In-silico optimization and molecular validation of putative anti-HIV antimicrobial peptides for therapeutic purpose

Philosophiae Doctor - PhDAIDS is considered a pandemic causing millions of deaths worldwide and a cure for this disease is still not available. Failure to implement early treatments due to the poor diagnostic methods and ineffective therapeutic regimens to treat HIV patients to achieve complete viral eradication from the human body has encouraged the escalation of this disease at an exponential rate. Though the current treatment regimens (High Active Antiretroviral Therapy) have aided in increasing the lifespan of HIV patients, it still suffers from some shortcomings such as adverse side effects and non-eradication of the virus. Thus, there is a need for a non-toxic therapeutic regimen to stop further infection of HIV-infected patients. Antimicrobial Peptides (AMPs) are naturally occurring peptides which are components of the first line of defence of many organisms against infections and have been proven to be promising therapeutic agents against HIV. The use of AMPs as anti-microbial agents is due to the fact that most AMPs have a net positive charge and are mostly hydrophobic molecules. These features allow AMPs to be site directed electro-statistically to the mostly negatively charged pathogens. In a previous study, a number of novel anti-HIV AMPs was identified using a predictive algorithm Profile Hidden Markov Models (HMMER). The AMP's threedimensional structures were predicted using an in-silico modelling tool I-TASSER and an insilico protein-peptide interaction study of the AMPs to HIV protein gp120 was performed using PatchDock. Five AMPs were identified to bind gp120, at the site where gp120 interacts with CD4 to prevent HIV invasion and HIV replication. Therefore, the aims of this research were to perform in-silico site-directed mutation on the parental anti-HIV AMPs to increase their binding affinity to the gp120 protein, validate the anti-HIV activity of these peptides and confirm the exclusivity of this activity by testing possible anti-bacterial and anti-cancer activities of the AMPs. Firstly, the five parental anti-HIV AMPs were used to generate mutated AMPs through insilico site-directed mutagenesis. The AMPs 3-D structures were determined using I-TASSER and the modelled AMPs were docked against the HIV protein gp120 using PatchDock. Secondly, an "in house" Lateral Flow Device (LFD) tool developed by our industrial partner, Medical Diagnostech (Pty) Ltd, was utilised to confirm the in-silico docking results. Furthermore, the ability of these AMPs to inhibit HIV-1 replication was demonstrated and additional biological activities of the peptides were shown on bacteria and cancer cell lines. In an effort to identify AMPs with increased binding affinity, the in-silico results showed that two mutated AMPs Molecule 1.1 and Molecule 8.1 bind gp120 with high affinity, at the point where gp120 bind with CD4. The molecular binding however showed that only Molecule 3 and Molecule 7 could prevent the interaction of gp120 protein and CD4 surface protein of human cells, in a competitive binding assay. Additionally, the testing of the anti-HIV activity of the AMPs showed that Molecule 7, Molecule 8 and Molecule 8.1 could inhibit HIV-1 NL4-3 with maximal effective concentration (EC₅₀) values of 37.5 μg/ml and 93.75 μg/ml respectively. The EC₅₀ of Molecule 8.1 was determined to be around 12.5 μg/ml. This result looks promising since 150 μg/ml of the AMPs could not achieve 80% toxicity of the human T cells, thus high Therapeutics Index (TI) might be obtained if 50% cytotoxic concentration (CC₅₀) is established. Further biological activity demonstrates that Molecule 3 and Molecule 7 inhibited P. aeruginosa completely after 24 hours treatment with peptide concentrations ranging from 0.5 mg/ml to 0.03125 mg/ml. Nevertheless, moderate inhibition was observed when CHO, HeLa, MCF-7 and HT-29 were treated with these peptides at peptides concentration of 100 μg/ml. The ability of these AMPs to block the entrance of HIV via the binding to CD4 of the host cells is a good concept since they pave the way for the design of anti-HIV peptide-based drugs Entry Inhibitors (FIs) or can be exploited in the production microbicide gels/films to suppress the propagation of the virus.DST-NIC/Minte

Biosynthesis of silver nanoparticles using Bersama engleriana fruits extracts and their potential inhibitory effect on resistant bacteria

The absence of novel, safe, and effective bactericide is an urgent concern worldwide and remains a challenge in scientific communities. The unique proprieties of silver nanoparticles (SNPs) synthesized from plant extracts make them a suitable candidate to overcome these limitations. Herein, we synthesized SNPs from Bersama engleriana fruit (BEfr) extracts and determined their potential antibacterial activity and mode of action. SNPs were synthesized from BEfr methanolic fruit extracts at 25 and 70 C, and the antibacterial effectiveness of SNPs against bacterial strains was investigated. The surface plasmon resonance peaked at 430.18 and 434.08 nm, respectively, for SNPs synthesized at 25 and 70 C, confirming SNPs synthesis

Enhanced anti-bacterial activity of biogenic silver nanoparticles synthesized from terminalia mantaly extracts

The global increase in outbreaks and mortality rates associated with multidrug- resistant (MDR) bacteria is a major health concern and calls for alternative treatments. Natural-derived products have shown potential in combating the most dreadful diseases, and therefore serve as an effective source of bioactive compounds that can be used as antibacterial agents. These compounds are able to reduce metal ions and cap nanoparticles to form biogenic nanoparticles (NPs) with remarkable anti-bacterial activities. This study explores the use of Terminalia mantaly (TM) extracts for the synthesis of biogenic silver NPs (TM-AgNPs) and the evaluation of their antibacterial activity. TM-AgNPs were synthetized by the reduction of AgNO3 with aqueous andmethanolic TM extracts. UV–visible (UV-vis) spectrophotometry, Dynamic Light Scattering (DLS), Transmission Electron Microscopy, and Fourier Transform Infrared (FTIR) analyses were used to characterise the TM-AgNPs. Anti-bacterial activity of the TM extracts and TM-AgNPs was evaluated against eight bacterial strains using the broth microdilution assay

In silico prediction of new antimicrobial peptides and proteins as druggable targets towards alternative anti-schistosomal therapy

Schistosomiasis is a debilitating disease caused by a parasitic flatworm found in fresh- water. With the exponential increase in prevalence, Praziquantel (PZQ) remains the only effective treatment drug, however, resistance to PZQ has been reported recently. There- fore, it is imperative to develop effective alternative anti-schistosomal compounds using bioinformatics-based tools utilizing the broad-spectrum therapeutic capabilities of antimi- crobial peptides (AMPs). AMPs are essential components of the innate immune system and are responsible for complete destruction and immunomodulatory effects in the host defence against pathogens. Here, Hidden Markov model was used to identify six anti- microbial peptides (TAK1–TAK6) with potential anti-schistosomal capabilities. Also, glyco- syltransferase and axonemal dynein intermediate chain protein were identified as impor- tant druggable Schistosome proteins. The 3-D structures of the AMPs and proteins were modelled using I-TASSER and it was shown that the six putative anti-schistosomal AMPs and the two proteins had low C-score, possibly due to lack of available templates for their modelling. Finally, PatchDock was employed to ascertain the interaction between the schis- tosome proteins and the putative AMPs

Biosynthesis of Silver Nanoparticles Using Bersama engleriana Fruits Extracts and Their Potential Inhibitory Effect on Resistant Bacteria

The absence of novel, safe, and effective bactericide is an urgent concern worldwide and remains a challenge in scientific communities. The unique proprieties of silver nanoparticles (SNPs) synthesized from plant extracts make them a suitable candidate to overcome these limitations. Herein, we synthesized SNPs from Bersama engleriana fruit (BEfr) extracts and determined their potential antibacterial activity and mode of action. SNPs were synthesized from BEfr methanolic fruit extracts at 25 and 70 ◦C, and the antibacterial effectiveness of SNPs against bacterial strains was investigated. The surface plasmon resonance peaked at 430.18 and 434.08 nm, respectively, for SNPs synthesized at 25 and 70 ◦C, confirming SNPs synthesis. BEfr-SNPs had minimum inhibitory concentrations (MIC) range of 0.234 to >50 µg/mL, which was 30-fold greater than extract alone (MIC of 500 µg/mL). BEfrSNPs-25 ◦C was potent against six bacterial strains (S. aureus, S. enterica, MRS. aureus, K. pneumonia, and S. pyogenes), with MIC range of 0.339 to 6.25 µg/mL. The mode of action of BEfr-SNPs-25 ◦C was achieved by an MRSA bacteria strain outer membrane and DNA nucleotide linkage. These results suggest that our synthesized SNPs, especially BEfr-SNPs-25 ◦C, demonstrated an enhanced antibacterial effect and could be potential candidates for bacterial infection treatment

Identification and validation of putative therapeutic and diagnostic antimicrobial peptides against HIV: An in silico approach

>Magister Scientiae - MScBackground: Despite the effort of scientific research on HIV therapies and to reduce the rate of HIV infection, AIDS still remains one of the major causes of death in the world and mostly in Sub-Saharan Africa. To date, neither a cure, nor an HIV vaccine had been found and the disease can only be managed by using High Active Antiretroviral Therapy (HAART) if detected early. The need for an effective early diagnostic and non-toxic therapeutic treatment has brought about the necessity for the discovery of additional HIV diagnostic methods and treatment regimens to lower mortality rates. Antimicrobial Peptides (AMPs) are components of the first line of defence of prokaryotes and eukaryotes and have been proven to be promising therapeutic agents against HIV. Methods: With the utility of computational biology, this work proposes the use of profile search methods combined with structural modelling to identify putative AMPs with diagnostic and anti-HIV activity. Firstly, experimentally validated anti-HIV AMPs were retrieved from various publicly available AMP databases, APD, CAMP, Bactibase and UniprotKB and classified according to super-families. Hidden Markov Model (HMMER) and Gap Local Alignment of Motifs (GLAM2) profiles were built for each super-family of anti- HIV AMPs. Putative anti-HIV AMPs were identified after scanning genome sequence databases using the trained models, retrieved AMPs and ranked based on their E-values. The 3-D structures of the 10 peptides that were ranked highest were predicted using 1-TASSER. These peptides were docked against various HIV proteins using PatchDock and putative AMPs showing highest affinity and having the correct orientation to the HIV -1 proteins gp 120 and p24 were selected for future work so as to establish their function in HIV therapy and diagnosis. Results: The results of the in silica analysis showed that the constructed models using the HMMER algorithm had better performances compare to that of the models built by the GLAM2 algorithm. Furthermore, the former tool has better statistical and probability explanation compared to the latter tool. Thus only the HMMER scanning results were considered for further study. Out of 1059 species scanned by the HMMER models, 30 putative anti-HIV AMPs were identified from genome scans with the family specific profile models after elimination of duplicate peptides. Docking analysis of putative AMPs against HIV proteins showed that from the 10 best performing anti-HIV AMPs with the highest Escores, molecules 1,3, 8 and 10 firmly binds the gp120 binding pocket at the VIN2 domain and at the point of interaction between gp120 and T cells, with the 1st and 3rd highest scoring anti-HIV AMPs having the highest binding affinities. However, all 10 putative anti-HIV AMPs bind to the N-terminal domain of p24 with large surface interaction, rather than the C-terminal. Conclusion: The in silica approach has made it possible to construct computational models having high performances, and which enabled the identification of putative anti-HIV peptides from genome sequence scans. The in silica validation of these putative peptides through docking studies has shown that some of these AMPs may be involved in HIV/AIDS therapeutics and diagnostics. The molecular validation of these findings will be the way forward for the development of an early diagnostic tool and as a consequence initiate early treatment. This will prevent the invasion of the immune system by blocking the VIN2 domain and thus designing of a successful vaccine with broad neutralizing activity against this domain

Cytotoxicity Potential of Endophytic Fungi Extracts from Terminalia catappa against Human Cervical Cancer Cells

Endophytic fungi are potential sources of novel bioactive metabolites from a natural product drug discovery perspective. This study reports the bioactivity-directed fractionation of the secondary metabolites of the ethyl acetate extract of a fermentation culture of endophytic fungi from Terminalia catappa which were then evaluated for their cytotoxicity against human cervical cancer (HeLa) cells and human foreskin fibroblast (HFF) cells. Furthermore, apoptosis was determined using the Annexin V/propidium iodide (PI) flow cytometry assay. Endophyte extracts N2, N7, N8, N97, N169, and N233 were obtained from Trichoderma sp, Phoma sp, Phomopsis phyllanticola, Fusarium oxyporum, Collectotrichum sp, and Cryptococcus flavescens, respectively. The N97 extract was most active with a 50% inhibitory concentration (IC50) of 33.35 µg/ml. A 50% cytotoxic concentration (CC50) of 268.4 µg/ml was obtained with HFF cells and the selectivity index (SI) was 8.01. The percentages of cell populations were increased at late apoptosis (Annexin+/PI+), with the percentages of 27.4 ± 0.3 and 19.2 ± 0.01 obtained, respectively, for 50 µg/ml and 80 µg/ml of the N97 extract and 2.1 ± 0.1 obtained for the control in late apoptosis (Annexin V+/PI+) . Moreover, a higher reduction in the percentage of viable cells was observed in the HeLa control cells (93.6 ± 0.3), but the percentages of viable HeLa cells were 37 ± 0.05 and 45 ± 0.1, respectively, for the 50 µg/ml and 80 µg/ml treatments with the N97 extract. Also, the percentages of 34.7 ± 0.1 and 33.9 ± 0.4 were, respectively, obtained for 50 µg/ml and 80 µg/ml compared to the control with 4.6 ± 0.2, in early apoptosis (Annexin V+/PI-). These findings highlight the anticancer potential of the N97 extract of endophytic fungi from Terminalia catappa, which is mediated through apoptosis and presumably also attenuation of chemoresistance

Biosynthesis of Silver Nanoparticles Using Bersama engleriana Fruits Extracts and Their Potential Inhibitory Effect on Resistant Bacteria

The absence of novel, safe, and effective bactericide is an urgent concern worldwide and remains a challenge in scientific communities. The unique proprieties of silver nanoparticles (SNPs) synthesized from plant extracts make them a suitable candidate to overcome these limitations. Herein, we synthesized SNPs from Bersama engleriana fruit (BEfr) extracts and determined their potential antibacterial activity and mode of action. SNPs were synthesized from BEfr methanolic fruit extracts at 25 and 70 °C, and the antibacterial effectiveness of SNPs against bacterial strains was investigated. The surface plasmon resonance peaked at 430.18 and 434.08 nm, respectively, for SNPs synthesized at 25 and 70 °C, confirming SNPs synthesis. BEfr-SNPs had minimum inhibitory concentrations (MIC) range of 0.234 to >50 µg/mL, which was 30-fold greater than extract alone (MIC of 500 µg/mL). BEfr-SNPs-25 °C was potent against six bacterial strains (S. aureus, S. enterica, MRS. aureus, K. pneumonia, and S. pyogenes), with MIC range of 0.339 to 6.25 µg/mL. The mode of action of BEfr-SNPs-25 °C was achieved by an MRSA bacteria strain outer membrane and DNA nucleotide linkage. These results suggest that our synthesized SNPs, especially BEfr-SNPs-25 °C, demonstrated an enhanced antibacterial effect and could be potential candidates for bacterial infection treatment

Adolescent transport and unintentional injuries: a systematic analysis using the Global Burden of Disease Study 2019

Background Globally, transport and unintentional injuries persist as leading preventable causes of mortality and morbidity for adolescents. We sought to report comprehensive trends in injury-related mortality and morbidity for adolescents aged 10-24 years during the past three decades. Methods Using the Global Burden of Disease, Injuries, and Risk Factors 2019 Study, we analysed mortality and disability-adjusted life-years (DALYs) attributed to transport and unintentional injuries for adolescents in 204 countries. Burden is reported in absolute numbers and age-standardised rates per 100 000 population by sex, age group (10-14, 15-19, and 20-24 years), and sociodemographic index (SDI) with 95% uncertainty intervals (UIs). We report percentage changes in deaths and DALYs between 1990 and 2019. Findings In 2019, 369 061 deaths (of which 214337 [58%] were transport related) and 31.1 million DALYs (of which 16.2 million [52%] were transport related) among adolescents aged 10-24 years were caused by transport and unintentional injuries combined. If compared with other causes, transport and unintentional injuries combined accounted for 25% of deaths and 14% of DALYs in 2019, and showed little improvement from 1990 when such injuries accounted for 26% of adolescent deaths and 17% of adolescent DALYs. Throughout adolescence, transport and unintentional injury fatality rates increased by age group. The unintentional injury burden was higher among males than females for all injury types, except for injuries related to fire, heat, and hot substances, or to adverse effects of medical treatment. From 1990 to 2019, global mortality rates declined by 34.4% (from 17.5 to 11.5 per 100 000) for transport injuries, and by 47.7% (from 15.9 to 8.3 per 100000) for unintentional injuries. However, in low-SDI nations the absolute number of deaths increased (by 80.5% to 42 774 for transport injuries and by 39.4% to 31 961 for unintentional injuries). In the high-SDI quintile in 2010-19, the rate per 100 000 of transport injury DALYs was reduced by 16.7%, from 838 in 2010 to 699 in 2019. This was a substantially slower pace of reduction compared with the 48.5% reduction between 1990 and 2010, from 1626 per 100 000 in 1990 to 838 per 100 000 in 2010. Between 2010 and 2019, the rate of unintentional injury DALYs per 100 000 also remained largely unchanged in high-SDI countries (555 in 2010 vs 554 in 2019; 0.2% reduction). The number and rate of adolescent deaths and DALYs owing to environmental heat and cold exposure increased for the high-SDI quintile during 2010-19. Interpretation As other causes of mortality are addressed, inadequate progress in reducing transport and unintentional injury mortality as a proportion of adolescent deaths becomes apparent. The relative shift in the burden of injury from high-SDI countries to low and low-middle-SDI countries necessitates focused action, including global donor, government, and industry investment in injury prevention. The persisting burden of DALYs related to transport and unintentional injuries indicates a need to prioritise innovative measures for the primary prevention of adolescent injury