Publications by authors named "Sajjad Ahmad"

317 Publications

Role of Insect Gut Microbiota in Pesticide Degradation: A Review.

Front Microbiol 2022 3;13:870462. Epub 2022 May 3.

Department of Entomology, South China Agricultural University, Guangzhou, China.

Insect pests cause significant agricultural and economic losses to crops worldwide due to their destructive activities. Pesticides are designed to be poisonous and are intentionally released into the environment to combat the menace caused by these noxious pests. To survive, these insects can resist toxic substances introduced by humans in the form of pesticides. According to recent findings, microbes that live in insect as symbionts have recently been found to protect their hosts against toxins. Symbioses that have been formed are between the pests and various microbes, a defensive mechanism against pathogens and pesticides. Insects' guts provide unique conditions for microbial colonization, and resident bacteria can deliver numerous benefits to their hosts. Insects vary significantly in their reliance on gut microbes for basic functions. Insect digestive tracts are very different in shape and chemical properties, which have a big impact on the structure and composition of the microbial community. Insect gut microbiota has been found to contribute to feeding, parasite and pathogen protection, immune response modulation, and pesticide breakdown. The current review will examine the roles of gut microbiota in pesticide detoxification and the mechanisms behind the development of resistance in insects to various pesticides. To better understand the detoxifying microbiota in agriculturally significant pest insects, we provided comprehensive information regarding the role of gut microbiota in the detoxification of pesticides.
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http://dx.doi.org/10.3389/fmicb.2022.870462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9111541PMC
May 2022

Vaccinomics to Design a Multi-Epitopes Vaccine for .

Int J Environ Res Public Health 2022 05 4;19(9). Epub 2022 May 4.

Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan.

Antibiotic resistance (AR) is the result of microbes' natural evolution to withstand the action of antibiotics used against them. AR is rising to a high level across the globe, and novel resistant strains are emerging and spreading very fast. is a multidrug resistant Gram-negative bacteria, responsible for causing severe nosocomial infections that are treated with several broad spectrum antibiotics: carbapenems, β-lactam, aminoglycosides, tetracycline, gentamicin, impanel, piperacillin, and amikacin. The genome is superplastic to acquire new resistant mechanisms and, as there is no vaccine in the development process for this pathogen, the situation is more worrisome. This study was conducted to identify protective antigens from the core genome of the pathogen. Genomic data of fully sequenced strains of were retrieved from the national center for biotechnological information (NCBI) database and subjected to various genomics, immunoinformatics, proteomics, and biophysical analyses to identify potential vaccine antigens against . By doing so, four outer membrane proteins were prioritized: TonB-dependent siderphore receptor, OmpA family protein, type IV pilus biogenesis stability protein, and OprD family outer membrane porin. Immuoinformatics predicted B-cell and T-cell epitopes from all four proteins. The antigenic epitopes were linked to design a multi-epitopes vaccine construct using GPGPG linkers and adjuvant cholera toxin B subunit to boost the immune responses. A 3D model of the vaccine construct was built, loop refined, and considered for extensive error examination. Disulfide engineering was performed for the stability of the vaccine construct. Blind docking of the vaccine was conducted with host MHC-I, MHC-II, and toll-like receptors 4 (TLR-4) molecules. Molecular dynamic simulation was carried out to understand the vaccine-receptors dynamics and binding stability, as well as to evaluate the presentation of epitopes to the host immune system. Binding energies estimation was achieved to understand intermolecular interaction energies and validate docking and simulation studies. The results suggested that the designed vaccine construct has high potential to induce protective host immune responses and can be a good vaccine candidate for experimental in vivo and in vitro studies.
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http://dx.doi.org/10.3390/ijerph19095568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9104312PMC
May 2022

Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan.

Sci Rep 2022 May 11;12(1):7703. Epub 2022 May 11.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.

Tuberculosis, caused by Mycobacterium tuberculosis, is a high-burden disease in Pakistan, with multi-drug (MDR) and extensive-drug (XDR) resistance, complicating infection control. Whole genome sequencing (WGS) of M. tuberculosis is being used to infer lineages (strain-types), drug resistance mutations, and transmission patterns-all informing infection control and clinical decision making. Here we analyse WGS data on 535 M. tuberculosis isolates sourced across Pakistan between years 2003 and 2020, to understand the circulating strain-types and mutations related to 12 anti-TB drugs, as well as identify transmission clusters. Most isolates belonged to lineage 3 (n = 397; 74.2%) strain-types, and were MDR (n = 328; 61.3%) and (pre-)XDR (n = 113; 21.1%). By inferring close genomic relatedness between isolates (< 10-SNPs difference), there was evidence of M. tuberculosis transmission, with 55 clusters formed consisting of a total of 169 isolates. Three clusters consist of M. tuberculosis that are similar to isolates found outside of Pakistan. A genome-wide association analysis comparing 'transmitted' and 'non-transmitted' isolate groups, revealed the nusG gene as most significantly associated with a potential transmissible phenotype (P = 5.8 × 10). Overall, our study provides important insights into M. tuberculosis genetic diversity and transmission in Pakistan, including providing information on circulating drug resistance mutations for monitoring activities and clinical decision making.
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http://dx.doi.org/10.1038/s41598-022-11795-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9095715PMC
May 2022

Engineering processive cellulase of Clostridium thermocellum to divulge the role of the carbohydrate-binding module.

Biotechnol Appl Biochem 2022 Apr 28. Epub 2022 Apr 28.

School of Biological Science, University of the Punjab, Lahore, Pakistan.

The processive cellulase (CelO) is an important modular enzyme of Clostridium thermocellum. To study the effect of the carbohydrate-binding module (CBM3b) on the catalytic domain of CelO (GH5), four engineered derivatives of CelO were designed by truncation and terminal fusion of CBM3b. These are CBM at the N-terminus, native form (CelO-BC, 62 kDa); catalytic domain only (CelO-C, 42 kDa); CBM at the C-terminus (CelO-CB, 54 kDa) and CBM attached at both termini (CelO-BCB, 73 kDa). All constructs were cloned into pET22b (+) and expressed in Escherichia coli BL21 (DE3) star. The expression levels of CelO-C, CelO-CB, CelO-BC, and CelO-BCB were 35%, 35%, 30%, and 20%, respectively. The enzyme activities of CelO-C, CelO-CB, CelO-BC, and CelO-BCB against 1% regenerated amorphous cellulose (RAC) were 860, 758, 985, and 1208 units per μmole of the enzyme, respectively. The enzymes were partially purified from the lysate of E. coli cells by heat treatment followed by anion exchange FPLC purification. Against RAC, CelO-C, CelO-CB, CelO-BC, and CelO-BCB showed K values of 32, 33, 45, and 43 mg⋅mL and V values of 3571, 3846, 3571, and 4545 U⋅min , respectively. CBM3b at the N-terminus of GH5 linked through a P/T-rich linker was found to enhance the catalytic activity and thermostability of the enzyme.
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http://dx.doi.org/10.1002/bab.2352DOI Listing
April 2022

Microbial adaptation and impact into the pesticide's degradation.

Arch Microbiol 2022 Apr 28;204(5):288. Epub 2022 Apr 28.

Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47906, USA.

The imprudent use of agrochemicals to control agriculture and household pests is unsafe for the environment. Hence, to protect the environment and diversity of living organisms, the degradation of pesticides has received widespread attention. There are different physical, chemical, and biological methods used to remediate pesticides in contaminated sites. Compared to other methods, biological approaches and their associated techniques are more effective, less expensive and eco-friendly. Microbes secrete several enzymes that can attach pesticides, break down organic compounds, and then convert toxic substances into carbon and water. Thus, there is a lack of knowledge regarding the functional genes and genomic potential of microbial species for the removal of emerging pollutants. Here we address the knowledge gaps by highlighting systematic biology and their role in adaptation of microbial species from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Moreover, by co-metabolism, the microbial species fulfill their nutritional requirements and perform more efficiently than single microbial-free cells. But in an open environment, free cells of microbes are not much prominent in the degradation process due to environmental conditions, incompatibilities with mechanical equipment and difficulties associated with evenly distributing inoculum through the agroecosystem. This review highlights emerging techniques involving the removal of pesticides in a field-scale environment like immobilization, biobed, biocomposites, biochar, biofilms, and bioreactors. In these techniques, different microbial cells, enzymes, natural fibers, and strains are used for the effective biodegradation of xenobiotic pesticides.
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http://dx.doi.org/10.1007/s00203-022-02899-6DOI Listing
April 2022

Alternatives to endokeratoplasty: an attempt towards reducing global demand of human donor corneas.

Regen Med 2022 Jul 28;17(7):461-475. Epub 2022 Apr 28.

Institute of Ophthalmology, University College London, London, EC1V 9EL,UK.

The cornea is an anterior transparent tissue of the eye that enables the transmission of surrounding light to the back of the eye, which is essential for maintaining clear vision. Corneal endothelial diseases can lead to partial or total blindness; hence, surgical replacement of the diseased corneal tissue with a healthy cadaveric donor graft becomes necessary when the endothelium is damaged. Keratoplasties face a huge challenge due to a worldwide shortage in the supply of human donor corneas. Hence, alternative solutions such as cell or tissue engineering-based therapies have been investigated for reducing the global demand of donor corneas. This review aims at highlighting studies that have been successful at replacing partial or total endothelial keratoplasty.
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http://dx.doi.org/10.2217/rme-2021-0149DOI Listing
July 2022

Synthesis, crystal structure investigation and computational approach to discover potential hydrazide derivatives as a potent inhibitor of cyclooxygenase-2 enzyme.

J Biochem Mol Toxicol 2022 Apr 18:e23082. Epub 2022 Apr 18.

Department of Chemistry, Tulane University, New Orleans, Louisiana, USA.

This study reports the synthesis of two new hydrazide derivatives, namely, (E)-N'-(4- bromobenzylidene)-2-(4-isobutylphenyl)propanehydrazide (4a) and (E)-N'-benzylidene-2-(4-isobutylphenyl)propanehydrazide (4b), respectively. The compounds were synthesized by the reaction of benzaldehyde with Ibuprofen acid hydrazide. Their structures were confirmed by X-ray crystallography. To try to do a more detailed investigation, computational studies including Hirshfeld surface analyses, energy frameworks, density functional theory (DFT) optimizations, frontier orbital analyses, molecular electrostatic potential analyses, and natural bond orbital analyses of the studied compounds are performed. Moreover, molecular docking and dynamics simulations of complexes of the compounds with the cyclooxygenase-2 (COX-2) enzyme were performed to determine the anti-inflammatory potential of the compounds. These analyses predicted the compounds to show maximum chemical interactions and be dynamically stable during simulation time. Furthermore, estimation of binding free energies confirmed the high binding affinity of the compounds for the COX-2 enzyme.
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http://dx.doi.org/10.1002/jbt.23082DOI Listing
April 2022

Designing a multi-epitope vaccine against Chlamydia pneumoniae by integrating the core proteomics, subtractive proteomics and reverse vaccinology-based immunoinformatics approaches.

Comput Biol Med 2022 06 9;145:105507. Epub 2022 Apr 9.

Department of Bioinformatics and Biotechnology, Government College University Faisalabad, 38000, Faisalabad, Pakistan. Electronic address:

Chlamydia pneumoniae, a pneumonia causing specie belonging to chlamydia bacterium. C. pneumonia is considered as a leading cause of pneumonia. Apart from that, C. pneumoniae infection can also cause a variety of inflammatory disorders. There is an urgent need to tackle the major concerns arises due to infections causing by C. pneumoniae as no licensed vaccine available against this bacterial infection. In the framework of this study, a core proteome was generated C. pneumoniae strains was generated which revealed a total of 4754 core proteins. Later, 4 target proteins were obtained from 4754 core proteins by applying subtractive proteomics pipeline. Finally, MEV construct was designed by applying reverse vaccinology-based immunoinformatics approach on four target proteins. Molecular docking analysis were conducted to better understand thermodynamic stability, binding affinities, and interaction of vaccine. The binding interactions of MEV construct against TLR4, MHCII and MHCII showed that these candidate vaccines perfectly fit into the binding domains of the receptors. In addition, MEV construct has a better binding energy of 103.7 ± 15.4, 72.1 ± 9.1, and 70.4 ± 16.0 kcal/mol against TLR4, MHCII and MHCI. MD simulation was run at 200ns on docked complexes which further strengthened the current findings. Respective codon of vaccine construct was optimized and then in silico cloned into an E. coli expression host to ensure maximum vaccine protein expression. Despite the fact that the in-silico analysis used in this research produced reliable results, more studies are needed to validate the effectiveness and performance of proposed vaccine candidate.
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http://dx.doi.org/10.1016/j.compbiomed.2022.105507DOI Listing
June 2022

Incidence of SARS-CoV-2 re-infection in anti-nucleocapsid IgG-positive healthcare workers: a prospective cohort study.

Ir J Med Sci 2022 Apr 12. Epub 2022 Apr 12.

Department of Medicine, Peshawar Medical College, Riphah International University, Islamabad, Pakistan.

BACKGROUND : Since the pandemic of SARS-CoV-2 began, our understanding of the pathogenesis and immune responses to this virus has continued to evolve. It has been shown that this infection produces natural detectable immune responses in many cases. However, the duration and durability of immunity and its effect on the severity of the illness are still under investigation. Moreover, the protective effects of antibodies against new SARS-CoV-2 variants still remain unclear.

Objectives: To assess the incidence and associated demographic features of SARS-CoV-2 infection in anti-nucleocapsid IgG-positive and anti-nucleocapsid IgG-negative healthcare workers.

Material And Methods: This prospective longitudinal cohort study was conducted in Peshawar Medical College group of hospitals of Prime Foundation. Anti-nucleocapsid IgG sero-positive and anti-nucleocapsid IgG sero-negative healthcare workers were followed for a period of 6 months (from 1 Aug 2020 to 31 Jan 2021), and the incidence of SARS-CoV-2 was confirmed by RT-PCR.

Results: A total number of 555 cohorts were followed for a period of 6 months; of them 365 (65.7%) were anti-nucleocapsid-negative (group A) and 190 (34.3%) were anti-nucleocapsid-positive (group B) healthcare workers. The mean age of the study cohort was 33.85 ± 9.80 (anti-N (-), 34.2 ± 10.58; anti-N ( +), 33.5 ± 9.50). The median antibody level in anti-nucleocapsid-positive HCWs was 15.95 (IQR: 5.24-53.4). Male gender was the majority in both groups (group A, 246 (67%), group B, 143 (48%)) with statistically significant difference (P < 0.05). Majority of the HCWs were blood group B in both groups (34% each). None of the 190 anti-nucleocapsid-positive HCWs developed subsequent SARS-CoV-2 re-infection, while 17% (n = 65) HCWs developed infection in anti-nucleocapsid-negative group during the 6-month follow-up period.

Conclusion: In conclusion, none of the anti-nucleocapsid-positive HCWs developed SARS-CoV-2 re-infection in this study, and the presence of IgG anti-nucleocapsid antibodies substantially reduce the risk of re-infection for a period of 6 months.
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http://dx.doi.org/10.1007/s11845-022-02997-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9001818PMC
April 2022

PSRR: A Web Server for Predicting the Regulation of miRNAs Expression by Small Molecules.

Front Mol Biosci 2022 21;9:817294. Epub 2022 Mar 21.

University Hospital for Gynecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg, Germany.

MicroRNAs (miRNAs) play key roles in a variety of pathological processes by interacting with their specific target mRNAs for translation repression and may function as oncogenes (oncomiRs) or tumor suppressors (TSmiRs). Therefore, a web server that could predict the regulation relations between miRNAs and small molecules is expected to achieve implications for identifying potential therapeutic targets for anti-tumor drug development. Upon obtaining positive/known small molecule-miRNA regulation pairs from SM2miR, we generated a multitude of high-quality negative/unknown pairs by leveraging similarities between the small molecule structures. Using the pool of the positive and negative pairs, we created the Dataset1 and Dataset2 datasets specific to up-regulation and down-regulation pairs, respectively. Manifold machine learning algorithms were then employed to construct models of predicting up-regulation and down-regulation pairs on the training portion of pairs in Dataset1 and Dataset2, respectively. Prediction abilities of the resulting models were further examined by discovering potential small molecules to regulate oncogenic miRNAs identified from miRNA sequencing data of endometrial carcinoma samples. The random forest algorithm outperformed four machine-learning algorithms by achieving the highest AUC values of 0.911 for the up-regulation model and 0.896 for the down-regulation model on the testing datasets. Moreover, the down-regulation and up-regulation models yielded the accuracy values of 0.91 and 0.90 on independent validation pairs, respectively. In a case study, our model showed highly-reliable results by confirming all top 10 predicted regulation pairs as experimentally validated pairs. Finally, our predicted binding affinities of oncogenic miRNAs and small molecules bore a close resemblance to the lowest binding energy profiles using molecular docking. Predictions of the final model are freely accessible through the PSRR web server at https://rnadrug.shinyapps.io/PSRR/. Our study provides a novel web server that could effectively predict the regulation of miRNAs expression by small molecules.
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http://dx.doi.org/10.3389/fmolb.2022.817294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8979021PMC
March 2022

Complexes of 1-(2-R(F, CH, Cl)-phenyl)-1,4-dihydro-5H-tetrazole-5-thiones with cadmium chloride: Synthesis, molecular, crystal structures and computational investigation approach.

J Inorg Biochem 2022 Jun 11;231:111791. Epub 2022 Mar 11.

Alekseev State Technical University, Nizhny Novgorod 603950, Russia.

New complex compounds (I) - (IV) were synthesized by the reaction of 1-(2-fluorofluorophenyl) -1,4-dihydro-5H-tetrazole-5-thione (HL), 1-(2-methylphenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL) and 1-(2-chlorochlorophenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL) with cadmium chloride. By X-ray diffraction analysis, molecular and crystal structures of complexes (I), (II), (III) and (IV) are determined. (CIF files CCDC № 2,003,797 (I), 1,993,454 (II), 2,151,359 (III), 2,098,997 (IV)). Hirshfeld surface analysis, frontier orbital analysis, atomic charges, electrostatic potential, nonlinear optical properties, and natural bond analysis of all three‑cadmium metal-organic complexes were discussed. A molecular docking study was used to investigate compounds' binding and interactions with DNA molecules, which predicted compound I as the best binder at the DNA minor groove and demonstrated closed distance interactions. In a long run of molecular dynamics simulations, the compound I complex was also depicted with good dynamics.
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http://dx.doi.org/10.1016/j.jinorgbio.2022.111791DOI Listing
June 2022

Whole Proteome-Based Therapeutic Targets Annotation and Designing of Multi-Epitope-Based Vaccines against the Gram-Negative XDR- Bacterium.

Vaccines (Basel) 2022 Mar 17;10(3). Epub 2022 Mar 17.

Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan.

This study involved therapeutic targets mining for the extremely drug-resistant bacterial species called , which is known to infect humans. The infections caused by this species in different parts of the human body have been linked with a higher degree of resistance to several classes of antibiotics. Meanwhile, alternate therapeutic options are needed to treat these bacterial infections in clinical settings. In the current study, a subtractive proteomics approach was adapted to annotate the whole proteome of and prioritize target proteins for vaccine-related therapeutics design. This was followed by targeted protein-specific immune epitope prediction and prioritization. The shortlisted epitopes were further subjected to structural design and in silico validation of putative vaccines against . The final vaccine designs were also evaluated for potential interaction analysis with human TLR-2 through molecular docking. Finally, the putative vaccines were subjected to in silico cloning and immune simulation approaches to ensure the feasibility of the target-specific vaccine constructs in further experimental designs.
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http://dx.doi.org/10.3390/vaccines10030462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8955209PMC
March 2022

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

Vaccines (Basel) 2022 Feb 28;10(3). Epub 2022 Feb 28.

Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan.

Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the current research, a reverse vaccinology approach was applied to design a multi-epitope-based vaccine against hantavirus. A set of 340 experimentally reported epitopes were retrieved from Virus Pathogen Database and Analysis Resource (ViPR) and subjected to different analyses such as antigenicity, allergenicity, solubility, IFN gamma, toxicity, and virulent checks. Finally, 10 epitopes which cleared all the filters used were linked with each other through specific GPGPG linkers to construct a multi-antigenic epitope vaccine. The designed vaccine was then joined to three different adjuvants-TLR4-agonist adjuvant, β-defensin, and 50S ribosomal protein L7/L12-using an EAAAK linker to boost up immune-stimulating responses and check the potency of vaccine with each adjuvant. The designed vaccine structures were modelled and subjected to error refinement and disulphide engineering to enhance their stability. To understand the vaccine binding affinity with immune cell receptors, molecular docking was performed between the designed vaccines and TLR4; the docked complex with a low level of global energy was then subjected to molecular dynamics simulations to validate the docking results and dynamic behaviour. The docking binding energy of vaccines with TLR4 is -29.63 kcal/mol (TLR4-agonist), -3.41 kcal/mol (β-defensin), and -11.03 kcal/mol (50S ribosomal protein L7/L12). The systems dynamics revealed all three systems to be highly stable with a root-mean-square deviation (RMSD) value within 3 Å. To test docking predictions and determine dominant interaction energies, binding free energies of vaccine(s)-TLR4 complexes were calculated. The net binding energy of the systems was as follows: TLR4-agonist vaccine with TLR4 (MM-GBSA, -1628.47 kcal/mol and MM-PBSA, -37.75 kcal/mol); 50S ribosomal protein L7/L12 vaccine with TLR4 complex (MM-GBSA, -194.62 kcal/mol and MM-PBSA, -150.67 kcal/mol); β-defensin vaccine with TLR4 complex (MM-GBSA, -9.80 kcal/mol and MM-PBSA, -42.34 kcal/mol). Finally, these findings may aid experimental vaccinologists in developing a very potent hantavirus vaccine.
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http://dx.doi.org/10.3390/vaccines10030378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953224PMC
February 2022

Finite Element Analysis of the Ballistic Impact on Auxetic Sandwich Composite Human Body Armor.

Materials (Basel) 2022 Mar 11;15(6). Epub 2022 Mar 11.

Department of Mechanical Engineering, International Islamic University, Islamabad 44000, Pakistan.

In this study, the ballistic impact behavior of auxetic sandwich composite human body armor was analyzed using finite element analysis. The auxetic core of the armor was composed of discrete re-entrant unit cells. The sandwich armor structure consisted of a front panel of aluminum alloy (Al 7075-T6), UHMWPE (sandwich core), and a back facet of silicon carbide (SiC) bonded together with epoxy resin. Numerical simulations were run on Explicit Dynamics/Autodyne 3-D code. Various projectile velocities with the same boundary conditions were used to predict the auxetic armor response. These results were compared with those of conventional monolithic body armor. The results showed improved indentation resistance with the auxetic armor. Deformation in auxetic armor was observed greater for each of the cases when compared to the monolithic armor, due to higher energy absorption. The elastic energy dissipation results in the lower indentation in an auxetic armor. The armor can be used safely up to 400 m/s; being used at higher velocities significantly reduced the threat level. Conversely, the conventional monolithic modal does not allow the projectile to pass through at a velocity below 300 m/s; however, the back face becomes severely damaged at 200 m/s. At a velocity of 400 m/s, the front facet of auxetic armor was destroyed; however, the back facet was completely safe, while the monolithic panel did not withstand this velocity and was completely damaged. The results are encouraging in terms of resistance offered by the newly adopted auxetic armor compared to conventional monolithic armor.
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http://dx.doi.org/10.3390/ma15062064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8950186PMC
March 2022

Designing of a Recombinant Multi-Epitopes Based Vaccine against Using Bioinformatics and Immunoinformatics Approaches.

Int J Environ Res Public Health 2022 03 21;19(6). Epub 2022 Mar 21.

Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan.

Enterococcus species are an emerging group of bacterial pathogens that have a significant role in hospital-associated infections and are associated with higher mortality and morbidity rates. Among these pathogens, is one of the causative agents of multiple hospital associated infections. Currently, no commercially available licensed vaccine is present, and multi-drug resistant strains of the pathogen are prominent. Due to several limitations of experimental vaccinology, computational vaccine designing proved to be helpful in vaccine designing against several bacterial pathogens. Herein, we designed a multi-epitope-based vaccine against using in silico approaches. After an in-depth analysis of the core genome, three probable antigenic proteins (lytic polysaccharide monooxygenase, siderophore ABC transporter substrate-binding protein, and lytic polysaccharide monooxygenase) were shortlisted for epitope prediction. Among predicted epitopes, ten epitopes-GPADGRIAS, TTINHGGAQA, SERTALSVTT, GDGGNGGGEV, GIKEPDLEK, KQADDRIEA, QAIGGDTSN, EPLDEQTASR, AQWEPQSIEA, QPLKFSDFEL-were selected for multi-epitope vaccine construct designing. The screened B- and T-cell epitopes were joined with each other via specific linkers and linked to the cholera toxin B subunit as an adjuvant to enhance vaccine immune protection efficacy. The designed vaccine construct induced cellular and humoral immune responses. Blind docking with immune cell receptors, followed by molecular dynamic simulation results confirms the good binding potency and stability of the vaccine in providing protection against the pathogen.
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http://dx.doi.org/10.3390/ijerph19063729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8949936PMC
March 2022

Identifying higher risk subgroups of health care workers for priority vaccination against COVID-19.

Ther Adv Vaccines Immunother 2022 10;10:25151355221080724. Epub 2022 Mar 10.

Peshawar Medical College, Riphah International University, Warsak Road Peshawar, Islamabad, Pakistan.

Background: Health care workers (HCWs) are exposed to high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection due to close contact with infected patients in hospital. The objective of this study was to estimate the seroprevalence and to identify the exposure risk of various subgroups among HCWs to prioritize them for early vaccination.

Methods: This was a multicentre cross-sectional study conducted between 15 and 29 June 2020. A total of 987 HCWs were recruited randomly from two major tertiary-care hospitals of Peshawar city, Pakistan. The HCWs included doctors, nurses, paramedics and hospital support staff. The US Food and Drug Administration (FDA)-approved kit was used for the detection of SARS-CoV-2 antibodies.

Results: Overall, 310 (31.4%) HCWs were seropositive for SARS-CoV-2 antibodies (95% confidence interval, CI: 28.5-34.4). Seroprevalence was higher in males (33.5%) and in age group 51-60 years (40.9%). Seropositivity increased with increasing age from 8.3% in age group ⩽20 to 40.9% in 51-60 years of age group ( < 0.05). The highest seroprevalence was identified in paramedical staff (42·5%, 95% CI: 36.6-48.6) followed by nursing staff (38·8%, 95% CI: 32.1-45.7). In logistic regression, being a male HCW led to higher risk of seropositivity (odds ratio, OR: 1.50, 95% CI: 1·06-2.13.  < 0.05) compared with female staff members. The odds of seropositivity was higher in nurses (OR: 3·47, 95% CI: 1.99-6.05.  < 0.01), paramedical staff (OR: 3·19, 95% CI: 1.93-5.28.  < 0.01) and hospital support staff (OR: 2·47, 95% CI: 1.29-4.7.  < 0.01) compared with consultants.

Conclusion: Overall, our results concluded that nursing and paramedical staff are at higher risk and should be vaccinated on priority.
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http://dx.doi.org/10.1177/25151355221080724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8918754PMC
March 2022

Rational design, synthesis, antiproliferative activity against MCF-7, MDA-MB-231 cells, estrogen receptors binding affinity, and computational study of indenopyrimidine-2,5-dione analogs for the treatment of breast cancer.

Bioorg Med Chem Lett 2022 05 8;64:128668. Epub 2022 Mar 8.

Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, 22060 Abbottabad, Pakistan. Electronic address:

Based on the structural architecture of estrogen receptors (ER) agonists/antagonists, we rationally designed and synthesized indenopyrimidine-2,5-dione analogs as a starting point of current research targeting estrogen receptors. These analogs were evaluated for their antiproliferative activities against breast cancer MCF-7 (ER), MDA-MB-231 (ER) and non-cancerous HEK-293 cells using MTT assay. Compounds with high antiproliferative activity against MCF-7 breast cancer cells were found devoid of cytotoxicity against HEK-293 cells. Competitive binding assay of estrogen receptors ERα and ERβ showed that diethanolamine derivative of 4-trifluoromethyl phenyl derivative 30 displayed 77.5-fold strong binding affinity towards ERα (IC = 0.004 μM) as compared to ERβ (IC = 0.31 μM). The calculated RBA value of compound 30 indicated that it has greater affinity with ER than estradiol. By docking studies, we demonstrated that high binding affinity with ERα is due to binding orientation and interaction of CF with a number of key amino acid residues present in the active site of ERα.
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http://dx.doi.org/10.1016/j.bmcl.2022.128668DOI Listing
May 2022

Anatomical Characterization, HPLC Analysis, and Biological Activities of .

Plants (Basel) 2022 Feb 24;11(5). Epub 2022 Feb 24.

Department of Mechatronics Engineering, Jeju National University, Jeju-si 63243, Korea.

Wall (), is a traditional medicinal plant abundantly found in India and Pakistan. In the current research work, initially, the anatomical characteristics were recorded through microscopic examination of selected plant parts, such as leaf, petiole, and midrib. Then, the quantitative phytochemical screening was performed using standard tests reported in literature. The whole-plant powdered sample was then soaked in methanol to obtain crude extract, which was then fractionated into solvents of different polarities to obtain ethyl acetate, chloroform, butanol, hexane, and aqueous extracts. The phytochemical composition of the crude ethyl acetate and chloroform extracts (being the most active fractions) was then confirmed through HPLC analyses, where the possible phytochemical present were predicted through comparison of retention time of a given compound peak with the available standards. The extracts were also evaluated for their in vitro antioxidant and ani-lipoxygenase potentials using standard methods. The microscopic examination revealed the presence of anomocytic type stomata on the abaxial side of the leaf as well as unicellular trichrome and calcium oxalate druses crystals in the midrib and petiole, with a single, centered U-shaped collateral arterial bundle, which was directed toward the adaxial and the phloem toward the abaxial sides of the selected plant parts, respectively. Almost all tested representative groups of phytochemicals and essential minerals were detected in the selected plant, whereas five possible phytochemicals were confirmed in crude and chloroform extract and seven in ethyl acetate fraction. As antioxidant, chloroform fraction was more potent, which exhibited an IC value of 64.99, 69.15, and 268.52 µg/mL, determined through DPPH, ABTS, and FRAP assays. Ethyl acetate extract was also equally potent against the tested free radicals. Chloroform and ethyl acetate extracts were also potent against lipoxygenase, with IC value of 75.99 and 106.11 µg/mL, respectively. Based on the results of biological studies, was found to good inhibitor of free radicals and lipoxygenase that could be further investigated to isolate compounds of medicinal importance.
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http://dx.doi.org/10.3390/plants11050617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8912459PMC
February 2022

An Update on Synthesis of Coumarin Sulfonamides as Enzyme Inhibitors and Anticancer Agents.

Molecules 2022 Feb 28;27(5). Epub 2022 Feb 28.

Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3-go Maja 54, 08-110 Siedlce, Poland.

Coumarin is an important six-membered aromatic heterocyclic pharmacophore, widely distributed in natural products and synthetic molecules. The versatile and unique features of coumarin nucleus, in combination with privileged sulfonamide moiety, have enhanced the broad spectrum of biological activities. The research and development of coumarin, sulfonamide-based pharmacology, and medicinal chemistry have become active topics, and attracted the attention of medicinal chemists, pharmacists, and synthetic chemists. Coumarin sulfonamide compounds and analogs as clinical drugs have been used to cure various diseases with high therapeutic potency, which have shown their enormous development value. The diversified and wide array of biological activities such as anticancer, antibacterial, anti-fungal, antioxidant and anti-viral, etc. were displayed by diversified coumarin sulfonamides. The present systematic and comprehensive review in the current developments of synthesis and the medicinal chemistry of coumarin sulfonamide-based scaffolds give a whole range of therapeutics, especially in the field of oncology and carbonic anhydrase inhibitors. In the present review, various synthetic approaches, strategies, and methodologies involving effect of catalysts, the change of substrates, and the employment of various synthetic reaction conditions to obtain high yields is cited.
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http://dx.doi.org/10.3390/molecules27051604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8911621PMC
February 2022

Computational Design of a Multi-Epitope Vaccine Against .

Front Immunol 2022 18;13:806825. Epub 2022 Feb 18.

Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea.

is a Gram-negative pathogenic bacterium associated with chronic periodontitis. The development of a chimeric peptide-based vaccine targeting this pathogen could be highly beneficial in preventing oral bone loss as well as other severe gum diseases. We applied a computational framework to design a multi-epitope-based vaccine candidate against . The vaccine comprises epitopes from subunit proteins prioritized from the reference strain ( ATCC 33277) using several reported vaccine properties. Protein-based subunit vaccines were prioritized through genomics techniques. Epitope prediction was performed using immunoinformatic servers and tools. Molecular modeling approaches were used to build a putative three-dimensional structure of the vaccine to understand its interactions with host immune cells through biophysical techniques such as molecular docking simulation studies and binding free energy methods. Genome subtraction identified 18 vaccine targets: six outer-membrane, nine cytoplasmic membrane-, one periplasmic, and two extracellular proteins. These proteins passed different vaccine checks required for the successful development of a vaccine candidate. The shortlisted proteins were subjected to immunoinformatic analysis to map B-cell derived T-cell epitopes, and antigenic, water-soluble, non-toxic, and good binders of DRB1*0101 were selected. The epitopes were then modeled into a multi-epitope peptide vaccine construct (linked epitopes plus adjuvant) to enhance immunogenicity and effectively engage both innate and adaptive immunity. Further, the molecular docking approach was used to determine the binding conformation of the vaccine to TLR2 innate immune receptor. Molecular dynamics simulations and binding free energy calculations of the vaccine-TLR2 complex were performed to highlight key intermolecular binding energies. Findings of this study will be useful for vaccine developers to design an effective vaccine for chronic periodontitis pathogens, specifically .
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http://dx.doi.org/10.3389/fimmu.2022.806825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8894597PMC
May 2022

Designing a Recombinant Vaccine against Using Immunoinformatics Approach.

Vaccines (Basel) 2022 Jan 25;10(2). Epub 2022 Jan 25.

Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.

Antibiotic resistance (AR) is the resistance mechanism pattern in bacteria that evolves over some time, thus protecting the bacteria against antibiotics. AR is due to bacterial evolution to make itself fit to changing environmental conditions in a quest for survival of the fittest. AR has emerged due to the misuse and overuse of antimicrobial drugs, and few antibiotics are now left to deal with these superbug infections. To combat AR, vaccination is an effective method, used either therapeutically or prophylactically. In the current study, an in silico approach was applied for the design of multi-epitope-based vaccines against , a major cause of traveler's diarrhea. A total of six proteins: fimbrial protein, flagellar hook protein (FlgE), flagellar basal body L-ring protein (FlgH), flagellar hook-basal body complex protein (FliE), flagellar basal body P-ring formation protein (FlgA), and Gram-negative pili assembly chaperone domain proteins, were considered as vaccine targets and were utilized for B- and T-cell epitope prediction. The predicted epitopes were assessed for allergenicity, antigenicity, virulence, toxicity, and solubility. Moreover, filtered epitopes were utilized in multi-epitope vaccine construction. The predicted epitopes were joined with each other through specific GPGPG linkers and were joined with cholera toxin B subunit adjuvant via another EAAAK linker in order to enhance the efficacy of the designed vaccine. Docking studies of the designed vaccine construct were performed with MHC-I (PDB ID: 1I1Y), MHC-II (1KG0), and TLR-4 (4G8A). Findings of the docking study were validated through molecular dynamic simulations, which confirmed that the designed vaccine showed strong interactions with the immune receptors, and that the epitopes were exposed to the host immune system for proper recognition and processing. Additionally, binding free energies were estimated, which highlighted both electrostatic energy and van der Waals forces to make the complexes stable. Briefly, findings of the current study are promising and may help experimental vaccinologists to formulate a novel multi-epitope vaccine against .
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http://dx.doi.org/10.3390/vaccines10020189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8876559PMC
January 2022

A Method for Pipeline Leak Detection Based on Acoustic Imaging and Deep Learning.

Sensors (Basel) 2022 Feb 17;22(4). Epub 2022 Feb 17.

Department of Electrical, Electronic and Computer Engineering, University of Ulsan, Ulsan 44610, Korea.

This paper proposes a reliable technique for pipeline leak detection using acoustic emission signals. The acoustic emission signal of a pipeline contains leak-related information. However, the noise in the signal often obscures the leak-related information, making traditional acoustic emission features, such as count and peaks, less effective. To obtain leak-related features, first, acoustic images were obtained from the time series acoustic emission signals using continuous wavelet transform. The acoustic images (AE images) were the wavelet scalograms that represent the time-frequency scales of the acoustic emission signal in the form of an image. The acoustic images carried enough information about the leak, as the leak-related information had a high-energy representation in the scalogram compared to the noise. To extract leak-related discriminant features from the acoustic images, they were provided as input into the convolutional autoencoder and convolutional neural network. The convolutional autoencoder extracts global features, while the convolutional neural network extracts local features. The local features represent changes in the energy at a finer level, whereas the global features are the overall characteristics of the acoustic signal in the acoustic image. The global and local features were merged into a single feature vector. To identify the pipeline leak state, the feature vector was fed into a shallow artificial neural network. The proposed method was validated by utilizing a data set obtained from the industrial pipeline testbed. The proposed algorithm yielded a high classification accuracy in detecting leaks under different leak sizes and fluid pressures.
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http://dx.doi.org/10.3390/s22041562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8875737PMC
February 2022

Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA.

Appl Biochem Biotechnol 2022 Feb 23. Epub 2022 Feb 23.

Department of Theoretical and Applied Chemistry, South Ural State University, Lenin prospect 76, Chelyabinsk, 454080, Russian Federation.

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.
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http://dx.doi.org/10.1007/s12010-022-03849-0DOI Listing
February 2022

Molecular docking study and molecular dynamics simulation of ethyl 3,5-diphenyl-1H-pyrrole-2-carboxylate and (Z)-ethyl-2-(3-oxo-1,3-diphenylprop-1-enylamino)acetate.

J Biochem Mol Toxicol 2022 May 21;36(5):e23013. Epub 2022 Feb 21.

Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation.

The present analysis has been performed in the wet-lab and computational environments. First, the synthesis of the latest heterocyclic compounds containing the alkyl organic compound fragment of acetate and glycine acid were obtained and then their crystal structure and biological activity were studied. (Z)-ethyl-2-(3-oxo-1,3-diphenylprop-1-enylamino) acetate (1) was initially retrieved on the supported reaction of dibenzene gas with glycine alkyl organic compound-complex within the presence of Y(OTF) catalyst in liquid medium. At an identical time, ethyl-3,5-diphenyl-1H-pyrrole-2-carboxylate (2) was synthesized from the interaction of amino alkane with tert-BuOK in the presence of tert-BuOH/DMFA solvent. The structure of the latest compounds has been studied by H, C NMR. Additionally, the crystal structure of ethyl-3,5-diphenyl-1H-pyrrole-2-carboxylate (2) is conferred. Moreover, computational drug-likeness and pharmacokinetics indicated the compounds' good drug-like molecules and friendly pharmacokinetics, making the compound valuable candidates to be explored for additional structural modification to act as a potential inhibitor of AChE and α-glycosidase enzymes.
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http://dx.doi.org/10.1002/jbt.23013DOI Listing
May 2022

Extracellular Vesicles Derived From Human Corneal Endothelial Cells Inhibit Proliferation of Human Corneal Endothelial Cells.

Front Med (Lausanne) 2021 4;8:753555. Epub 2022 Feb 4.

Institute of Ophthalmology, Faculty of Brain Sciences, University College London, London, United Kingdom.

Corneal endothelial cells (CEnCs) are a monolayer of hexagonal cells that are responsible for maintaining the function and transparency of the cornea. Damage or dysfunction of CEnCs could lead to blindness. Human CEnCs (HCEnCs) have shown limited proliferative capacity hence, their maintenance is crucial. Extracellular vesicles (EVs) are responsible for inter- and intra-cellular communication, proliferation, cell-differentiation, migration, and many other complex biological processes. Therefore, we investigated the effect of EVs (derived from human corneal endothelial cell line-HCEC-12) on corneal endothelial cells. HCEC-12 cells were starved with serum-depleted media for 72 h. The media was ultracentrifuged at 100,000xg to isolate the EVs. EV counting, characterization, internalization and localization were performed using NanoSight, flow cytometry, Dil labeling and confocal microscopy respectively. HCEC-12 and HCEnCs were cultured with media supplemented with EVs. Extracted EVs showed a homogeneous mixture of exosomes and microvesicles. Cells with EVs decreased the proliferation rate; increased apoptosis and cell size; showed poor wound healing response and on human, porcine, and rabbit CECs. Thirteen miRNAs were found in the EV sample using next generation sequencing. We observed that increased cellular uptake of EVs by CECs limit the proliferative capacity of HCEnCs. These preliminary data may help in understanding the pathology of corneal endothelial dysfunction and provide further insights in the development of future therapeutic treatment options.
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http://dx.doi.org/10.3389/fmed.2021.753555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8854366PMC
February 2022

Evaluation and identification of essential therapeutic proteins and vaccinomics approach towards multi-epitopes vaccine designing against Legionella pneumophila for immune response instigation.

Comput Biol Med 2022 Feb 6;143:105291. Epub 2022 Feb 6.

Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China. Electronic address:

The Legionellaceae group comprises the Legionella, containing 58 species with 70 serotypes. For instance, Legionella pneumophila is the deadliest serotype to cause Legionnaires infectious and is responsible for 90% of the infections in humans. The bacterial pathogen is associated with a severe lung infection, known as legionaries' disease. It is resistant to multiple drugs, thus warranting novel vaccine candidates identification to immune the host against infections caused by the said pathogen. For this, we applied the subtractive proteomics and reverse vaccinology approaches to annotate the most essential genes suitable for vaccine designing. From the whole proteome, only five proteins (Q5ZVG4, Q5ZRZ1, Q5ZWE6, Q5ZT09, and Q5ZUZ8) as the best targets for further processing as they fulfill all the standard parameters set for in silico vaccine design. Immuno-informatics approaches were further applied to the selected protein sequences to prioritized antigenic epitopes for design a multi-epitope subunit vaccine. A multi-epitopes vaccine was designed by using suitable linkers to link the CTL (cytotoxic T lymphocytes), HTL (Helper T lymphocytes), B cell epitopes, and adjuvant to strengthen the vaccine's immunogenicity. The MEVC(multi-epitopes vaccine construct) was reported to interact with human immune receptor TLR-2 (toll-like receptor) robustly (docking score = -357.18 kcal/mol), and a higher expression was achieved in the Escherichia coli system (CAI = 0.88, and GC contents = 54.34%). Moreover, immune simulation revealed that on the 3rd day, the neutralization of the antigen started, while on the 5th day, the antigen was completely neutralized by the secreted immune factors. In conclusion, the designed vaccine candidate effectively triggered the immune response against eh pathogen; however, wet lab-based experimentations are highly recommended to prove the protective immunological proficiency of the vaccine against L. pneumophila.
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http://dx.doi.org/10.1016/j.compbiomed.2022.105291DOI Listing
February 2022

Epithelial Cell-Derived Extracellular Vesicles Trigger the Differentiation of Two Epithelial Cell Lines.

Int J Mol Sci 2022 Feb 2;23(3). Epub 2022 Feb 2.

Department of Eye and Vision Science, University of Liverpool, Liverpool L7 8TX, UK.

Extracellular vesicles (EVs), specifically exosomes, carry a cell-type dependent cargo that is transported to the recipient cell and translated in the presence of a required machinery. Differences in the cargo carried by the corneal and conjunctival-derived EVs could be the agent that triggers the transdifferentiation of these two cell populations. Therefore, this study investigates the role of EVs in triggering the plasticity of corneal and conjunctival epithelial cells and identifies prospective miRNA and genes responsible for maintaining ocular surface homeostasis. The EVs were extracted from the conditioned media (after starving) of corneal epithelial (hTCEpi) and conjunctival (HCjE-Gi) cell lines using ultracentrifugation. HCjE-Gi cells were cultured with hTCEpi-derived EVs and vice-versa. The EVs were characterized as exosomes using Nanosight and Flow cytometry. KRT3 and KRT12 were used as associated corneal markers, whereas KRT7 and KRT13 were used as associated conjunctival markers with ΔNp63 as a differentiation marker. Shift of these markers was an indication of transdifferentiation. The cargo of the extracted exosomes from both the cell types was explored using next-generation sequencing. The hTCEpi-derived EVs induced conjunctival epithelial cells to express the corneal-associated markers KRT3 and KRT12, losing their conjunctival phenotype at both the mRNA and protein level. Simultaneously, HCjE-Gi-derived EVs induced corneal epithelial cells to express the conjunctival associated markers KRT7 and KRT13, losing their corneal phenotype. This process of differentiation was accompanied by an intermediate step of cell de-differentiation showed by up-regulation in the expression of epithelial stem cell marker ΔNp63, also shown on the ex vivo human cadaveric donor corneas. miRNA molecules (total of 11 including precursor and mature) with significant differences in their relative abundance between the two populations ( < 0.05) were found and investigated. miR-9-5p expression was higher in HCjE-Gi cells and HCjE-Gi-derived EVs when compared to hTCEpi cells and hTCEPi-derived EVs ( < 0.001). The results suggest that EVs released by the two cell types have the ability to influence the transdifferentiation of human conjunctival and corneal epithelial cells. miR-9-5p could have a role in stem cell homeostasis and cell differentiation via gene.
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http://dx.doi.org/10.3390/ijms23031718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8836104PMC
February 2022

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

J Mol Model 2022 Feb 2;28(2):51. Epub 2022 Feb 2.

Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.

Humans are a major reservoir of the hepatitis B virus (HBV), therefore promising treatment and control vaccination strategies are needed to eradicate the virus. Though promising drugs and vaccines are available against HBV, still efforts are required to enrich the therapy options. Herein, the HBV assembly protein was explored to identify novel targets for future use against HBV. Computer-aided drug designing and immune-informatics techniques were employed for the identification of putative inhibitors and vaccine ensemble against HBV using capsid assembly protein. The identified drug molecule binds with high affinity to the active pocket of the protein, and several epitopes are scanned in the protein sequence. The drug molecule, besides being a good putative inhibitor, has acceptable drug-like properties. A multi-epitope vaccine is also constructed to overcome the limitations of weakly immunogenic epitopes. In contrast to the MHC II level, the set of predicted epitopes has been recognized to interact with significant numbers of HLA alleles of MHC I. Selected epitopes are extremely virulent, antigenic, nontoxic, nonallergic, have suitable affinity to bind with the prevailing DRB*0101 allele, and also spectacle 86% mediocre population coverage. A multi-epitope peptide-based vaccine chimera having 73 amino acids was designed. It emerged as substantially immunogenic, thermally stable, robust in producing cellular as well as humoral immune responses, and had competent physicochemical properties to analyze in vitro and in vivo studies. The capsid assembly protein is a in more stable nature in the presence of the drug molecule compared to the TLR3 receptor in the vaccine presence. These particulars were confirmed by exposing the docked molecules to absolute and relative binding free energy approaches of MMGBSA/PBSA. The purpose to investigate the interactions between the vaccine and a representative TLR3 immune receptor can reveal the intermolecular affinity and possible presentation mechanism of the vaccine by TLR3 to the host immune system. It was revealed that the vaccine is showing a very good affinity of binding for the TLR3 and forming a network of hydrophobic and hydrophilic interactions. Overall, the findings of this study are promising and might be useful for further experimental validations.
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http://dx.doi.org/10.1007/s00894-022-05042-wDOI Listing
February 2022

Revisiting the Synthesis of Betti Bases: Facile, One-pot, and Efficient Synthesis of Betti Bases Promoted by FeCl3•6H2O.

Curr Org Synth 2022 Jan 27. Epub 2022 Jan 27.

Department of Chemistry, Government College University Faisalabad, 38000-Faisalabad, Pakistan.

Background: Betti bases are pharmaceutically and synthetically important scaffolds due to their diverse range of biological activities and applications in key synthetic transformations in organic synthesis.

Objective: This work has been sought to contribute to the development, design, and implementation of an improved green methodology with higher atom economy and lower E-factor values for the synthesis of Betti bases.

Method: To realize our objectives, we screened out different catalysts and reaction conditions using one-pot multicomponent modified Mannich reaction/Betti reaction by employing 2-naphthol, benzaldehyde and pyrrolidine as model substrates.

Results: The developed methodology afforded functionalized Betti bases via FeCl3•6H2O catalyzed one-pot multicomponent Betti reaction under neat conditions at 110 °C (5-15 min) to afford functionalized Betti bases by using several aromatic aldehydes and secondary amines in 60-100% yields.

Conclusion: A facile synthetic methodology with higher atom economy and lower E-factor values to synthesize Betti bases via FeCl3•6H2O catalyzed one-pot multicomponent Betti reaction of 2-naphthol, aromatic aldehydes, and secondary amines under neat conditions at 110 °C has been reported. The developed methodology offers various advantages such as excellent yields (60-100%), short reaction time (5-15 min), wide substrate scope (12 examples), green reaction conditions, readily available catalyst, and easy purification (without column chromatography).
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http://dx.doi.org/10.2174/1570179419666220127144352DOI Listing
January 2022

Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches.

Molecules 2022 Jan 16;27(2). Epub 2022 Jan 16.

Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan.

Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson-Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds ()-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study.
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http://dx.doi.org/10.3390/molecules27020554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8779602PMC
January 2022
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