Binding Mechanism and Structural Optimization of Plant‐Derived Inhibitors for <i>Cryptosporidium parvum</i> Adenylate Kinase

ABSTRACT Cryptosporidiosis, caused by the parasite Cryptosporidium parvum , is still a serious health concern, especially in places with limited medical care. It tends to hit infants and people with weak immune systems the hardest. Right now, there are not many effective treatments available, and resistance to current drugs is becoming more common. So, this study focused on finding small molecules that could block the activity of C. parvum ’s adenylate kinase enzyme, which is considered a good drug target. We looked at 1226 phytochemicals taken from plants known for their antiparasitic properties. First, we used Lipinski's rule of five to narrow down the list, then grouped similar compounds, and ran molecular docking to see which ones had the best fit with the target enzyme. Out of all of them, compound 9865515 showed the strongest binding with a score of −10.5 kcal/mol. To check if this compound had the right properties for a drug, we ran absorption, distribution, metabolism, excretion, and toxicity (ADMET) tests and some density functional theory (DFT) calculations. The results looked promising, and the compound seemed stable, with favorable absorption and safety profiles. Then we conducted a molecular dynamics simulation lasting 600 ns, during which the compound remained stable (root mean square deviation [RMSD] around 0.75 nm). It also formed steady interactions with important parts of the enzyme, like Arg176, Ile129, Pro14, Tyr142, and Ile141. When we calculated the binding energy using molecular mechanics–general born surface area (MM/GBSA), the value came out to –27.30 kcal/mol, which is a sign of solid binding. Steered molecular dynamics (SMD) simulations showed that this compound could be removed with less force (∼650 kJ/mol/nm) compared to a control compound (∼1200 kJ/mol/nm), suggesting it is less tightly stuck, but still effective. Umbrella sampling also showed a lower potential of mean force (∼70 kJ/mol), which means that the binding is stable but could still be reversible. Overall, compound 9865515 looks like a strong drug candidate. The next step is to test it further in the lab to see how it works in real biological systems against C. parvum .