression and pathway profiles in the mouse hippocampus following treatment with different effective compounds for ischemia-reperfusion injury.

In order to elucidate the overlapping and diverse pharmacological protective mechanisms of different Chinese medicinal compounds, we investigated the alteration of gene expression and activation of signaling pathways in the mouse hippocampus after treatment of cerebral ischemia–reperfusion injury with various compounds. A microarray including 16,463 genes was used to identify differentially expressed genes among six treatment groups: baicalin (BA), jasminoidin (JA), cholic acid (CA), concha margaritiferausta (CM), sham, and vehicle. The US Food and Drug Administration (FDA) ArrayTrack system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to screen significantly altered genes and pathways (P < 0.05, fold change >1.5). Vehicle treatment alone resulted in alteration of 726 genes (283 upregulated, 443 downregulated) compared to the sham treatment group. BA, JA, and CA treatments, but not CM treatment, were effective in reducing infarct volume compared with vehicle treatment (P < 0.05). Compared with the CM group, a total of 167 (73 upregulated, 94 downregulated), 379 (211 upregulated, 168 downregulated), and 181 (76 upregulated, 105 downregulated) altered genes were found in the BA, JA, and CA groups, respectively. The numbers of overlapping genes between the BA and JA, BA and CA, and JA and CA groups were 28 (16 upregulated, 12 downregulated), 14 (4 upregulated, 10 downregulated), and 31 (8 upregulated, 23 downregulated), respectively. Three overlapping genes were identified among the BA, JA, and CA treatment groups: Il1rap, Gnb5, and Wdr38. Based on KEGG pathway analysis, two, seven, and four pathways were significantly activated in the BA, JA, and CA groups, respectively, when compared to the CM group. The ATP-binding cassette (ABC) transporters general pathway was activated by BA and JA treatment, and the mitogen-activated protein kinase (MAPK) signaling pathway was activated by JA and CA treatment. Alteration of IL-1 and Hspa1a expression was found by real time reverse transcription polymerase chain reaction, confirming the results of the microarray analysis. Our data demonstrated that polytypic profiles of 167–379 altered genes exist in the mouse hippocampus treated with different compounds known to be therapeutically effective in cerebral ischemia–reperfusion injury, and we were able to identify overlapping genes and pathways among these groups. Therefore, these different compounds may function through both overlapping and distinct pharmacological mechanisms to exert their therapeutic action.

Outcome-Dependent Global Similarity Analysis of Imbalanced Core Signaling Pathways in Ischemic Mouse Hippocampus

Analysis of the diverse interactions of multiple signaling pathways is an emerging challenge in the era of networking pharmacology. To reveal imbalanced signaling pathways and pharmacological mechanisms involved in ischemic process, we designed systemic experiments from top-down to bottom-up for investigating the variations of multiple pathways in mouse hippocampal cells. A total of 711 focal cerebral ischemia-reperfused animals (504 mice and 207 rats), induced by occlusion of the middle cerebral artery, were obtained to conduct 4 experiments. The mice were used to analyze the pharmacological effects of four single compounds, baicalin (BA), jasminoidin (JA), ursodeoxycholic acid (UA) and concha margaritifera (CM) and two combination therapies (BA+JA, and JA+UA). Moreover, the mouse models were also used for microarray and western blotting test. The rat models were used for infarction volume test, magnetic resonance imaging (MRI) test and neurological score analysis to validate the pharmacological effects in another species. The results of western blotting confirmed that the expression of the key proteins involved in the ischemiaactivated Wnt and nuclear factor κB (NF-κB) pathway was markedly altered. In addition, based on the screened gene expression profiles of ischemia hippocampus, a variety of altered genes contributed to the 9 stroke-related pathways based on literature review [Wnt, extracellular signal-regulated kinase (ERK), janus kinase (JAK), mitogen-activated protein kinase (MAPK), gonadotropin-releasing hormone (GnRH), calcium/calmodulin-dependent protein kinase (CaMK), vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), and platelet-derived growth factor (PDGF)] in different groups. Thus, we believed that the 9 signaling pathways were significantly imbalanced in different groups. However, analysis of overlapping genes was insufficient to reveal the expression profiles of imbalanced pathways between or within various conditions treated with different compounds or compound mixtures. Therefore, global similarity index (GSI) is introduced to quantify the genotypic outcomes of gene expression profiles. Independent experiments in mice on the effects of infarction volume, neurologic deficit score and the results of MRI in rats showed that GSI was suitable for the spectral measurement of imbalance in those 9 biochemical pathways with a predictive accuracy of 81.0% as assessed by leave-one-out cross-validation.

Hierarchical Profiles of Signaling Pathways and Networks Reveal Two Complementary Pharmacological Mechanisms

Until now the overlapping and diverse pharmacological protective mechanisms of different compounds in the treatment of cerebral ischemia, both on the signaling pathway and network levels have not been revealed. In order to find differential pathway networks from gene expression profiles of hippocampus of ischemic mice treated with baicalin (BA), ursodeoxycholic acid (UA) and jasminoidin (JA), a microarray comprising 16,463 genes, FDA Arraytrack software and Ingenuity Pathway Analysis, was employed. A total of 5, 8, 11, 9 networks and 6, 7, 40, 16 pathways were found in vehicle (vs sham), BA, UA and JA (vs vehicle), respectively. Only 4 and 7 overlapping pathways were shared between BA and UA, UA and JA, accounting for 9.3% and 14.3% of the total number of all pathways, respectively. BA, UA and JA all acted on Ca(2+)-dependent signaling cascades in diverse links. BA intervened in arachidonic acid metabolism. UA affected eicosanoid, cyclin-dependent kinase 5, nuclear factor-kB, and T-helper 1 cell cytokine production. It was found that JA might decrease oxidative damage via nuclear factor erythroid 2-related factor 2-mediated antioxidant response. Compared to vehicle, no overlapping pathways were found among three groups. However, the total of 60 (71.4%) overlapping functions could be approximately divided into diseases and disorders, molecular and cellular functions, physiological system development and function as categories with ratio of 1:1:1. Analysis of network functions and known pathways may be two complementary paradigms for revealing potential pharmacological mechanisms based on the same phenotype variation.

Fangjiomics: revealing adaptive omics pharmacological mechanisms of the myriad combination therapies to achieve personalized medicine.

Fangjiomics: revealing adaptive omics pharmacological mechanisms of the myriad combination therapies to achieve personalized medicine

Spatiotemporal positioning of multipotent modules in diverse biological networks

A biological network exhibits a modular organization. The modular structure dependent on functional module is of great significance in understanding the organization and dynamics of network functions. A huge variety of module identification methods as well as approaches to analyze modularity and dynamics of the inter- and intra-module interactions have emerged recently, but they are facing unexpected challenges in further practical applications. Here, we discuss recent progress in understanding how such a modular network can be deconstructed spatiotemporally. We focus particularly on elucidating how various deciphering mechanisms operate to ensure precise module identification and assembly. In this case, a system-level understanding of the entire mechanism of module construction is within reach, with important implications for reasonable perspectives in both constructing a modular analysis framework and deconstructing different modular hierarchical structures.

Variation of pathways and network profiles reveals the differential pharmacological mechanisms of each effective component to treat middle cerebral artery ischemia-reperfusion mice.

Using a system pharmacology strategy, this study evaluated the unique pharmacological characteristics of three different neuroprotective compounds for the treatment of cerebral ischemia-reperfusion. A microarray including 374 brain ischemia-related genes was used to identify the differentially expressed genes among five treatment groups: baicalin, jasminoidin, ursodeoxycholic acid, sham, and vehicle, and MetaCore analysis software was applied to identify the significantly altered pathways, processes and interaction network parameters. At pathway level, 46, 25, and 31 pathways were activated in the baicalin, jasminoidin, and ursodeoxycholic acid groups, respectively. Thirteen pathways mainly related with apoptosis and development were commonly altered in the three groups. Additionally, baicalin also targeted pathways related with development, neurophysiologic process and cytoskeleton remodeling, while jasminoidin targeted pathways related with cell cycle and ursodeoxycholic acid targeted those related with apoptosis and development. At process level, three processes were commonly regulated by the three groups in the top 10 processes. Further interaction network analysis revealed that baicalin, jasminoidin, and ursodeoxycholic acid displayed unique features either on network topological parameters or network structure. Additional overlapping analysis demonstrated that compared with ursodeoxycholic acid, the pharmacological mechanism of baicalin was more similar with that of jasminoidin in treating brain ischemia. The data presented in this study may contribute toward the understanding of the common and differential pharmacological mechanisms of these three compounds.

Vertical and Horizontal Convergences of Targeting Pathways in Combination Therapy with Baicalin and Jasminoidin for Cerebral Ischemia.

Baicalin (BA) and jasminoidin (JA) exert an additive effect in the treatment of cerebral ischemia, but the underlying molecular mechanism is still unclear. One hundred mice with focal cerebral ischemia/re-perfusion injury were divided into 5 groups: BA, JA, combination therapy (BJ), sham and vehicle. The differentially expressed genes identified by microarray consisting of 374 cDNAs were uploaded into GeneGo MetaCore software for pathway analyses. Networks were constructed to visualize the interactions of the differentially expressed genes. Among the top ten pathways and processes, we found 5, 3, 2 overlapping pathways and 6, 4, 6 overlapping processes between the BA and JA, BA and BJ, JA and BJ groups, respectively; of which 1 pathway and 3 processes were shared by all the three groups. Six representative pathways and 3 processes were activated only in BJ, such as Gamma-secretase proteolytic targets,etc. These BJ representative targeting pathways showed both vertical (e.g. Cytoplasmic/mitochondrial transport of proapoptotic Bid Bmf and Bim) and horizontal (e.g. Endothelin-1/EDNRA signaling) convergences with those of the BA and JA groups based on the upstream and downstream relationship of cerebral ischemia network, which may help to reveal their additive mechanism in the treatment of cerebral ischemia. Network comparison identified important transcription factors that regulated some of the other BJ related genes, such as cMyb and NF-AT. Such a systemic approach based on multiple pathways and networks may provide a robust path to understand the complex pharmacological variations of combination therapies.

Editorial (Thematic Issue: Combination Therapy of Vascular Diseases and Fangjiomics: When West Meets East in the Era of Phenomics)

Combination drug therapy is now a common clinical practice in the treatment of complex vascular disease [1–5]. Different from monotherapy which uses a single drug that targets a pure molecule to treat a clinical condition, combination therapy uses a variety of drugs simultaneously to form a multi-drug regimen, usually a cocktail of several monotherapies that target at different molecules, to treat disease. Historically, combination therapy of vascular disease is designed by either empiric- or mechanism-based optimization of pharmacodynamics and pharmacokinetics for the purpose of improving drug efficacy and reducing toxicity or adverse reactions. However, combination drug therapy of vascular diseases is currently facing major challenges in terms of how to translate the knowledge of genomic research into clinical guidelines for the practice of personalized combination therapy of the phenotypically-complex vascular diseases [1–5]. On the other hand, multiple-target therapies of complex diseases, including vascular disorders, have been exploited for over 3000 years in Chinese medicine (CM). While these multi-target combination therapies with proven efficacy are mainly empiric-based, the underlying mechanisms remain mysteries [6–9]. In the era of post-genomics, the mega-scale data generation and integration of genomics, proteomics, metabolomics, and systems biology have not only advanced our understanding of the molecular basis of vascular biology, pathophysiology, and pharmacology but also highlighted the limitation of the conventional combination drug therapy in both CM and Western medicine and the urgent demand for new paradigm and approaches to develop genome-guided and personalized combination therapy of vascular disease [10, 11]. Fangjiomicsa new emerging discipline developed from the CM focusing on design and evaluation of different combination therapy [8], seeks to systematically study myriad compatible combinations that may act through multiple targets and modes of action balancing between on-target and off-target. The development of Fangjiomics is based on 1) collecting diverse evidences of combination therapies from literatures; 2) revealing different mechanisms of combination therapies; 3) understanding dynamic characteristics of combination therapies; and 4) designing optimal pattern of combination therapies. By prioritizing targets, pathways and ingredient spectrum, Fangjiomics may lead to the discovery of controllable array-designed therapies to combine less potent elements with more on-target effects and fewer off-target effects than monotherapy. In many aspects, Fangjiomics addresses the key components and issues in treating vascular diseases with combination therapies, which may represent the next generation of strategies of clinical pharmacology and therapeutics for the personalized adequate treatment of complex disease [8, 12]. In this Special Issue of Current Vascular Pharmacology, we have assembled a series of articles of reviews, perspectives and original contributions from experts in current research of combination therapy of vascular disease. These articles summarize recent advances in phenomics of vascular disease [13], clinical Zheng-hou pharmacology [12], potential new targets for combination therapy including the volume-regulated Cl− channels (VRCCs) and calcium-activated Cl− channels (CaCCs) [14], microparticles (MPs) [15], adrenomedullin [16], and the endothelin-1 (ET-1) mediated ERK1/2 signaling pathways [17], and the application of CM and Chinese Patent Medicine (CPM) as new approaches to the treatment of cerebral [18] and coronary artery disease [19], hypertension [20] and diabetic complications [21, 22]. Selecting combination therapies based on different horizontal or vertical targets, such as the VRCCs and CaCCs [14], circulating MPs [15], and the ET-1-mediated ERK1/2 signaling pathways in hypertension-induced myocardial hypertrophic response [17], may be very promising in the treatment of variant vascular disease. The combination of CPM with routine anti angina therapy appears to be more effective in the treatment of angina pectoris than the routine treatment [23]. CM interventions of combination therapies to diabetic foot also displayed effectiveness [21]. The combination therapy could not only improve the quality of life and the symptoms of hypertensive patients, but also stabilize blood pressure variability based on systematic reviews (including meta-analyses) [19]. Besides, randomized controlled trials in the last decade demonstrated CPMs had the potential benefits in reducing the incidence of the endpoints and improving neurologic impairments, body movements, Barthel index, and quality of life. It is also noticed, however, that while most current literature indicated that the combination therapy of diabetic nephropathies with the angiotensin-converting enzyme inhibitors (ACEI) and/or angiotensin receptor blockers (ARBs) plus effective CM drugs might have anti-proteinuric and renal protective effects, the clinical outcomes are not always consistent [22]. Clearly, newer strategies are needed for better rational design of combination therapy. The phenomics strategy will allow the transition from focused genotype/phenotype studies to a global genome/phenome approach to the understanding of vascular diseases. The application of phenomics will identify a systemically integrated set of biomarkers for diagnosis and prognosis of vascular disease and provide treatment targets for combination therapy and thus make a significant paradigm shift in the clinical treatment of vascular diseases [13]. In the phenomic standpoint of view [13], Zheng-hou in CM can be regarded as an identifiable clinical phenome, which is the sum total of a patient’s phenotypic traits (Zheng-hou) that signify the expression of genome, proteome, and metabolome under specific environmental influence [12]. Accordingly, more attention should be directed to the translation of the diagnosis of a patient’s Zheng-hou into the identification of dynamic variation of clinical phenome in our future clinical practice. Pharmacokinetics is becoming a useful approach to resolve the growing and complex issue of drug combinations to devise reasonable treatment regimens and to make physicians recognize the mechanisms of combined therapies [24]. In order to leverage breakthroughs in the genome-wide solutions for complex disease and drug responses through a combination of the current “omics” technology a new discipline in the modern translational Chinese medical science (CMS), the clinical Zheng-hou pharmacology (CZP), has been recently emerged [12]. It is hoped that CZP can help us better understand the clinical phenomics, including the disease phenome (Zheng-hou) and its response to the combination drug therapy (Fangjiomics) so that the personalized medicine with rational holistic diagnosis and individualized treatment can be finally achieved [12]. We believe that publication of this special issue will further promote international academic exchange and collaborations to accelerate understanding of mechanisms for human vascular disease and discovery of better designed regimens for personalized combination therapy of these devastating diseases.