ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus

Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs’ absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (−8.47 kcal/mol) and average global energy (−70.78 kcal/mol) compared to ACAP-IV (−7.60 kcal/mol and −57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation

ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus

Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs’ absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (−8.47 kcal/mol) and average global energy (−70.78 kcal/mol) compared to ACAP-IV (−7.60 kcal/mol and −57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation

Molecular Characterization of African Swine Fever Viruses from Outbreaks in Peri-Urban Kampala, Uganda

African swine fever (ASF) is an infectious transboundary disease of domestic pigs and wild swine and is currently the most serious constraint to piggery in Uganda. The causative agent of ASF is a large double-stranded linear DNA virus with a complex structure. There are twenty-four ASFV genotypes described to date; however, in Uganda, only genotypes IX and X have been previously described. Inadequate ASF outbreak investigation has contributed to the delayed establishment of effective interventions to aid the control of ASF. Continuous virus characterization enhances the understanding of ASF epidemiology in terms of viral genome variations, extent, severity, and the potential source of the viruses responsible for outbreaks. We collected samples from pigs that had died of a hemorrhagic disease indicative of ASF. DNA was extracted from all samples and screened with the OIE recommended diagnostic PCR for ASF. Partial B646L (p72), full-length E183L (p54) genes, and CVR region of the P72 gene were amplified, purified, and sequenced. Web-based BLAST and MEGA X software were used for sequence analysis. ASF was confirmed in 10 of the 15 suspected pig samples. Phylogenetic analysis confirmed circulation of genotype IX by both full-length E183 (p54) and partial B646L (p72) gene sequencing. Intragenotypic resolution of the CVR region revealed major deletions in the virus genome, in some isolates of this study. The marked reduction in the number of tetrameric tandem repeats in some isolates of this study could potentially play a role in influencing the virulence of this particular genotype IX in Uganda

Distribution and prevalence of ixodid tick species (Acari: Ixodidae) infesting cattle in Karamoja region of northeastern Uganda

Abstract Background Ticks and tick-borne diseases (TTBDs) are a significant threat to livestock production in sub-Saharan Africa. Transhumance pastoralism practiced in Karamoja region and other factors like cattle trade, communal grazing and the presence of wildlife predispose cattle to TTBDs. Tick species abundance and distribution data can be used as a tool for early disease diagnosis and inform tick control strategies. However, these data for north-eastern Uganda are currently limited; previous surveys were relatively localized and targeted fewer cattle kraals and numbers. Methods We randomly collected tick specimens from 1,534 cattle spread across Karamoja region in both the peak month of the rainy (May 2020) and the dry (February2021) seasons. The ticks were identified using morpho-taxonomic keys and the tick species identities confirmed by the 16 S rRNA gene sequencing and phylogenetic analysis. Results A collection of 18,637 ticks was examined and fifteen tick species from three genera (ten Rhipicephalus; three Amblyomma; two Hyalomma species) were identified. Rhipicephalus appendiculatus was the most dominant (37.9%) tick species, followed by Amblyomma variegatum (32.3%); A. lepidum (17.3%); R. evertsi evertsi (7.8%); and R. decoloratus (1.4%). Eight of these tick species were ubiquitous in the study districts while six were found in isolated areas. The peak month of the dry season collection was associated with a higher proportion of tick-infested cattle (91%) compared to the peak month of the rainy season (89.8%); a difference that was not found statistically significant (χ 2  = 0.5077, n = 1385, p = 0.476). The overall cattle infestation rate was mainly dominated by five tick species namely: A. variegatum (55%), R. appendiculatus (53%), A. lepidum (41%), R. evertsi (22%), and R. decoloratus (8%). The proportion of tick-infested cattle was highest in Napak District (95.4%) and lowest in Amudat District (80.9%) during the peak month of the rainy season. Napak and Amudat Districts also had the highest and lowest proportion of tick-infested cattle (94.8% and 80.7% respectively) during the peak month of the dry season. Rhipicephalus microplus was confirmed in Amudat, Kaabong and Napak districts. Conclusion This study demonstrates high tick infestation rates in cattle by a battery of tick species in Karamoja region. We identified both R. microplus and R. decoloratus which indicates that R. microplus has recently been introduced in this region. This calls for effective tick control responses to prevent further spread of this invasive cattle tick specie

Molecular Detection of <i>Cryptosporidium</i> Species in Wildlife and Humans at the Wildlife-Human Interface around Queen Elizabeth National Park, Uganda

To date, information on Cryptosporidium spp. infection status among people and wild animals living at the wildlife-human interface such as Queen Elizabeth National Park (QENP) is scarce. The aim of this study is to document the molecular detection of Cryptosporidium spp. in wild animals, and people, around QENP in the Kasese District. A total of 308 patients from four health centres and 252 wildlife animals from six species across 13 sampling areas were analysed microscopically and with PCR for Cryptosporidium spp. detection. The parasitological and molecular prevalence of Cryptosporidium spp. in humans was 40% and 53%, respectively; Kasenyi Health Centre recorded the highest percentage of positive stool samples for both tests. Wildlife species had an overall molecular percentage positivity of 30.16%; however, considering individual animal species that were sampled, the Waterbucks had the highest positivity rate, that is, 54.54%. All the samples were confirmed as genus Cryptosporidium with less species discrimination as our PCR target was a short fragment. There is a need to investigate the risk factors that predispose to high Cryptosporidium infection in the study area, especially in Kasenyi. In-depth investigation of the genetic diversity of Cryptosporidium spp. circulating at the human, livestock, and wildlife interface is imperative in devising disease management strategies

Additional file 1: of Spatial and temporal distribution of lumpy skin disease outbreaks in Uganda (2002–2016)

Mean annual Lumpy skin disease outbreaks across different regions (agro-ecological zones) from 2002 to 2016. The mean annual Lumpy skin disease outbreaks reported in the Central, East, North, Northeast, Southwest, West and Westnile regions of Uganda from 2002 to 2016. (DOCX 33 kb

Invasive cattle ticks in East Africa : morphological and molecular confirmation of the presence of Rhipicephalus microplus in south‑eastern Uganda

BACKGROUND : Rhipicephalus microplus, an invasive tick species of Asian origin and the main vector of Babesia species, is considered one of the most widespread ectoparasites of livestock. The tick has spread from its native habitats on translocated livestock to large parts of the tropical world, where it has replaced some of the local populations of Rhipicephalus decoloratus ticks. Although the tick was reported in Uganda 70 years ago, it has not been found in any subsequent surveys. This study was carried out to update the national tick species distribution on livestock in Uganda as a basis for tick and tick-borne disease control, with particular reference to R. microplus. METHODS : The study was carried out in Kadungulu, Serere district, south-eastern Uganda, which is dominated by small scale livestock producers. All the ticks collected from 240 cattle from six villages were identified microscopically. Five R. microplus specimens were further processed for phylogenetic analysis and species confirmation. RESULTS : The predominant tick species found on cattle was Rhipicephalus appendiculatus (86.9 %; n = 16,509). Other species found were Amblyomma variegatum (7.2 %; n = 1377), Rhipicephalus evertsi (2.3 %; n = 434) and R. microplus (3.6 %; n = 687). Phylogenetic analysis of the 12S rRNA, 16S rRNA and ITS2 gene sequences of R. microplus confirmed the morphological identification. CONCLUSIONS : It is concluded that R. microplus has replaced R. decoloratus in the sampled villages in Kadungulu subcounty, since the latter was not any longer found in this area. There is currently no livestock movement policy in force in Uganda, which could possibly limit the further spread of R. microplus ticks. Future surveys, but also retrospective surveys of museum specimens, will reveal the extent of distribution of R. microplus in Uganda and also for how long this tick has been present on livestock without being noticed.The Bill & Melinda Gates Foundation (BMGF) through ClinVet International (Pty), the Makerere University-Uganda Virus Research Institute Centre of Excellence for Infection and Immunity Research and Training (MUII), the DELTAS Africa Initiative, the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), the New Partnership for Africa’s Development Planning and Coordinating Agency, the Wellcome Trust and the UK government.http://www.parasitesandvectors.comam2021Veterinary Tropical Disease

Retrospective in silico mutation profiling of SARS-CoV-2 structural proteins circulating in Uganda by July 2021 : towards refinement of COVID-19 disease vaccines, diagnostics, and therapeutics

The SARS-CoV-2 virus, the agent of COVID-19, caused unprecedented loss of lives and economic decline worldwide. Although the introduction of public health measures, vaccines, diagnostics, and therapeutics disrupted the spread of the SARS-CoV-2, the emergence of variants poses substantial threat. This study traced SARS-CoV-2 variants circulating in Uganda by July 2021 to inform the necessity for refinement of the intervention medical products. A comprehensive in silico analysis of the SARS-CoV-2 genomes detected in clinical samples collected from COVID-19 patients in Uganda revealed occurrence of structural protein variants with potential of escaping detection, resisting antibody therapy, or increased infectivity. The genome sequence dataset was retrieved from the GISAID database and the open reading frame encoding the spike, envelope, membrane, or nucleocapsid proteins was translated. The obtained protein sequences were aligned and inspected for existence of variants. The variant positions on each of the four alignment sets were mapped on predicted epitopes as well as the 3D structures. Additionally, sequences within each of the sets were clustered by family. A phylogenetic tree was constructed to assess relationship between the encountered spike protein sequences and Wuhan-Hu-1 wild-type, or the Alpha, Beta, Delta and Gamma variants of concern. Strikingly, the frequency of each of the spike protein point mutations F157L/Del, D614G and P681H/R was over 50%. The furin and the transmembrane serine protease 2 cleavage sites were unaffected by mutation. Whereas the Delta dominated the spike sequences (16.5%, 91/550), Gamma was not detected. The envelope protein was the most conserved with 96.3% (525/545) sequences being wild-type followed by membrane at 68.4% (397/580). Although the nucleocapsid protein sequences varied, the variant residue positions were less concentrated at the RNA binding domains. The dominant nucleocapsid sequence variant was S202N (34.5%, 205/595). These findings offer baseline information required for refining the existing COVID-19 vaccines, diagnostics, and therapeutics

Identification of Antimicrobial Peptides Isolated From the Skin Mucus of African Catfish, (Burchell, 1822).

Antimicrobial peptides (AMPs) constitute a broad range of bioactive compounds in diverse organisms, including fish. They are effector molecules for the innate immune response, against pathogens, tissue damage and infections. Still, AMPs from African Catfish, , skin mucus are largely unexplored despite their possible therapeutic role in combating antimicrobial resistance. In this study, African Catfish Antimicrobial peptides (ACAPs) were identified from the skin mucus of African Catfish, . Native peptides were extracted from fish mucus scrapings in 10% acetic acid (v/v) and ultra-filtered using 5 kDa molecular weight cut-off membrane. The extract was purified using C Solid-Phase Extraction. The antibacterial activity was determined using the Agar Well Diffusion method and broth-dilution method utilizing (ATCC 25923) and (ATCC 25922). Thereafter, Sephadex G-25 gel filtration was further utilized in bio-guided isolation of the most active fractions prior to peptide identification using Orbitrap Fusion Lumos Tribrid Mass Spectrometry. The skin mucus extracted from African Catfish from all the three major lakes of Uganda exhibited antimicrobial activity on and . Lake Albert's demonstrated the best activity with the lowest MIC of 2.84 and 0.71 μg/ml on and , respectively. Sephadex G-25 peak I mass spectrometry analysis (Data are available ProteomeXchange with identifier PXD029193) alongside analysis revealed seven short peptides (11-16 amino acid residues) of high antimicrobial scores (0.561-0.905 units). In addition, these peptides had a low molecular weight (1005.57-1622.05 Da) and had percentage hydrophobicity above 54%. Up to four of these AMPs demonstrated α-helix structure conformation, rendering them amphipathic. The findings of this study indicate that novel AMPs can be sourced from the skin mucus of . Such AMPs are potential alternatives to the traditional antibiotics and can be of great application to food and pharmaceutical industries; however, further studies are still needed to establish their drug-likeness and safety profiles