Exploring Novel 1-Hydroxynaphthalene-2-Carboxanilides Based Inhibitors Against C-Jun N-Terminal Kinases Through Molecular Dynamic Simulation and WaterSwap Analysis

Cancer is a disease of mutation and lifestyle modifications. A large number of normal genes can transform normal cells to cancer cells due to their deregulations including overexpression and loss of expression. Signal transduction is a complex signaling process that involves multiple interactions and different functions. C-Jun N-terminal kinases (JNKs) is an important protein involved in signaling process. JNK mediated pathways can detect, integrate, and amplify various external signals that may cause alterations in gene expression, enzyme activities, and different cellular functions that affect cellular behavior like metabolism, proliferation, differentiation, and cell survival. In this study, we performed molecular docking protocol (MOE) to predict the binding interactions of some known anticancer 1-hydroxynaphthalene-2-carboxanilides candidates. A set of 10 active compounds was retrieved after initial screening on the basis of docking scores, binding energies, and number of interactions and was re-docked in the active site of JNK protein. The results were further validated through molecular dynamics simulation and MMPB/GBSA calculations. The active compounds 4p and 5 k were ranked on top. After computationally exploring interactions of 1-hydroxynaphthalene-2-carboxanilides with JNK protein, we believe compounds 4p and 5 k can serve as potential inhibitors of JNK protein. It is believed that the results of current research would help to develop novel and structurally diverse anticancer compounds that will be useful not only treat cancer but also for the medication for the other diseases caused by protein deregulation.

Discovery of novel inhibitor via molecular dynamics simulations against D-alanyl-D-alanine carboxypeptidase of Enterobacter cloacae

Antibiotics resistance by bacterial pathogens is a major concern to public health worldwide resulting in high health care costs and rising mortality. Subtractive proteomics prioritized D-alanyl-D-alanine carboxypeptidas (DacB) enzyme from Enterobacter cloacae ATCC 13047 as a potential candidate for drugs designing to block pathogen cell wall biosynthesis. Virtual screening of an antibacterial library against the target unraveled a hit compound (2-[(1-methylsulfonylpiperidin-3-yl)methyl]-6-(1H-pyrazol-4-yl) pyrazine) showing high affinity and stability with the target. The N-methyl-N-propyl-methanesulfonamide of the compound is seen as a closed affinity towards domain involving strong hydrogen bonds with Ser41, Lys44, Ser285, and Asn287. The 4-methyl-1H-pyrazole is posed towards the open cavity of domain I and II and formed hydrophobic and hydrophilic contacts. The system is highly stable with average carbon-alpha deviations of 1.69 Å over trajectories of 400-ns. Three vital residues projected: Arg437, Arg438 and Leu400 from enzyme pocket via Radial distribution function (RDF) assay, which actively engaged the inhibitor. Further confirmation is done by estimating binding free energies, which confirms the very low delta energy of -7.24 kcal/mol in Generalized Born (GB) method and -7.4363 kcal/mol in Poisson-Boltzmann (PB) method. WaterSwap calculations were performed that revealed the energies highly converged, an agreement on good system stability. Lastly, three DacB mutants were created to investigate the role of functional active residues and a decline in binding affinity of the residues was noticed. These computational results provide a gateway for experimentalists to further confirm their efficacy both in-vitro and in-vivo.Communicated by Ramaswamy H. Sarma.

Computational design of experimentally validated multi-epitopes vaccine against hepatitis E virus: An immunological approach

Hepatitis E virus (HEV) is one of the leading acute liver infections triggered by viral hepatitis. Patients infected with HEV usually recover and the annual death rate is negligible. Currently, there is no HEV licensed vaccine available globally. This study was carried out to design a multi-epitope HEV peptide-based vaccine by retrieving already experimentally validated epitopes from ViPR database leading to epitope prioritization. Epitopes selected as potential vaccine candidates were non-allergen, immunogenic, soluble, non-toxic and IFN gamma positive. The epitopes were linked together by AAY linkers and the linker EAAAK was used to join adjuvant with epitopes. Toll-like receptor (TLR)-4 agonist was used as an adjuvant to boost efficacy of the vaccine. Furthermore, codon optimization followed by disulfide engineering was performed to analyse the designed vaccine's structural stability. Computational modeling of the immune simulation was done to examine the immune response against the vaccine. The designed vaccine construct was docked with TLR-3 receptor for their interactions and then subjected to molecular dynamic simulations. The vaccine model was examined computationally towards the capability of inducing immune responses which showed the induction of both humoral and cell mediated immunity. Taken together, our study suggests an In-silico designed HEV based multi-epitope peptide-based vaccine (MEPV) that needs to be examined in the wet lab-based data that can help to develop a potential vaccine against HEV.

Ocular manifestations of HIV infection at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa

BACKGROUND

The pattern of HIV-associated eye disease has changed with ongoing advancements in highly active antiretroviral therapy (HAART). HIV-infected individuals now live longer, enabling us to observe the long-term effects of HIV and HAART on the eye. There are few recent studies on HIV-related ocular disease in sub-Saharan Africa.

OBJECTIVES

To describe the ocular manifestations of HIV in patients attending the Nthabiseng HIV clinic at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa.

METHODS

A cross-sectional study was conducted in 2021 and 2022 using convenience sampling of patients at the HIV clinic. The participants' clinical history was taken, their files were reviewed, and they underwent ocular examination. Correlation between eyes was managed by taking disease in one eye as the presence of disease in the participant. Descriptive statistics were used to summarise participant characteristics. Univariate and multivariate logistic regression models were used to assess the odds ratio (OR) of developing HIV-associated ocular diseases, and a p-value of <0.05 was used to define statistical significance.

RESULTS

There were 182 participants (139 females and 43 males), with a mean (standard deviation) age of 48.9 (10.6) years. The most common anterior segment diagnoses were conjunctival microangiopathy (34.6%), pinguecula (31.3%) and cataracts (30.2%), while the most common posterior segment finding was peripheral retinal scarring with features in keeping of previous cytomegalovirus retinitis (24.2%). Notably, only 1.1% of patients had HIV retinopathy. A CD4 count <200 cells/μL showed an increased OR for cataracts (OR 4.24; p=0.003) and any anterior segment diagnoses (OR 10.05; p=0.029), while a CD4 count ≥200 cells/μL showed an increased risk of conjunctival microangiopathy (OR 2.14; p=0.017).

CONCLUSION

With the advent of HAART, ocular manifestations of HIV are changing and the incidence of severe ocular opportunistic infections and HIV retinopathy has decreased precipitously. Although this study has shown that patients with a CD4 count <200 cells/μL are at increased risk of developing anterior ocular manifestations of HIV, including cataracts, these diseases are relatively innocuous or easily treatable. Routine ocular screening of HIV patients seems to be substantially less important now than it was in the pre-HAART era.

Stress perceived by drivers in public healthcare facilities in Negeri Sembilan during the first year of the COVID-19 pandemic

INTRODUCTION

Healthcare drivers, including ambulance drivers, were less concerned about health and safety during the COVID-19 pandemic, with not only the risk of COVID-19 infection but also a higher risk of prolonged states of alertness, stress, burnout, fatigue and road traffic accident. This study aimed to determine the prevalence of stress and its associated factors among healthcare drivers, especially during the COVID-19 pandemic.

MATERIALS AND METHODS

This study employs a crosssectional study design and utilises self-reported data obtained from locally validated personal stress inventory questionnaires. The data collection period spanned from August 1 to 31, 2020. The study sample consisted of 163 healthcare drivers affiliated with the Negeri Sembilan State Health Department. The Chi-square test and Fisher's exact test were the first used to determine the association between variables prior to conducting multiple logistic regression to predict the relationship between dependent and independent variables.

RESULTS

In COVID-19's first year, 7.4% (n = 12) of healthcare drivers reported perceived stress with ambulance drivers reporting more stress (10.6%; n = 5) than non-ambulance drivers (6.0%; n = 7). Simple statistical analysis identified perceived stress significantly associated with household income, smoking status and performing on-call. Further analysis by multiple logistic regression found that perceived stress was significantly related to smoking (aOR 19.9, 95% CI: 1.86-213.90), and performing on-call (aOR 8.69, 95% CI 1.21-62.28). Nevertheless, no association was found between perceived stress and age, ethnicity, marital status, education, household income, co-morbidities, driving assignment, employment duration, needing a part-time job or motor vehicle accident history.

CONCLUSION

The study found that the perceived stress amongst Malaysian healthcare drivers during the COVID-19 pandemic was relatively low. This could be due to fewer lifethreatening tasks, emergencies, assigned tasks and increase income due to overtime during the COVD-19 pandemic. The OSH team's efforts to provide consistent safety and health training, including stress management, may have contributed to the healthcare driver's ability to effectively manage the stressful circumstances encountered during the pandemic. In order to enhance salary competitiveness, employers should provide financial management education alongside subsidised housing and childcare provisions. Healthcare drivers who smoke should be taught different stress reduction techniques so that they can handle their stress in a healthy way.

Computational Design of a Chimeric Vaccine against Plesiomonas shigelloides Using Pan-Genome and Reverse Vaccinology

The swift emergence of antibiotic resistance (AR) in bacterial pathogens to make themselves adaptable to changing environments has become an alarming health issue. To prevent AR infection, many ways can be accomplished such as by decreasing the misuse of antibiotics in human and animal medicine. Among these AR bacterial species, Plesiomonas shigelloides is one of the etiological agents of intestinal infection in humans. It is a gram-negative rod-shaped bacterium that is highly resistant to several classes of antibiotics, and no licensed vaccine against the aforementioned pathogen is available. Hence, substantial efforts are required to screen protective antigens from the pathogen whole genome that can be subjected easily to experimental evaluations. Here, we employed a reverse vaccinology (RV) approach to design a multi-antigenic epitopes based vaccine against P. shigelloides. The complete genomes of P. shigelloides were retrieved from the National Center for Biotechnological Information (NCBI) that on average consist of 5226 proteins. The complete proteomes were subjected to different subtractive proteomics filters, and in the results of that analysis, out of total proteins, 2399 were revealed as non-redundant and 2827 as redundant proteins. The non-redundant proteins were further checked for subcellular localization analysis, in which three were localized in the extracellular matrix, eight were outer membrane, and 13 were found in the periplasmic membrane. All surface localized proteins were found to be virulent. Out of a total of 24 virulent proteins, three proteins (flagellar hook protein (FlgE), hypothetical protein, and TonB-dependent hemoglobin/transferrin/lactoferrin family receptor protein) were considered as potential vaccine targets and subjected to epitopes prediction. The predicted epitopes were further examined for antigenicity, toxicity, and solubility. A total of 10 epitopes were selected (GFKESRAEF, VQVPTEAGQ, KINENGVVV, ENKALSQET, QGYASANDE, RLNPTDSRW, TLDYRLNPT, RVTKKQSDK, GEREGKNRP, RDKKTNQPL). The selected epitopes were linked with each other via specific GPGPG linkers in order to design a multi-epitopes vaccine construct, and linked with cholera toxin B subunit adjuvant to make the designed vaccine construct more efficient in terms of antigenicity. The 3D structure of the vaccine construct was modeled ab initio as no appropriate template was available. Furthermore, molecular docking was carried out to check the interaction affinity of the designed vaccine with major histocompatibility complex (MHC-)I (PDB ID: 1L1Y), MHC-II (1KG0), and toll-like receptor 4 ((TLR-4) (PDB: 4G8A). Molecular dynamic simulation was applied to evaluate the dynamic behavior of vaccine-receptor complexes. Lastly, the binding free energies of the vaccine with receptors were estimated by using MMPB/GBSA methods. All of the aforementioned analyses concluded that the designed vaccine molecule as a good candidate to be used in experimental studies to disclose its immune protective efficacy in animal models.

Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine

Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world’s population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.

Computational Based Designing of a Multi-Epitopes Vaccine against Burkholderia mallei

The emergence of antibiotic resistance in bacterial species is a major threat to public health and has resulted in high mortality as well as high health care costs. Burkholderia mallei is one of the etiological agents of health care-associated infections. As no licensed vaccine is available against the pathogen herein, using reverse vaccinology, bioinformatics, and immunoinformatics approaches, a multi-epitope-based vaccine against B. mallei was designed. In completely sequenced proteomes of B. mallei, 18,405 core, 3671 non-redundant, and 14,734 redundant proteins were predicted. Among the 3671 non-redundant proteins, 3 proteins were predicted in the extracellular matrix, 11 were predicted as outer membrane proteins, and 11 proteins were predicted in the periplasmic membrane. Only two proteins, type VI secretion system tube protein (Hcp) and type IV pilus secretin proteins, were selected for epitope prediction. Six epitopes, EAMPERMPAA, RSSPPAAGA, DNRPISINL, RQRFDAHAR, AERERQRFDA, and HARAAQLEPL, were shortlisted for multi-epitopes vaccine design. The predicted epitopes were linked to each other via a specific GPGPG linker and the epitopes peptide was then linked to an adjuvant molecule through an EAAAK linker to make the designed vaccine more immunologically potent. The designed vaccine was also found to have favorable physicochemical properties with a low molecular weight and fewer transmembrane helices. Molecular docking studies revealed vaccine construct stable binding with MHC-I, MHC-II, and TLR-4 with energy scores of −944.1 kcal/mol, −975.5 kcal/mol, and −1067.3 kcal/mol, respectively. Molecular dynamic simulation assay noticed stable dynamics of the docked vaccine-receptors complexes and no drastic changes were observed. Binding free energies estimation revealed a net value of −283.74 kcal/mol for the vaccine-MHC-I complex, −296.88 kcal/mol for the vaccine-MHC-II complex, and −586.38 kcal/mol for the vaccine-TLR-4 complex. These findings validate that the designed vaccine construct showed promising ability in terms of binding to immune receptors and may be capable of eliciting strong immune responses once administered to the host. Further evidence from experimentations in mice models is required to validate real immune protection of the designed vaccine construct against B. mallei.

Pan-Genome-Assisted Computational Design of a Multi-Epitopes-Based Vaccine Candidate against Helicobacter cinaedi

Helicobacter cinaedi is a Gram-negative bacterium from the family Helicobacteraceae and genus Helicobacter. The pathogen is a causative agent of gastroenteritis, cellulitis, and bacteremia. The increasing antibiotic resistance pattern of the pathogen prompts the efforts to develop a vaccine to prevent dissemination of the bacteria and stop the spread of antibiotic resistance (AR) determinants. Herein, a pan-genome analysis of the pathogen strains was performed to shed light on its core genome and its exploration for potential vaccine targets. In total, four vaccine candidates (TonB dependent receptor, flagellar hook protein FlgE, Hcp family type VI secretion system effector, flagellar motor protein MotB) were identified as promising vaccine candidates and subsequently subjected to an epitopes' mapping phase. These vaccine candidates are part of the pathogen core genome: they are essential, localized at the pathogen surface, and are antigenic. Immunoinformatics was further applied on the selected vaccine proteins to predict potential antigenic, non-allergic, non-toxic, virulent, and DRB*0101 epitopes. The selected epitopes were then fused using linkers to structure a multi-epitopes' vaccine construct. Molecular docking simulations were conducted to determine a designed vaccine binding stability with TLR5 innate immune receptor. Further, binding free energy by MMGB/PBSA and WaterSwap was employed to examine atomic level interaction energies. The designed vaccine also stimulated strong humoral and cellular immune responses as well as interferon and cytokines' production. In a nutshell, the designed vaccine is promising in terms of immune responses' stimulation and could be an ideal candidate for experimental analysis due to favorable physicochemical properties.

Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach

Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.

Pan-Genome Analysis of Oral Bacterial Pathogens to Predict a Potential Novel Multi-Epitopes Vaccine Candidate

Porphyromonas gingivalis is a Gram-negative anaerobic bacterium, mainly present in the oral cavity and causes periodontal infections. Currently, no licensed vaccine is available against P. gingivalis and other oral bacterial pathogens. To develop a vaccine against P. gingivalis, herein, we applied a bacterial pan-genome analysis (BPGA) on the bacterial genomes that retrieved a total number of 4908 core proteins, which were further utilized for the identification of good vaccine candidates. After several vaccine candidacy analyses, three proteins, namely lytic transglycosylase domain-containing protein, FKBP-type peptidyl-propyl cis-trans isomerase and superoxide dismutase, were shortlisted for epitopes prediction. In the epitopes prediction phase, different types of B and T-cell epitopes were predicted and only those with an antigenic, immunogenic, non-allergenic, and non-toxic profile were selected. Moreover, all the predicted epitopes were joined with each other to make a multi-epitopes vaccine construct, which was linked further to the cholera toxin B-subunit to enhance the antigenicity of the vaccine. For downward analysis, a three dimensional structure of the designed vaccine was modeled. The modeled structure was checked for binding potency with major histocompatibility complex I (MHC-I), major histocompatibility complex II (MHC-II), and Toll-like receptor 4 (TLR-4) immune cell receptors which revealed that the designed vaccine performed proper binding with respect to immune cell receptors. Additionally, the binding efficacy of the vaccine was validated through a molecular dynamic simulation that interpreted strong intermolecular vaccine-receptor binding and confirmed the exposed situation of vaccine epitopes to the host immune system. In conclusion, the study suggested that the model vaccine construct has the potency to generate protective host immune responses and that it might be a good vaccine candidate for experimental in vivo and in vitro studies.

Epidemiology and risk factors of colorectal cancer in Syria: a single-center retrospective study

OBJECTIVE

Colorectal cancer represents the third most common malignancy and the second leading cause of cancer deaths worldwide. Many factors contribute to the risk of developing colorectal carcinoma including diet, lifestyle, age, and genetic abnormalities.  Recent findings have shown a considerable increase in the incidence rate of CRC in developing countries. However, there is little information regarding its incidence in the Middle East countries, including Syria. With our manuscript we aimed at presenting the first large epidemiological study regarding colorectal carcinoma incidence in Syria.

PATIENTS AND METHODS

We conducted a retrospective study on colorectal carcinoma cases at our institution from 2014 to 2018. The data include the cases that were diagnosed and recorded based on multiple parameters including gender, age, year of diagnosis, city of origin, and profession.

RESULTS

The number of colorectal cancer cases was 1,117 out of 13,589 cases of all malignant tumors recorded from 2014 to 2018, with an annual average incidence of 8.2%. There was a statistically significant difference in CRC cases according to age and gender. We also found a statistically significant difference according to physical activity and occupation.

CONCLUSIONS

These results demonstrate that risk factors related to colorectal cancer incidence in Syria mainly include male sex, age over 50 years old, and occupation with no physical activity.

OP0003 DOES IMMUNOSUPPRESSIVE THERAPY IMPROVE GASTROINTESTINAL SYMPTOMS IN PATIENTS WITH SYSTEMIC SCLEROSIS?

Background

The gastrointestinal (GI) tract is frequently affected in systemic sclerosis (SSc), leading to considerable morbidity and even mortality. While important progress has been made in the last years regarding treatment of SSc, there is no disease-modifying treatment available for SSc-related GI involvement.

Objectives

We aimed to identify, in an observational cohort study of real-life patients with SSc, an association between immunosuppressive therapy and the severity of GI symptoms, measured by the University of California at Los Angeles / Scleroderma Clinical Trial Consortium Gastro-Intestinal Tract instrument 2.0 (UCLA GIT 2.0).

Methods

We selected patients from our EUSTAR centre who met the 2013 ACR/EULAR classification criteria for SSc and had at least two visits with completed UCLA GIT 2.0 questionnaires, with an interval of 12±3 months between visits. We defined the first visit with a completed UCLA GIT 2.0 questionnaire as baseline visit. Immunosuppressive therapy was defined as exposure for at least 6 months between the two visits to at least one of the following drugs, regardless of indication: mycophenolate mofetil (MMF), cyclophosphamide, methotrexate, azathioprine, leflunomide, glucocorticoids (>10mg/d prednisone-equivalent), rituximab, tocilizumab, and abatacept. The study outcome was the UCLA GIT 2.0 score at the follow-up visit. We performed multivariable linear regression with this outcome as dependent variable and immunosuppressive therapy during follow-up, immunosuppressive therapy before baseline, baseline UCLA GIT 2.0 score and several baseline parameters selected by clinical judgment as potentially influencing GI symptoms, as independent variables. Multiple imputation was implemented to handle missing values.

Results

We included 209 patients. Baseline characteristics were: 82.3% female, median (IQR) age 59.0 (48.6, 68.2) years, median disease duration 6.0 (2.7, 12.5) years, 40 (19.1%) diffuse cutaneous SSc, median baseline UCLA GIT 2.0 score 0.19 (0.06, 0.43). Of these, 71 patients were exposed to immunosuppressive therapy during the observation period: 27/71 methotrexate, 1/71 cyclophosphamide, 17/71 MMF, 3/71 leflunomide, 3/71 azathioprine, 6/71 glucocorticoids >10mg/d, 16/34 rituximab, 18/34 tocilizumab. Patients on immunosuppressive therapy during the observation period had, compared to patients without such treatment, overall more severe SSc, higher prevalence of treatment with proton pump inhibitors, similar UCLA GIT 2.0 scores at baseline and at follow up and tendentially less severe GI symptoms at baseline and follow-up by medical history. In multivariable linear regression, immunosuppressive therapy, lower body mass index, longer disease duration and lower baseline UCLA GIT 2.0 score were significantly associated with lower (better) UCLA GIT 2.0 scores at follow-up (Table 1).

Table 1.Predictors of UCLA GIT 2.0 score at follow-upEstimates95% CIpAge0.002-0.001 – 0.0060.136Sex [male]-0.056-0.172 – 0.0610.347Disease duration-0.005-0.009 – -0.0000.030Body mass index0.0140.002 – 0.0250.017UCLA GIT 2.0 total score baseline0.6900.571 – 0.809<0.001Immunosuppressive therapy during observation period-0.119-0.228 – -0.0100.032Immunosuppressive therapy before baseline0.080-0.032 – 0.1920.160Modified Rodnan Skin Score-0.001-0.008 – 0.0070.860Forced vital capacity-0.001-0.004 – 0.0010.302Erythrocyte sedimentation rate0.003-0.001 – 0.0060.116Proton pump inhibitors-0.034-0.120 – 0.0520.435(Intercept)-0.120-0.531 – 0.2910.566

Baseline factors associated with the total UCLA GIT 2.0 score at the end of the observation period. Multiple linear regression model with imputation for missing variables. N=209 patients

Conclusion

Immunosuppressive treatment was associated with lower UCLA GIT 2.0 scores, which suggests potential effects of immunosuppressants on GI manifestations in patients with SSc. These results need verification in additional studies and randomised controlled clinical trials.

References

[1]Khanna D et al. Arthritis Rheum, 2009; 61: 1257-63.

Disclosure of Interests

Lea Stamm: None declared, Alexandru Garaiman: None declared, Norina Zampatti: None declared, Mike O. Becker Speakers bureau: Mepha, MSD, Novartis, GSK, Bayer and Vifor, Consultant of: Mepha, MSD, Novartis, GSK, Bayer and Vifor, Grant/research support from: Mepha, MSD, Novartis, GSK, Bayer and Vifor, Cosimo Bruni Speakers bureau: Actelion, Eli-Lilly, Boehringer-Ingelheim, Grant/research support from: Abbvie, EUSTAR, Gruppo Italiano Lotta alla Sclerodermia (GILS), SCTC, Rucsandra Dobrota Consultant of: Boehringer-Ingelheim, Grant/research support from: Iten-Kohaut Foundation, Muriel Elhai: None declared, Sherif Ismail Grant/research support from: EULAR scientific training grant for young fellows 2021, Suzana Jordan: None declared, Aurora Tatu: None declared, Oliver Distler Speakers bureau: Bayer, Boehringer Ingelheim, Janssen, Medscape, Consultant of: Abbvie, Acceleron, Alcimed, Amgen, AnaMar, Arxx, AstraZeneca, Baecon, Blade, Bayer, Boehringer Ingelheim, Corbus, CSL Behring, 4P Science, Galapagos, Glenmark, Horizon, Inventiva, Kymera, Lupin, Miltenyi Biotec, Mitsubishi Tanabe, MSD, Novartis, Prometheus, Roivant, Sanofi and Topadur, Grant/research support from: Kymera, Mitsubishi Tanabe, Boehringer Ingelheim, Carina Mihai Speakers bureau: Boehringer-Ingelheim, Mepha, MED Talks Switzerland, Consultant of: Boehringer-Ingelheim, Janssen, Grant/research support from: Boehringer-Ingelheim, Janssen, Roche.

Design of a Multi-Epitopes Vaccine against Hantaviruses: An Immunoinformatics and Molecular Modelling Approach

Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the current research, a reverse vaccinology approach was applied to design a multi-epitope-based vaccine against hantavirus. A set of 340 experimentally reported epitopes were retrieved from Virus Pathogen Database and Analysis Resource (ViPR) and subjected to different analyses such as antigenicity, allergenicity, solubility, IFN gamma, toxicity, and virulent checks. Finally, 10 epitopes which cleared all the filters used were linked with each other through specific GPGPG linkers to construct a multi-antigenic epitope vaccine. The designed vaccine was then joined to three different adjuvants-TLR4-agonist adjuvant, β-defensin, and 50S ribosomal protein L7/L12-using an EAAAK linker to boost up immune-stimulating responses and check the potency of vaccine with each adjuvant. The designed vaccine structures were modelled and subjected to error refinement and disulphide engineering to enhance their stability. To understand the vaccine binding affinity with immune cell receptors, molecular docking was performed between the designed vaccines and TLR4; the docked complex with a low level of global energy was then subjected to molecular dynamics simulations to validate the docking results and dynamic behaviour. The docking binding energy of vaccines with TLR4 is -29.63 kcal/mol (TLR4-agonist), -3.41 kcal/mol (β-defensin), and -11.03 kcal/mol (50S ribosomal protein L7/L12). The systems dynamics revealed all three systems to be highly stable with a root-mean-square deviation (RMSD) value within 3 Å. To test docking predictions and determine dominant interaction energies, binding free energies of vaccine(s)-TLR4 complexes were calculated. The net binding energy of the systems was as follows: TLR4-agonist vaccine with TLR4 (MM-GBSA, -1628.47 kcal/mol and MM-PBSA, -37.75 kcal/mol); 50S ribosomal protein L7/L12 vaccine with TLR4 complex (MM-GBSA, -194.62 kcal/mol and MM-PBSA, -150.67 kcal/mol); β-defensin vaccine with TLR4 complex (MM-GBSA, -9.80 kcal/mol and MM-PBSA, -42.34 kcal/mol). Finally, these findings may aid experimental vaccinologists in developing a very potent hantavirus vaccine.

An in silico study to unveil potential drugs and vaccine chimera for HBV capsid assembly protein: combined molecular docking and dynamics simulation approach

Humans are a major reservoir of the hepatitis B virus (HBV), therefore promising treatment and control vaccination strategies are needed to eradicate the virus. Though promising drugs and vaccines are available against HBV, still efforts are required to enrich the therapy options. Herein, the HBV assembly protein was explored to identify novel targets for future use against HBV. Computer-aided drug designing and immune-informatics techniques were employed for the identification of putative inhibitors and vaccine ensemble against HBV using capsid assembly protein. The identified drug molecule binds with high affinity to the active pocket of the protein, and several epitopes are scanned in the protein sequence. The drug molecule, besides being a good putative inhibitor, has acceptable drug-like properties. A multi-epitope vaccine is also constructed to overcome the limitations of weakly immunogenic epitopes. In contrast to the MHC II level, the set of predicted epitopes has been recognized to interact with significant numbers of HLA alleles of MHC I. Selected epitopes are extremely virulent, antigenic, nontoxic, nonallergic, have suitable affinity to bind with the prevailing DRB*0101 allele, and also spectacle 86% mediocre population coverage. A multi-epitope peptide-based vaccine chimera having 73 amino acids was designed. It emerged as substantially immunogenic, thermally stable, robust in producing cellular as well as humoral immune responses, and had competent physicochemical properties to analyze in vitro and in vivo studies. The capsid assembly protein is a in more stable nature in the presence of the drug molecule compared to the TLR3 receptor in the vaccine presence. These particulars were confirmed by exposing the docked molecules to absolute and relative binding free energy approaches of MMGBSA/PBSA. The purpose to investigate the interactions between the vaccine and a representative TLR3 immune receptor can reveal the intermolecular affinity and possible presentation mechanism of the vaccine by TLR3 to the host immune system. It was revealed that the vaccine is showing a very good affinity of binding for the TLR3 and forming a network of hydrophobic and hydrophilic interactions. Overall, the findings of this study are promising and might be useful for further experimental validations.

Salmonella-induced pulmonary and pericardial abscesses in a patient presenting with subacute cough

The non-typhoid Salmonella (NTS) species are commonly associated with gastroenteritis and other forms of intestinal disease. Thoraco-pulmonary infections are less commonly reported. We describe the case of a 66-year-old Qatari lady who presented with subacute cough. Chest imaging revealed multiple pulmonary and a pericardial cavitary lesion with air fluid levels. Bronchoalveolar lavage culture grew Salmonella species group D. The patient was treated with 4 weeks of appropriate antibiotics. Clinical and radiological improvement were documented on subsequent follow up. To our knowledge, this is the first reported case of pulmonary and pericardial salmonella abscesses in the state of Qatar.

SARS-CoV-2 associated pathogenesis, immune dysfunction and involvement of host factors: a comprehensive review

Infectious diseases, especially viral infections, have emerged as a major concern for public health in recent years. Recently emerged COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has been declared a pandemic by World Health Organization since March 2020. It was first identified in Wuhan, China, in December 2019 and has since claimed more than a million lives. Complicated symptoms are associated with rising incidence and fatality rates, while many of the vaccine candidates are in the final stages of clinical trials. This review encompasses a summary of existing literature on COVID-19, including the basics of the disease such as the causative agent's genome characterization, modes of transmission of the virus, pathogenesis, and clinical presentations like associated immune responses, neurological manifestations, the variety of host genetic factors influencing the disease and the vulnerability of different groups being affected by COVID-19.

Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii

Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.

Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance

Antimicrobial resistance (AMR) in bacterial pathogens is a major global distress. Due to the slow progress of antibiotics development and the fast pace of resistance acquisition, there is an urgent need for effective vaccines against such bacterial pathogens. In-silico approaches including pan-genomics, subtractive proteomics, reverse vaccinology, immunoinformatics, molecular docking, and dynamics simulation studies were applied in the current study to identify a universal potential vaccine candidate against the 18 multi-drug resistance (MDRs) bacterial pathogenic species from a WHO priority list. Ten non-redundant, non-homologous, virulent, and antigenic vaccine candidates were filtered against all targeted species. Nine B-cell-derived T-cell antigen epitopes which show a great affinity to the dominant HLA allele (DRB1*0101) in the human population were screened from selected vaccine candidates using immunoinformatics approaches. Screened epitopes were then used to design a multi-epitope peptide vaccine construct (MEPVC) along with β-defensin adjuvant to improve the immunogenic properties of the proposed vaccine construct. Molecular docking and MD simulation were carried out to study the binding affinity and molecular interaction of MEPVC with human immune receptors (TLR2, TLR3, TLR4, and TLR6). The final MEPVC construct was reverse translated and in-silico cloned in the pET28a(+) vector to ensure its effectiveness. This in silico construct is expected to be helpful for vaccinologists to assess its immune protection effectiveness in vivo and in vitro to counter rising antibiotic resistance worldwide.

Molecular screening of glycyrrhizin-based inhibitors against ACE2 host receptor of SARS-CoV-2

The interaction between SARS-CoV-2 Spike protein and angiotensin-converting enzyme 2 (ACE2) is essential to viral attachment and the subsequent fusion process. Interfering with this event represents an attractive avenue for the development of therapeutics and vaccine development. Here, a hybrid approach of ligand- and structure-based virtual screening techniques were employed to disclose similar analogues of a reported antiviral phytochemical, glycyrrhizin, targeting the blockade of ACE2 interaction with the SARS-CoV-2 Spike. A ligand-based similarity search using a stringent cut-off revealed 40 FDA-approved compounds in DrugBank. These filtered hits were screened against ACE2 using a blind docking approach to determine the natural binding tendency of the compounds with ACE2. Three compounds, deslanoside, digitoxin, and digoxin, were reported to show strong binding with ACE2. These compounds bind at the H1-H2 binding pocket, in a manner similar to that of glycyrrhizin which was used as a control. To achieve consistency in the docking results, docking calculations were performed via two sets of docking software that predicted binding energy as ACE2-Deslanoside (AutoDock, -10.3 kcal/mol and DockThor, -9.53 kcal/mol), ACE2-Digitoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.84 kcal/mol), and ACE2-Digoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.81 kcal/mol). The docking results were validated by running molecular simulations in aqueous solution that demonstrated the stability of ACE2 with no major conformational changes in the ligand original binding mode (~ 2 Å average RMSD). Binding interactions remained quite stable with an increased potential for getting stronger as the simulation proceeded. MMGB/PBSA binding free energies were also estimated and these supported the high stability of the complexes compared to the control (~ -50 kcal/mol net MMGB/PBSA binding energy versus ~ -30 kcal/mol). Collectively, the data demonstrated that the compounds shortlisted in this study might be subjected to experimental evaluation to uncover their real blockade capacity of SARS-CoV-2 host ACE2 receptor.

Development of a Novel Multi-Epitope Vaccine Against Crimean-Congo Hemorrhagic Fever Virus: An Integrated Reverse Vaccinology, Vaccine Informatics and Biophysics Approach

Crimean-Congo hemorrhagic fever (CCHF) is a highly severe and virulent viral disease of zoonotic origin, caused by a tick-born CCHF virus (CCHFV). The virus is endemic in many countries and has a mortality rate between 10% and 40%. As there is no licensed vaccine or therapeutic options available to treat CCHF, the present study was designed to focus on application of modern computational approaches to propose a multi-epitope vaccine (MEV) expressing antigenic determinants prioritized from the CCHFV genome. Integrated computational analyses revealed the presence of 9 immunodominant epitopes from Nucleoprotein (N), RNA dependent RNA polymerase (RdRp), Glycoprotein N (Gn/G2), and Glycoprotein C (Gc/G1). Together these epitopes were observed to cover 99.74% of the world populations. The epitopes demonstrated excellent binding affinity for the B- and T-cell reference set of alleles, the high antigenic potential, non-allergenic nature, excellent solubility, zero percent toxicity and interferon-gamma induction potential. The epitopes were engineered into an MEV through suitable linkers and adjuvating with an appropriate adjuvant molecule. The recombinant vaccine sequence revealed all favorable physicochemical properties allowing the ease of experimental analysis in vivo and in vitro. The vaccine 3D structure was established ab initio. Furthermore, the vaccine displayed excellent binding affinity for critical innate immune receptors: TLR2 (-14.33 kcal/mol) and TLR3 (-6.95 kcal/mol). Vaccine binding with these receptors was dynamically analyzed in terms of complex stability and interaction energetics. Finally, we speculate the vaccine sequence reported here has excellent potential to evoke protective and specific immune responses subject to evaluation of downstream experimental analysis.

Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology

Mycobacteroides abscessus (Previously Mycobacterium abscessus) is an emerging microorganism of the newly defined genera Mycobacteroides that causes mainly skin and tissue diseases in humans. The recent availability of total 34 fully sequenced genomes of different strains belonging to this species has provided an opportunity to utilize this genomics data to gain novel insights and guide the development of specific antimicrobial therapies. In the present study, we collected collectively 34 complete genome sequences of M. abscessus from the NCBI GenBank database. Pangenome analysis was conducted on these genomes to understand the genetic diversity and to obtain proteins associated with its core genome. These core proteins were then subjected to various subtractive filters to identify potential antigenic targets that were subjected to multi-epitope vaccine design. Our analysis projected the open pangenome of M. abscessus containing 3443 core genes. After applying various stepwise filtration steps on the core proteins, a total of four potential antigenic targets were identified. Utilizing their constituent CD4 and CD8 T-cell epitopes, a multi-epitope based subunit vaccine was computationally designed. Sequence-based analysis as well as structural characterization revealed the immunological effectiveness of this designed vaccine. Further molecular docking, molecular dynamics simulation and binding free energy estimation with Toll-like receptor 2 indicated strong structural associations of the vaccine with the immune receptor. The promising results are encouraging and need to be validated by additional wet laboratory studies for confirmation.

Rational design of potent anti-COVID-19 main protease drugs: An extensive multi-spectrum in silico approach

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a novel coronavirus and the etiological agent of global pandemic coronavirus disease (COVID-19) requires quick development of potential therapeutic strategies. Computer aided drug design approaches are highly efficient in identifying promising drug candidates among an available pool of biological active antivirals with safe pharmacokinetics. The main protease (M^Pro) enzyme of SARS-CoV-2 is considered key in virus production and its crystal structures are available at excellent resolution. This marks the enzyme as a good starting receptor to conduct an extensive structure-based virtual screening (SBVS) of ASINEX antiviral library for the purpose of uncovering valuable hits against SARS-CoV-2 M^Pro. A compound hit (BBB_26580140) was stand out in the screening process, as opposed to the control, as a potential inhibitor of SARS-CoV-2 M^Pro based on a combined approach of SBVS, drug likeness and lead likeness annotations, pharmacokinetics, molecular dynamics (MD) simulations, and end point MM-PBSA binding free energy methods. The lead was further used in ligand-based similarity search (LBSS) that found 33 similar compounds from the ChEMBL database. A set of three compounds (SCHEMBL12616233, SCHEMBL18616095, and SCHEMBL20148701), based on their binding affinity for M^Pro, was selected and analyzed using extensive MD simulation, hydrogen bond profiling, MM-PBSA, and WaterSwap binding free energy techniques. The compounds conformation with M^Pro show good stability after initial within active cavity moves, a rich intermolecular network of chemical interactions, and reliable relative and absolute binding free energies. Findings of the study suggested the use of BBB_26580140 lead and its similar analogs to be explored in vivo which might pave the path for rational drug discovery against SARS-CoV-2 M^Pro.

123 Use of The Induction Mobile Application in A Busy General Surgery Department

Introduction

Contacting other hospital professionals, or accessing local guidelines is a common task for surgeons, which is usually facilitated by inefficient switchboard and intranet systems. Induction is a mobile application which includes crowd-sourced hospital directories and local guidelines, which could theoretically expedite these tasks. To assess this, we undertook a QIP within the General Surgery department using a bespoke Induction group.

Method

A private Induction group was created with the features mentioned above. We audited Induction against local trust processes (Switchboard and Intranet Trust Guidelines). We estimated cost saving using the 2019 junior doctor pay-scales. We also surveyed our department to evaluate their experiences using the application with a Likert scale.

Results

The timesaving from using Induction compared to current methods was on average 9.93 hours/week accumulated by 16 staff members, giving an estimated cost saving of £10,636.54/year. In a qualitative analysis, respondents rated Induction 4.8/5 for speed and 3.4/5 for completeness of directory, compared to 1.5/5 and 4.5/5 respectively for switchboard. Regarding accessing clinical guidelines, respondents rated the app as ‘easier’ and ‘quicker’ than the intranet.

Conclusions

We have demonstrated significant time and cost-savings using Induction compared to standard practices. Our QIP provides a replicable model to increase efficiency in surgery departments.

Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme

With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. The purpose of the current study was to predict a library of phytochemicals derived from diverse plant families with high binding affinity to SARS-CoV-2 helicase (Nsp13) enzyme. High throughput virtual screening of the Medicinal Plant Database for Drug Design (MPD3) database was performed on SARS-CoV-2 helicase using AutoDock Vina. Nilotinib, with a docking value of -9.6 kcal/mol, was chosen as a reference molecule. A compound (PubChem CID: 110143421, ZINC database ID: ZINC257223845, eMolecules: 43290531) was screened as the best binder (binding energy of -10.2 kcal/mol on average) to the enzyme by using repeated docking runs in the screening process. On inspection, the compound was disclosed to show different binding sites of the triangular pockets collectively formed by Rec1A, Rec2A, and 1B domains and a stalk domain at the base. The molecule is often bound to the ATP binding site (referred to as binding site 2) of the helicase enzyme. The compound was further discovered to fulfill drug-likeness and lead-likeness criteria, have good physicochemical and pharmacokinetics properties, and to be non-toxic. Molecular dynamic simulation analysis of the control/lead compound complexes demonstrated the formation of stable complexes with good intermolecular binding affinity. Lastly, affirmation of the docking simulation studies was accomplished by estimating the binding free energy by MMPB/GBSA technique. Taken together, these findings present further in silco investigation of plant-derived lead compounds to effectively address COVID-19.

A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum

The nucleocapsid (N) protein of SARS-COV-2, a virus responsible for the current COVID-19 pandemic, is considered a potential candidate for the design of new drugs and vaccines. The protein is central to several critical events in virus production, with its highly druggable nature and rich antigenic determinants making it an excellent anti-viral biomolecule. Docking-based virtual screening using the Asinex anti-viral library identified binding of drug molecules at three specific positions: loop 1 region, loop 2 region and β-sheet core pockets, the loop 2 region being the most common binding and stable site for the bulk of the molecules. In parallel, the protein was characterized by vaccine design perspective and harboured three potential B cell-derived T cell epitopes: PINTNSSPD, GVPINTNSS, and DHIGTRNPA. The epitopes are highly antigenic, virulent, non-allergic, non-toxic, bind with good affinity to the highly prevalent DRB*0101 allele and show an average population coverage of 95.04%. A multi-epitope vaccine ensemble which was 83 amino acids long was created. This was highly immunogenic, robust in generating both humoral and cellular immune responses, thermally stable, and had good physicochemical properties that could be easily analyzed in in vivo and in vitro studies. Conformational dynamics of both drug and vaccine ensemble with respect to the receptors are energetically stable, shedding light on favourable conformation and chemical interactions. These facts were validated by subjecting the complexes to relative and absolute binding free energy methods of MMGB/PBSA and WaterSwap. A strong agreement on the system stability was disclosed that supported ligand high affinity potential for the receptors. Collectively, this work sought to provide preliminary experimental data of existing anti-viral drugs as a possible therapy for COVID-19 infections and a new peptide-based vaccine for protection against this pandemic virus.

Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging health concern due to its high mortality rate of 35%. At present, no vaccine is available to protect against MERS-CoV infections. Therefore, an in silico search for potential antigenic epitopes in the non-redundant proteome of MERS-CoV was performed herein. First, a subtractive proteome-based approach was employed to look for the surface exposed and host non-homologous proteins. Following, immunoinformatics analysis was performed to predict antigenic B and T cell epitopes that were used in the design of a multi-epitopes peptide. Molecular docking study was carried out to predict vaccine construct affinity of binding to Toll-like receptor 3 (TLR3) and understand its binding conformation to extract ideas about its processing by the host immune system. We identified membrane protein, envelope small membrane protein, non-structural protein ORF3, non-structural protein ORF5, and spike glycoprotein as potential candidates for subunit vaccine designing. The designed multi-epitope peptide then linked to β-defensin adjuvant is showing high antigenicity. Further, the sequence of the designed vaccine construct is optimized for maximum expression in the Escherichia coli expression system. A rich pattern of hydrogen and hydrophobic interactions of the construct was observed with the TLR3 allowing stable binding of the construct at the docked site as predicted by the molecular dynamics simulation and MM-PBSA binding energies. We expect that the panel of subunit vaccine candidates and the designed vaccine construct could be highly effective in immunizing populations from infections caused by MERS-CoV and could possible applied on the current pandemic COVID-19.

Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

The COVID-19 pandemic caused by SARS-CoV-2 is a public health emergency of international concern and thus calling for the development of effective and safe therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for a vaccine, antibodies, and inhibitors development because of the many roles it plays in attachment, fusion and entry into the host cell. In the present investigation, we characterized the SARS-CoV-2 spike glycoprotein by immunoinformatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in aqueous milieu aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel axial frequency distribution (AFD) analytical tool. Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus could be considered in experimental studies.

Understanding the structure of a country’s health service providers for defence health engagement

There are a variety of structural and systems frameworks for describing the building blocks of country’s public health and health systems. In this paper, we propose a conceptual framework for a holistic view of a country’s health service providers in order to inform the plan for Defence Health Engagement activities with partner countries. This includes all potential government ministries involved in healthcare provision, the independent, private sector and the non-government organisation/charity sector. The framework provides a visualisation to support the analysis of a country’s health services providers. We propose that recognising and analysing the different contributions of all these national health providers is essential for understanding the wider political economy of a nation’s health systems. This can inform a plan of Defence Health Engagement for capacity building in crisis response, development and health systems strengthening.

Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis

The global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, has resulted in a negative impact on human health and on social and economic activities worldwide. Researchers around the globe need to design and develop successful therapeutics as well as vaccines against the novel COVID-19 disease. In the present study, we conducted comprehensive computer-assisted analysis on the spike glycoprotein of SARS-CoV-2 in order to design a safe and potent multiepitope vaccine. In silico epitope prioritization shortlisted six HLA I epitopes and six B-cell-derived HLA II epitopes. These high-ranked epitopes were all connected to each other via flexible GPGPG linkers, and at the N-terminus side, the sequence of Cholera Toxin β subunit was attached via an EAAAK linker. Structural modeling of the vaccine was performed, and molecular docking analysis strongly suggested a positive association of a multiepitope vaccine with Toll-like Receptor 3. The structural investigations of the vaccine-TLR3 complex revealed the formation of fifteen interchain hydrogen bonds, thus validating its integrity and stability. Moreover, it was found that this interaction was thermodynamically feasible. In conclusion, our data supports the proposition that a multiepitope vaccine will provide protective immunity against COVID-19. However, further in vivo and in vitro experiments are needed to validate the immunogenicity and safety of the candidate vaccine.

Prevalence of Cryptosporidium spp. infection among children admitted to Hospital Tengku Ampuan Afzan

INTRODUCTION

Cryptosporidium spp. is identified as an important cause of diarrhoeal morbidity and mortality worldwide particularly in children below five years of age and immunocompromised individuals. Infections are present among cattle and humans. Until now, there is no report on its prevalence in humans in Kuantan. The aim of this study is to record the prevalence and associated risk factors of Cryptosporidium spp. infection among children admitted to Hospital Tengku Ampuan Afzan (HTAA), Kuantan.

METHODS

This is a cross-sectional study conducted among children admitted to the Paediatrics ward in HTAA between December 2017 and May 2018. Faecal samples were examined using wet smear and Modified Ziehl-Neelsen (MZN) staining techniques. Data on demography and hygiene practices was collected using a pretested questionnaire, and analysed using SPSS version 22.

RESULTS

One hundred thirty five children (95.6% were of Malay ethnicity) were included in the study. The overall prevalence of Cryptosporidium spp. infection was 25.2%. The prevalence was slightly higher in females (28.1%) than males (23.1%). The prevalence was higher than expected. This study showed that some risk factors namely children's age and trash disposal methods were significantly associated with Cryptosporidium spp. infection (p<0.05).

CONCLUSION

Higher prevalence could possibly be due to an outbreak of this infection or until now undetected.

Intranasal inoculation of recombinant DNA vaccine ABA392 against haemorrhagic septicaemia disease

We evaluate the efficacy of recombinant DNA vaccine ABA392 against haemorrhagic septicaemia infection through intranasal administration route by targeting the mucosal immunity. The DNA vaccine was constructed and subjected to animal study using the Sprague Dawley (SD) rat. The study was divided into two major parts: (i) active and (ii) passive immunization studies, involving 30 animals for each part. Each group was then divided into five test groups: two test samples G1 and G2 with 50 and 100 µg ml^-1 purified DNA vaccine; one positive control G5 with 10⁶  CFU per ml formalin-killed PMB2; and two negative controls, G3 and G4 with normal saline and pVAX1 vector. Both studies were conducted for the determination of immunogenicity by total white blood cell count (TWBC), indirect ELISA and histopathological changes for the presence of the bronchus-associated lymphoid tissue (BALT). Our findings demonstrate that TWBC, IgA and IgG increased after each of the three vaccination regimes: groups G1, G2 and G5. Test samples G1 and G2 showed significant differences (P < 0·05) compared to the negative controls, G3 and G4, but no significant differences from the positive control G5. Groups G1, G2 and G5 showed more formation of BALT compared to the negative controls, G3 and G4. Our results show that intranasal inoculation of recombinant DNA vaccine ABA392 can provoke mucosal immunity which makes it a potential prophylactic against HS. SIGNIFICANCE AND IMPACT OF THE STUDY: New approach of combating haemorrhagic septicaemia disease among bovines by recombinant DNA vaccine is crucial to overcome the loss of edible products from the infected bovines. DNA vaccine can potentially serve as a better immunogen which would elicit both cellular and humoral immunity, and it is also stable for its molecular reproduction. This research report demonstrates an effective yet simple way of administering the DNA vaccine via the intranasal route in rats, to provoke the mucosal immunity through the development of immunoglobulins IgA, IgG and bronchus-associated lymphoid tissue which guard as the first-line defence at the host's mucosal lining.

Effect And Predictive Value Of Routine Preoperative Laboratory Testing For Endoscopic Retrograde Cholangiopancreatography

BACKGROUND AND AIMS

Several studies and guidelines are questioning routine preoperative laboratory tests in surgical and endoscopic procedures. Their effect in endoscopic retrograde cholangiopancreatography is not currently known. This study was carried out to evaluate the risk of adverse effects in endoscopic retrograde cholangiopancreatography and their association with preoperative lab tests.

MATERIALS AND METHODS

A single-center, prospective observational study on all 956 patients undergoing 1196 endoscopic retrograde cholangiopancreatographies in the Endoscopy Unit of Helsinki University Central Hospital from 1 March 2012 to 28 February 2013. Routine preoperative laboratory test results (basic blood count, creatinine, potassium, sodium, international normalized ratio/thromboplastin time, and amylase), health status, medication, and demographic information of all patients were analyzed in relation to adverse effects related to endoscopic retrograde cholangiopancreatography and procedural sedation.

RESULTS

Multivariate analysis showed post-endoscopic retrograde cholangiopancreatography pancreatitis (43 cases, 3.6%) to have no association with abnormal routine preoperative laboratory tests. Respiratory depression caused by sedation (128 cases, 11%) was not associated with abnormal routine preoperative laboratory tests, and anemia was found to be a slightly protecting factor. Cardiovascular depression caused by sedation was associated with thrombocytopenia (odds ratio = 1.87, p = 0.025) and, in male patients, hyponatremia (odds ratio = 3.66, p < 0.001). Incidence of other adverse effects was too low for statistical analysis.

CONCLUSION

Routine universal preoperative lab testing was not found to be successful in predicting adverse effects in endoscopic retrograde cholangiopancreatography procedures. Laboratory testing should be done focusing on each patient's individual needs.

Encapsulation of Bacillus salmalaya 139SI using double coating biopolymer technique

Sustainable crop production for a rapidly growing human population is one of the current challenges faced by the agricultural sector. However, many of the chemical agents used in agriculture can be hazardous to humans, non-targeted organism and environment. Plant growth promoting rhizobacteria have demonstrated a role in promoting plant growth and health under various stress conditions including disease. Unfortunately, bacterial viability degrades due to temperature and other environmental factors (Bashan et al., Plant Soil 378: 1-33, 2014). Encapsulation of bacteria into core-shell biopolymers is one of the promising techniques to overcome the problem. This study deals with the encapsulation of Bacillus salmalaya 139SI using simple double coating biopolymer technique which consist of brown rice protein/alginate and 0·5% low molecular weight chitosan of pH 4 and 6. The influence of biopolymer to bacteria mass ratio and the chitosan pH on the encapsulation process, physic-chemical, morphology and bioactivity properties of encapsulated B. salmalaya 139SI have been studied systematically. Based on the analysis of physico-chemical, morphology and bioactivity properties, B. salmalaya 139S1 encapsulated using double coating encapsulation technology has promising viability pre- and postfreeze-drying with excellent encapsulation yields of 99·7 and 89·3% respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: The need of a simple yet effective way of encapsulating plant growth promoting rhizobacteria is crucial to further improve their benefits to global sustainable agriculture practice. Effective encapsulation allows for protection, controlled release and function of the micro-organism, as well as providing a longer shelf life for the product. This research report offers an innovative yet simple way of encapsulating using double coating technology with environmentally friendly biopolymers that could degrade and provide nutrients when in soil. Importantly, the bioactivity of the bacteria is maintained upon encapsulation.

An Empirical Study of Service Quality and Customer Satisfaction of Malaysian Air Passenger

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Summary of the NACI Update on Herpes Zoster Vaccines

BACKGROUND

Steep increases in herpes zoster (HZ) incidence, hospitalization due to HZ and the risk of post-herpetic neuralgia as a complication of HZ occur in people over 50 years of age. Two HZ vaccines are currently authorized for use in those 50 years of age and older in Canada: a live attenuated zoster vaccine (LZV) authorized in 2008; and a recombinant subunit vaccine (RZV) authorized in October 2017.

OBJECTIVES

To review current evidence and develop guidance on whether the previously authorized LZV (Zostavax®) and/or the recently authorized RZV (Shingrix®) vaccine should be offered to Canadians 50 years of age and older: 1) at a population-level, in publicly funded immunization programs; and 2) at an individual-level, to individuals wishing to prevent HZ, or by clinicians wishing to advise individual patients about preventing HZ.

METHODS

The National Advisory Committee on Immunization (NACI) Herpes Zoster Working Group developed a predefined search strategy to identify all eligible studies, assessed their quality, and summarized and analyzed the findings. A Cost Utility Analysis of LZV and RZV was also conducted from a health care system perspective. Recommendations were proposed according to NACI's evidence-based process. The strength of these recommendations was defined, and the Grade of evidence supporting them was identified. In light of the evidence, the recommendations were then considered and approved by NACI.

RESULTS

Five recommendations were developed for public health and individual-level decision-making. 1) RZV should be offered to populations/individuals >50 years of age without contraindications (Strong NACI Recommendation, Grade A evidence). 2) RZV should be offered to populations/individuals >50 years of age without contraindications who have previously been vaccinated with LZV (Strong NACI Recommendation, Grade A evidence). Re-immunization with two doses of RZV may be considered one year after LZV (Discretionary NACI Recommendation, Grade I evidence). 3) RZV should be offered to populations/individuals >50 years of age without contraindications who have had a previous episode of HZ (Strong NACI Recommendation, Grade B evidence). Immunization with two doses of RZV may be considered one year after the HZ episode (Discretionary NACI Recommendation, Grade I evidence). 4) LZV may be considered for immunocompetent populations/individuals >50 years of age without contraindications when RZV is contraindicated, unavailable or inaccessible (Discretionary NACI Recommendation, Grade A evidence). 5) RZV (not LZV) may be considered in immunocompromised adults >50 years of age on a case-by-case basis (Discretionary NACI Recommendation, Grade I evidence).

CONCLUSION

Both vaccines have been shown to be safe and immunogenic and to reduce the incidence of HZ and post-herpetic neuralgia. Vaccine efficacy of LZV against HZ decreases with age at, and time since vaccination. The vaccine efficacy of RZV remains higher and appears to decline more slowly than vaccine efficacy of LZV across all age groups. Both vaccines are cost-effective in those 50 years of age and older compared with no vaccination, especially in those 65-79 years of age. RZV is more cost-effective than LZV.

HIV-2 Infection in Malaysia: Current situation and the use of in-house real-time reverse transcription PCR for HIV-2

HIV-2 surveillance has been carried out in Malaysia for more than 25 years ago. Tests to discriminate HIV-1 and HIV-2 are available but the options of test are limited and the need to develop a new in-house HIV-2 real-time reverse transcription PCR (RT-PCR) is crucial. A study was done on 29 samples from hospitals in Malaysia which were found to be positive screening for HIV-2 antibodies by the commercial Western Blot assay. These samples were further tested by a Western Blot assay that detects specific antibodies to HIV-2. Detection of HIV-2 genome was then performed by using a commercial kit. Fifteen samples were evaluated by using in-house real-time RT-PCR for HIV-2. Ninety-three percent (27/29) of samples have positive results for HIV-2 on HIV-2 Western Blot with only 2 samples showing indeterminate results. All samples showed negative results for HIV-2 genomes by using a PCR commercial kit and the 15 samples that were subjected to our in-house real-time RT-HIV-2 PCR were also tested negative for HIV-2 RNA. Results of HIV-2 Western Blot did not reflect the actual positivity as both HIV-1 and HIV-2 antibodies may cross-react with either viral proteins. None of the samples was confirmed positive for HIV-2 by the commercial and in-house real-time RTPCR. In-house real-time RT-HIV-2 PCR assay can be further used to confirm the presence of HIV-2 genome. Up to the year 2015, Malaysia is still free from HIV-2 infection.

A clinicopathologic study of 173 odontogenic tumours in Northern Peninsular Malaysia (2007-2014)

INTRODUCTION

The objectives of this study were to analyse, compare and contrast the demographic, clinical and pathological data of odontogenic tumours seen at a regional oral pathology centre in the Northern part of Peninsular Malaysia with other international data as an aid to clinicians in diagnosing odontogenic tumours.

MATERIALS AND METHODS

This was a descriptive, retrospective study of odontogenic tumours diagnosed from January 2007 to December 2014 at this centre. The odontogenic tumours were classified using the 2005 World Health Organization classification system.

RESULTS

Among 2,733 biopsy specimens, 173 cases were diagnosed as odontogenic tumours (6.3%), of which 171 (98.8%) are benign and 2 (1.2%) are malignant. The most frequently encountered tumour was ameloblastoma (n=96, 55.5%), followed by keratocystic odontogenic tumour (KCOT) (n=38, 22.0%) and odontomas (n=16, 9.2%). Malignant tumours accounted for 1.2% of the tumours. Most ameloblastomas and KCOTs affected the mandible preferentially. The mean age was 33.5 (± 17.8) years and 64.7% of patients were in the age group of 10 to 39. Odontogenic tumours were slightly more common in males, with a male to female ratio of 1.4:1.

CONCLUSION

The findings of this study are similar to the other studies in Asia in which the most common tumour encountered is the ameloblastoma, followed by KCOT. The most common signs and symptoms are pain and swelling, while paraesthesia and root resorption are less frequently reported. Such clinical and radiographic features should alert the clinician of a possible odontogenic tumour and though rare, malignant tumours should also be included in the differential diagnoses.

Change in Mallampati class during labor: Hypertensive versus normotensive parturients

BACKGROUND

Mallampati class has been shown to increase during labor. There are no prospective studies evaluating airway changes in hypertensive parturients during labor. The aim of our study was to observe the frequency of change in Mallampati class during labor in hypertensive compared to normotensive parturients.

METHODS

In this prospective observational cohort study, 60 parturients were enrolled and divided into two groups of 30 each: hypertensive parturients and normotensive parturients. The Mallampati class was evaluated in each parturient at two points; during early labor (cervical dilation 1-3 cm and regular contractions) taken as T1 and at 20 minutes after delivery taken as T2. The change in Mallampati class from T1 to T2 was compared between the two groups. Post-stratification chi-square test was applied and P value <.05 was considered as significant.

RESULTS

The change in Mallampati class was significantly more frequent in hypertensive group as compared to normotensive group [80% (24/30) vs 46.7% (14/30); P = .002]. Overall, an increase in Mallampati class during labor was found with statistically significant difference between the hypertensive and normotensive group [80% (24/30) vs 42.9% (12/28); P = .004]. The risk of increase in Mallampati class was 2 times higher in hypertensive women as compared to normotensive 2.44; 95% CI: 1.19 to 5.02].

CONCLUSION

Mallampati class showed 2-fold increase in hypertensive compared to normotensive parturients during labor; requiring additional caution during airway management.

An insight into frequency and predictors leading psychiatric patients to visit faith healers: A hospital-based cross-sectional survey, Karachi, Pakistan

BACKGROUND

Psychiatric illnesses have recently escalated in numbers, with patients resorting to various forms of healthcare providers, including faith healers. This delays early psychiatric treatment, resulting in further mental health deterioration of the patient. Various factors impact the mode of treatment preferred by psychiatric patients.

AIMS

To determine the frequency of psychiatric patients visiting faith healers, presenting at the outpatient department of Liaquat National Hospital, Karachi, Pakistan, and to explore the predictors that direct them toward visiting faith healers.

METHODS

This cross-sectional survey was conducted using a semi-structured pre-tested questionnaire, employing a total of 219 male and female psychiatric patients. Patients were recruited through non-random consecutive sampling technique. SPSS 18 was used for statistical analysis.

RESULTS

About 32% of the patients had visited a faith healer in their lifetime. Frequency of current visitors declined; the most frequent reason being stated was no relief from their treatment. Students, patients of upper middle class and those coming for initial visit to a psychiatrist were more likely to visit a faith healer. Patients who knew of someone previously visiting a faith healer were less likely to have visited a faith healer.

CONCLUSION

This study highlights the importance of a multisectoral approach to dealing with psychiatric patients to help in bridging the treatment gap in mental health.

Evaluation of reference values of standard semen parameters in fertile Egyptian men

The reference values of human semen, published in the WHO's latest edition in 2010, were lower than those previously reported. The objective of this study was to evaluate reference values of standard semen parameters in fertile Egyptian men. This cross-sectional study included 240 fertile men. Men were considered fertile when their wives had recent spontaneous pregnancies with time to pregnancy (TTP) ≤12 months. The mean age of fertile men was 33.8 ± 0.5 years (range 20-55 years). The 5th percentiles (95% confidence interval) of macroscopic semen parameters were 1.5 ml for volume and 7.2 for pH. The 5th percentiles of microscopic parameters were 15 million/ml for sperm concentration, 30 million per ejaculate for total sperm count, 50% for total motility, 40% for progressive motility, 62% for vitality, 4% for normal sperm forms and 0.1 million/ml for seminal leucocyte counts. In conclusion, fertile Egyptian men had higher reference values of sperm total motility, progressive motility and vitality, and lower reference values for total sperm counts as compared to those determined by the latest edition of the WHO laboratory manual in 2010. Other semen parameters were identical to those defined by the WHO 2010 manual.