Proteome Exploration of Human Coronaviruses for Identifying Novel Vaccine Candidate: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach.

BACKGROUND: The SARS-CoV-2 has been responsible for infecting more than 613,615,658 people in 222 countries by September 11, 2022, of which 6,516,076 have died. COVID-19 was introduced by World Health Organization as a global concern and a pandemic disease due to its prevalence. OBJECTIVE: Developing preventive or therapeutic medications against 2019-nCoV is an urgent need, and has been deemed as a high priority among scientific societies; in this regard, the production of effective vaccines is one of the most significant and high-priority requirements. Because of costly and time-consuming process of vaccine design, different immunoinformatics methods have been developed. METHODS: At the beginning of vaccine design, the proteome study is essential. In this investigation, the whole human coronavirus proteome was evaluated using the proteome subtraction strategy. Out of 5945 human coronavirus proteins, five new antigenic proteins were selected by analyzing the hierarchical proteome subtraction, and then their various physicochemical and immunological properties were investigated bioinformatically. RESULTS: All five protein sequences are antigenic and non-allergenic proteins; moreover, the spike protein group, including spike glycoprotein (E2) (Peplomer protein), spike fragment and spike glycoprotein fragment, showed acceptable stability, which can be used to design new vaccines against human coronaviruses. CONCLUSION: The selected peptides and the other proteins introduced in this study (HE, orf7a, SARS_X4 domain-containing protein and protein 8) can be employed as a suitable candidate for developing a novel prophylactic or therapeutic vaccine against human coronaviruses.

Challenge of Politico-Economic Sanctions on Pharmaceutical Procurement in Iran: A Qualitative Study.

Background: Politico-economic sanctions over the recent years have led to significant challenges in the pharmaceutical supply chain (PSC) in Iran. Given the importance of the chain's resilience for the health system and its impact on accessibility, equity, and public health, this study was conducted to determine the major challenges facing pharmaceutical procurement in Iran after the imposition of these sanctions. Methods: This study was a qualitative research with a content analysis approach conducted in 2019. Eighteen policymakers and administrative managers in food and drug administration of two Iranian Medical Universities and Iran's Ministry of Health were included in the present study via snowball sampling and semi-structured interview. The data were analyzed using the framework analysis of MAX QDA10. Results: Five main themes and 15 sub-themes were identified, which addressed pharmaceutical supply chain challenges under politico-economic sanctions. These included the challenges in financing, purchasing, importing, and manufacturing domestic products in addition to storing and distributing medicines, along with challenges facing the general public, particularly patients. Conclusion: The results revealed that pharmaceuticals are not immune to politico-economic sanctions, although they are not directly subjected to them. Sanctions, similar to any economic crisis, can affect public health and limit their access to healthcare. Identifying supply chain challenges and planning to address them could help policymakers find solutions to enhance PSC resilience in the future.

Design of a multi-epitope protein vaccine against herpes simplex virus, human papillomavirus and Chlamydia trachomatis as the main causes of sexually transmitted diseases.

Sexually transmitted diseases (STDs) have a profound effect on reproductivity and sexual health worldwide. According to world health organization (WHO) 375 million new case of STD, including chlamydia trachomatis (chlamydia), Neisseria gonorrhoeae, HSV, HPV has been reported in 2016. More than 30 diverse pathogenesis have identified to be transmitted through sexual intercourse. Of these, viral infections (hepatitis B, herpes simplex virus (HSV or herpes), HIV, and human papillomavirus (HPV) are incurable. However, symptoms caused by the incurable viral infections can be alleviated through treatment. Antimicrobial resistance (AMR) of sexually transmitted infections (STIs) to antibiotics has increased recent years, in this regard, vaccination is proposed as an important strategy for prevention or treatment of STDs. Vaccine against HPV 16 and 18 suggests a new approach for controlling STDs but until now, there is no prophylactic or therapeutic vaccine have been approved for HSV-2 and Chlamydia trachomatis (CT); in this reason, developing an efficient vaccine is inevitable. Recently, different combinatorial forms of subunit vaccines against two or three type of bacteria have been designed. In this study, to design a combinatorial vaccine against HSV, CT, and HPV, the E7 and L2 from HPV, glycoprotein D from HSV-2 and ompA from CT were selected as final antigens. Afterward, the immunodominant helper T lymphocytes (HTLs) and cytolytic T lymphocytes (CTLs) epitopes were chosen from aforesaid antigens. P30 (tetanus toxoid epitope) as universal T-helper were also added to the vaccine. Moreover, flagellin D1/D0 as TLR5 agonist and the RS09 as a TLR4 ligand were incorporated to N and C-terminals of peptide vaccine, respectively. Finally, all selected parts were fused together by appropriate linkers to enhance vaccine efficiency. The physicochemical, structural, and immunological properties of the designed vaccine protein were assessed. To achieve the best 3D model of the protein vaccine, modeling, refinement, and validation of modeled structures were also done. Docking evaluation demonstrated suitable interaction between the vaccine and TLR5. Moreover, molecular dynamics (MD) studies showed an appropriate and stable structure of protein and TLR5. Based on immunoinformatic analysis, our vaccine candidate could potentially incite humoral and cellular immunities, which are critical for protection against HPV, HSV-2, and chlamydia trachomatis. It should be noted that, experimental studies are needed to confirm the efficacy of the designed vaccine.

Strategies to improve pharmaceutical supply chain resilience under politico-economic sanctions: the case of Iran.

BACKGROUND: Given the impact of politico-economic sanctions on the pharmaceutical supply chain, this study aims to identify practical strategies to improve the resilience of the Iranian supply chain in pharmaceutical procurement under politico-economic sanctions. METHODS: This is a qualitative content analysis study conducted in 2018. Semi-structured interviews were conducted using snowball sampling, and saturation was achieved after 18 interviews. Guba and Lincoln's criteria, namely credibility, confirmability, transferability, and dependability, were considered to ensure the validity and transparency of the study. A five-step framework analysis was applied to analyze the data using MAX QDA10. RESULTS: The results led to the identification of nine main themes and 26 subthemes as strategies to improve the resilience of the pharmaceutical chain. According to the thematic map, some of these strategies have an extra-sectoral character: 'insurance organizations', 'strengthening relations with other countries', 'mechanization of the distribution system', and 'suppliers and manufacturers'. At the same time, some inter-sectoral strategies can help the pharmaceutical chain maintain its resilience: 'healthcare management and policy', 'exploiting local potential', 'pricing', and 'integrated health information systems.' As a strategy, 'Medical community and consumers' also plays a crucial role in this regard. According to the subthemes, revisions of health management, more supervision, privatization, clinical policies, strategic purchasing, improvement of the referral system, inter-sectoral cooperation, support of indigenous medicines, rational pricing, insurance system, improvement of medical coverage, and development of electronic prescription should be considered by health systems. Sufficient support for indigenous medication and supervision of the distribution system should be considered by the pharmaceutical industry, taking into account the cooperation between consumers and patients. CONCLUSIONS: Integration of the pharmaceutical supply chain and modern technologies, more attention to business complexity, economic development, intense competition, rapid changes in customer needs, and appropriate relationship between manufacturers, distributors, prescribers, and insurance organizations as purchasers should be considered by policymakers to improve supply chain resilience.

Production and Immunological Evaluation of Epitope-based Preventative Pneumococcal Candidate Vaccine Comprising Immunodominant Epitopes from PspA, CbpA, PhtD and PiuA Antigens.

BACKGROUND: Streptococcus pneumoniae is the leading cause of pneumonia, mostly in children less than five years and elderly people. Although the Pneumoniae Polysaccharide Vaccine (PPV) and Pneumonia Conjugate Vaccines (PCV) are the efficient pneumococcal vaccine in adults and children, the serotype replacement of S. pneumoniae strains causes the reduction in the efficacy of PPV and PCV vaccines. Epitope-based vaccines are a promising alternative to the present capsular antigen vaccines. METHODS: In this study, we evaluated cellular and humoral immune responses induced by our novel designed multi-epitope vaccine in BALB/c mice. CD8+ Cytolytic T Lymphocytes (CTLs) epitopes were selected from PspA and CbpA antigens, and CD4+ Helper T Lymphocytes (HTLs) epitopes were chosen from PhtD and PiuA antigens. PorB, the TLR2 agonist, as an adjuvant, was employed to increase the immunogenicity of the vaccine. RESULTS AND CONCLUSION: The high levels of specific anti-peptide vaccine IgG and an increase in the level of IgG2 in the vaccinated group demonstrated our vaccine could elicit robust antibody production. The significant increase in IFN-γ, IL-2, TNF-α, IL-4, IL-6, and decrease in IL-10 showed that the designed vaccine could be proposed as the efficient preventative pneumococcal vaccine in the mouse model.

Lessons from one year experience of pooled procurement of pharmaceuticals: exploration of indicators and assessing pharmacies` performance.

BACKGROUND: Joint procurement of medicines is a way to improve access and justice in developing countries. The aim of this study is to determine local indicators for assessing the performance of joint procurement agencies and compare the indicators in those pharmacies which use centralized purchasing before and after this change. METHODS: This was a mixed method study. In the first qualitative phase, 3 expert panels were held including 20 national experts who were selected through purposeful sampling. Data was analyzed applying a five-stage framework analysis using MAXQDA. In the second quantitative phase, financial, supply and procurement, physical and functional indicators of two hospitals affiliated with joint procurement were assessed and the satisfactions of patients from the pharmacy performance were compared applying a valid questionnaire. Data was analyzed using SPSS through independent test, Paired t-test and ANOVA. RESULTS: Results show that after settlement of joint procurement, the cost of transportation has increased by 54%, a part of the cost of overhead has increased by 30%, the cost of manpower has increased by 88.9% and cost of insurance of warehouses has increased by 71.85% in 2016 compared to 2015. In addition, the total costs of holding were 89.8% of selling revenue. In other words, the profit was about 10% of revenue in total. Moreover the average score of pharmacies under the Holding has been higher than similar ones in all aspects of satisfaction from the patients` points of view. CONCLUSION: The one-year experience of deploying centralized purchasing to supply medicine has led to increased income and patient satisfaction. However, increase in staffing costs, longevity, overhead and warehouse costs have been significant that need appropriate monitoring and interventions. Graphical abstract Graphical abstract of lessons from one year experience of pooled procurement of pharmaceuticals in south of Iran.

Designing self-assembled peptide nanovaccine against Streptococcus pneumoniae: An in silico strategy.

Streptococcus pneumoniae is the main cause of diseases such as meningitis, pneumoniae and sepsis, especially in children and old people. Due to costly antibiotic treatment, and increasing resistance of pneumococcus, developing high-efficient protective vaccine against this pathogen is an urgent need. Although the pneumoniae polysaccharide vaccine (PPV) and pneumonia conjugate vaccines (PCV) are the efficient pneumococcal vaccine in children and adult groups, but the serotype replacement of S. pneumoniae strains causes the reduction in efficacy of such vaccines. For overcoming the aforesaid drawbacks epitope-based vaccines are introduced as the relevant alternative. In our previous research, the epitope vaccine was designed based on immunodominant epitopes from PspA, CbpA antigens as cellular stimulants and PhtD, PiuA as humoral stimulants. Because the low immunogenicity is the main disadvantage of epitope vaccine, in the current study, we applied coiled-coil self-assembled structures for developing our vaccine. Recently, self-assembled peptide nanoparticles (SAPNs) have gained much attention in the field of vaccine development due to their multivalency, self-adjuvanticity, biocompatibility, and size similarity to pathogen. In this regard, the final designed vaccine is comprised of cytotoxic T lymphocytes (CTL) epitopes from PspA and CbpA, helper T lymphocytes (HTL) epitopes from PhtD and PiuA, the pentamer and trimmer oligomeric domains form 5-stranded and 3-stranded coiled-coils as self-assembled scaffold, Diphtheria toxoids (DTD) as a universal T-helper, which fused to each other with appropriate linkers. The four different arrangements based on the order of above-mentioned compartments were constructed, and each of them were modeled, and validated to find the 3D structure. The structural, physicochemical, and immunoinformatics analyses of final vaccine construct represented that our vaccine could stimulate potent immune response against S. pneumoniae; however, the potency of that should be approved via various in vivo and in vitro immunological tests.

Vaccinomics approach for developing multi-epitope peptide pneumococcal vaccine.

Streptococcus pneumoniae is a leading cause of some diseases such as pneumonia, sepsis, and meningitis mostly in children less than 5 years of age. Presently, two types of pneumococcal vaccine are available on the market: polysaccharide vaccines (PPV) that are based on capsular polysaccharides of at least 92 different serotypes, and protein-conjugated polysaccharide vaccine (PCV). The PPVs such as PPV23 do not stimulate efficient protective immunity in children under 2 years old, while the PCVs such as PCV7, PCV10, and PCV13 that cover 7, 10, and 13 serotypes, respectively, highly protect newborns, but have some disadvantages such as complications in manufacturing, costly production, and also requires refrigeration and multiple injections. Epitope-based vaccines, including varied mixtures of conserved virulence proteins, are a promising alternative to the existing capsular antigen vaccines. In this study, it has been tried to design an efficient subunit vaccine in order to elicit both CTL and HTL responses. The immunodominant epitopes from highly protective antigens of S. pneumoniae (PspA, CbpA, PiuA, and PhtD) were selected from different databanks, such as IEDB, PROPRED, RANKPEP, and MHCPRED. The PspA and CbpA were chosen as CTL epitope stimulants, and PhtD and PiuA were defined as helper epitopes. Because of low immunogenicity of epitope vaccines, PorB protein as a TLR2 agonist was employed to increase the immunogenicity of the vaccine. All the peptide segments were fused to each other by proper linkers, and the physicochemical, structural, and immunological characteristics of the construct were also evaluated. To achieve a high-quality 3 D structure of the protein, modeling, refinement, and validation of the final construct were done. Docking and molecular dynamics analyses demonstrated an appropriate and stable interaction between the vaccine and TLR2 during the simulation period. The computational studies suggested the designed vaccine as a novel construct, capable to elicit efficient humoral and cellular immunities, which are crucial for protection against S. pneumoniae. Communicated by Ramaswamy H. Sarma.

Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus.

Dengue, a mosquito-borne disease, is caused by four known dengue serotypes. This infection causes a range of symptoms from a mild fever to a sever homorganic fever and death. It is a serious public health problem in subtropical and tropical countries. There is no specific vaccine currently available for clinical use and study on this issue is ongoing. In this study, bioinformatics approaches were used to predict antigenic, immunogenic, non-allergenic, and conserved B and T-cell epitopes as promising targets to design an effective peptide-based vaccine against dengue virus. Molecular docking analysis indicated the deep binding of the identified epitopes in the binding groove of the most popular human MHC I allele (human leukocyte antigens [HLA] A*0201). The final vaccine construct was created by conjugating the B and T-cell identified epitopes using proper linkers and adding an appropriate adjuvant at the N-terminal. The characteristics of the new subunit vaccine demonstrated that the epitope-based vaccine was antigenic, non-toxic, stable, and soluble. Other physicochemical properties of the new designed construct including isoelectric point value, aliphatic index, and grand average of hydropathicity were biologically considerable. Molecular docking of the engineered vaccine with Toll-like receptor 2 (TLR2) model revealed the hydrophobic interaction between the adjuvant and the ligand binding regions in the hydrophobic channel of TLR2. The study results indicated the high potential capability of the new multi-epitope vaccine to induce cellular and humoral immune responses against the dengue virus. Further experimental tests are required to investigate the immune protection capacity of the new vaccine construct in animal models. Communicated by Ramaswamy H. Sarma.

Accreditation status of hospital pharmacies and their challenges of medication management: A case of south Iranian largest university.

Considering the importance of accreditation for hospital pharmacies, this study was to determine the challenges of medication management in hospital pharmacies affiliated with Shiraz University of Medical Sciences, Iran. The study was a mix-method research conducted in two qualitative and quantitative phases during the years 2014-2015 in Shiraz, Iran. National Accreditation Standard checklist for hospitals was used for data collection in the first phase, and Delphi method was applied in three rounds to achieve the most challenges of medication management and the related solutions. Results indicated a medium status of accreditation for all three dimensions in the above hospital pharmacies (3.53, 42.15 and 7, respectively). Lack of clinical pharmacists, nonparticipation of the pharmacy director in annual budgeting, lack of access to patient information, discontinuity of pharmaceutical care for patients discharged, defects in pharmacy staff training, lack of legislation in support of pharmacists and lack of adequate access to physicians' prescriptions, shortages in reporting medication errors, and lack of evidence related to microbial contamination are the most challenges extracted from the second phase. It seems that the studied hospital pharmacies encounter numerous problems regarding accreditation, pharmaceutical care as well as appropriate medication management and supply chain. Attempts to solve these problems can play an important role in improving the efficiency and effectiveness of pharmacies in Iran.