Acinetobacter baumannii as an oro-dental pathogen: a red alert!!

OBJECTIVES

This review highlights the existence and association of Acinetobacter baumannii with the oro-dental diseases, transforming this systemic pathogen into an oral pathogen. The review also hypothesizes possible reasons for the categorization of this pathogen as code blue due to its stealthy entry into the oral cavity.

METHODOLOGY

Study data were retrieved from various search engines reporting specifically on the association of A. baumannii in dental diseases and tray set-ups. Articles were also examined regarding obtained outcomes on A. baumannii biofilm formation, iron acquisitions, magnitude of antimicrobial resistance, and its role in the oral cancers.

RESULTS

A. baumannii is associated with the oro-dental diseases and various virulence factors attribute for the establishment and progression of oro-mucosal infections. Its presence in the oral cavity is frequent in oral microbiomes, conditions of impaired host immunity, age related illnesses, and hospitalized individuals. Many sources also contribute for its prevalence in the dental health care environment and the presence of drug resistant traits is also observed. Its association with oral cancers and oral squamous cell carcinoma is also evident.

CONCLUSIONS

The review calls for awareness on the emergence of A. baumannii in dental clinics and for the need for educational programs to monitor and control the sudden outbreaks of such virulent and resistant traits in the dental health care settings.

Genetic Association of Toll-Like Receptor 4 (TLR4) Gene Polymorphism (rs4986790) With Oral Squamous Cell Carcinoma (OSCC): A Pilot Case-Control Study

Introduction Oral squamous cell carcinoma (OSCC) is a highly prevalent and most common form of oral malignancy in the Indian population. Toll-like receptors belong to an important family of receptors that are involved in the process of pathogen recognition and mounting immune response. The expression of this receptor is dysregulated on the tumor cells as reported across several cancer types. The genetic variants in this gene could have a profound impact on the expression of the Toll-like receptor 4 (TLR4) gene.  Objective This study aimed to understand the association of TLR4 gene polymorphism (rs4986790) with OSCC. The objective of this study was to compare the allele and genotype frequencies between the two groups, viz., OSCC and normal healthy subjects, recruited in the study. Materials and methods The blood samples were collected from normal healthy subjects (N = 25) and OSCC patients (N = 25). Genomic DNA was isolated from all samples, and genotyping was performed for the TLR4 gene polymorphism (rs4986790) employing the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. The frequency distribution of genotypes and alleles across the study groups was determined by the Chi-square test.  Results The allele frequency for TLR4 gene polymorphism (rs4986790) in the case group was found to be 60% (A allele) and 40% (G allele), respectively. The study population in both groups were found to agree with the Hardy-Weinberg equilibrium (HWE). The genotype frequency did not differ significantly among the two study groups which was evident from the p-value = 0.8285.  Conclusion The present study did not report any significant association of the TLR4 polymorphic marker rs4986790 with OSCC. Further investigations into the association of other polymorphic markers in the TLR4 gene, among the larger population of OSCC patients, could provide evidence of their association with OSCC.

Molecular Detection of Secreted Aspartyl Proteinases (Saps) From Dental Isolates of Candida albicans and Targeting With Psidium guajava Biocompounds: An In Vitro and In Silico Analysis

Introduction Candida albicans (C. albicans) is an opportunistic yeast-like fungus and is considered a functional biome of the oral and gut microbiomes. The sap gene and its types play a vital role in the pathogenesis of C. albicans. The emergence of resistance traits is a major problem, and targeting the same with alternative medicines has sparked renewed interest in recent years. Objectives This study is thus aimed at detecting the frequency of sap gene types in the clinical isolates of C. albicans and evaluating the antifungal effect of the crude methanolic extract of Psidium guajava (P. guajava). Further in silico assessments will assess the inhibitory effect of six compounds of P. guajava against the Sap protein. Materials and methods C. albicans was characterized phenotypically in 20 patients with root caries, and the sap gene was detected by PCR. The crude methanolic extract was prepared, and its antifungal efficacy was evaluated by the agar well diffusion method. Auto-docking was performed to assess the best compound based on the docking and overall interactions. Results Six isolates were identified as C. albicans and sap gene types 1-3 were detected in the four strains. P. guajava methanolic extracts showed a promising antifungal effect at varying concentrations. In silico analysis showed myricetin possessing the maximum number of hydrogen bonds and high docking energy with one violation. Conclusion The study concludes that P. guajava has a promising inhibitory effect against C. albicans with myricetin as the best compound to target the sap gene of C. albicans. However, further experimental studies are to be considered for its effectiveness in treating the infections caused by C. albicans.

Prediction of Antigenic Vaccine Peptide Candidates From BfmRS Associated With Biofilm Formation in Acinetobacter baumannii

INTRODUCTION

 A. baumannii is categorized as a priority pathogen due to its propensity for multi-drug resistance, exhibiting resistance against the last resort of antibiotics. It is also considered a potent nosocomial pathogen, so targeting the microbe using novel strategies would be the need of the hour. In this context, the in-silico computational approach would serve the best to design the possible epitope peptides, which may be further considered for the experimental trials for their immunological response.  Objective: To predict the immune-dominant epitope peptide candidates against the bfmR and bfmS proteins mediating the two-component system adaptation in the formation of biofilm in A. baumannii.

MATERIALS AND METHODS

11 different FASTA sequences of bfmR and bfmS from A. baumannii strains retrieved based on the blast-p similarity search tool were subjected to linear epitope B-cell epitope predictions under the IEDB B-cell epitope prediction server. Further analysis on antigenicity, allergenicity, and toxigenicity was achieved using the AntigenPro, Vaxijen, and AlgPred tools, with the physical and chemical properties evaluated using the Expasy Protparam server. Selection of the immunodominant peptides for T-cells was done through the databases under IEDB. The final assessment of protein-TLR2 interactions was done by MHC cluster servers.

RESULTS

Four peptide sequences (E1-E4) were predicted for B-cell dominance, with E1, E2, and E4 as probable antigens. All were soluble and non-toxigenic. E1 and E3 were considered non-allergens. GRAVY values were negative for all the peptides, indicating the protein to be hydrophilic in nature. Analysis of the T-cell epitopes was promising, with 100% conservancy for class-I HLA alleles, high interaction scores for similarity with TLR2, and more hydrogen bonds for E2, followed by other epitope peptides.

CONCLUSION

The promising four epitopes, as predicted for bfmR and bfmS in the present study, suggest their potent role as possible candidates for the design of vaccines targeting the TCS of A. baumannii, recommending further in vitro and in vivo experimental validation.

The Implementation of HIV Self-Testing in Resource-Limited Settings Where the HIV Disease Burden is High

In resource-limited settings, there is growing evidence that HIV testing is lacking among high-risk key populations such as men having sex with men, injection drug users, and transgenders largely due to stigma, discrimination, and lack of confidentiality. Findings from recent studies among high-risk key populations and the general population from various regions including resource-limited settings support the need for wider accessibility of HIV self-testing (HIV-ST) to reach those who may not otherwise have access to testing. Therefore, HIV-ST has untapped potential as a strategy to improve access to HIV testing and to increase testing frequency among key high-risk populations and their partners. Though HIV-ST has emerged as a safe, acceptable, and effective way to reach people, there are several roadblocks to implementing the HIV-ST policy, and fast-track policy implementation needs to be necessitated with newer or modified strategic plans.

Moonlighting proteins [ML proteins]: The pandora's box of insidious oro-dental diseases

Oral pathogens survive in the harsh niche of the oral microbiome on account of a plethora of moonlighting [ML] proteins that can multitask in the oro-mucosal layers. ML proteins are considered as the complex protein hyperspace expressed in many oral bacterial pathogens and encompass many hypothetical and experimentally evidenced proteins that can efficiently assist in the initiation and progression of various oro-dental infections. With the propensity of multi-drug resistance and biofilm formation, unravelling the mysterious functions associated with the oral ML proteins could be essential in targeting the vital oral bacteria and their associated infections. This commentary thus throws insights onto the key clues on various ML proteins that can be considered for the development of therapeutic versatility to curtail the complications caused by various oral bacterial species.

Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in Acinetobacter baumannii Using an In Silico Approach

Background and Objectives: The BaeR protein is involved in the adaptation system of A. baumannii and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope peptides for the design of vaccines against BaeR protein, using an immune-informatic approach. Materials and Methods: FASTA sequences of BaeR from five different strains of A. baumannii were retrieved from the UNIPROT database and evaluated for their antigenicity, allergenicity and vaccine properties using BepiPred, Vaxijen, AlgPred, AntigenPro and SolPro. Their physio-chemical properties were assessed using the Expasy Protparam server. Immuno-dominant B-cell and T-cell epitope peptides were predicted using the IEDB database and MHC cluster server with a final assessment of their interactions with TLR-2. Results: A final selection of two peptide sequences (36aa and 22aa) was made from the 38 antigenic peptides. E1 was considered a soluble, non-allergenic antigen, and possessed negative GRAVY values, substantiating the hydrophilic nature of the proteins. Further analysis on the T-cell epitopes, class I immunogenicity and HLA allele frequencies yielded T-cell immuno-dominant peptides. The protein-peptide interactions of the TLR-2 receptor showed good similarity scores in terms of the high number of hydrogen bonds compared to other protein-peptide interactions. Conclusions: The two epitopes predicted from BaeR in the present investigation are promising vaccine candidates for targeting the TCS of A. baumannii in systemic and nosocomial infections. This study also demonstrates an alternative strategy to tackling and mitigating MDR strains of A. baumannii and provides a useful reference for the design and construction of novel vaccine candidates against this bacteria.

Probiotic curd as antibacterial agent against pathogens causing oral deformities - in vitro microbiological study

Major oral deformities fall under dental caries and periodontal diseases hence active prevention of these two diseases can contribute to good oral health and preserves oral hygiene. Streptococcus mutans, Staphylococcus aureus, Lactobacillus, Candida, and anaerobic organisms are the organisms responsible for causing oral cavity-related deformities. Probiotics which is the useful and nonpathogenic bacteria are added to food products which tend to be advantageous to human health. A wide range of studies indicates that these probiotics are useful against oral tissues. Hence, the primary goal of the study aims to determine the antibacterial potential of probiotic curd against pathogens causing various oral diseases and deformities. A laboratory-oriented in vitro microbiological study design was framed to detect the antimicrobial potential of the probiotic curd. Subgingival calculus specimens were collected and anaerobic organisms were isolated in thioglycollate broth. Lawn cultures were subjected to the surface of brain heart infusion agar and 100 μl of probiotic curd, normal curd, and filtrate were taken in a micropipette and inoculated over the specific wells. The culture plates were incubated anaerobically at 37°C for 24 h. The culture plates were monitored for the zone of inhibition to assess the antibacterial activity against the test pathogens. The results showed that there was no antibacterial activity against the anaerobic bacteria cultivated from subgingival calculus. However, further validation must be done on the same with purified components from the probiotic curd. Probiotic curd is normally considered a vital immune-boosting nutritional supplement. However, the antibacterial activity must be evaluated with care with the purified filtrates of the curd to substantiate its exact role against dental pathogens.

Protean role of epigenetic mechanisms and their impact in regulating the Tregs in TME

Constitutive expression of Foxp3+ Tregs in the tumor microenvironment (TME) specifically renders immune suppression in the tumor tissues. Being highly stable and self-tolerant, Tregs may be influenced by various epigenetic-associated mechanisms while exhibiting their functions. DNA methylation, histone acetylation, epigenetic silencing, alteration in chromatin networks, etc., are some of the main factors underlying the epigenetic-based Treg cell functional modulations in the TME. The possible reasons on why these epigenetic modulations should be specifically targeted are thus discussed, so that enhanced anti-tumor immunity in TME can be achieved.

Biofilm-Associated Agr and Sar Quorum Sensing Systems of Staphylococcus aureus Are Inhibited by 3-Hydroxybenzoic Acid Derived from Illicium verum

Biofilm-producing Staphylococcus aureus (S. aureus) is less sensitive to conventional antibiotics than free-living planktonic cells. Here, we evaluated the antibiofilm activity of Illicium verum (I. verum) and one of its constituent compounds 3-hydroxybenzoic acid (3-HBA) against multi-drug-resistant S. aureus. We performed gas chromatography-mass spectroscopy (GC-MS) to identify the major constituents in the methanolic extract of I. verum. Ligand-receptor interactions were studied by molecular docking, and in vitro investigations were performed using crystal violet assay, spreading assay, hemolysis, proteolytic activity, and growth curve analysis. The methanolic extract of I. verum inhibited S. aureus at 4.8 mg/mL, and GC-MS analysis revealed anethole, m-methoxybenzaldehyde, and 3-HBA as the major constituents. Molecular docking attributed the antibiofilm activity to an active ligand present in 3-HBA, which strongly interacted with the active site residues of AgrA and SarA of S. aureus. At a subinhibitory concentration of 2.4 mg/mL, the extract showed biofilm inhibition. Similarly, 3-HBA inhibited biofilm activity at 25 μg/mL (90.34%), 12.5 μg/mL (77.21%), and 6.25 μg/mL (62.69%) concentrations. Marked attrition in bacterial spreading was observed at 2.4 mg/mL (crude extract) and 25 μg/mL (3-HBA) concentrations. The methanol extract of I. verum and 3-HBA markedly inhibited β-hemolytic and proteolytic activities of S. aureus. At the lowest concentration, the I. verum extract (2.4 mg/mL) and 3-HBA (25 μg/mL) did not inhibit bacterial growth. Optical microscopy and SEM analysis confirmed that I. verum and 3-HBA significantly reduced biofilm dispersion without disturbing bacterial growth. Together, we found that the antibiofilm activity of I. verum and 3-HBA strongly targeted the Agr and Sar systems of S. aureus.

Decoding the Genetic Alteration in Genes of PARP Family and the Possible Association with HNSCC

Introduction: Genetic alterations have long been associated with the transformation of normal cells into malignant cells. Several genes are related to exhibiting the phenotype. The PARP gene family is mainly involved in maintaining genome stability. They play an important role in DNA repair and the programmed cell death process. Aim: To analyse the genetic alteration in PARP family and to determine its association with HNSCC. Materials and Methods: Cbioportal was used as the primary database for identifying the mutations and variations. The data generated in the form of oncoprint was further assessed for frequency of occurrence, type and novelty. Results and Discussion: It can be observed that greater amplification was found in the TIPARP gene which is 14% among all the 17 genes of the family. Also to add on, PARP 14 and PARP 15 show amplification patterns in similar groups of patients. Several types of mutations such as truncated, splicing deep deletion were found in most of the genes. The TIPARP gene was up-regulated in HNSCC patients. The Caucasians experiencing low/medium expression of TIPARP showed greater rates of survival than highly expressed African Americans. Similarly, males presenting with low or medium expression of TIPARP showed a greater rate of survival than the highly expressed females. Conclusion: TIPARP could be a promising prognostic marker for screening populations vulnerable to acquiring HNSCC.

Virtual Screening to Identify the Protein Network Interaction of Theophylline in Red Complex Pathogens

Background: Plants, herbs and plant derived compounds have been used since decades in folk and traditional medicine. These compounds were found to be non-toxic and compatible with the human cells. Screening of this exhaustive collection of compounds seems to be a herculean task. Hence, virtual screening methods have been developed to predict the potential targets of these compounds enabling researchers to acquire preliminary data on the compound intended to be tested in vitro. Aim: The present study aims to identify protein targets of theophylline in red complex pathogens which are mainly associated with periodontitis. Methods: The STITCH v5.0 pipeline was mainly used to classify drug-protein interactions, while VirulentPred and VICMPred were used to determine the proteins' virulence properties and functional classes. PSORTb v3.0 was used to determine the subcellular localization of viral proteins, and BepiPred v1.0 Linear Epitope Prediction was used to classify epitopes. Results: Proteins of red complex pathogens implicated in cellular process, metabolism, and virulence were identified to interact with theophylline. The virulent proteins attacked by the drugs were present in the cytoplasm, which would improve the drugs' antimicrobial efficacy even more. Finally, epitope prediction showed a number of epitopes in virulent proteins that can be targeted. Conclusions: Proteins involved in the cellular process, metabolism, and virulence of red complex pathogens targeted by theophylline were identified. To substantiate the true interactions between the drugs and the protein arsenal of pathogens, further in vitro experiments on a broad range of pathogens are required.

Genetic Alterations in CDH (Cadherin) Family of Genes and their Putative Association with Head and Neck Squamous Cell Carcinoma

Background: Head and neck squamous cell carcinoma is considered to be a common type of human cancer. It is highly invasive with limited therapeutic options outside surgery, chemotherapy and radiation.  Cadherin family genes comprises a family with more than 110 members which are calcium dependent transmembrane proteins which helps in cellular adhesion, signaling etc. There exist different functions of Cadherin genes in malignant cells. Uncontrolled mesenchymal- epithelial transition is seen in malignant situations where the cadherins serve as tumour suppressor genes but gets down regulated drastically to create tumour initiation and invasions. This study aims to study the association between genetic alterations in the cadherin family of genes and HNSCC patients. Materials and Methods: The datas were collected from a promising database, cBioportal and the demographic details of the selected individuals(HNSCC patients) were tabulated and noted. The genetic variations in the genes were analysed using GnomAD analysis, oncoprint analysis and their various genetic alterations,frequency were tabulated and represented figuratively. Results and Discussion: On analysing the various genetic alterations discovered in cadherin family genes of HNSCC patients, CDH2 gene showed maximum genetic alteration(%). The different genetic alterations documented were splicing, deep deletion, amplification, etc. the oncoprint data analysis shows the frequency of the types of different genetic alteration in the five genes considered, their combination with any other genetic alteration seen in the other genes along with their frequency. The graphical representation of Kaplan meier analysis, showing over expression of CDH2 genes helps understand the survival rate of HNSCC patients. These analysis and tabulated documents, figures prove the association between genetic alterations in the cadherin family of genes and HNSCC. Conclusion: There exists a significant association between HNSCC and genetic alterations seen in the cadherin family of genes.

Aerosol Contamination in the Dental Operatory During Oral Prophylaxis: An Occupational Hazard

Aim: To investigate the level of aerosol contamination following oral prophylaxis using ultrasonic scalers at different positions in the dental operatory at different time. Methodology: In a pre-fumigatedroom of 10m*15m scaling was performed using ultrasonic scalers along with high volume suction while maintaining all aseptic precautions. Blood agar plates were positioned at the level of patient’s chest (P1), doctor’schest (P2), assistant’s chest (P3), on the floor directly below the patients headrest (P4) and 4 feet away from the dental chair at a height 3 feet above the ground (P5) to assess aerosol contamination occurring during scaling procedure. Similarly, blood agar plates were position at P3,P4,P5 for a time interval of 15 minutes after 1 and 3 hours of the procedure respectively to assess the levels of aerosol post procedure. All the blood agar plates were incubated at 37°C for 24 hours, following which bacterial colony forming unit (CFU) was calculatedfor each plate and gram staining was performed to identify the organism present. Results: At the time of procedure the patient was most exposed to the aerosol. At the end of 3 hours the percentage of aerosol reduction was 81 %. Gram staining showed that the streptococci were predominant organisms with a few short rods as observed on the plates obtained during the procedure, while gram positive bacilli were seen abundantly in samples obtained at the end of 3 hours. Conclusion: The study examined the spreading characteristics of aerosol during and after scaling procedure. Even after 3 hours of completion of the procedure some amount of aerosol present in the room. Hence, the dentist must ensure proper precautionary measures to prevent air-borne nosocomial infections.

Detection of 11 Multidrug Resistance Genes among the Strains of A. Baumannii by Computational Approach

Background: Acinetobacter baumannii is typically short, rod shaped gram negative bacterium. The World Health Organisation has declared it as an opportunistic pathogen in humans. Multi drug resistance involves different genetic determinants making the pathogen difficult to treat. So this study is undertaken to characterize the 11 different drug resistant genes from 19  virulent strains of A. baumannii using in-silico PCR. Aim: Detect the 11 multidrug resistance genes among strains of A. baumannii by computational approach. Materials & Methods: 11 multidrug resistance genes of A. baumannii were selected. Forward and reverse primers of the 11 genes as reported from earlier studies were used for in-silico PCR amplification. 19 strains of A .baumannii set as default strains on the server were chosen and the amplicon bands were observed.  Result: Among the 11 multidrug resistance genes only blaOXA-51like and blaADC were detected among the 19 virulent strains of A. bauamannii. Conclusion: The findings of the study documents the frequency of blaADC and blaOXA-51 like from the selected strains of A. baumannii. However further experimental validation must be done towards the periodical surveillance on the drug resistant strains of A. baumannii in hospital settings.

Prediction of Epitope Peptides for PTK Gene of Acinetobacter baumannii

Background: Acinetobacter baumannii is a gramnegative bacilli acquiring both intrinsic and adaptive patterns of multi drug resistance and virulence. Immune-informatics approach holds promise to detect putative epitope peptides from vital virulence factors which can be further synthesized and evaluated for their immunological response. Aim: The aim of the study was to predict the immuno-dominant peptides from the ptk gene of A. baumannii. Materials and Methods: Protein retrieval of the Ptk gene using CELLO V.2.5 was done with the evaluation of antigenicity and allergenicity of the predicted epitopes, using Vaxijen V2.0 server and AlgPred servers. Epitope structure prediction and validation by using RAMPAGE revealed the homology peptides. Molecular Docking of epitopes with HLA-alleles using ClusterPro server, and further identification of B cell epitope was performed by using Kolaskar and Tonganokar antigenicity method. Results: A total of 20 epitopes were predicted and 18 peptides were chosen based on antigenicity and stability analysis prediction. The structure predictions were carried out using pepfold server and based on Ramachandran plot analysis 10 epitopes were taken for further analysis. Conclusion: The present finding has detected and evaluated the desirable epitope as LFFSLIAQW using an immune-informatic approach. However, it needs further experimental validation for its immunological response using standard in-vitro studies.

Epitope Based Vaccine Peptide Predictions for fimH gene of Acinetobacter baumannii

Background: Acinetobacter baumannii is an opportunistic bacterial pathogen that is primarily associated with hospital-acquired infections. Recently, there is a dramatic increase in the incidence of multidrug-resistant (MDR) strains, which has significantly raised the profile of this emerging opportunistic pathogen. MDR is often associated with the formation of biofilms and various other virulence factors. Amidst all the genes, fimH gene is our area of interest in this research, because it is an important virulence factor in A. baumannii which encodes the Type 1 fimbriae, that helps bacteria bind to the surface of host cells initiating further infection. Aim: The aim of this study was to assess the epitope based vaccine epitope peptide predictions for the fimH protein of A. baumannii. Materials and Methods: The fimH gene for epitope prediction was selected. Druggability and physico-chemical properties were analysed. Antigenicity was predicted. Epitope mapping of T-cell MHC class 1, Class 1 immunogenicity, conservancy and toxicity analysis was done. T-cell class II epitopes were further mapped together with the immuno-dominant B-cell epitopes.  Results: From the selected 20 epitopes, 2 best epitopes (AALVASVCL and YSSGANAFT) were selected after analysing their antigenicity and allergenicity. The epitope YSSGANAFT showed better values in association with HLA alleles - HLA-DP, HLA-DQ, HLA-DR and TLR-2. Conclusion: The finding of the study documents a single immunodominant peptide (sequence) as a promising vaccine candidate to treat infections caused by A. baumannii. However further experimental analysis must be performed to assess the immunological memory and response of the peptide in both in-vitro and in-vivo studies.

Screening and in Silico Validation of Anti-Microbial Peptides Derived from Lysostaphin, Entero and Endolysin

Introduction: Antimicrobial peptides (AMPs) are small molecules which are known to exert destructive effects upon pathogenic microorganisms. AMPs are designed from proteins obtained from various sources and tested under in vitro conditions to deduce their antimicrobial activity. Materials and Methods: A few of the peptidoglycan hydrolases such as lysostaphin (AAB53783.1), enterolysin (AGG79281.1), and endolysin (YP_009901016.1) were selected for the study based on an extensive text mining process. The protein sequences of the proteins were retrieved from the NCBI (National Centre for Biotechnology Information) database in the FASTA format (https://www.ncbi.nlm.nih.gov/protein/). Results and Discussion :In the antimicrobial protein lysostaphin, three antimicrobial peptide are been found, in which two is active and other is inactive, and one has antifungal property with a score of -0.15, and one having cell penetrating property, in which all are non toxic. Conclusion: The present study predicts AMPs from lysostaphin, entero and endolysins. These peptides were found to possess antifungal, anti-biofilm properties. Most of the peptides predicted were found to be non-cell penetrating and non-toxic.

Effect of Ocimum Sanctum Bio Compounds against csuE Gene Protein of Acinetobacter baumanii

Background: Acinetobacter baumannii is a Gram-negative bacillus that is aerobic, pleomorphic and non-motile. Multi-drug resistance and biofilm formation contributes to the virulence and pathogenicity of the bacterium. Among many virulence factors, csuE is critical for initiation and assembly, showing much homology to type 1 and P pili. With much propensity of drug resistance, in recent years alternative medications have spurred renewed interest in targeting potent pathogens. Ocimum sanctum, also known as holy basil or tulsi possess various bio-active properties and can be used as alternative medicine to treat systemic ailments. Aim: This study was aimed to analyze the drug-ligand interactions between csuE protein of A. baumannii and the bio-compounds from O.sanctum using in-silico docking analysis. Material and Methods: csuE protein was retrieved and optimisation of protein was done. Ligands were selected and were assessed for drug likeness using molinspiration parameters. Further the compounds were subjected for docking analysis and the interacted molecules were visualized for binding energy and hydrogen bonds. Results: Out of the 9 compounds of Ocimum sanctum, benzofuran showed good interaction with csuE protein of Acinetobacter baumannii with a least docking energy of -5.31Kcal/Mol. Conclusion: The present study recommends benzofuran as the potent candidate for novel drug design to treat the infections caused by A.baumannii upon further evaluations for its safety and immunological response.

Distribution of Four Biofilm Associated Gene among A. baumannii by in Silico-PCR

Background: A.baumannii is an opportunistic pathogen known for its efficient biofilm formation that is attributed for its virulence. Acinetobacter baumannii is an inhabitant of oral biofilms as well. Many gene operons are involved in the biofilm formation that need to be monitored frequently. Aim: The aim of the present study was to detect the distribution of four biofilm associated genes among A.baumannii. Materials and Methods: Four biofilm forming genes viz., bfms, ptk, pgaB, and fimH of A.baumannii were selected. Forward and reverse primers of those four genes were used for in-silico PCR amplification. 19 strains of A.baumannii set as default on the server were chosen and the amplicon bands were observed Results: The present investigation documents the distribution of four vital biofilm associated gene among 19 different strains of A.baumannii among which bfms was distributed at a higher frequency followed by pgaB and ptk Conclusion: The finding of the study suggests the presence of pgaB, bfms, ptk among the 19 different strains of A.baumannii. However further experimental validation must be done to frequently monitor the presence of the genes among the clinical strains of A.baumannii.

A Computational Approach on the Anti-biofilm Effect of Ocimum sanctum Bio-compounds Against ptk of Acinetobacter baumannii

Introduction: Acinetobacter baumannii is a gram negative coccobacilli often considered as a nosocomial pathogen and as an opportunistic pathogen in immunocompromised patients. It is considered to be multi-drug resistant and a potent bacteria forming vital biofilms. Ptk which is protein tyrosine kinase is a protein coding gene involved with the synthesis of capsular polysaccharide. Ocimum sanctum is a perennial plant belonging to the Lamiaceae family. Tulsi and holy basil are the common names of this plant. In-silico docking approach method is much more convenient and cost effective to assess the bioactive properties of the natural drugs against any target ligands. Aim: The aim of the study to assess the inhibitory effect of Ocimum sanctum bio-compounds against ptk of Acinetobacter baumannii using a computational approach. Materials and Methods: Retrieval of the structure of ptk was followed by Ligand preparation and optimisation. Further drug likeliness was assessed using Molinspiration parameters, docking simulations and visualisation for the binding energy and hydrogen bonds. Results: Among the bio compounds of O.sanctum, benzofuran is selected as an active inhibitory compound with -11.12 as its binding energy showing a high affinity. Conclusion: The findings of the present study documents benzofuran as the promising candidate to design novel drugs from O.sanctum and to target the ptk of A.baumannii. However further experimental validation must be done to observe its efficacy and safety in the treatment of nosocomial infections caused by A.baumannii.

Distribution of Biofilm-associated Genes among Acinetobacter baumannii by in-silico PCR

Background: Acinetobacter baumannii is a coccobacillus that is Gram negative, non motile, non fermentative and oxidase negative. It is the most common and successful nosocomial pathogen recognised by WHO. This dreadful pathogen causes urinary tract infections, ventilator associated pneumonia (VAP), bacteremia, etc., These infections are most common in hospital wards especially Intensive Care Unit (ICU). The infections are due to biofilm formation by the virulent genes of A. baumannii, and the common biofilm-associated genes of A. baumannii were bap, csuE, fimH, epsA, bfmS, ptk, pgaB, ompA, blaPER-1. Among these, bap, epsA and ompA genes are highly prevalent among the clinical strains of A. baumannii. Aim:  To detect the three vital biofilm-associated genes of A. baumannii by in-silico PCR analysis. Materials and Methods: 19 isolates of A. baumannii were selected and 3 target genes, namely epsA, ompA and bap gene were used for the amplification process through in-silico PCR simulation tools. Evolutionary analysis was done for the ompA gene. Results: The epsA gene was expressed in 10.52% of the total strains selected with the highest occurrence of ompA gene as 57.89%. bap gene was not observed from the study strains included. From evolutionary analysis based on ompA distributed strains, the Acinetobacter baumannii SDF and Acinetobacter baumannii BJAB0715 might be the parental strains where the evolution of strains would have started. Through successive generations, the Acinetobacter baumannii MDR-ZJ06 and Acinetobacter baumannii TYTH-1 had become the multidrug resistant strains present in the environment. Conclusion: The findings of the study confirms the distribution of epsA and ompA genes among the 19 different strains of A. baumannii. The study suggests periodical monitoring of biofilm based virulence genes among the clinical strains and to curtail the A. baumannii infections.

Characterization of biofilm producing methicillin resistant coagulase negative Staphylococci from India

Methicillin-resistant coagulase-negative staphylococci (MR-CoNS) cause infectious diseases due to their potential to form biofilm and further colonization in hospital materials. This study evaluated the antibiotic susceptible phenotypes, biofilm-producing ability, and biofilm-associated genes (mecA, icaAD, bap, cna, and fnbA). Biofilm formation was detected through Congo red agar (CRA) method and MTP method. The presence of biofilm and associated genes in MR-CoNS were detected by PCR. A total of 310 (55.95%) isolates produced the biofilm. Among these isolates, Staphylococcus haemolyticus (34.83%), Staphylococcus epidermis (31.93%), Staphylococcus capitis (16.77%), Staphylococcus cohnii (10.96%), and Staphylococcus hominis (5.48%) were identified. The antimicrobial susceptibility pattern of CoNS isolates indicated resistance to cefoxitin (100%), erythromycin (94.8%), ciprofloxacin (66.7%), sulfamethoxazole/trimethoprim (66.7%), gentamicin (66.12%), and clindamycin (62.9%). Resistance rate to mupirocin was 48.5% in S. epidermidis and 38.9% in S. haemolyticus isolates. All isolates were sensitive to vancomycin and linezolid. The prevalence rates of icaAD, bap, fnbA, and cna were 18.06%, 12.5%, 47.4%, and 27.4%, respectively. icaAD and bap genes were detected in 18.06% and 12.5% of MR-CoNS isolates. fnbA and cna genes were detected in 47.41% and 27.41% of MRCoNS isolates. icaAD positive strains exhibited a significant increase in the biofilm formation compared with those that lacked icaAD (0.86 (0.42, 1.39) versus 0.36 (0.14, 0.75), respectively; P < 0.001). In conclusion, the majority of MR-CoNS isolates were biofilm producers, and S. capitis, which possessed icaAD genes, ranked as the great biofilm producer than other Staphylococcus. The study's findings are important to form a strategy to control biofilm formation as an alternative strategy to counter the spread of MR-CoNS in healthcare settings.

Detection of Drug Resistant Genes among A. baumannii by In silico PCR Method

Background: Acinetobacter baumannii is a gram-negative bacterium classified as an opportunistic pathogen in humans by the World Health Organization. Different genetic determinants contribute to multidrug resistance, and transform it as a nosocomial pathogen. Aim: Using in-silico PCR, this analysis aims to characterize the 13 distinct drug resistant genes found in 19 virulent A.baumannii strains. Materials & Methods: There were 11 A.baumannii multidrug resistance genes chosen. In-silico PCR amplification was performed using forward and reverse primers from the 11 genes described in previous research. The amplicon bands were detected in 19 strains of A.baumannii that were set as default on the server. Results: Among the 13 multidrug resistance genes studied, tet A, tet B, Sul 1, Sul 2, DfrA1,  ISAba-1 and ISAba-125 were detected among the 19 virulent strains of ​A.baumannii​. Conclusion: The findings of the study documents the frequency of tet A, tet B, Sul 1, Sul 2, DfrA1, ISAba-1 and ISAba-125 like from the selected strains of A. baumannii. However, more experimental validation is needed in order to conduct routine surveillance on drug-resistant A. baumannii strains in hospital settings.

In silico Analysis of Plant Based Quorum Sensing Inhibitor against Chromobacterium violaceum CviR

Background: Chromobacterium violaceum (C. violaceum), a Gram-negative, facultative anaerobic, non-sporing coccobacillus has a quorum-sensing system consisting of CviI/CviR, a homologous gene. Quorum sensing (QS) is a mechanism of intercellular communication in bacteria that received substantial attention as an alternate strategy for combating bacterial resistance and the development of new anti-infective agents. Methods: DATA SET Information of photochemical from the natural source deposited as a machine readable format in PubChem database was utilized to retrieve the compound for the study. To study ligand - receptor interactions, docking paves way to accomplish the protein ligand interaction was docked through rigid docking CviR protein (PDB ID: 3QP5) was prepared and energy minimized to evaluate the best affinity among the complex. Results: The results showed that the Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One had high affinity for CviR receptor protein and Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One binds to the active site of CviR with binding energy of -9.6 kcal/mol. Conclusion: Overall study concluded that 1. Alpha., 2. Alpha.- Epoxy-1.Beta.-Methyl Cholesta-4,6-Dien-3-One with highest binding affinity for the CviR protein possessing strong inhibitory binding interaction. Hence, we concluded that 1.Alpha.,2.Alpha.-Epoxy-1.Beta.- Methyl Cholesta-4, 6-Dien-3-One good serves as potential an anti-quorum sensing molecule for treating C. violaceum infection.

Virtual Screening to Identify the Protein Network Interaction of Hypericin with Red Complex Pathogens

Introduction: Hypericin is the anthraquinone derivative and has many properties like antiviral, antifungal and antibacterial. The red complex pathogens which include Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in association with other microbes found in the periodontal pockets, cause severe inflammation resulting in periodontitis. Novel bioactive agents from several sources have been tested against the microbial pathogens to deduce antimicrobial activity.  Aim: The aim of the study is to virtually screen and identify the protein network interaction of hypericin in red complex pathogens. Methodology: The STITCH v5.0 pipeline was primarily used to identify the drug-protein interactions. The VirulentPred and VICMPred software were used for elucidating the functional class of the proteins and virulence property. The sub cellular localization of virulent proteins was analysed with pSORTb v3.0 software. Further, the epitopes in virulent proteins were identified using BepiPred v1.0 linear epitope prediction tool. Results: Heat shock protein 90 of Porphyromonas gingivalis were found to involve in the cellular process and DNA topoisomerase IV subunit B, heat shock protein 90, DNA gyrase subunit A and DNA gyrase subunit B of Treponema denticola were found to be the virulent factors. The virulent proteins were located in the cytoplasm, which would further increase the potential effect of the drug to serve as antimicrobial agents. Finally, epitopes were predicted on the virulent proteins which can be specifically docked to further ascertain their interactions with the phytocompound. Conclusion: Hypericin with all its potential and biological benefits can be addressed, can be used as an antimicrobial agent to eradicate dental pathogens which are recalcitrant to treatment. The mode of action of hypericin is, it is targeting crucial proteins in red complex pathogens. Further in vitro studies should be performed on a wide range of pathogens to substantiate the true interactions between the drugs and the protein repertoire of pathogens.

Targeting Omp-A Protein of Acinetobacter Baumannii with the Bio-Active Compounds from Azadirachta Indica - an in-silico Approach

Background: Acinetobacter baumannii is a gram negative bacterium which is typically short, round, coccobacillus and was named after the bacteriologist Paul Baumann. It is an emerging dental pathogen since it acquires  drug resistance and expression of several virulence genes. It is an opportunistic pathogen in humans, affecting people with compromised immune systems. Acinetobacter baumannii is an arising nosocomial microorganism causing serious complications because of the propensity of its multi-drug resistant property. Aim: The aim of the present study was to target omp-A protein of Acinetobacter baumannii with the bio active compounds from Azadirachta indica an in-silico approach. Materials and Methods: The crystal structure of ompA protein was obtained from the PDB protein data bank. The structures of the bio-active derivatives of A. indica were obtained from the chemsketch software. The generated 3D structures were then optimised. Auto Dock instrument was utilized for docking investigation to interpret the affinity between bio-compounds of A. indica against ompA protein of A. baumannii. Results: The 3D crystal structure of OmpA-like domain from A.baumannii was retrieved from PDB database and its PDB ID was 3TD3 – A chain. 3D Structure of OmpA visualization using Biovia-Discovery studio visualizer. The 2D structure of compounds from Azadirachta indica was drawn using ACD chemsketch and saved in MDL-mol format and converted to PDB format using open babel converter. The final docked structures for the drug ligand interactions were assessed for their binding energies and hydrogen bonds. Conclusion: The present study had achieved the anti-biofilm inhibitory effect of imidazole-2-carboxylic acid from A. indica exhibiting a great interaction between activity with ompA utilizing computational investigation.

Effect of Azadirachta indica Bio-Compounds against KpsM Protein of Acinetobacter baumannii

Background: Acinetobacter baumannii was considered as a low priority pathogen earlier, and is been now reported as a priority pathogen causing nosocomial infections. Selection of natural compounds to target the organism is the need of the hour. Aim: This study is aimed to target the KpsM protein of A. baumannii with the bio-compounds from Azadirachta indica using in-silico docking analysis. Materials and Methods: KpsM protein was retrieved and optimisation of protein was done. After that optimization and ligand preparation was carried out. It was continued by molinspiration assessment of the molecular properties of selected compounds. It was followed by docking simulation and docking visualisation. Results: Out of the 7 compounds of Azadirachta indica, dihydro diisoeugenol is the best compound to act on the KpsM protein of Acinetobacter baumannii and a binding energy of -6.83Kcal/Mol. Conclusion: The findings of the study reports isoeugenol with more binding energy than other compounds towards the selected protein KpsM of Acinetobacter baumannii. However it requires further experimental studies to understand the mechanism of its actions and safety.

Attenuation of Quorum Sensing Controlled Virulence Factors and Biofilm Formation by Edible Fruit Extract of Coccinia indica against Pseudomonas aeruginosa

Background: Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that mainly infects immunocompromised individuals and patients with urinary tract infection and chronic infections of the respiratory pathways, including cystic fibrosis. Many quorum sensing (QS) controlled components such as bio surfactants and swarming motilities play an important role in the establishment of biofilms. Targeting these factors through anti-QS strategies prevent biofilm formation and treating infections. Coccinia indica commonly called little gourd is used to treat diabetes, wound, burn infections and has antioxidant, antibacterial and antitussive properties. Methods: The methanolic fruit extract of C. indica was prepared and screened for anti-QS and anti-biofilm formation activity. Pyocyanin inhibition, rhamnolipid, crystal violet staining assay tests was performed and the extract was observed under fluorescent microscope. Results: The results obtained are as follows - the fruit extract inhibits the pyocyanin at 58.13% and 42.27% at 0.5 mg/ml and 1.0 mg/ml, biofilm at 69.86% and 49.06% at 0.5 mg/ml and 1.0 mg/ml, inhibits rhamnolipid assay and under fluorescent microscope it is seen scattered whereas control produce biofilm matrix like appearance. Conclusion: Since less study has been made on the quorum sensing and biofilm activity of C.indica our study aimed to fulfil it and it was found that it exhibits good biofilm formation and thus can be used for treating infections.

Virtual Screening to Identify the Protein Network Interactions of Triclosan with Streptococcus mutans and Enterococcus faecalis

Introduction: Triclosan is considered to be an important ingredient in toothpastes and mouth rinses. Several studies have reported contradictory results regarding the antimicrobial effect of triclosan. Hence, the present in silico study intends to identify the potential targets of triclosan in two common dental pathogens Streptococcus mutans and Enterococcus faecalis. Aim: To identify the protein network interactions of triclosan in Streptococcus mutans and Enterococcus faecalis by virtual screening method. Materials and Methods: The STITCH v5.0 database was initially used for identifying drug-protein interactions followed by VICMPred and VirulentPred which was employed to identify functional class of the proteins and its virulence property. Finally, BepiPred v1.0 Linear Epitope Prediction tool was used to identify the potential epitopes of the virulent proteins. Results: Triclosan was found to interact with crucial proteins in S. mutans and E. faecalis which could contribute to severe forms of periodontitis and endodontic diseases. Conclusion: Taken together, the present study provides the preliminary data on the potential targets of triclosan in common dental pathogens. Further experimental validation is warranted to provide concrete evidence on the molecular targets of dental pathogens. 

Detection of Immuno Dominant Peptides against pgaB of Acinetobacter baumannii

Background: Acinetobacter baumannii is a gram negative non-motile coccobacillus, which was considered as a low priority pathogen with low virulence. Recently, it was declared as the priority pathogen under the critical category of the most dangerous pathogen by WHO. Acinetobacter Baumannii is an inhabitant of oral biofilms, and it also increases the risk of refractory periodontitis. It causes nosocomial infections with pgaB, a part of pgaABCD operon which is involved in the biofilm formation. Aim: The aim of the present study was to detect the immunodominant peptides against pgaB of Acinetobacter baumannii using bioinformatic tools and databases. Materials and Methods: The present study was carried out using immune informatics. The protein sequence of the pgaB protein from A.baumannii was subjected to assess allergenicity, secondary structure, antigenicity and stability prediction of selected T cell epitopes, physico-chemical analysis, Identification of MHC class 2 binders, Final selection of B-cell epitopes was done with IEDB B-cell epitope tool Results: Final docking of the peptides were interpreted by hydrogen bonds and interac- tion scores with TLR-2. Promising scores on antigenicity, instability were obtained. Based on the combinatorial scores, one vaccine peptide (LNLTLGLAL) was suggested to be a promising vaccine candidate against pgaB of A.baumannii. Conclusion: The findings of the present study suggest epitope LNLTLGLAL as a promising vaccine candidate against pgaB of A.baumannii. The vaccine peptides targeting the pgaB Gene in A.baumannii using an immune-informatics approach suggests promising results in the present study. However, the predicted epitope peptides need further experimentation in animal models for its application against A.baumannii.

Virtual Screening to Identify the Protein Network Interaction of Berberine with Red Complex Pathogens

Introduction: Periodontal disease is an infection of the tissues that hold your teeth in place. It's typically caused by poor brushing and flossing habits that allow plaque, a sticky film of bacteria, to build up on the teeth and harden. Elimination of these pathogens from the site of infection remains a perplexing task, which demands the use of antibiotics. The emergence of drug resistant forms has spurred interest into identifying novel therapeutic targets against these pathogens. Aim: The present study employs virtual screening method to identify the protein network interaction of berberine with red complex pathogens. Materials and Methods: Computational tools were used to identify the targets, assess their functional role and virulence property. Further, the peptide epitopes present in the virulence factors were identified using the BepiPred tool. The subcellular location of the virulence proteins was also elucidated using PSORTb. Results: Berberine was found to target vital protein transporters such as TetR family transcriptional regulator and MerR family transcriptional regulator, which is known to play a crucial role in the survival of bacterial cells. Conclusion: Hence the present study provides preliminary data on the protein targets of berberine against red complex pathogens. However, in vitro studies using the compound is warranted to further confirm the efficacy of the compound.

Decoding the Genetic Alterations in Genes of Fibroblast Growth Factor Family and Their Possible Association with HNSCC

Introduction: HNSCC is a type of cancer in the oral and pharynx region. Several mutations/variations are observed in these cancer phenotypes. Fibroblast growth factor belongs to the family of heparin binding growth factors. FGFs are multifunctional proteins with a wide variety of effects; they are most commonly mitogens. Their expression pattern correlates with invasion of HNSCC. Aim: To assess the genetic alterations in genes of the fibroblast growth factor family and their association with HNSCC. Materials and Methods: The demographic data and samples of 528 HNSCC patients was collected from the cBioportal database. Oncoprint analysis was done to assess the amplification and genetic alterations of the members of the FGF gene family. String analysis was performed to evaluate the protein-protein interaction. The information about previous reported mutation and correlation with novel and reported mutation was obtained using GnomAD analysis. Results and Discussion: FGF3,4 and 19 genes showed maximum variation (25%). FGF4 and FGF19 genes showed maximum amplification in addition to deletion mutation. Excitingly FGF3, FGF4 and FGF19 genes showed similar amplification patterns in most of the HNSCC patients. Statistical significant difference in the gene expression of FGF3 9.578 x 10-3 observed between normal and primary tumour. S.  Findings showed many novel mutations and also 4 reported mutations ie:FGF1, FGF12, FGF20, FGF21 Conclusion: Our present study concludes that more evidence is required to confirm their association with HNSCC.

Virtual Screening to Identify the Protein Network Interaction of Triclosan in Red Complex Pathogens

Background: Antimicrobial drug resistance is the major problem encountered world-wide. Novel therapeutic leads have been identified and are regularly tested for their activity against microbial pathogens. Aim: To identify the protein network interactions of triclosan in red complex pathogens. Materials and Methods: The present study follows an observational study design which aims to screen for the interaction of triclosan in red complex pathogens. The interaction was analyzed using the STITCH v.5 pipeline. The functional class of proteins identified were assessed using VICMPred and VirulentPred softwares. The microbial pathogens Treponema denticola ATCC 35405, Tannerella forsythia ATCC 43037, Porphyromonas gingivalis ATCC 33277 are the strains of red complex pathogens that are included in the present study. Results and Discussion: Several proteins were found to interact with triclosan. Among the protein interactions, interactions of triclosan with virulent proteins seems to have a greater impact. The NAD-dependent nucleotide-diphosphate-sugar epimerase [PGN_1370], Putative NAD dependent epimerase [PGN_1886], GDP-fucose synthetase [PGN_1079], Probable oxidoreductase [PGN_1360] of Porphyromonas gingivalis, Conserved hypothetical protein [TDE_2401],  Epimerase/dehydratase family protein [TDE_1439] of Treponema denticola, NAD dependent epimerase/dehydratase family protein [BFO_2919], Hypothetical protein [BFO_1782],  Nitroreductase family protein [BFO_1604] and Nitroreductase family protein [BFO_1516] Tannerella forsythia were found to be exhibit virulence nature. Conclusion: This study identifies the molecular targets of triclosan on red complex pathogens. As triclosan interacts with the red complex pathogens, in future it can be used as a primary medicine for periodontitis and some oral conditions.

In silico Analysis of a Novel Peptide Vaccine against Hepatitis B Virus (HBV)

Background : Hepatitis B is a potentially life-threatening liver infection caused by the Hepatitis B virus (HBV). It is a major global health problem and the most serious type of viral hepatitis. It can cause chronic liver disease and puts people at high risk of death from cirrhosis of the liver and liver cancer. HBV is found in highest concentrations in blood and in lower concentrations in other body fluids. Methods: Target protein was retrieved from the swissprot database. Epitopes were predicted using the BCEPRED server. After running the BLAST algorithm for the target protein, the template with the best identity was selected. After modeling, target protein is verified by using the swiss model workspace and after this process the obtained target protein is allowed to interact with the MHC which is studied by using patchdock, finally these results were viewed by using the deepview tool. Results: The target protein for vaccine development was downloaded from the SwissProt database. Its SwissProt ID was p29178. The protein was isolated from hepatitis B virus genotype G. The virus was isolated from the United States of America. The length of the target protein was found to be 195 amino acids. To confirm that the target protein could be used for vaccine development, the Presence of epitopes in the protein was confirmed using the BCEPRED tool. Results from the SAVS server showed 95.80 of the residues of the protein had an average 3D-1D score greater than 0.2. The protein attained a pass with an ERRAT value of 90.299. Conclusion: The present investigation recognized the promising complex formed between the HBV peptide and MHC molecules. All the downloaded MHC molecules were found to interact with the target protein through the formation of hydrogen bonds. Since these interactions are necessary during an immune response to invading pathogens, the target protein would ultimately trigger an immune response if it is administered as a vaccine for Hepatitis B virus genotype G.

Genetic Alterations in HSPA Family of Genes and their Putative Association with HNSCC

Introduction: Head and neck squamous cell carcinoma (HNSCC) is an aggressive life-threatening disease associated with high mortality rates. Several genes related to stress response have been studied extensively to reveal their possible association with HNSCC. Members of the HSPA (heat shock protein family A) family are exclusively expressed under stress conditions suggesting that these are specialised to function in the stress response. Aim: The aim of the present study is to demonstrate the genetic alterations in the HSPA gene family and their putative association with HNSCC. Materials and Methods: The source of the patient's data was procured from the cBioportal database. The TCGA Firehose Legacy comprised 528 head and neck squamous cell carcinoma cases. Oncoprint data analysis can be used to derive a putative association between the disease phenotype and genotype, to identify the variations and to identify any novel variations which can be associated with the disease phenotype. The gnomAD data analysis was used to compare between the observed variants documented in the present study with that of reported variants deposited in the gnomAD repository. Results and Discussion: The HSPA1A&HSPA1B genes harboured high frequency of amplification and deep deletions. The expression of two genes HSPA8 and HSPA13 was found to be up-regulated in the primary tumor sample in comparison to normal tissues. In Kaplan Meier analysis, HSPA8 gene expression was compared with gender, here, high expression in females shows low survival rate. Similarly, HSPA13 gene expression was compared with race, here low expression in africanamerican population shows low survival rate. Conclusion: The present study provides preliminary data on the involvement of the HSPA family of genes with HNSCC, which has to be validated using experimental evidence in other populations.

Delineating the potential targets of thymoquinone in ESKAPE pathogens using a computational approach

The present study was designed to identify and analyze the targets of thymoquinone on drug resistant pathogens employing in silico tools. The target identification was performed using STITCH tool, followed by the functional analysis of protein targets by VICMPred. Further, VirulentPred was used to determine the nature of virulence of target proteins. The putative epitopes present on the virulent proteins were identified using BepiPred tool. The subcellular location of the virulent proteins was assessed using PSORTb. The results showed multiple targets of the pathogens being targeted. The nitric-oxide synthase-like protein of Staphylococcus aureus and acetyltransferase family protein, histone acetyltransferase HPA2, GNAT family acetyltransferase of Acinetobacter baumannii was found to be the virulent proteins interacting with thymoquinone. Molinspiration assessments showed zero violations suggesting the druggability of TQ. The study unveils the molecular mechanisms underlying the antimicrobial effect of thymoquinone as demonstrated by in silico procedures.

Decoding The Genetic Alterations In Cytochrome P450 Family 3 Genes And Its Association With HNSCC

INTRODUCTION

Cytochrome P450 (CYPs) are enzymes belonging to the family of heme-containing proteins, most commonly found in the endoplasmic reticulum and mitochondria. These enzymes catalyze a variety of functions including metabolism of steroids, fatty acids, natural compounds, drugs and carcinogenic chemicals. The inherent association of CYPs with disease conditions have turned the focus into the genetic alterations or variations associated with phenotypes such as drug responsiveness, chemical toxicity and bioconversion of procarcinogens to active carcinogens.

RESULTS

A total of 8 genes of the CYP3 family were analyzed, among which 4 genes were found to harbour gross abnormalities and variations. The genes CYP3A4, CYP3A5, CYP3A7, CYP3A43 showed a common pattern of gene amplification in a group of patients. Truncating and missense variants were also identified of which rs199908125 of CYP3A4 and rs768530577 of CYP3A5 were reported in different populations.

MATERIALS AND METHODS

The present observation study utilizes several computational tools to identify and predict the possible outcomes of gene alterations in CYP3 family of genes with head and neck squamous cell carcinoma (HNSCC). cBioportal hosts an exhaustive collection of datasets of various cancers which was the primary source of analysis. Oncoprint data obtained was further analysed using tools such as PROVEAN, I-Mutant and gnomAD.

DISCUSSION

The gnomAD analysis revealed a few polymorphic rare variants with minor allele frequency less than 0.01, which could have a putative association with HNSCC. Five out of eight variants identified were found to be deleterious exhibiting decreased protein stability.

CONCLUSION

Further screening of the genetic abnormalities through experimental validation in different populations are warranted to derive an association between the gene identifiers and disease phenotype.

Hijacking of the Host's Immune Surveillance Radars by Burkholderia pseudomallei

Burkholderia pseudomallei (B. pseudomallei) causes melioidosis, a potentially fatal disease for which no licensed vaccine is available thus far. The host-pathogen interactions in B. pseudomallei infection largely remain the tip of the iceberg. The pathological manifestations are protean ranging from acute to chronic involving one or more visceral organs leading to septic shock, especially in individuals with underlying conditions similar to COVID-19. Pathogenesis is attributed to the intracellular ability of the bacterium to ‘step into’ the host cell’s cytoplasm from the endocytotic vacuole, where it appears to polymerize actin filaments to spread across cells in the closer vicinity. B. pseudomallei effectively evades the host’s surveillance armory to remain latent for prolonged duration also causing relapses despite antimicrobial therapy. Therefore, eradication of intracellular B. pseudomallei is highly dependent on robust cellular immune responses. However, it remains ambiguous why certain individuals in endemic areas experience asymptomatic seroconversion, whereas others succumb to sepsis-associated sequelae. Here, we propose key insights on how the host’s surveillance radars get commandeered by B. pseudomallei.

Genetic alterations in Wnt family of genes and their putative association with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most frequent type of head and neck cancer that usually arises from the mucosal surfaces of several organs including nasal cavity, paranasal sinuses, oral cavity, tongue, pharynx, and larynx. The Wnt signaling pathway is a crucial mechanism for cellular maintenance and development. It regulates cell cycle progression, apoptosis, proliferation, migration, and differentiation. Dysregulation of this pathway correlates with oncogenesis in various tissues including breast, colon, pancreatic as well as head and neck cancers. The present study aims to assess the gene alterations in the Wnt family of genes so as to derive an association with HNSCC. Computational approaches have been utilized for the identification of gene alterations in the Wnt family of genes. Several databases such as cBioportal, STRING, and UALCAN were used for the purpose. The frequency of alteration was high in case of Wnt family member 11 (5%). Gene amplification, deep deletions, missense and truncating mutations were observed in HNSCC patients. There was a marked difference in the gene expression profile of WNT11 between grades as well as normal samples. The survival probability measured using the Kaplan-Meier curve also presented with a significant difference among male and female subjects experiencing a low/medium level expression. The female patients showed less survival probability when compared to the male subjects. This provides the prognostic significance of the WNT11 gene in HNSCC. Taken together, the present study provides clues on the possible association of WNT11 gene alterations with HNSCC, which has to be further validated using experimental approaches.

Molecular characterization and epitope-based vaccine predictions for ompA gene associated with biofilm formation in multidrug-resistant strains of A.baumannii

The present study was conducted to molecularly characterize the biofilm associated ompA gene from the drug resistant strains of A. baumannii and its immuno-dominant vaccine epitope predictions through immuno-informatic approach. ompA was amplified by PCR from the genomic DNA and was sequenced. Using the ORF, ompA protein sequence was retrieved and was subjected for IEDB T cell and B cell epitope analysis for the selection of the epitope peptides. Selected peptides were evaluated using appropriate servers and tools to assess the propensity for its antigenicity, solubility, physico-chemical property, toxigenicity and class-I immunogenicity. MHC class I and II restriction of HLA alleles was also performed. 48% (n = 24) of the strains possessed ompA gene. Protein structure was successfully retrieved with the selection of two epitopes viz., E1- FDGVNRGTRGTSEEGTLGNA and E2-KLSEYPNATARIEGHTDNTGPRKL. Final docking with TLR-2, showed E2 as the best epitope candidate predicted with the highest number of hydrogen bonds.

Asymptomatic SARS-CoV-2 infection: is it all about being refractile to innate immune sensing of viral spare-parts?-Clues from exotic animal reservoirs

A vast proportion of coronavirus disease 2019 (COVID-19) individuals remain asymptomatic and can shed severe acute respiratory syndrome (SARS-CoV) type 2 virus to transmit the infection, which also explains the exponential increase in the number of COVID-19 cases globally. Furthermore, the rate of recovery from clinical COVID-19 in certain pockets of the globe is surprisingly high. Based on published reports and available literature, here, we speculated a few immunovirological mechanisms as to why a vast majority of individuals remain asymptomatic similar to exotic animal (bats and pangolins) reservoirs that remain refractile to disease development despite carrying a huge load of diverse insidious viral species, and whether such evolutionary advantage would unveil therapeutic strategies against COVID-19 infection in humans. Understanding the unique mechanisms that exotic animal species employ to achieve viral control, as well as inflammatory regulation, appears to hold key clues to the development of therapeutic versatility against COVID-19.

Deciphering the Genetic Alterations in SPARC Gene Family and Its Association with HNSCC

The aim of this study is to identify the genetic alteration in SPARC gene family and its association with head and neck squamous cell carcinoma (HNSCC). Head and neck cancer is a set of cancerous lesions arising from the squamous cell of the mucous membrane of the oral cavity, nose throat, larynx and pharynx. SPARC gene encodes for cysteine rich acid matrix metalloprotein, osteonectin whose expression in metastatic OSCC (Oral squamous cell carcinoma) was found to be higher. This expression pattern also correlated with the worst pattern of invasion and differentiation of OSCC tumors. In line with the above facts, the present study was carried out to ascertain the gene alterations and their consequences. Also the putative association of gene alterations with HNSCC was analyzed using computational tools. The Cancer Gene Atlas (TCGA, Firehose Legacy) dataset hosted by the cBioportal server was used in the present study. The non-synonymous variants identified were further assessed for protein stability and pathogenicity employing IMutant and PROVEAN tools. Gene amplification was observed in the FSTL1 gene, which was also shown to present with the highest frequency of gene alterations (5%) among eight genes. Furthermore, the expression of the FSTL1 gene was found to differ significantly among different grades of HNSCC. In conclusion, the study throws light on the possible association of the FSTL1 gene of the SPARC family with HNSCC.

Delineating the Immuno-Dominant Antigenic Vaccine Peptides Against gacS-Sensor Kinase in Acinetobacter baumannii: An in silico Investigational Approach

Objectives

To predict the novel vaccine peptide candidates against gacS protein involved with the citrate utilization in the two-component system of A. baumannii-associated virulence as an alternative strategy to combat the multi-drug resistant strains using an immuno-informatic approach.

Methods

The study is designed as an observational in silico study design with the application of BepiPred, AlgPred, VaxiJen, AntigenPro, SolPro, Expasy ProtParam server, IEDB database, and MHC cluster analytical tools and servers to predict the immuno-dominant B-cell and T-cell epitopes from gacS FASTA sequences retrieved from UNIPROT database. Further peptide interactions with TLR-4 was assessed based on the number of hydrogen bonds.

Results

Nine peptides (20aa) with the highest score of 1 were selected from the 137 epitopes, and five were predicted as antigenic epitopes (E1-E5). E3 was selected as the potent antigen (score: 0.939537) and E1 as the best vaccine candidate (score: 0.9803) under AntigenPro and Vaxijen server, respectively. SolPro predicted all epitopes as soluble peptides. ProtParam predictions showed E3 and E5 as stable proteins with a shelf life of 3.5 and 1.9 h and possessed negative GRAVY values. PsortB server predicted a final localization score of 7.88 for the gacS protein sequence as a cytoplasmic membrane protein. IEDB conservancy analysis showed 100% conserved sequences within the gacS sequence, and class I conservancy yielded positive values for all epitopes. Cluster analysis showed strong interactions, and the protein-peptide interactions with TLR-2 finally detected E5 as the best interacting peptide (H bonds = 14) followed by E3 (H bonds = 12).

Conclusion

The study suggests five antigenic peptides as promiscuous vaccine candidates to target the gacS of A. baumannii using immuno-informatic approach toward the peptide synthesis and in vitro analysis. However, the study recommends further experimental validation for immunological response and memory through in vivo studies.

Virtual Screening to Identify the Protein Targets in Common Dental Pathogens Interacting with Menthol

Deducing the molecular pathway underlying the antimicrobial effect of phytocompounds is an inevitable part of drug discovery. Selection of potential targets on the microbial pathogens will eventually lead to eradication of microbes and effective treatment. In this context, the present insilico study identifies vital targets in the dental pathogens interacting with menthol. The STITCHtool was used for identifying the protein drug interaction, VICMPred and VirulentPred tools were used for identifying the functional class and virulence nature of proteins. PSORTb was used to locate the sub-cellular location of the virulent proteins. The study results indicate that menthol interacts with virulence factors of Treponema denticola. These factors play a crucial role in cell survival and hence can be a good target for further in vitro and in vivo studies. To conclude, menthol was found to interact with crucial proteins of dental pathogens which can be targeted to achieve promising results.

Decoding the Genetic Alterations in PRAME Gene Family and Its Association with Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most common form of cancer with an incidence rate greater in male than in female. Advancements in molecular diagnostics have identified several pathways which can have a direct or indirect role in the development and progression of HNSCC. The PRAME (PReferentially Antigen expressed in MElanoma) gene family is yet another group of genes which has been recently implicated in HNSCC. The present study aims to identify the genetic alterations, the pattern of gene expression and the consequence of mutations in the PRAME family of genes in HNSCC patients. Several databases such as cBioportal, gnomAD, IMutant, PROVEAN were used to assess genetic alterations. The alterations included deep deletions, amplification, inframe, missense, truncating mutations. The gene showing the highest frequency of alteration (PRAME - 3%) was further assessed for its gene expression profile using the UALCAN database. The expression profile relative to normal samples was found to be significantly higher in HNSCC patients (p = 1.11 x 10-16). Further, the survival curve based on high and low/medium expression of the PRAME gene was assessed by Kaplan-Meier method. The analysis revealed a significant difference in the survival rate of patients with high and low/medicum level expression (0.0095). In addition, the high level expression was found to be associated with poor survival rate in HNSCC patients compared to those exhibiting low and medium level expression. In conclusion the study provides insights into the putative association of genes of the PRAME family with HNSCC. The preliminary results have to be further validated using experimental procedures.

Computational Approach to Identify Mutations in Genes of Notch Signaling Pathway and Its Association with OSCC

Derailments in signal transduction pathways are associated with the development of tumors. One such vital pathway is the Notch signaling pathway which is associated with various processes of carcinogenesis such as proliferation of cells, cell renewal, angiogenesis and oncogenic microenvironment preservation. Interestingly, Notch also plays a pivotal role in tumor development by acting as an oncogene as well as tumor suppressor gene. In view of this fact, the present study was designed to analyze mutations in Notch signalling pathway which might have a crucial role in the etiology of oral squamous cell carcinoma (OSCC) using computational approach. The Cancer Gene Atlas data set hosted in the cBioportal was used in the present study. These samples were queried for the presence of mutations in Notch signalling genes which included a predefined list of 55 genes. Further, the Oncoprint data obtained was compared to that of gnomAD database which identified novel and reported mutations in the genes analyzed. Additionally, I-Mutant and MutPred analysis was carried out to determine the stability and pathogenicity of the variations recorded. Among 55 genes analysed, SPEN gene was shown to possess the highest frequency of mutation (5%) followed by FBXW7, Notch1, EP300, NUMB, and RBPJL genes. Most of the mutations identified were novel as assessed using the control dataset from the gnomAD database. The stability of the protein was found to decrease upon nucleotide substitution. Finally, the MutPred score revealed that most of the mutant proteins were pathogenic.  Several novel mutations have been identified in the pathway analyzed. Functional analysis of these variants using experimental approaches would aid in dissecting their association with OSCC.