Experimental trials of predicted CD4+ and CD8+ T-cell epitopes of respiratory syncytial virus

Background

Respiratory syncytial virus (RSV) is the most common cause of viral lower respiratory tract infections (LRTIs) in young children around the world and an important cause of LRTI in the elderly. The available treatments and FDA-approved vaccines for RSV only lessen the severity of the infection and are recommended for infants and elderly people.

Methods

We focused on developing a broad-spectrum vaccine that activates the immune system to directly combat RSV. The objective of this study is to identify CD4+ and CD8+ T-cell epitopes using an immunoinformatics approach to develop RSV vaccines. The efficacy of these peptides was validated through in-vitro and in-vivo studies involving healthy and diseased animal models.

Results

For each major histocompatibility complex (MHC) class-I and II, we found three epitopes of RSV proteins including F, G, and SH with an antigenic score of >0.5 and a projected SVM score of <5. Experimental validation of these peptides on female BALB/c mice was conducted before and after infection with the RSV A2 line 19f. We found that the 3RVMHCI (CD8+) epitope of the F protein showed significant results of white blood cells (19.72 × 103 cells/μl), neutrophils (6.01 × 103 cells/μl), lymphocytes (12.98 × 103 cells/μl), IgG antibodies (36.9 µg/ml), IFN-γ (86.96 ng/L), and granzyme B (691.35 pg/ml) compared to control at the second booster dose of 10 µg. Similarly, 4RVMHCII (CD4+) of the F protein substantially induced white blood cells (27.08 × 103 cells/μl), neutrophils (6.58 × 103 cells/μl), lymphocytes (16.64 × 103 cells/μl), IgG antibodies (46.13 µg/ml), IFN-γ (96.45 ng/L), and granzyme B (675.09 pg/ml). In-vitro studies showed that 4RVMHCII produced a significant level of antibodies in sera on day 45 comparable to mice infected with the virus. 4RVMHCII also induced high IFN-γ and IL-2 secretions on the fourth day of the challenge compared to the preinfectional stage.

Conclusion

In conclusion, epitopes of the F protein showed considerable immune response and are suitable for further validation.

Designing, cloning and simulation studies of cancer/testis antigens based multi-epitope vaccine candidates against cutaneous melanoma: An immunoinformatics approach

Background

Melanoma is the most fatal kind of skin cancer. Among its various types, cutaneous melanoma is the most prevalent one. Melanoma cells are thought to be highly immunogenic due to the presence of distinct tumor-associated antigens (TAAs), which includes carcinoembryonic antigen (CEA), cancer/testis antigens (CTAs) and neo-antigens. The CTA family is a group of antigens that are only expressed in malignancies and testicular germ cells.

Methods

We used integrative framework and systems-level analysis to predict potential vaccine candidates for cutaneous melanoma involving epitopes prediction, molecular modeling and molecular docking to cross-validate the binding affinity and interaction between potential vaccine agents and major histocompatibility molecules (MHCs) followed by molecular dynamics simulation, immune simulation and in silico cloning.

Results

In this study, three cancer/testis antigens were targeted for immunotherapy of cutaneous melanoma. Among many CTAs that were studied for their expression in primary and malignant melanoma, NY-ESO-1, MAGE1 and SSX2 antigens are most prevalent in cutaneous melanoma. Cytotoxic and Helper epitopes were predicted, and the finest epitopes were shortlisted based on binding score. The vaccine construct was composed of the four epitope-rich domains of antigenic proteins, an appropriate adjuvant, His tag and linkers. This potential multi-epitope vaccine was further evaluated in terms of antigenicity, allergencity, toxicity and other physicochemical properties. Molecular interaction estimated through protein-protein docking unveiled good interactions characterized by favorable binding energies. Molecular dynamics simulation ensured the stability of docked complex and the predicted immune response through immune simulation revealed elevated levels of antibodies titer, cytokines, interleukins and immune cells (NK, DC and MA) population.

Conclusion

The findings indicate that the potential vaccine candidates could be effective immunotherapeutic agents that modify the treatment strategies of cutaneous melanoma.

Recurrent Rhabdomyolysis Induced by a Viral Illness in a Young Patient

Rhabdomyolysis is a syndrome caused by skeletal muscle disruption that results in the release of muscle proteins into circulation, which can lead to life-threatening systemic complications. These complications include acute kidney injury (AKI), renal failure, compartment syndrome, and disseminated intravascular coagulopathy. Patients commonly present with muscle pain, fatigue, weakness, and dark-colored urine. We present the case of a 37-year-old male who presented to the hospital with pain in the lower limbs and difficulty in mobility for the past two days after returning from Jamaica. He had a mild cold and body aches but denied any sore throat, cough, or shortness of breath (SOB). He tested negative for COVID-19. He had attended his local hospital the previous night, but due to the long waiting time, he presented to the accident and emergency department at our hospital. His physical examination was normal, and his urine was dark in color. All laboratory test results were normal, except for creatinine kinase (CK) levels >100,000 IU/L (reference: 40-320 IU/L) and an alanine transaminase (ALT) level of 376 U/L (reference: 30-130 U/L). Magnetic resonance imaging of both femurs revealed a high signal in multiple muscle compartments bilaterally on a short TI inversion recovery (STIR) sequence. Autoimmune screening results were negative. He had a similar episode last year due to COVID-19 with elevated CK levels. He received conservative treatment with IV fluids and was discharged eight days after hospital admission.

Pangenomic and immunoinformatics based analysis of Nipah virus revealed CD4+ and CD8+ T-Cell epitopes as potential vaccine candidates

Introduction: Nipah (NiV) is the zoonotic deadly bat-borne virus that causes neurological and respiratory infections which ultimately lead to death. There are 706 infected cases reported up till now especially in Asia, out of which 409 patients died. There is no vaccine and effective treatment available for NiV infections and we have to timely design such strategies as world could not bear another pandemic situation. Methods: In this study, we screened viral proteins of NiV strains based on pangenomics analysis, antigenicity, molecular weight, and sub-cellular localization. The immunoproteomics based approach was used to predict T-cell epitopes of MHC class-I and II as potential vaccine candidates. These epitopes are capable to activate CD4+, CD8+, and T-cell dependent B-lymphocytes. Results: The two surface proteins including fusion glycoprotein (F) and attachment glycoprotein (G) are antigenic with molecular weights of 60 kDa and 67 kDa respectively. Three epitopes of F protein (VNYNSEGIA, PNFILVRNT, and IKMIPNVSN) were ranked and selected based on the binding affinity with MHC class-I, and 3 epitopes (VILNKRYYS, ILVRNTLIS, and VKLQETAEK) with MHC-II molecules. Similarly, for G protein, 3 epitopes each for MHC-I (GKYDKVMPY, ILKPKLISY, and KNKIWCISL) and MHC-II (LRNIEKGKY, FLIDRINWI, and FLLKNKIWC) with substantial binding energies were predicted. Based on the physicochemical properties, all these epitopes are non-toxic, hydrophilic, and stable. Conclusion: Our vaccinomics and system-level investigation could help to trigger the host immune system to prevent NiV infection.

Comparison of the effect of zinc oxide nanoparticles and extract of Acorus calamus applied topically on surgical wounds inflicted on the skin of rabbits

Antibiotics are used for postsurgical wound healing purposes but unfortunately, resistance against them demands some alternatives for quick recovery. Sepsis of wounds is a challenge for medical as well as veterinary professionals. Nanoparticles have significant advantages in wound treatment and drug resistance reversal. This study was conducted to appreciate emerging alternates of antibiotics like zinc oxide nanoparticles and plant extracts in topical application. Zinc oxide is considered a good wound healer and its nanoparticles are easy to access. So, the efficacies of zinc oxide nanoparticles and sweet flag plant extract ointments were tested to compare modern and traditional therapeutics as sweet flag is considered a pure medicinal plant. Rabbits were selected for this study due to the healing properties of their skin. Wounds were inflicted on the thoracolumbar region and treated for 29 days post-surgically daily with normal saline and the ointment of zinc oxide nanoparticles and sweet flag extract ointment, prepared in a hydrophilic solvent. Wound shrinkage was observed daily and histopathological analysis was made and results were compared. Zinc oxide nanoparticles ointment showed the most satisfactory results for every parameter included in the study. No side effects of its topical application were observed. Healing was normal without any complications. The preparations of zinc oxide nanoparticles may help in the era of antibiotic resistance as topical drugs in the future.

Remitting Seronegative Symmetrical Synovitis with Pitting Oedema Following Administration of the Chadox1-S/NCOV-19 Coronavirus Vaccine

Introduction

We describe a case of remitting seronegative symmetrical synovitis with pitting oedema (RS3PE) syndrome following administration of the ChAdOx1-S/nCoV-19 [recombinant] vaccine, suggesting a possible causal link.

Case Description

A 72-year-old man presented to his general practitioner with swollen, oedematous hands and legs 2 weeks after receiving a coronavirus vaccine. He had raised inflammatory markers but remained systemically well. He was initially presumed to have cellulitis, but his symptoms persisted despite several courses of antibiotics. Deep vein thromboses, cardiac failure, renal failure and hypoalbuminaemia were ruled out. Upon Rheumatology review, he was diagnosed as having RS3PE syndrome with the Covid vaccine suspected of being an immunogenic trigger. Following initiation of steroid therapy, his symptoms improved dramatically, as is characteristic of RS3PE syndrome.

Discussion

The pathophysiology of RS3PE is unclear. It is known to have various triggers and associations including infections, certain vaccines and malignancy. This case highlights that a coronavirus vaccine (ChAdOx1-S/nCoV-19 [recombinant] vaccine) is also a possible trigger. Factors that make the diagnosis likely include an acute onset of symptoms including pitting oedema in a typical distribution, age above 50, and unremarkable autoimmune serology. Other learning points from this case include the importance of antibiotic stewardship and the need to explore non-infectious causes of illness when antibiotics do not improve symptoms.

Conclusion

The ChAdOx1-S/nCoV-19 [recombinant] vaccine is a possible trigger of RS3PE. However, the benefits of vaccines against coronavirus outweigh the risks in the majority of patients.

LEARNING POINTS

This case demonstrates a possible link between the ChAdOx1-S/nCoV-19 [recombinant] vaccine and autoimmune conditions such as RS3PE.It is important to consider alternative diagnoses when antibiotic regimes fail to work.A barrier to accurate diagnosis includes an episodic approach, where a patient presents to multiple clinicians acutely rather than having a long-term, continuous relationship with a single multi-disciplinary team, where response to treatment can be monitored.

The Effect of Vitamin D Supplementation on Incidence of Type 2 Diabetes: A Systematic Review

With the clinical increase in Type 2 Diabetes worldwide, several interventions to decrease its incidence have been investigated. One such intervention is Vitamin D supplementation, as it affects Insulin secretion from the pancreas and Insulin receptors in the cells of the body. This systematic review addresses whether or not Vitamin D supplementation has a role in reducing the risk of developing Type 2 Diabetes. Systematic searches were conducted on PubMed, and Cochrane Library mainly but also checked Google Scholar. Randomized controlled trials, systematic trials and cohort studies were retrieved that included keywords pertaining to Vitamin D supplementation and the incidence of Type 2 Diabetes. Exclusion criteria included studies that looked at different forms of Diabetes, studies including patients aged less than 18 or more than 85 years of age and studies that were not English language. For all the trials identified, the incidence of Type 2 Diabetes among the cohort receiving vitamin D supplementation was compared to the cohort receiving placebo medication. Additionally, the Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) was analyzed to observe if there was a difference between Insulin resistance among these two cohorts between the start of the trials and the end. Thirteen randomized controlled trials were identified. Seven of these identified incidences of Type 2 Diabetes as a research outcome, out of which six showed no statistically significant impact of vitamin D on the incidence of Type 2 Diabetes. Out of the 13 trials, 10 analyzed the impact of vitamin D supplementation on patients' HOMA-IR. In six of these trials, patients receiving vitamin D supplementation had a decrease in their HOMA-IR, while it increased in 4 trials. In seven of the ten trials that analyzed for HOMA-IR, the HOMA-IR was less in the vitamin D cohort than the placebo cohort. There is insufficient evidence to suggest that vitamin D supplementation significantly reduces the incidence of Type 2 Diabetes despite its effects on insulin resistance. Further research in this area would be helpful in order to influence clinical guidelines on vitamin D supplementation among patients at risk of Type 2 Diabetes.

Experimental Validation of MHC Class I and II Peptide-Based Potential Vaccine Candidates for Human Papilloma Virus Using Sprague-Dawly Models

Human papilloma virus (HPV) causes cervical and many other cancers. Recent trend in vaccine design is shifted toward epitope-based developments that are more specific, safe, and easy to produce. In this study, we predicted eight immunogenic peptides of CD4+ and CD8+ T-lymphocytes (MHC class I and II as M1 and M2) including early proteins (E2 and E6), major (L1) and minor capsid protein (L2). Male and female Sprague Dawly rats in groups were immunized with each synthetic peptide. L1M1, L1M2, L2M1, and L2M2 induced significant immunogenic response compared to E2M1, E2M2, E6M1 and E6M2. We observed optimal titer of IgG antibodies (>1.25 g/L), interferon-γ (>64 ng/L), and granzyme-B (>40 pg/mL) compared to control at second booster dose (240 µg/500 µL). The induction of peptide-specific IgG antibodies in immunized rats indicates the T-cell dependent B-lymphocyte activation. A substantial CD4+ and CD8+ cell count was observed at 240 µg/500 µL. In male and female rats, CD8+ cell count for L1 and L2 peptide is 3000 and 3118, and CD4+ is 3369 and 3484 respectively compared to control. In conclusion, we demonstrated that L1M1, L1M2, L2M1, L2M2 are likely to contain potential epitopes for induction of immune responses supporting the feasibility of peptide-based vaccine development for HPV.

Correction: Carbimazole-Induced Agranulocytosis in a Previously Stable Patient: A Case Report and Literature Review

[This corrects the article DOI: 10.7759/cureus.24115.].

Recent advances in immune checkpoint inhibitors for non-small lung cancer treatment

Lung cancer is one of the deadliest types of cancer responsible for thousands of cancer-related deaths. Its treatment has remained a challenge for researchers, but an increase in the knowledge of molecular pathways and biology of lung cancer has dramatically changed its management in recent decades. Immunotherapies and immunomodulation of lung cancer have previously failed for a long time but thanks to continuous research work and enthusiasm, now, this field is emerging as a novel effective therapy. Now, it is hope with potential benefits and promising results in the treatment of lung cancer. This review article focuses on immune checkpoints inhibitors: CTLA-4 inhibitors (ipilimumab and tremelimumab) and PDL-1 inhibitors (durvalumab and atezolizumab) that can be blocked to treat lung carcinoma. It is also focused on critically analyzing different studies and clinical trials to determine the potential benefits, risks, and adverse events associated with immunotherapeutic treatment.

Genome-wide Meta-analysis Reveals New Gene Signatures and Potential Drug Targets of Hypertension

The prevalence of hypertension reported around the world is increasing and is an important public health challenge. This study was designed to explore the disease's genetic variations and to identify new hypertension-related genes and target proteins. We analyzed 22 publicly available Affymetrix cDNA datasets of hypertension using an integrated system-level framework involving differential expression genetic (DEG) analysis, data mining, gene enrichment, protein-protein interaction, microRNA analysis, toxicogenomics, gene regulation, molecular docking, and simulation studies. We found potential DEGs after screening out the extracellular proteins. We studied the functional role of seven shortlisted DEGs (ADM, EDN1, ANGPTL4, NFIL3, MSR1, CEBPD, and USP8) in hypertension after disease gene curation analysis. The expression profiling and cluster analysis showed significant variations and enriched GO terms. hsa-miR-365a-3p, hsa-miR-2052, hsa-miR-3065-3p, hsa-miR-603, hsa-miR-7113-3p, hsa-miR-3923, and hsa-miR-524-5p were identified as hypertension-associated miRNA targets for each gene using computational algorithms. We found functional interactions of source DEGs with target and important gene signatures including EGFR, AGT, AVP, APOE, RHOA, SRC, APOB, STAT3, UBC, LPL, APOA1, and AKT1 associated with the disease. These DEGs are mainly involved in fatty acid metabolism, myometrial pathways, MAPK, and G-alpha signaling pathways linked with hypertension pathogenesis. We predicted significantly disordered regions of 71.2, 48.8, and 45.4% representing the mutation in the sequence of NFIL3, USP8, and ADM, respectively. Regulation of gene expression was performed to find upregulated genes. Molecular docking analysis was used to evaluate Food and Drug Administration-approved medicines against the four DEGs that were overexpressed. For each elevated target protein, the three best drug candidates were chosen. Furthermore, molecular dynamics (MD) simulation using the target's active sites for 100 ns was used to validate these 12 complexes after docking. This investigation establishes the worth of systems genetics for finding four possible genes as potential drug targets for hypertension. These network-based approaches are significant for finding genetic variant data, which will advance the understanding of how to hasten the identification of drug targets and improve the understanding regarding the treatment of hypertension.

COVID-19 Vaccine-Induced Myocarditis: A Systemic Review and Literature Search

Myocarditis is one of the complications reported with COVID-19 vaccines, particularly both Pfizer-BioNTech and Moderna vaccines. Most of the published data about this association come from case reports and series. Integrating the geographical data, clinical manifestations, and outcomes is therefore important in patients with myocarditis to better understand the disease. A thorough literature search was conducted in Cochrane library, PubMed, ScienceDirect, and Google Scholar for published literature till 30 March 2022. We identified 26 patients eligible from 29 studies; the data were pooled from these qualifying case reports and case series. Around 94% of patients were male in this study, the median age for onset of myocarditis was 22 years and 85% developed symptoms after the second dose. The median time of admission for patients to hospitals post-vaccination was three days and chest pain was the most common presenting symptom in these patients. Most patients had elevated troponin on admission and about 90% of patients had cardiac magnetic resonance imaging (CMR) that showed late gadolinium enhancement. All patients admitted with myocarditis were discharged home after a median stay of four days. Results from this current analysis show that post-mRNA vaccination myocarditis is mainly seen in young males after the second dose of vaccination. The pathophysiology of vaccine-induced myocarditis is not entirely clear and late gadolinium enhancement is a common finding on CMR in these patients that may indicate myocardial fibrosis or necrosis. Prognosis remains good and all patients recovered from myocarditis, however further studies are advisable to assess long-term prognosis of myocarditis.

Carbimazole-Induced Agranulocytosis in a Previously Stable Patient: A Case Report and Literature Review

Carbimazole-induced agranulocytosis is a rare condition. A 48-year-old female patient with a history of hyperthyroidism for several years presented with generalized fatigue and chest pain associated with palpitations; the patient was stable on carbimazole therapy. She was previously on carbimazole 15 mg once daily (OD) and, three months later, was reduced to 10 mg OD as symptoms were controlled. She was taking propranolol, and it was stopped as she was not having any palpitations. This time, however, she presented mainly with palpitations at night associated with chest pain and generalized fatigue ongoing for the last one week. Her laboratory results showed agranulocytosis with reduced white cell count and neutrophil count in the absence of any evidence of infection. Her carbimazole was stopped, and the patient was referred to ear, nose, and throat surgeons for consideration of thyroidectomy. The patient underwent subtotal thyroidectomy, and her symptoms resolved following surgery.

A Case Report on the Incidental Diagnosis of a Left Atrial Myxoma in a Patient Presenting With Right Shoulder Pain and Inter-scapular Back Pain

Primary cardiac tumors are rare, and myxoma is a rare benign primary cardiac tumor in adults, commonly found within the left atrium. The presentation can vary from patients being asymptomatic to pulmonary embolism or stroke. Smaller atrial myxomas are usually asymptomatic, however, larger ones can cause symptoms such as dyspnea, orthopnea, cough, peripheral edema, palpitations, and fatigue. We present a case report of a 72-year-old patient presenting with right shoulder pain and chest pain on breathing to the accident and emergency department. The patient was complaining of right shoulder pain for five days and pleuritic chest pain for the last 48 hours. Initial electrocardiogram showed normal sinus rhythm, however, repeat electrocardiograms showed atrial fibrillation. An echocardiogram showed a homogeneous, relatively round mass seen in the left atrium, close to the inter-atrial septum, and close to the roof of the left atrium, and the patient underwent surgical removal of the benign tumor.

Synthesis, Biological Evaluation, 2D-QSAR, and Molecular Simulation Studies of Dihydropyrimidinone Derivatives as Alkaline Phosphatase Inhibitors

The presence of alkaline phosphatases has been observed in several species and has been known to play a crucial role in various biological functions. Higher expressions of alkaline phosphatase have been found in several multifactorial disorders and cancer patients, which has led it to be an interesting target for drug discovery. A strong structural similarity exists between intestinal alkaline phosphatases (IAPs) and tissue-nonspecific alkaline phosphatases (TNAPs), which has led to the discovery of only a few selective inhibitors. Therefore, a series of 22 derivatives of 6-(chloromethyl)-4-(4-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (1) and ethyl 6-(chloromethyl)-4-(2-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (2) were synthesized to evaluate the anticancer potential of these compounds against breast cancer. The compounds were characterized through spectral and elemental analyses. The inhibitory effect of dihydropyrimidinone derivatives on alkaline phosphatases was evaluated using the calf alkaline phosphatase assay. The antioxidant activity of these compounds was performed to study the radical scavenging effect. In silico molecular docking and molecular dynamic simulations were performed to elucidate the binding mode of active compounds. Moreover, the two-dimensional qualitative-structure-activity relationship (2D-QSAR) was performed to study the structural requirements for enzyme inhibition. The calf alkaline phosphatase inhibitory assay revealed significant inhibition of the enzyme by compound 4d with IC₅₀ 1.27 μM at 0.1 mM concentration as compared to standard KH₂PO₄ having IC₅₀ 2.80 μM. The compounds 4f, 4e, and 4i also showed very good inhibition with IC₅₀ values of 2.502, 2.943, and 2.132 μM, respectively, at the same concentration. The antioxidant assay revealed efficient radical scavenging activity of compounds 4f, 4e, and 4g at 100 μg/mL with IC₅₀ values of 0.48, 0.61, and 0.75 μg/mL, respectively. The molecular docking and simulation studies revealed efficient binding of active compounds in the active binding site of the target enzyme. The final QSAR equation revealed good predictivity and statistical validation having R ² = 0.958 and Q ² = 0.903, respectively, for the generated model. The compound 4d showed the highest inhibitory activity with stable binding modes acting as a future lead for identifying alkaline phosphatase inhibitors. The molecular simulations suggested the stable binding of this compound, and the QSAR studies revealed the importance of autocorrelated descriptors in the inhibition of alkaline phosphatase. The investigated compounds may serve as potential pharmacophores for potent and selective alkaline phosphatase inhibitors. We intend to further investigate the biological activities of these compounds as alkaline phosphatase inhibitors.

Drug Reaction With Eosinophilia and Systemic Symptoms Syndrome in a Patient Taking Lamotrigine: A Case Report Based Literature Review

A 29-year-old patient presented to the hospital with worsening generalized rash for the last two days from a mental health facility. The patient was commenced on lamotrigine two weeks earlier, and he developed fever and generalized macular rash on his body. His blood tests showed deranged liver function tests (LFTs) and clotting with raised eosinophil count, and he was treated for lamotrigine-induced drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome. The patient was commenced on prednisolone 50 mg once daily with a proton pump inhibitor cover, and lamotrigine was suspended on advice from Dermatology. The patient showed improvement after 3-4 days of treatment. His skin biopsy showed prominent suppurative granulomatous folliculitis, mild perivascular chronic inflammation, and red blood cell extravasation, including the rare eosinophil. He was weaned off from prednisolone by 5 mg weekly and had complete resolution of symptoms.

A Rare Case of Clopidogrel-Induced Migratory Polyarthritis in a Patient With Recent Myocardial Infarction

Clopidogrel is an antiplatelet drug used for secondary prevention of myocardial infarction, and it is also used in patients with cerebrovascular ischemia. Patients with acute myocardial infarction tend to be on dual antiplatelet therapy for 12 months followed by aspirin lifelong to prevent the risk of stent thrombosis. The most common side effects of clopidogrel are bleeding, neutropenia, and rash; however, arthritis is also one of the rare side effects. We present a case of a 53-year-old patient who had a recent myocardial infarction and was commenced on dual antiplatelet therapy in the form of aspirin and clopidogrel. He started to have severe joint pain, particularly in his knees and shoulders, and was not able to mobilize anymore only three weeks after starting the medications. His clopidogrel was stopped and the patient showed dramatic improvement within three to four days after discontinuation with complete resolution one week later.

Quantitative Real-Time Analysis of Differentially Expressed Genes in Peripheral Blood Samples of Hypertension Patients

Hypertension (HTN) is considered one of the most important and well-established reasons for cardiovascular abnormalities, strokes, and premature mortality globally. This study was designed to explore possible differentially expressed genes (DEGs) that contribute to the pathophysiology of hypertension. To identify the DEGs of HTN, we investigated 22 publicly available cDNA Affymetrix datasets using an integrated system-level framework. Gene Ontology (GO), pathway enrichment, and transcriptional factors were analyzed to reveal biological information. From 50 DEGs, we ranked 7 hypertension-related genes (p-value < 0.05): ADM, ANGPTL4, USP8, EDN, NFIL3, MSR1, and CEBPD. The enriched terms revealed significant functional roles of HIF-1-α transcription; endothelin; GPCR-binding ligand; and signaling pathways of EGF, PIk3, and ARF6. SP1 (66.7%), KLF7 (33.3%), and STAT1 (16.7%) are transcriptional factors associated with the regulatory mechanism. The expression profiles of these DEGs as verified by qPCR showed 3-times higher fold changes (2−ΔΔCt) in ADM, ANGPTL4, USP8, and EDN1 genes compared to control, while CEBPD, MSR1 and NFIL3 were downregulated. The aberrant expression of these genes is associated with the pathophysiological development and cardiovascular abnormalities. This study will help to modulate the therapeutic strategies of hypertension.

Investigation of anti-diabetic potential and molecular simulation studies of dihydropyrimidinone derivatives

In an attempt to find new targets for α-amylase and α-glucosidase for the treatment of type 2 diabetes mellitus, the present study aims in determining the anti-diabetic potential of synthesized dihydropyrimidinone derivatives. The in vitro α-glucosidase and α-amylase inhibitory activity was performed and the molecular docking analysis of the ligand in the active binding site of target protein was determined. The results revealed significant percent inhibition of α-glucosidase by the compound 6-benzyl-4-(4-hydroxyphenyl)-3,4,6,7-tetrahydro-1H-pyrrolo[3,4-d]pyrimidine-2,5-dione (compound A). The active compound showed 81.99% inhibition when compared to standard ascorbic acid having percent inhibition 81.18%. The IC₅₀ of active compound (A) showed to be 1.02 µg/ml. The molecular docking analysis revealed that the ligand bound to the active binding site of protein with the lowest binding energy of -7.9 kcal/mol that was also significantly similar to standard having -7.8 kcal/mol binding energy. The molecular dynamic simulation studies also revealed stable binding of ligand in the active binding site of protein with low RMSD of 1.7 Å similar to the protein RMSD 1.6Å In conclusion, the study revealed a potential new target against α-glucosidase to treat type 2 diabetes mellitus.

Cytotoxic Evaluation and Molecular Docking studies of Aminopyridine derivatives as Potential Anticancer Agents

BACKGROUND

The development of resistance to available anticancer drugs is increasingly becoming a major challenge and new chemical entities could be unveiled to compensate for this therapeutic failure.

OBJECTIVES

The current study demonstrated whether N-protected and deprotected amino acid derivatives of 2-aminopyridine could attenuate tumor development using colorectal cancer cell lines.

METHODS

Biological assays were performed to investigate the anticancer potential of synthesized compounds. The in silico ADME profiling and docking studies were also performed by docking the designed compounds against the active binding site of beta-catenin (CTNNB1) to analyze the binding mode of these compounds. Four derivatives 4a, 4b, 4c, and 4d were selected for investigation of in vitro anticancer potential using colorectal cancer cell line HCT 116. The anti-tumor activities of synthesized compounds were further validated by evaluating the inhibitory effects of these compounds on the target protein beta-catenin through in vitro enzyme inhibitory assay.

RESULTS

The docking analysis revealed favorable binding energies and interactions with the target proteins. The in vitro MTT assay on colorectal cancer cell line HCT 116 and HT29 revealed potential anti-tumor activities with an IC50 range of 3.7-8.1µM and 3.27-7.7 µM, respectively. The inhibitory properties of these compounds on the concentration of beta-catenin by ELISA revealed significant percent inhibition of target protein at 100 µg/ml.

CONCLUSION

In conclusion, the synthesized compounds showed significant anti-tumor activities both in silico and in vitro, having potential for further investigating its role in colorectal cancer.

Novel oxadiazole derivatives as potent inhibitors of α-amylase and α-glucosidase enzymes: Synthesis, in vitro evaluation, and molecular docking studies

Objectives

Alpha-amylase and alpha-glucosidase enzyme inhibition is an effective and rational approach for controlling postprandial hyperglycemia in type II diabetes mellitus (DM). Several inhibitors of this therapeutic class are in clinical use but are facing challenges of safety, efficacy, and potency. Keeping in view the importance of these therapeutic inhibitors, in this study we are reporting 10 new oxadiazole analogs 5 (a-g) & 4a (a-c) as antidiabetic agents.

Materials and Methods

The newly synthesized derivatives 5 (a-g) & 4a (a-c) were characterized using different spectroscopic techniques including FTIR,¹HNMR, ¹³CNMR, and elemental analysis data. All compounds were screened for their in vitro α-amylase and α-glucosidase enzyme inhibitory potential, while two selected compounds (5a and 5g) were screened for cytotoxicity using MTT assay.

Results

Two analogues 5a and 4a (a) exhibited strong inhibitory potential against α-glucosidase enzyme, i.e., IC₅₀ value=12.27±0.41 µg/ml and 15.45±0.20 µg/ml, respectively in comparison with standard drug miglitol (IC₅₀ value=11.47±0.02 µg/ml) whereas, one compound 5g demonstrated outstanding inhibitory potential (IC₅₀ value=13.09±0.06 µg/ml) against α-amylase enzyme in comparison with standard drug acarbose (IC₅₀ value=12.20±0.78 µg/ml). The molecular interactions of these active compounds in the enzymes' active sites were evaluated following molecular docking studies.

Conclusion

Our results suggested that these new oxadiazole derivatives (5a, 5g & 4a (a)) may act as promising drug candidates for the development of new alpha-amylase and alpha-glucosidase inhibitors. Therefore, we further recommend in vitro and in vivo pharmacological evaluations and safety assessments.

Association study of NAT2 gene polymorphism and risk of oral cancer in Southern Punjab, Pakistan

OBJECTIVE

To investigate the single nucleotide polymorphic variations of N-acetyltransferase 2, phase-II metabolising enzyme, and associated risk factors for oral cancer.

METHODS

The case-control study was conducted from November 2017 to April 2018 after approval from the Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan, and comprised oral cancer patients and healthy controls. Single nucleotide polymorphism of the N-acetyltransferase 2 gene associated with oral cancer was analysed. Factors assessed using tetra-primer amplification refractory mutation system polymerase chain reaction included age, smoking, naswar, betel leaves and nuts.

RESULTS

Of the 201 subjects, 94(47%) were patients and 107(53%) were controls, while 108(54%) were aged 10-30 years. Single nucleotide polymorphism rs1208 of N-acetyltransferase 2 gene was primarily A803G and Lys268Arg, with allelic frequency of G/A. Age range 51-70 was significantly (p=0.00001) associated with the prevalence of oral cancer in terms of genotypic relationship with A803G. Substantial allelic association was found between the gene and oral cancer (p=0.006895). Smoking increased the cacner risk 7-fold (odds ratio: 7.0).

CONCLUSIONS

The genetic variant of N-acetyltransferase 2 rs1208 was found to be significantly associated with oral cancer progression and development of associated risk factors.

Cisplatin's potential for type 2 diabetes repositioning by inhibiting CDKN1A, FAS, and SESN1

Cisplatin is a DNA-damaging chemotherapeutic agent used for treating cancer. Based on cDNA dataset analysis, we investigated how cisplatin modified gene expression and observed cisplatin-induced dysregulation and system-level variations relating to insulin resistance and type 2 diabetes mellitus (T2DM). T2DM is a multifactorial disease affecting 462 million people in the world, and drug-induced T2DM is a serious issue. To understand this etiology, we designed an integrative, system-level study to identify associations between cisplatin-induced differentially expressed genes (DEGs) and T2DM. From a list of differential expressed genes, cisplatin downregulated the cyclin-dependent kinase inhibitor 1 (CDKN1A), tumor necrosis factor (FAS), and sestrin-1 (SESN1) genes responsible for modifying signaling pathways, including the p53, JAK-STAT, FOXO, MAPK, mTOR, P13-AKT, Toll-like receptor (TLR), adipocytokine, and insulin signaling pathways. These enriched pathways were expressively associated with the disease. We observed significant gene signatures, including SMAD3, IRS, PDK1, PRKAA1, AKT, SOS, RAS, GRB2, MEK1/2, and ERK, interacting with source genes. This study revealed the value of system genetics for identifying the cisplatin-induced genetic variants responsible for the progression of T2DM. Also, by cross-validating gene expression data for T2DM islets, we found that downregulating IRS and PRK families is critical in insulin and T2DM signaling pathways. Cisplatin, by inhibiting CDKN1A, FAS, and SESN1, promotes IRS and PRK activity in a similar way to rosiglitazone (a popular drug used for T2DM treatment). Our integrative, network-based approach can help in understanding the drug-induced pathophysiological mechanisms of diabetes.

Design, synthesis and biological evaluations of 2-aminothiazole scaffold containing amino acid moieties as anti-cancer agents

Due to the emerging mortality rate of colorectal cancer there is a high need for the management and control of this disease. Although several treatment approaches are being developed day by day yet the high incidence rate of colorectal cancer is still not controlled. To ease in the development of treatment therapies for colorectal cancer two derivatives of ethyl 2-aminothiazole 4-carboxylate were designed and synthesized. The compounds Ethyl 2-(2-(1,3-dioxoisoindolin-2-yl)acetamido)thiazole-4-carboxylate (5a) and ethyl 2-(2-(1,3-dioxoisoindolin-2-yl)-3-phenylpropanamido)thiazole-4-carboxylate (5b) were characterized and studied for their anti-cancer activities. The in silico molecular modeling studies were performed against the target protein beta-catenin which is an important player in the progression of colorectal cancer. The in silico ADMET studies were performed to assess the basic physicochemical properties of these compounds. The in vitro antiproliferative assay and the enzyme inhibitory assay was performed to validate the role of these compounds in the colorectal cancer. The preliminary cytotoxic assay and the MTT assay of the compounds 5a and 5b against the colorectal cancer cell line HCT 116 showed 60% inhibition of cell proliferation with IC50 of 0.72μM and 1.55μM, respectively. The standard methotrexate showed IC50 of 0.7μM showing potent inhibitory action of these compounds. The in vitro validation of the anti-cancer effect of both compounds revealed significant inhibition of beta-catenin concentration at higher doses as compared to control. Both the in vitro and in vivo assays of compounds showed effective anti-cancer activities and depicts the future potential of these compounds in colorectal cancer.

Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

BACKGROUND

Respiratory syncytial virus (RSV) infection is a public health epidemic, leading to around 3 million hospitalization and about 66,000 deaths each year. It is a life-threatening condition exclusive to children with no effective treatment.

METHODS

In this study, we used system-level and vaccinomics approaches to design a polyvalent vaccine for RSV, which could stimulate the immune components of the host to manage this infection. Our framework involves data accession, antigenicity and subcellular localization analysis, T cell epitope prediction, proteasomal and conservancy evaluation, host-pathogen-protein interactions, pathway studies, and in silico binding affinity analysis.

RESULTS

We found glycoprotein (G), fusion protein (F), and small hydrophobic protein (SH) of RSV as potential vaccine candidates. Of these proteins (G, F, and SH), we found 9 epitopes for multiple alleles of MHC classes I and II bear significant binding affinity. These potential epitopes were linked to form a polyvalent construct using AAY, GPGPG linkers, and cholera toxin B adjuvant at N-terminal with a 23.9 kDa molecular weight of 224 amino acid residues. The final construct was a stable, immunogenic, and nonallergenic protein containing cleavage sites, TAP transport efficiency, posttranslation shifts, and CTL epitopes. The molecular docking indicated the optimum binding affinity of RSV polyvalent construct with MHC molecules (-12.49 and -10.48 kcal/mol for MHC classes I and II, respectively). This interaction showed that a polyvalent construct could manage and control this disease.

CONCLUSION

Our vaccinomics and system-level investigation could be appropriate to trigger the host immune system to prevent RSV infection.

Prediction of Prophylactic Peptide Vaccine Candidates for Human Papillomavirus (HPV): Immunoinformatics and Reverse Vaccinology Approaches

Background:

Human Papillomavirus (HPV) is responsible for substantial morbidity and mortality worldwide. We predicted immunogenic promiscuous monovalent and polyvalent T-cell epitopes from the polyprotein of the Human Papillomavirus (HPV) using a range of bioinformatics tools and servers.

Methods:

We used immunoinformatics and reverse vaccinology-based approaches to design prophylactic peptides by antigenicity analysis, T-cell epitopes prediction, proteasomal and conservancy evaluation, host-pathogen protein interactions, and in silico binding affinity analysis.

Results:

We found two early proteins (E2 and E6) and two late proteins (L1 and L2) of HPV as potential vaccine candidates. Of these proteins (E2, E6, L1 & L2), 2-epitopes of each candidate protein for multiple alleles of MHC class I and II bearing significant binding affinity (>-6.0 kcal/mole). These potential epitopes for CD4+ and CD8+ T-cells were also linked to design polyvalent construct using GPGPG linkers. Cholera toxin B and mycobacterial heparin-binding hemagglutinin adjuvant with a molecular weight of 12.5 and 18.5 kDa were used for epitopes of CD4+ and CD8+ T-cells respectively. The molecular docking indicated the optimum binding affinity of HPV peptides with MHC molecules. This interaction showed that our predicted vaccine candidates are suitable to trigger the host immune system to prevent HPV infections.

Conclusion:

The predicted conserved T-cell epitopes would contribute to the imminent design of HPV vaccine candidates, which will be able to induce a broad range of immune-responses in a heterogeneous HLA population.

Genome-scale meta-analysis of breast cancer datasets identifies promising targets for drug development

Background

Because of the highly heterogeneous nature of breast cancer, each subtype differs in response to several treatment regimens. This has limited the therapeutic options for metastatic breast cancer disease requiring exploration of diverse therapeutic models to target tumor specific biomarkers.

Methods

Differentially expressed breast cancer genes identified through extensive data mapping were studied for their interaction with other target proteins involved in breast cancer progression. The molecular mechanisms by which these signature genes are involved in breast cancer metastasis were also studied through pathway analysis. The potential drug targets for these genes were also identified.

Results

From 50 DEGs, 20 genes were identified based on fold change and p-value and the data curation of these genes helped in shortlisting 8 potential gene signatures that can be used as potential candidates for breast cancer. Their network and pathway analysis clarified the role of these genes in breast cancer and their interaction with other signaling pathways involved in the progression of disease metastasis. The miRNA targets identified through miRDB predictor provided potential miRNA targets for these genes that can be involved in breast cancer progression. Several FDA approved drug targets were identified for the signature genes easing the therapeutic options for breast cancer treatment.

Conclusion

The study provides a more clarified role of signature genes, their interaction with other genes as well as signaling pathways. The miRNA prediction and the potential drugs identified will aid in assessing the role of these targets in breast cancer.

Are extracellular vesicles new hope in clinical drug delivery for neurological disorders?

Cells secrete extracellular vesicles (EVs) for intercellular communication. EVs are natural nanovesicles that are surrounded by lipid bilayer for delivery of assorted cargoes for therapeutic purposes. In addition to their therapeutic roles, these vesicles are potential drug delivery systems. Exosomes are the most studied EVs as the delivery carriers that can cross the blood-brain barrier (BBB) because of their nanosize. BBB is a diffusion barrier that is selective for small molecules to transit from blood to the brain. This barrier has been an obstacle for the delivery of drugs to the brain for the treatment of neurological disorders (NDs). For efficient drug delivery, synthetic vesicles such as liposomes have been employed as carriers for delivery of therapeutic molecules in clinical practice. However, these delivery systems are not without drawbacks. Among the limitations of these drug carriers include recognition by the body as foreign particles that encounter multiple defence systems that could recognize, neutralize and eliminate them. EVs are natural vesicles that may circumvent the body defence system to remain in systemic circulation for a long time. This unique property made them excellent drug delivery vehicles for clinical application. Here I discuss the progress, challenges and future directions of EVs (especially exosomes) as vehicles for targeted delivery of drug and at the same time deliver their cargoes for regenerative purposes in NDs. Recent developments in bioengineering and microfluidic technologies, which hold promise for clinical-grade production of EVs as drug delivery systems for NDs are also highlighted.

qPCR Analysis Reveals Association of Differential Expression of SRR, NFKB1, and PDE4B Genes With Type 2 Diabetes Mellitus

BACKGROUND

Type 2 diabetes mellitus (T2DM) is a heterogeneous, metabolic, and chronic condition affecting vast numbers of the world's population. The related variables and T2DM associations have not been fully understood due to their diverse nature. However, functional genomics can facilitate understanding of the disease. This information will be useful in drug design, advanced diagnostic, and prognostic markers.

AIM

To understand the genetic causes of T2DM, this study was designed to identify the differentially expressed genes (DEGs) of the disease.

METHODS

We investigated 20 publicly available disease-specific cDNA datasets from Gene Expression Omnibus (GEO) containing several attributes including gene symbols and clone identifiers, GenBank accession numbers, and phenotypic feature coordinates. We analyzed an integrated system-level framework involving Gene Ontology (GO), protein motifs and co-expression analysis, pathway enrichment, and transcriptional factors to reveal the biological information of genes. A co-expression network was studied to highlight the genes that showed a coordinated expression pattern across a group of samples. The DEGs were validated by quantitative PCR (qPCR) to analyze the expression levels of case and control samples (50 each) using glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as the reference gene.

RESULTS

From the list of 50 DEGs, we ranked three T2DM-related genes (p < 0.05): SRR, NFKB1, and PDE4B. The enriched terms revealed a significant functional role in amino acid metabolism, signal transduction, transmembrane and intracellular transport, and other vital biological functions. DMBX1, TAL1, ZFP161, NFIC (66.7%), and NR1H4 (33.3%) are transcriptional factors associated with the regulatory mechanism. We found substantial enrichment of insulin signaling and other T2DM-related pathways, such as valine, leucine and isoleucine biosynthesis, serine and threonine metabolism, adipocytokine signaling pathway, P13K/Akt pathway, and Hedgehog signaling pathway. The expression profiles of these DEGs verified by qPCR showed a substantial level of twofold change (FC) expression (2-ΔΔCT) in the genes SRR (FC ≤ 0.12), NFKB1 (FC ≤ 1.09), and PDE4B (FC ≤ 0.9) compared to controls (FC ≥ 1.6). The downregulated expression of these genes is associated with pathophysiological development and metabolic disorders.

CONCLUSION

This study would help to modulate the therapeutic strategies for T2DM and could speed up drug discovery outcomes.

Correction to: Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach

An amendment to this paper has been published and can be accessed via the original article.

Antibacterial activity and characterization of zinc oxide nanoparticles synthesized by microalgae

Biosynthesis of zinc oxide nanoparticles (ZnO-NPs) using microalgae is novel and cost-effective approach. We studied production, molecular characterization, and antibacterial activity. Filtrates of isolated microalgae strain ZAA1 (MF140241), ZAA2 (MF114592) and ZAA3 (MF114594) were used. Incubation of these strains in 5mM solution of zinc nitrate was resulted in the synthesis of ZnO-NPs. Fourier-transform infrared, UV-visible spectroscopy and scanning electron microscopy were used to characterize the nanoparticles. Significant antibacterial activity of ZnO-NPs was measured against Escherichia coli, Staphylococcus aureus, Micrococcus luteus, Klebsiella pneumoniae and Citrobacter freundii. The microalgae mediated ZnO-NPs production is a successful procedure that can be used in a wide range of biomedical applications.

Systems-level differential gene expression analysis reveals new genetic variants of oral cancer

Oral cancer (OC) ranked as eleventh malignancy worldwide, with the increasing incidence among young patients. Limited understanding of complications in cancer progression, its development system, and their interactions are major restrictions towards the progress of optimal and effective treatment strategies. The system-level approach has been designed to explore genetic complexity of the disease and to identify novel oral cancer related genes to detect genomic alterations at molecular level, through cDNA differential analysis. We analyzed 21 oral cancer-related cDNA datasets and listed 30 differentially expressed genes (DEGs). Among 30, we found 6 significant DEGs including CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13 and studied their functional role in OC. Our genomic and interactive analysis showed significant enrichment of xenobiotics metabolism, p53 signaling pathway and microRNA pathways, towards OC progression and development. We used human proteomic data for post-translational modifications to interpret disease mutations and inter-individual genetic variations. The mutational analysis revealed the sequence predicted disordered region of 14%, 12.5%, 10.5% for ADCY2, CYP1B1, and C7 respectively. The MiRNA target prediction showed functional molecular annotation including specific miRNA-targets hsa-miR-4282, hsa-miR-2052, hsa-miR-216a-3p, for CYP1B1, C7, and ADCY2 respectively associated with oral cancer. We constructed the system level network and found important gene signatures. The drug-gene interaction of OC source genes with seven FDA approved OC drugs help to design or identify new drug target or establishing novel biomedical linkages regarding disease pathophysiology. This investigation demonstrates the importance of system genetics for identifying 6 OC genes (CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13) as potential drugs targets. Our integrative network-based system-level approach would help to find the genetic variants of OC that can accelerate drug discovery outcomes to develop a better understanding regarding treatment strategies for many cancer types.

Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences

BACKGROUND

The coronavirus SARS-CoV-2 is a member of the Coronaviridae family that has caused a global public health emergency. Currently, there is no approved treatment or vaccine available against it. The current study aimed to cover the diversity of SARS-CoV-2 strains reported from all over the world and to design a broad-spectrum multi-epitope vaccine using an immunoinformatics approach.

METHODS

For this purpose, all available complete genomes were retrieved from GISAID and NGDC followed by genome multiple alignments to develop a global consensus sequence to compare with the reference genome. Fortunately, comparative genomics and phylogeny revealed a significantly high level of conservation between the viral strains. All the Open Reading Frames (ORFs) of the reference sequence NC_045512.2 were subjected to epitope mapping using CTLpred and HLApred, respectively. The predicted CTL epitopes were then screened for antigenicity, immunogenicity and strong binding affinity with HLA superfamily alleles. HTL predicted epitopes were screened for antigenicity, interferon induction potential, overlapping B cell epitopes and strong HLA DR binding potential. The shortlisted epitopes were arranged into two multi-epitope sequences, Cov-I-Vac and Cov-II-Vac, and molecular docking was performed with Toll-Like Receptor 8 (TLR8).

RESULTS

The designed multi-epitopes were found to be antigenic and non-allergenic. Both multi-epitopes were stable and predicted to be soluble in an Escherichia coli expression system. The molecular docking with TLR8 also demonstrated that they have a strong binding affinity and immunogenic potential. These in silico analyses suggest that the proposed multi-epitope vaccine can effectively evoke an immune response.

Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

Background

Type 2 diabetes mellitus (T2DM) is a worldwide disease that have an impact on individuals of all ages causing micro and macro vascular impairments due to hyperglycemic internal environment. For ultimate treatment to cure T2DM, association of diabetes with immune components provides a strong basis for immunotherapies and vaccines developments that could stimulate the immune cells to minimize the insulin resistance and initiate gluconeogenesis through an insulin independent route.

Methodology

Immunoinformatics based approach was used to design a polyvalent vaccine for T2DM that involved data accession, antigenicity analysis, T-cell epitopes prediction, conservation and proteasomal evaluation, functional annotation, interactomic and in silico binding affinity analysis.

Results

We found the binding affinity of antigenic peptides with major histocompatibility complex (MHC) Class-I molecules for immune activation to control T2DM. We found 13-epitopes of 9 amino acid residues for multiple alleles of MHC class-I bears significant binding affinity. The downstream signaling resulted by T-cell activation is directly regulated by the molecular weight, amino acid properties and affinity of these epitopes. Each epitope has important percentile rank with significant ANN IC₅₀ values. These high score potential epitopes were linked using AAY, EAAAK linkers and HBHA adjuvant to generate T-cell polyvalent vaccine with a molecular weight of 35.6 kDa containing 322 amino acids residues. In silico analysis of polyvalent construct showed the significant binding affinity (− 15.34 Kcal/mol) with MHC Class-I. This interaction would help to understand our hypothesis, potential activation of T-cells and stimulatory factor of cytokines and GLUT1 receptors.

Conclusion

Our system-level immunoinformatics approach is suitable for designing potential polyvalent therapeutic vaccine candidates for T2DM by reducing hyperglycemia and enhancing metabolic activities through the immune system.

Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach

Background

Colorectal cancer is known to be the most common type of cancer worldwide with high disease-related mortality. It is the third most common cancer in men and women and is the second major cause of death globally due to cancer. It is a complicated and fatal disease comprising of a group of molecular heterogeneous disorders.

Results

This study identifies the potential biomarkers of CRC through differentially expressed analysis, system biology, and proteomic analysis. Ten publicly available microarray datasets were analyzed and seven potential biomarkers were identified from the list of differentially expressed genes having a p value < 0.05. The expression profiling and the functional enrichment analysis revealed the role of these genes in cell communication, signal transduction, and immune response. The protein-protein interaction showed the functional association of the source genes (CTNNB1, NNMT, PTCH1, CALD1, CXCL14, CXCL8, and TNFAIP3) with the target proteins, such as AXIN, MAPK, IL6, STAT, APC, GSK3B, and SHH.

Conclusion

The integrated pathway analysis indicated the role of these genes in important physiological responses, such as cell cycle regulation, WNT, hedgehog, MAPK, and calcium signaling pathways during colorectal cancer. These pathways are involved in cell proliferation, chemotaxis, cellular growth, differentiation, tissue patterning, and cytokine production. The study shows the regulatory role of these genes in colorectal cancer and the pathways that can be effected after the dysregulation of these genes.

Experimental analysis of T cell epitopes for designing liver cancer vaccine predicted by system-level immunoinformatics approach

Liver cancer is a worldwide disease, and, currently, due to the poor prognostic and therapeutic options of liver cancer, we investigated the T cell epitopes as potential therapeutic vaccine candidates to get the benefit of experimental processes and utilize the complete ability of the immune system compared with other artificial ex vivo proliferation of T cells. Activation of T cells targets and kills several tumors, developing a strong rationale for the improvement of immunotherapeutic strategies to cancer therapy. To predict T cell epitopes for liver cancer, we designed a comprehensive immunoinformatics framework involving data mining, immunogenicity prediction, functional proteomic analysis, conservation studies, molecular modeling, and in vivo validation analysis. We found the binding affinity of antigenic peptides with major histocompatibility complex (MHC) I molecules to control the cancerous activity. Five extracellular antigenic proteins, including complement protein (C6), serotransferrin, coagulation factor XIII B, serum albumin (ALB), and prothrombin, were identified. We predicted and synthesized T cell epitopes to human leukocytes antigen-A*01:01 allele of MHC class I molecule. The hematological assay and IgG ELISA showed that C6 and ALB epitopes induced the production of lymphocytes, granulocytes, and peptide-specific IgG in immunized rats. We observed substantial high levels of granzymes B in serum samples of C6 and ALB compared with control, indicating the activity of cytotoxic T cells. We concluded that C6 and ALB are likely to contain potential epitopes for the induction of protective effector molecules, supporting the feasibility of therapeutic peptide-based vaccine for liver cancer.NEW & NOTEWORTHY We observed substantial high levels of granzymes B in serum samples of component C6 (C6) and albumin (ALB) compared with control, indicating the activity of cytotoxic T cells. We concluded that C6 and ALB are likely to contain potential epitopes for the induction of protective effector molecules, supporting the feasibility of therapeutic peptide-based vaccine for liver cancer.

Engineering and characterisation of BCG-loaded polymeric microneedles

The aim of this study was to fabricate Bacillus Calmette-Guérin (BCG)-loaded microneedle patches using micromould casting technique and compare their efficacy with the injectable counterparts. The microneedle patches were formulated using sodium alginate (10% w/v) and trehalose (20% of polymer). The patches were characterised using optical microscopy, scanning electron microscopy and folding endurance. Serum IgG, TLC, granulocyte count, lymphocyte count and CRP were assessed and results were compared to that of intradermal injections alongside controls. The results showed that polymeric patches had a thickness of 0.8 mm, microneedle projections of 272 ± 12 µm and folding endurance of more than 300. Based on haematological and IgG ELISA assays, microneedle-based BCG administration significantly activated the immune cells and induced production of lymphocytes, granulocytes and peptide-specific IgG in immunised rats that were comparable to injectable counterparts. There was an increase in IgG antibodies from 3 g/L to 5.98 g/L and an increase in leucocytes from 2.6 × 10⁹/L to 18.45 × 10⁹/L. There was also an increase in granulocytes from 14.4% to 29.15% and lymphocyte count from 58.75% to 85.3%. It was concluded that BCG-coated polymeric microneedle patches are suitable for the transdermal delivery of vaccine without inducing discomfort usually observed with injections.

Mini-Review: molecular elucidations of hutchinson-gilford progeria syndrome: A hope for managing horrors of premature aging in children

Hutchinson-Gilford Progeria syndrome (or Progeria) is an exceptionally rare genetic disorder in children. It is caused by a rare point mutation in the lamin gene. It encodes lamin A protein, resulting in the de-shaping of nuclear membrane. This altered structure of the nuclear membrane renders the nucleus unstable. The shortened lifespan of the nucleus makes the cell liable for rapid ageing. Children are healthy by appearance when they are born but the signs appear after 12-24 months of age. Cardiovascular system is greatly affected which became a reason for the death of most of the patients of progeria. Stiffened joints disturb the bone movements; and alopecia affects the appearance of the patient. Rate of occurrence of the disease is one per four hundred thousand of people, though both sexes are equally affected.

An Efficient Protocol for the Synthesis, Biological Screening and Molecular Docking Studies of 3,4-Dihydropyrimidine-2-one/thione Derivatives

Introduction:

Heterocyclic compounds are vital to life, since they constitute the most interesting part of the pharmacologically active drugs. Dihydropyrimidine-2-one/thione (DHPM) as the heterocyclic nucleus is the basic part of the most natural as well as synthetic drugs. Synthesis of new derivatives of DHPM and screening their pharmacological potential appear to be an important goal.

Methodology:

In this study, we have synthesized 15 derivatives of 3,4-dihydropyrimidin-2(1H)- ones/thiones through simple one-step synthetic method comprising one-pot condensation of variously substituted benzaldehydes, urea/thiourea and ethyl acetoacetate using ammonium chloride in methanol as well as under solvent-free conditions. In comparison, the former methodology was proved more efficient, convenient and gave higher yields. Moreover, those compounds were screened for their potential against bacterial strains (S. aureus and E. coli) and fungal strains (C. albicans and C. parapsilosis).

Results and Discussion:

The experimental results revealed that the synthesized compounds are more active against C. albicans fungus as compared to other tested microbes. Amongst all the synthesized derivatives, compound 3 showed significant non-competitive potential antifungal activity in vitro antimicrobial assay. Theoretically, molecular docking studies showed that these compounds can bind effectively to oxidoreductase enzyme of E. coli and CYP-51 oxidoreductase of C. albicans.

Conclusion:

Herein, we report improved and high yield reaction conditions for the synthesis of biologically active dihydropyrimidine-2-one, and-thione derivatives. Remarkably, most of the synthesized compounds demonstrated moderate to very good antifungal activity in comparison to the antibacterial activity.

Antitumor activity and combined inhibitory effect of ceritinib with gemcitabine in pancreatic cancer

Pancreatic cancer (PC) is predominantly incurable and is primarily treated with gemcitabine, but drug resistance commonly develops. Thus, new medicines are needed. Ceritinib (LDK378) is a second-generation tyrosine kinase inhibitor of anaplastic lymphoma kinase (ALK) with antitumor activity in various cancers. However, studies involving ceritinib for the treatment of PC are inadequate. We analyzed the combined effects of ceritinib and gemcitabine on PC and their mechanism of action. Three PC cell lines were used to evaluate the antitumor effects of ceritinib combined with gemcitabine. We analyzed cell viability using CCK-8 assays, determined apoptosis levels through flow cytometry, and analyzed autophagy and cell signaling pathways by Western blotting and tissue array analysis with samples from xenograft models. Ceritinib strongly inhibited the proliferation of PC cells in a dose-dependent manner, induced apoptosis, and inhibited autophagy and cell migration by regulating relevant factors. Ceritinib in combination with gemcitabine exhibited significant growth inhibition and additive antitumor effects in vitro. In vivo, gemcitabine and ceritinib reduced tumor size by up to 30%. In our study, ALK was shown to be highly expressed in various PC cells and tissues. Ceritinib strongly inhibited the levels of activated ALK in PC cells with subsequent effects on the downstream mediators STAT3, AKT, and ERK. In addition, ceritinib inhibited tumor progression in xenograft models. Overall, our research shows that ceritinib inhibits the ALK signaling pathway, leading to cell growth/angiogenesis inhibition in PC and the induction of apoptosis. We recommend using ceritinib as a new treatment for PC.NEW & NOTEWORTHY These data proved that ceritinib inhibits the anaplastic lymphoma kinase signaling pathway, leading to cell growth/angiogenesis inhibition and the induction of apoptosis by inhibiting STAT3, AKT, and ERK pathway in pancreatic cancer (PC). We recommend using ceritinib as a new treatment for PC.

REVIEW- Contemporary evidence on the dynamic role of probiotics in liver diseases

Currently probiotics are considered as an emerging therapeutic strategy in the treatment of many liver disorders. The use of probiotics beyond infection of intestinal flora is a very helpful approach. The optimistic effect of probiotics has been observed in treating the hepatic cirrhosis, hepatic encephalopathy, viral hepatitis, irritable bowel syndrome, non-alcoholic fatty liver and alcoholic liver disease. The characterize mechanisms of probiotics are still unknown but may involve in, maintaining a microbial barrier against potential pathogens, reducing the production of bacterial toxins, modulating the immune system, intestinal permeability, and the inflammatory response. Its safety issues, effectiveness, food supplements as its source are still to be studied. However, studies revealed that probiotic therapy in hepatocellular carcinoma and in portal hypertension are still weak. Larger clinical studies are required before probiotics can be recommended as a treatment modality in liver diseases.

Protective effects of maresin 1 against inflammation in experimentally induced acute pancreatitis and related lung injury

Severe acute pancreatitis (SAP) is an inflammatory disorder that progresses with local and systemic difficulties accompanied by a relatively high mortality rate. In recent years, maresin 1 (MaR1) has been shown to be a macrophage mediator with effective proresolving and anti-inflammatory properties that prevents the occurrence of various inflammatory conditions. The purpose of this study was to investigate the role of MaR1 in SAP and related lung injury. Experimental SAP was induced in mice with a combination of cerulean and lipopolysaccharide. MaR1 was administered 30 min before the primary injection of cerulean. Biochemical markers and histological injury scores were used to evaluate the severity of acute pancreatitis. To determine the degree of inflammation, serum cytokines and myeloperoxidase activity in pancreas and lung tissues were measured. Western blot analysis detected the activation of NF-κB. After MaR1 pretreatment, the activities of amylase, lipase, TNF-α, IL-1β, and IL-6 were decreased in serum, and the myeloperoxidase activity both in pancreas and in lung tissues significantly decreased, whereas the activity of anti-inflammatory cytokine IL-10 in serum was increased. MaR1-pretreated mice reduced the activation of pancreatic NF-κB and decreased the severity of pancreatic and lung-related injuries. These results confirm that MaR1 alleviated inflammation of the pancreas and lung by inhibiting the activity of NF-κB in experimentally induced acute pancreatitis and exerted anti-inflammatory effects. These findings suggest that MaR1 could be a new and useful drug in the treatment of SAP.NEW & NOTEWORTHY These results provided us evidence to confirm that maresin 1 (MaR1) can alleviate inflammation of the pancreas and lung by inhibiting the activity of NF-κB in experimental induced acute pancreatitis and exerts certain anti-inflammatory effects. These findings suggest that MaR1 could be a new and useful drug in the treatment of severe acute pancreatitis.

Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae

Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.

SHORT COMMUNICATION-Anticancer activity of Ziziphus mauritiana roots against human breast cancer cell line

This study was designed to evaluate the anticancer activity of Ziziphus mauritiana roots. The dichloromethane and methanol extracts were prepared and anticancer activity was investigated the by using MTT assay. Human breast cancer cell line (MCF-7) was used in this study. 50μg/ml of dichloromethane extract of the roots of plant exhibited significant anticancer activity (70%) against the breast cancer cell line with IC₅₀ 20.34±0.9 using doxorubicin as standard. The study indicated that Ziziphus mauritiana has anticancer activity against MCF-7 cell line.

A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia

Background

Alopecia or hair loss is a complex polygenetic and psychologically devastating disease affecting millions of men and women globally. Since the gene annotation and environmental knowledge is limited for alopecia, a systematic analysis for the identification of candidate biomarkers is required that could provide potential therapeutic targets for hair loss therapy.

Results

We designed an interactive framework to perform a meta-analytical study based on differential expression analysis, systems biology, and functional proteomic investigations. We analyzed eight publicly available microarray datasets and found 12 potential candidate biomarkers including three extracellular proteins from the list of differentially expressed genes with a p-value < 0.05. After expression profiling and functional analysis, we studied protein–protein interactions and observed functional associations of source proteins including WIF1, SPON1, LYZ, GPRC5B, PTPRE, ZFP36L2, HBB, PHF15, LMCD1, KRT35 and VAV3 with target proteins including APCDD1, WNT1, WNT3A, SHH, ESRI, TGFB1, and APP. Pathway analysis of these molecules revealed their role in major physiological reactions including protein metabolism, signal transduction, WNT, BMP, EDA, NOTCH and SHH pathways. These pathways regulate hair growth, hair follicle differentiation, pigmentation, and morphogenesis. We studied the regulatory role of β-catenin, Nf-kappa B, cytokines and retinoic acid in the development of hair growth. Therefore, the differential expression of these significant proteins would affect the normal level and could cause aberrations in hair growth.

Conclusion

Our integrative approach helps to prioritize the biomarkers that ultimately lessen the economic burden of experimental studies. It will also be valuable to discover mutants in genomic data in order to increase the identification of new biomarkers for similar problems.

Electronic supplementary material

The online version of this article (10.1186/s40709-019-0094-x) contains supplementary material, which is available to authorized users.