Core proteome mediated therapeutic target mining and multi-epitope vaccine design for Helicobacter pylori

Helicobacter pylori is a Gram-negative spiral-shaped bacterium that infects half of the human population worldwide and causes chronic inflammation. In the present study, we used the art of computational biology for therapeutic drug targets identification and a multi-epitope vaccine against multi-strains of H. pylori. For drug target identification, we used different tools and softwares to identify human non-homologous but pathogen essential proteins, with virulent properties and involved in unique metabolic pathways of H. pylori. For this purpose, the core proteome of 84 strains of H. pylori was retrieved from EDGAR 2.3 database. There were 59,808 proteins sequences in these strains. Duplicates and paralogous protein sequence removal was followed by human non-homologous protein miningPathogen essential and virulent proteins were subjected to pathway analysis Subcellular localization of the virulent proteins was predicted and druggability was also checked, leading to 30 druggable targets based on their similarity with the approved drug targets in Drugbank. For immunoinformatics analysis, we selected two outer membrane proteins (HPAKL86_RS06305 and HPSNT_RS00950) and subjected to determined immunogenic B and T-Cell epitopes. The B and T-Cell overlapped epitopes were selected to design 9 different vaccine constructs by using linkers and adjuvants. Least allergenic and most antigenic construct (C-8) was selected as a promiscuous vaccine to elicit host immune response. Cloning and in silico expression of the constructed vaccine (C-8) was done to produce a clone having the desired (gene) vaccine construct. In conclusion, the prioritized therapeutic targets for 84 strains of H.pylori will be useful for future therapy design. Vaccine design may also prove useful in the quest for targeting multi-strains of H. pylori in patients

Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction

<p>Abstract</p> <p>Background</p> <p>The hepatocyte growth factor (HGF) stimulates mitogenesis, motogenesis, and morphogenesis in a wide range of tissues, including epithelial cells, on binding to the receptor tyrosine kinase c-Met. Abnormal c-Met signalling contributes to tumour genesis, in particular to the development of invasive and metastatic phenotypes. The human microbial pathogen <it>Helicobacter pylori </it>can induce chronic gastritis, peptic ulceration and more rarely, gastric adenocarcinoma. The <it>H. pylori </it>effector protein cytotoxin associated gene A (CagA), which is translocated via a type IV secretion system (T4SS) into epithelial cells, intracellularly modulates the c-Met receptor and promotes cellular processes leading to cell scattering, which could contribute to the invasiveness of tumour cells. Using a logical modelling framework, the presented work aims at analysing the c-Met signal transduction network and how it is interfered by <it>H. pylori </it>infection, which might be of importance for tumour development.</p> <p>Results</p> <p>A logical model of HGF and <it>H. pylori </it>induced c-Met signal transduction is presented in this work. The formalism of logical interaction hypergraphs (LIH) was used to construct the network model. The molecular interactions included in the model were all assembled manually based on a careful meta-analysis of published experimental results. Our model reveals the differences and commonalities of the response of the network upon HGF and <it>H. pylori </it>induced c-Met signalling. As another important result, using the formalism of minimal intervention sets, phospholipase Cγ1 (PLCγ1) was identified as knockout target for repressing the activation of the extracellular signal regulated kinase 1/2 (ERK1/2), a signalling molecule directly linked to cell scattering in <it>H. pylori </it>infected cells. The model predicted only an effect on ERK1/2 for the <it>H. pylori </it>stimulus, but not for HGF treatment. This result could be confirmed experimentally in MDCK cells using a specific pharmacological inhibitor against PLCγ1. The <it>in silico </it>predictions for the knockout of two other network components were also verified experimentally.</p> <p>Conclusion</p> <p>This work represents one of the first approaches in the direction of host-pathogen systems biology aiming at deciphering signalling changes brought about by pathogenic bacteria. The suitability of our network model is demonstrated by an <it>in silico </it>prediction of a relevant target against pathogen infection.</p

Flavodoxins as novel therapeutic targets against helicobacter pylori and other gastric pathogens

Flavodoxins are small soluble electron transfer proteins widely present in bacteria and absent in vertebrates. Flavodoxins participate in different metabolic pathways and, in some bacteria, they have been shown to be essential proteins representing promising therapeutic targets to fight bacterial infections. Using purified flavodoxin and chemical libraries, leads can be identified that block flavodoxin function and act as bactericidal molecules, as it has been demonstrated for Helicobacter pylori (Hp), the most prevalent human gastric pathogen. Increasing antimicrobial resistance by this bacterium has led current therapies to lose effectiveness, so alternative treatments are urgently required. Here, we summarize, with a focus on flavodoxin, opportunities for pharmacological intervention offered by the potential protein targets described for this bacterium and provide information on other gastrointestinal pathogens and also on bacteria from the gut microbiota that contain flavodoxin. The process of discovery and development of novel antimicrobials specific for Hp flavodoxin that is being carried out in our group is explained, as it can be extrapolated to the discovery of inhibitors specific for other gastric pathogens. The high specificity for Hp of the antimicrobials developed may be of help to reduce damage to the gut microbiota and to slow down the development of resistant Hp mutants

Vaccine Development

Vaccination is the most effective and scientifically based means of protection against infectious diseases, especially in this era of the COVID-19 pandemic. This book examines several issues related to the development of vaccines against viral, bacterial, and parasitic infections

Annotation and curation of hypothetical proteins: prioritizing targets for experimental study

Completely sequenced organisms have some uncharacterized proteins that are gene-encoded products. These proteins can be predicted through in-silico approaches and their biological activities are not proved by experimental evidence and known as hypothetical proteins (HPs). These proteins are important due to their excessive involvement in different cellular and signaling pathways. Structural and functional characterization of HPs reveal crucial roles in microorganisms, especially in pathogens related to human diseases. Here, we discussed all possibilities of in-silico analysis tools and other recently reported methods for hypothetical protein characterization and biomedical applications, including drug and vaccine development. Different methodologies, including meta-proteomics have been used to study protein expression by identification of HPs and comparative genomics have also come under observation due to the emergence of evolutionary study among different organisms. Structural characterization of proteins acts as a base for their functional prediction, novel drug target identification for disease treatment, vaccine production and sero-diagnosis. HPs have played major roles in different vital phenomenon for life including host adaptation, wound healing and chemotaxis. In the current era of drug and antibiotic resistance, HPs can be novel targets to treat related diseases. Identification and characterization of most HPs are under observation and will be the most promising genomic and bioinformatics techniques in structure-based drug designing and vaccine production in future

Computational analysis of protein interaction networks for infectious diseases

Infectious diseases caused by pathogens, including viruses, bacteria and parasites, pose a serious threat to human health worldwide. Frequent changes in the pattern of infection mechanisms and the emergence of multidrug resistant strains among pathogens have weakened the current treatment regimen. This necessitates the development of new therapeutic interventions to prevent and control such diseases. To cater to the need, analysis of protein interaction networks (PINs) has gained importance as one of the promising strategies. The present review aims to discuss various computational approaches to analyse the PINs in context to infectious diseases. Topology and modularity analysis of the network with their biological relevance, and the scenario till date about host-pathogen and intra-pathogenic protein interaction studies were delineated. This would provide useful insights to the research community thereby enabling them to design novel biomedicine against such infectious diseases

CHALLENGES AND RECENT DEVELOPMENTS ASSOCIATED WITH VACCINE ANTIGENS PRODUCTION AGAINST HELICOBACTER PYLORI

Around half of the world’s population faces Helicobactor pylori (H. pylori) infection. Enormous progress has been made to understand the bacterial pathogenesis process and pathogen interaction with eukaryotic cells but infectious diseases are still the cause of premature death of humans around the world. H. pylori is categorized under class I carcinogen by the WHO based on clinical study results. This review paper discusses various attempts made to establish an efficient vaccine to manage H. pylori infection. Some of the problems in developing an efficient vaccine against H. pylori are recurrent or persistent infection, insufficient knowledge about the action specifically in case of probiotics, development of antibiotic resistance, and cost of therapy are noted. This research may come up with transient Nicotiana benthamiana with suitable H. pylori genes expressed as antigenic proteins, which can be used for further studies to develop a vaccine for gastric ulcer/cancer and generate good scientific data that can be helpful for scientists and researchers in this field. This review article for monitors’ current approaches monitoring&nbsp;H. pylori infection since 1998 to 2019 using world-wide recognized journals and books, questioning its efficacies and whether these strategies help eradicate or there is a need to focus on several diversions. We provide scientific recommendations in eliminating&nbsp;H. pylori through vaccination along with addressing the preventive vaccine for this pathogen rather than using defeated treatments with plant-based nil side effects solution. The information relies on the available content in Google Scholar and PubMed using the keywords listed below

The role of Helicobacter pylori outer membrane proteins in adherence and pathogenesis

Helicobacter pylori is one of the most successful human pathogens, whichcolonizes the mucus layer of the gastric epithelium of more than 50% of the world’spopulation. This curved, microaerophilic, Gram-negative bacterium induces a chronicactive gastritis, often asymptomatic, in all infected individuals. In some cases, this gastritisevolves to more severe diseases such as peptic ulcer disease, gastric adenocarcinoma, andgastric mucosa-associated lymphoid tissue lymphoma. H. pylori has developed a unique setof factors, actively supporting its successful survival and persistence in its natural hostileecological niche, the human stomach, throughout the individual’s life, unless treated. In thehuman stomach, the vast majority of H. pylori cells are motile in the mucus layer lining,but a small percentage adheres to the epithelial cell surfaces. Adherence to the gastricepithelium is important for the ability of H. pylori to cause disease because this intimateattachment facilitates: (1) colonization and persistence, by preventing the bacteria frombeing eliminated from the stomach, by mucus turnover and gastric peristalsis; (2) evasionfrom the human immune system and (3) efficient delivery of proteins into the gastric cell,such as the CagA oncoprotein. Therefore, bacteria with better adherence propertiescolonize the host at higher densities. H. pylori is one of the most genetically diversebacterial species known and is equipped with an extraordinarily large set of outermembrane proteins, whose role in the infection and persistence process will be discussed in this review, as well as the different receptor structures that have been so far described for mucosal adherence

Dynamic balance of pro‐ and anti‐inflammatory signals controls disease and limits pathology

Immune responses to pathogens are complex and not well understood in many diseases, and this is especially true for infections by persistent pathogens. One mechanism that allows for long‐term control of infection while also preventing an over‐zealous inflammatory response from causing extensive tissue damage is for the immune system to balance pro‐ and anti‐inflammatory cells and signals. This balance is dynamic and the immune system responds to cues from both host and pathogen, maintaining a steady state across multiple scales through continuous feedback. Identifying the signals, cells, cytokines, and other immune response factors that mediate this balance over time has been difficult using traditional research strategies. Computational modeling studies based on data from traditional systems can identify how this balance contributes to immunity. Here we provide evidence from both experimental and mathematical/computational studies to support the concept of a dynamic balance operating during persistent and other infection scenarios. We focus mainly on tuberculosis, currently the leading cause of death due to infectious disease in the world, and also provide evidence for other infections. A better understanding of the dynamically balanced immune response can help shape treatment strategies that utilize both drugs and host‐directed therapies.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146448/1/imr12671.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146448/2/imr12671_am.pd

Inhibitors of Helicobacter pylori Protease HtrA Found by ‘Virtual Ligand’ Screening Combat Bacterial Invasion of Epithelia

Background: The human pathogen Helicobacter pylori (H. pylori) is a main cause for gastric inflammation and cancer. Increasing bacterial resistance against antibiotics demands for innovative strategies for therapeutic intervention. Methodology/Principal Findings: We present a method for structure-based virtual screening that is based on the comprehensive prediction of ligand binding sites on a protein model and automated construction of a ligand-receptor interaction map. Pharmacophoric features of the map are clustered and transformed in a correlation vector (‘virtual ligand’) for rapid virtual screening of compound databases. This computer-based technique was validated for 18 different targets of pharmaceutical interest in a retrospective screening experiment. Prospective screening for inhibitory agents was performed for the protease HtrA from the human pathogen H. pylori using a homology model of the target protein. Among 22 tested compounds six block E-cadherin cleavage by HtrA in vitro and result in reduced scattering and wound healing of gastric epithelial cells, thereby preventing bacterial infiltration of the epithelium. Conclusions/Significance: This study demonstrates that receptor-based virtual screening with a permissive (‘fuzzy’) pharmacophore model can help identify small bioactive agents for combating bacterial infection