Biology subjects

Shonhai, A.

Publications and source records attributed to Shonhai, A..

4 recordsLinked to original sources

bioRxiv2024

Auto QSAR-based Active learning docking for hit identification of potential inhibitors ofPlasmodium falciparum Hsp90 as antimalarial agents

Malaria which is mainly caused by Plasmodium falciparum parasite remains a devastating public health concern, necessitating the need to develop new antimalarial agents. P. falciparum heat shock protein 90 (Hsp90), is indispensable for parasite survival and a promising drug target. Inhibitors targeting the ATP-binding pocket of the N-terminal domain have anti-Plasmodium effects. We proposed a de novo active learning (AL) driven method in tandem with docking to predict inhibitors with unique scaffolds and preferential selectivity towards PfHsp90. Reference compounds, predicted to bind PfHsp90 at the ATP-binding pocket and possessing anti-Plasmodium activities, were used to generate 10,000 unique derivatives and to build the Auto-quantitative structures activity relationships (QSAR) models. Glide docking was performed to predict the docking scores of the derivatives and > 15,000 compounds obtained from the ChEMBL database. Re-iterative training and testing of the models was performed until the optimum Kennel-based Partial Least Square (KPLS) regression model with a regression coefficient R2 = 0.75 for the training set and squared correlation prediction Q2 = 0.62 for the test set reached convergence. Rescoring using induced fit docking and molecular dynamics simulations enabled us to prioritize 15 ATP/ADP-like design ideas for purchase. The compounds exerted moderate activity towards P. falciparum NF54 strain with IC50 values of [≤] 6M and displayed moderate to weak affinity towards PfHsp90 (KD range: 13.5-19.9M) comparable to the reported affinity of ADP. The most potent compound was FTN-T5 (PfN54 IC50:1.44M; HepG2/CHO cells SI[≥] 29) which bound to PfHsp90 with moderate affinity (KD:7.7M), providing a starting point for optimization efforts. Our work demonstrates the great utility of AL for the rapid identification of novel molecules for drug discovery (i.e., hit identification). The potency of FTN-T5 will be critical for designing species-selective inhibitors towards developing more efficient agents against malaria.

biochemistry↗

bioRxiv2020

Biophysical characterization of the human K0513 protein

Glioblastoma multiforme (GBM) is an aggressive grade IV primary malignant tumour which accounts for 78 % of all brain tumours. K0513 is a GBM biomarker that is upregulated in the invasive phenotype. K0513 is expressed ubiquitously and is reportedly enriched in the cerebral cortex of the brain. K0513 is further implicated in signalling pathways involving neuroplasticity, cytoskeletal regulation and apoptosis. The protein encoded by K0513 is a prospective biomarker for pancreatic cancer prognosis. However, the gene product of K0153 is not well characterised. This study focused on structure-function characterisation of human K0513 protein. To this end, we employed bioinformatics analysis and biophysical approaches to characterize the protein. In silico structural characterisation of the human K0513 protein suggests the presence of a SET binding factor 2 (SBF2) domain and a transmembrane region. The SBF2 domain is found in the Myotubularin-related protein 13 (MTMR13), which may function as a nucleotide exchange factor for the RAS-associated GTPase, Rab28. K0513 was predicted to interact with RAS-associated GTPase, Rab3a. Secondary structure prediction revealed K0513 to be predominantly -helical in nature. The predicted three-dimensional model of K0513 showed a globular fold, suggesting that the protein is water-soluble. K0513 was heterologously expressed in E. coli XL1-Blue cells and subsequent purification yielded 80 % soluble protein. Biophysical characterisation using tryptophan-based fluorescence spectroscopy and limited proteolysis showed the conformation of K0513 is mostly unperturbed in the presence of nucleotides. Interestingly, K0513 was detected in lung carcinoma, fibrosarcoma and cervical adenocarcinoma cells, supporting its possible role in cancer signalling pathways.

biochemistry↗

bioRxiv2020

Comparative characterisation of Plasmodium falciparum Hsp70-1 relative to E. coli DnaK reveals functional specificity of the parasite chaperone

Hsp70 is one of the most prominent molecular chaperones. Although Hsp70s from various organisms are generally conserved, they exhibit specialised cellular functions. It remains to be fully understood how these highly conserved molecules exhibit specialised functional features. Plasmodium falciparum Hsp70-1 (PfHsp70-1) is a cytosol localised molecular chaperone that is implicated in the cyto-protection and pathogenicity of the malaria parasite. In the current study, we investigated the comparative structure-function features of PfHsp70-1 relative to its homologue, E. coli Hsp70 (DnaK) and a chimeric protein, KPf, that was constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of all the three Hsp70s exhibited similar secondary and tertiary structural fold. We further established that compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. A recombinant P. falciparum Hsp40 (PfHsp40) stimulated the ATPase activities of all the three Hsp70s. In addition, both PfHsp70-1 and KPf exhibited preference for asparagine rich peptides as opposed to DnaK. Furthermore, all the three proteins exhibited self-association capabilities in vitro. Recombinant P. falciparum adenosylmethionine decarboxylase (PfAdoMetDC) co-expressed in E. coli with either KPf or PfHsp70-1 was produced as a fully folded product. On the other hand, co-expression of PfAdoMetDC with heterologous DnaK in E. coli did not promote folding of the former. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins.

biochemistry↗

bioRxiv2019

Biophysical analysis of Plasmodium falciparum Hsp70-Hsp90 organizing protein (PfHop) reveals a monomer that is characterised by folded segments connected by flexible linkers

Plasmodium falciparum causes the most lethal form of malaria. The cooperation of heat shock protein (Hsp) 70 and 90 is important for folding of a select number of cellular proteins that are crucial for cyto-protection and development of the parasites. Hsp70 and Hsp90 are brought into a functional complex that allows substrate exchange by stress inducible protein 1 (STI1), also known as Hsp70-Hsp90 organizing protein (Hop). P. falciparum Hop (PfHop) co-localises and occurs in complex with the parasite cytosolic chaperones, PfHsp70-1 and PfHsp90. Here, we characterised the structure of recombinant PfHop using synchrotron radiation circular dichroism (SRCD) and small-angle X-ray scattering. Structurally, PfHop is a monomeric, elongated but folded protein, in agreement with its predicted TPR domain structure. Using SRCD, we established that PfHop is unstable at temperatures higher than 40 {degrees}C. This suggests that PfHop is less stable at elevated temperatures compared to its functional partner, PfHsp70-1, that is reportedly stable at temperatures as high as 80 {degrees}C. These findings contribute towards our understanding of the role of the Hop-mediated functional partnership between Hsp70 and Hsp90.

biochemistry↗