Molecular modeling and correlation of PFI1625c-peptide models of bioactive peptides with antimalarial properties

iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides

Antimalarial peptides (AMAPs) varying in length, amino acid composition, charge, conformational structure, hydrophobicity, and amphipathicity reflect their diversity in antimalarial mechanisms. Due to the worldwide major health problem concerning antimicrobial resistance, these peptides possess great therapeutic value owing to their low incidences of drug resistance as compared to conventional antibiotics. Although well-known experimental methods are able to precisely determine the antimalarial activity of peptides, these methods are still time-consuming and costly. Thus, machine learning (ML)-based methods that are capable of identifying AMAPs rapidly by using only sequence information would be beneficial for the high-throughput identification of AMAPs. In this study, we propose the first computational model (termed iAMAP-SCM) for the large-scale identification and characterization of peptides with antimalarial activity by using only sequence information. Specifically, we employed an interpretable scoring card method (SCM) to develop iAMAP-SCM and estimate propensities of 20 amino acids and 400 dipeptides to be AMAPs in a supervised manner. Experimental results showed that iAMAP-SCM could achieve a maximum accuracy and Matthew's coefficient correlation of 0.957 and 0.834, respectively, on the independent test dataset. In addition, SCM-derived propensities of 20 amino acids and selected physicochemical properties were used to provide an understanding of the functional mechanisms of AMAPs. Finally, a user-friendly online computational platform of iAMAP-SCM is publicly available at http://pmlabstack.pythonanywhere.com/iAMAP-SCM. The iAMAP-SCM predictor is anticipated to assist experimental scientists in the high-throughput identification of potential AMAP candidates for the treatment of malaria and other clinical applications.

Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum

Our current understanding of mitochondrial functioning is largely restricted to traditional model organisms, which only represent a fraction of eukaryotic diversity. The unusual mitochondrion of malaria parasites is a validated drug target but remains poorly understood. Here, we apply complexome profiling to map the inventory of protein complexes across the pathogenic asexual blood stages and the transmissible gametocyte stages of Plasmodium falciparum. We identify remarkably divergent composition and clade-specific additions of all respiratory chain complexes. Furthermore, we show that respiratory chain complex components and linked metabolic pathways are up to 40-fold more prevalent in gametocytes, while glycolytic enzymes are substantially reduced. Underlining this functional switch, we find that cristae are exclusively present in gametocytes. Leveraging these divergent properties and stage dynamics for drug development presents an attractive opportunity to discover novel classes of antimalarials and increase our repertoire of gametocytocidal drugs.

Plasmodium falciparum PFI1625c offers an opportunity to design potent anti-malarials: Biochemical characterization and testing potentials in drug discovery

Putative PFI1625c was cloned, over-expressed and purified to homogeneity. It is a 56.2 kDa monomeric protease which preferentially catalyzes the degradation of gelatin with a K_m = 30μM. It is a slow acting enzyme with optimal pH 8.5 and temperature 37 °C, and activity is sensitive to metalloprotease inhibitor 1,10-phenanthroline. PFI1625c active site was probed with a series of heterocyclic compounds and three molecules namely, BNPC-Inh2, DDBM-Inh1 and BHPM-Inh1 from the series were inhibiting PFI1625c protease activity. These heterocyclic compounds were found to irreversible inhibiting PFI1625c protease activity. Parasite culture was treated with these inhibitors and PFI1625c isolated from culture was found to be inactive without affecting other gelatinases present in the parasite. These inhibitors were used to generate chemically knockout PFI1625c in the parasite. PFI1625c knockout parasite remained at ring stage and was unable to complete its erythrocytic schizogony. Also, these knockout parasites were incapable to multiply. More careful analysis indicate these parasites develop oxidative stress as evident by the increase in lipid peroxidation, protein-carbonyl and a decrease of GSH level. In summary, the current study has employed biochemical, computational and pharmacological approaches to explore the role of PFI1625c in the parasite, its utility as a potential drug target to develop anti-malarials.

Versatile spider venom peptides and their medical and agricultural applications

Spiders have been evolving complex and diverse repertoires of peptides in their venoms with vast pharmacological activities for more than 300 million years. Spiders use their venoms for prey capture and defense, hence they contain peptides that target both prey (mainly arthropods) and predators (other arthropods or vertebrates). This includes peptides that potently and selectively modulate a range of targets such as ion channels, receptors and signaling pathways involved in physiological processes. The contribution of these targets in particular disease pathophysiologies makes spider venoms a valuable source of peptides with potential therapeutic use. In addition, peptides with insecticidal activities, used for prey capture, can be exploited for the development of novel bioinsecticides for agricultural use. Although we have already reviewed potential applications of spider venom peptides as therapeutics (in 2010) and as bioinsecticides (in 2012), a considerable number of research articles on both topics have been published since, warranting an updated review. Here we explore the most recent research on the use of spider venom peptides for both medical and agricultural applications.