Patrick Opare Sakyi

The escalation of bacterial resistance to existing antibiotics represents a growing global health challenge, exacerbated by the widespread misuse of antimicrobial agents. As a result, alternative antibacterial strategies are increasingly being explored, including phage-derived lytic proteins. In this study, we report a preliminary characterisation of a novel phage-derived lytic protein identified through computational screening of bacteriophage genome sequences. A putative open reading frame, designated SM07 (1383 bp), was selected from bacteriophage sequences contributed by the University of KwaZulu-Natal to a global phage repository. The gene was synthesised, sub-cloned into the pET-30b(+) vector with an N-terminal histidine tag, and recombinantly expressed in Escherichia coli BL-21(AI) cells. The protein was purified using affinity and ion-exchange chromatography. Purified SM07 exhibited in vitro antimicrobial activity against Pseudomonas aeruginosa, with a minimum inhibitory concentration of 4 µg/mL, while no significant cytotoxic effects were observed in Vero kidney cells at concentrations substantially above the effective dose. Together, these findings provide initial evidence supporting the antimicrobial potential of SM07 and highlight phage-derived lytic proteins as candidates for further investigation as alternative agents against P. aeruginosa-associated infections.

Alpha‐glucosidase (GAA), a crucial enzyme involved in carbohydrate metabolism, is found in the intestine. Glutamine:fructose‐6‐phosphate amidotransferase (GFAT), on the other hand, is a rate‐determining step enzyme in the hexosamine biosynthetic pathway implicated in insulin resistance. As glucose is released and enters the bloodstream, it can lead to the development of hyperglycemia in the absence of or with dysfunctional insulin. Accordingly, inhibiting GAA and GFAT activities reduces production of glucosamine‐6‐phosphate as well as the speed at which starch is broken down, preventing a rapid increase in glucose levels, and ultimately leading to reduced postprandial hyperglycemia. Inhibiting the activity of these enzymes holds promise for treating Type 2 diabetes mellitus (T2DM). This study aimed to identify potential therapeutic agents that can selectively target GAA and GFAT enzymes, in order to discover potent antidiabetic compounds. In this study, researchers performed triplicate screening of 194 phytocompounds from ten ethnomedicinal plants against GAA and GFAT using computational methods like molecular docking and molecular dynamics simulation studies. High‐throughput virtual screening identified 8 compounds registering binding energies ranging from −7 to −12 kcal/mol, some of which are akin to acarbose (−7.4 kcal/mol), a standard GAA inhibitor, and glucose‐6‐phosphate (−6.8 kcal/mol), a cocrystalized ligand of GFAT. Subjecting three of the compounds labeled 160503, 439533, and 441597 to a replicate of 100 ns molecular dynamics simulations analysis revealed that the compounds form stable complexes with GAA and GFAT compared to the known drug acarbose and glucose‐6‐phosphate, respectively. Molecular mechanics Poisson–Boltzmann surface area computations discovered favorable negative free binding energy for the compounds, depicting their dual potential in inhibiting GAA and GFAT. These findings suggest that the identified compounds have potential as novel therapeutics against GAA and GFAT, warranting further experimental biological evaluations to validate the in silico studies.

The pressing global challenges of parasitic diseases, particularly prevalent in tropical and subtropical regions, underscore the critical urgent need for innovative therapeutic strategies in identifying and developing new treatments. The immense chemical diversity inherent in nature has rendered natural product (NP) chemistry a promising avenue for the discovery of novel antiparasitic chemotypes. Despite challenges such as sourcing, synthetic complexity, and drug resistance, NPs continue to offer invaluable contributions to antiparasitic therapy. This review focuses on recent advancements in NP chemistry and their application in the development of antiparasitic therapeutics. Key highlights include the identification of new molecular targets such as enzymes, membrane proteins, and metabolic pathways in parasites, as well as the role of metabolomics, genomics, and high-throughput screening in accelerating drug development. Additionally, the exploration of microorganisms (including soil bacteria and fungi) and marine organisms as a latent reserve of bioactive compounds with potent antiparasitic activity is discussed. The review further examines emerging strategies such as chemoinformatics and combination and polypharmacology therapies, aimed at addressing the challenges of antiparasitic chemotherapeutic treatment and advancing the development of new and effective treatments. Ultimately, NP chemistry represents a frontier for the design of novel antiparasitic drugs, offering the potential for more effective and sustainable therapies for combating parasitic diseases.

The current therapeutic agents for the treatments of visceral leishmaniasis are ineffective, and cytotoxic. Therefore, there is the urgent need for new chemotypes for the treatment of the disease with novel mechanisms of action. In our previous investigation, we identified the triazolopyridazine, STOCK6S-84928 as a potential inhibitor of Leishmania donovani sterol methyltransferase (LdSMT) with IC₅₀ value of 118.3 µM. To improve the biological activity of the initial hit compound, we hereby describe the results of structural-activity relationship studies on STOCK6S-84928 via chemical modifications on the scaffold and virtually screening of 250 compounds obtained against the Modeller generated LdSMT structure. A total of 21 compounds were found to have binding energies ranging from − 7.0 to − 9.2 kcal/mol lower or comparable to the 22,26-azasterol (− 7.6 kcal/mol), the known inhibitor of the target. Molecular docking and molecular dynamics simulations revealed Ile272 and Tyr275 to be pivotal for ligand binding. The compounds were predicted to possess leishmanicidal activities with good drug-like properties. Significantly, the compounds 8, 9, 21, and 23 were predicted to possess antineoplastic, anti-inflammatory, analgesics, protein and MAP kinase inhibitory activities with probability of activity (Pa) > 0.2 and probability of inactivity (Pi) < 0.16. Through the applications of cyclization, amination, Williamson’s ether synthesis, and Suzuki cross-coupling reactions, the selected analogues of STOCK6S-84928 were synthesised in moderate to high yields and characterized by FTIR, LC–MS, and NMR spectroscopy methods. In vitro antileishmanial evaluation of the synthesized compounds identified 23 as the most potent, exhibiting L. donovani promastigotes inhibitory activities with IC₅₀ value of (1.9 ± 0.1) µM. The ortho-difluoropheneyl group as well as the triazolopyridine moieties were suspected to be responsible for the observed activity. Similarly, the compounds 10 and 16 required (0.8 ± 0.1) µM and (0.6 ± 0.0) µM, respectively to eliminate 50% of Trypanosoma brucei. Graphical abstract

Objective: Falciparum malaria is a major global health concern, affecting more than half of the world’s population and causing over half a million deaths annually. Red cell invasion is a crucial step in the parasite’s life cycle, where the parasite invade human erythrocytes to sustain infection and ensure survival. Two parasite proteins, Apical Membrane Antigen 1 (AMA-1) and Rhoptry Neck Protein 2 (RON2), are involved in tight junction formation, which is an essential step in parasite invasion of the red blood cell. Targeting the AMA-1 and RON2 interaction with inhibitors halts the formation of the tight junction, thereby preventing parasite invasion, which is detrimental to parasite survival. This study leverages machine learning (ML) to predict potential small molecule inhibitors of the AMA-1–RON2 interaction, providing putative antimalaria compounds for further chemotherapeutic exploration. Method: Data was retrieved from the PubChem database (AID 720542), comprising 364,447 inhibitors and non-inhibitors of the AMA-1–RON2 interaction. The data was processed by computing Morgan fingerprints and divided into training and testing with an 80:20 ratio, and the classes in the training data were balanced using the Synthetic Minority Oversampling Technique. Five ML models developed comprised Random Forest (RF), Gradient Boost Machines (GBMs), CatBoost (CB), AdaBoost (AB) and Support Vector Machine (SVM). The performances of the models were evaluated using accuracy, F1 score, and receiver operating characteristic—area under the curve (ROC-AUC) and validated using held-out data and a y-randomization test. An applicability domain analysis was carried out using the Tanimoto distance with a threshold set at 0.04 to ascertain the sample space where the models predict with confidence. Results: The GBMs model emerged as the best, achieving 89% accuracy and a ROC-AUC of 92%. CB and RF had accuracies of 88% and 87%, and ROC-AUC scores of 93% and 91%, respectively. Conclusions: Experimentally validated inhibitors of the AMA-1–RON2 interaction could serve as starting blocks for the next-generation antimalarial drugs. The models were deployed as a web-based application, known as PLASMOpred.

Malaria, caused by Plasmodium parasites, remains life-threatening, with Plasmodium falciparum responsible for severe cases. The parasite’s invasion of Red Blood Cells (RBCs) is critical for infection. The interaction between Reticulocyte Binding Protein Homologue 5 (RH5), Basigin, monoclonal antibodies and Cysteine-Rich Protective Antigen (CyRPA) with glycan on RBCs is essential for this process. This study aims to identify small molecules inhibiting the RH5-CyRPA-RIPr invasion complex. A library of 2299 compounds from FDA-approved drugs and African natural products in the ZINC database was screened using molecular docking. Binding sites for Basigin, monoclonal antibodies and glycans on RH5 and CyRPA were targeted, with binding affinity cutoffs of −8.5 kcal/mol for monoclonal antibodies and −7.0 kcal/mol for CyRPA and Basigin. Compounds were assessed for pharmacokinetics, solubility, drug-likeness, lead-likeness and biological activity using the PASS online server. Molecular dynamics simulations and free energy calculations evaluated stability and binding efficiency. Nine hits for RH5 and three for CyRPA showed favorable stability and anti-protozoal activity (up to 0.65). African natural products exhibited similarities with drugs like Nequinate and Cyanidin, supporting further research. Promising small molecules were identified as potential inhibitors of P. falciparum invasion, laying a foundation for experimental validation and drug development.

Background/Objectives: Pteridine reductase 1 (PTR1) has been one of the prime targets for discovering novel antileishmanial therapeutics in the fight against Leishmaniasis. This enzyme catalyzes the NADPH-dependent reduction of pterins to their tetrahydro forms. While chemotherapy remains the primary treatment, its effectiveness is constrained by drug resistance, unfavorable side effects, and substantial associated costs. Methods: This study addresses the urgent need for novel, cost-effective drugs by employing in silico techniques to identify potential lead compounds targeting the PTR1 enzyme. A library of 1463 natural compounds from AfroDb and NANPDB, prefiltered based on Lipinski’s rules, was used to screen against the LmPTR1 target. The X-ray structure of LmPTR1 complexed with NADP and dihydrobiopterin (Protein Data Bank ID: 1E92) was identified to contain the critical residues Arg17, Leu18, Ser111, Phe113, Pro224, Gly225, Ser227, Leu229, and Val230 including the triad of residues Asp181-Tyr194-Lys198, which are critical for the catalytic process involving the reduction of dihydrofolate to tetrahydrofolate. Results: The docking yielded 155 compounds meeting the stringent criteria of −8.9 kcal/mol instead of the widely used −7.0 kcal/mol. These compounds demonstrated binding affinities comparable to the known inhibitors; methotrexate (−9.5 kcal/mol), jatrorrhizine (−9.0 kcal/mol), pyrimethamine (−7.3 kcal/mol), hardwickiic acid (−8.1 kcal/mol), and columbamine (−8.6 kcal/mol). Protein–ligand interactions and molecular dynamics (MD) simulation revealed favorable hydrophobic and hydrogen bonding with critical residues, such as Lys198, Arg17, Ser111, Tyr194, Asp181, and Gly225. Crucial to the drug development, the compounds were physiochemically and pharmacologically profiled, narrowing the selection to eight compounds, excluding those with potential toxicities. The five selected compounds ZINC000095486253, ZINC000095486221, ZINC000095486249, 8alpha-hydroxy-13-epi-pimar-16-en-6,18-olide, and pachycladin D were predicted to be antiprotozoal (Leishmania) with Pa values of 0.642, 0.297, 0.543, 0.431, and 0.350, respectively. Conclusions: This study identified five lead compounds that showed substantial binding affinity against LmPTR1 as well as critical residue interactions. A 100 ns MD combined with molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculations confirmed the robust binding interactions and provided insights into the dynamics and stability of the protein–ligand complexes.

Cervical cancer is the fourth most diagnosed cancer and the fourth leading cause of cancer death in women globally. Its onset and progression have been attributed to high-risk human papillomavirus (HPV) types, especially 16 and 18, while the Epstein–Barr virus (EBV) is believed to also significantly contribute to cervical cancer growth. The E6 protein associated with high-risk HPV strains, such as HPV16 and HPV18, is known for its role in promoting cervical cancer and other anogenital cancers. E6 proteins contribute to the malignant transformation of infected cells by targeting and degrading tumor suppressor proteins, especially p53. On the other hand, EBV nuclear antigen 1 (EBNA1) plays a crucial role in the maintenance and replication of the EBV genome in infected cells. EBNA1 is believed to increase HPV E6 and E7 levels, as well as c-MYC, and BIRC5 cellular genes in the HeLa cell line, implying that HPV/EBV co-infection accelerates cervical cancer onset and growth. Thus, the E6 and EBNA1 antigens of HPV and EBV, respectively, are attractive targets for cervical cancer immunotherapy. This study, therefore, virtually screened for potential drug candidates with good binding affinity to all three oncoviral proteins, HPV16 E6, HPV18 E6, and EBNA1. The compounds were further subjected to ADMET profiling, biological activity predictions, molecular dynamics (MD) simulations, and molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculations. A total of six compounds comprising ZINC000013380012, ZINC000070454124, ZINC000014588133, ZINC000085568136, ZINC000095909247, and ZINC000085597263 demonstrated very strong affinity (≤−60 kJ/mol) to the three oncoviral proteins (EBNA1, HPV16 E6, and HPV18 E6) after being subjected to docking, MD, and MM/PBSA. These compounds demonstrated relatively stronger binding than the controls used, inhibitors of EBNA1 (VK-1727) and HPV E6 (baicalein and gossypetin). Biological activity predictions also corroborated their antineoplastic, p53-enhancing, Pin1 inhibitory, and JAK2 inhibitory activities. Further experimental testing is required to validate the ability of the shortlisted compounds to silence the insidious effects of HPV E6 and EBNA1 proteins in cervical cancers.

In exploring the potential of agricultural waste as an efficient adsorbent, acid‐activated coconut husk biochar was prepared, characterized and applied to remove amoxicillin from wastewater. The mechanism of adsorption was also investigated through isotherm and kinetic studies. The biochar was activated with HNO₃ for 2 h at 25°C and investigated under varying experimental conditions of pH (1–11), initial amoxicillin concentration (0.5–2.5 mg/L), adsorbent dosage (2–20 mg) and contact time (0–24 h). The adsorption process was characterized by rapid attainment of adsorption equilibrium and high values of adsorption capacity. Acid activation had a significant impact on the adsorptive capacity of biochar as removal efficiency improved from 90% (over an hour) to 98.9% (within 40 min). The FTIR results confirmed the characteristic adsorption peaks of C‐H, =C‐H, C=C, C‐O, C=O and O‐H, suggesting the dominant presence of aromatic and carbonyl functional groups on the surface of the biochar. Adjustments in peak shapes and transmittance were observed for these functional groups after the adsorption; highlighting the likely interaction between the biochar and the amoxicillin during the adsorption which has been succinctly proposed. The SEM micrographs showed the growth of leaf‐like flakes of irregular shapes and pores essential for the adsorption. The rate and mechanism of adsorption were driven by the variable surface charge of the adsorbent and the degree of ionization of the adsorbates, which were largely controlled by the solution pH. Adsorption rates were highest in the acidic medium, peaking around a pH of 3, then remained relatively stable between pHs of 5 and 7 before reducing dramatically with increasing pH in the alkaline region. The adsorption best followed the Langmuir model of isotherm while the kinetics mimicked the pseudo–second order (PSO). The findings suggest that HNO₃‐activated coconut biochar is a promising, low‐cost and porous adsorbent effective for amoxicillin removal.