Bio-computational evaluation of Cryptosporidium inosine monophosphate dehydrogenase as a viable target in the attenuation of cryptosporidiosis.
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2021
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Abstract
Cryptosporidiosis caused by Cryptosporidium species is an enteric disease infecting vertebrate. The disease is associated with poor living conditions, such as contamination of recreational water facilities with infective oocysts. Transmission can be zoonotic or anthroponotic through direct contact or faeco-oral routes. Cryptosporidiosis is a significant opportunistic parasitic organism of immune-compromised patients. Globally, The World Health Organisation (WHO) reported three million infections annually, mostly in developing countries. Notably, cryptosporidiosis self-resolve in immune-competent individuals after few days of watery diarrhea. However, infection is often treated by nitazoxanide, a thiazolide class of drug. Previous studies have reported nitazoxanide's ineffectiveness in immune-compromised patients (such as pregnant women, children, and HIV/AIDS individuals). Hence, there is a need for continuous research on effective drugs against cryptosporidiosis in individuals with a challenged immune system. This study investigates the pooled prevalence of Cryptosporidium infection in the southern Africa region and also the molecular mechanism of action of potential anticryptosporidials.
Meta-analysis was conducted by screening literature database (Google Scholar, PubMed, Ovid Medline, AJOL, and Web of Science) between 2000 and 2020 to estimate the recent pooled prevalence of Cryptosporidium infection in southern Africa. This thesis investigated the inhibitory dynamics of the promising anticryptosporidial drug P131 on Cryptosporidium parvum inosine monophosphate dehydrogenase (CpIMPDH) compared to the orthologous mouse protein (mIMPDH). Crucial moieties of P131 were identified and subsequently adopted to create a pharmacophore model for virtual screening in the ZINC database through the per residue energy decomposition approach. This was done to mine for compounds that could be as effective as or more effective than P131. The potential inhibitory mechanism of these compounds was probed using molecular dynamics simulation and Molecular Mechanics Generalized Poisson Boltzmann Surface Area (MM/PBSA) analyses. In addition, a dedicated library of 107,000 natural compounds available in the ZINC database was virtually screened against CpIMPDH –NAD+ binding site to determine the compounds that have the best complementarity to the binding site.
Cryptosporidium infection in southern Africa shows the pooled prevalence of 16.8% (95%CI 9.7-25.3), with subgroup analyses revealing the highest pooled prevalence of 25.2% in HIV/AIDS patients. The high prevalence of Cryptosporidium spp. infections among immune-compromised patients in southern Africa showed that the pathogen is of significant importance in this region. The relatively high-affinity interactions occurring at the CpIMPDH-NAD+ site were majorly mediated by SER22, VAL24, PRO26, SER354, GLY357 and, TYR358 located on chain D of CpIMPDH. These residues are unique to the parasite IMPDH and not in their eukaryotic host, thereby explaining the selective action of P131. Three compounds ZINC46542062, ZINC58646829, and ZINC89780094, which contained the pharmacophore of P131, showed a respective, favorable docking score of -8.3kcal/mol, -8.2 kcal/mol, and -7.5kcal/mol in CpIMPDH-NAD+ site. Results revealed that one of the hits (ZINC46542062) exhibited a higher binding free energy of -39.52kcal/mol than P131, which had -34.6 kcal/mol. Conformational perturbation induced by the binding of the identified hits to CpIMPDH was similar to P131, suggesting a similarity in inhibitory mechanisms. The top three natural compounds identified with the best complementarity to the CpIMPDH–NAD+ binding site included ZINC5225833, ZINC4258873, and ZINC3841381. The latter (ZINC3841381) had the best binding free energy of -58.43kcal/mol.
The high prevalence of Cryptosporidium infections among immune-compromised patients in southern Africa revealed that cryptosporidiosis is of significant importance in this region. The molecular dynamics approaches presented revealed positive prospects toward the identification of novel anticryptosporidials. Identified ZINC compounds from both inorganic and natural sources could serve as the basis for further experimental investigations, optimization for improved selectivity, thereby providing several therapeutic options of treatment.
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Doctoral Degree. University of KwaZulu-Natal, Durban.