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Background and objective: Cryptosporidiosis is a diarrheal disease that affects millions of people worldwide and can cause dire effects in immunocompromised, HIV/AIDS patients and younger children. Cryptosporidium species are causative agents for cryptosporidiosis. The presently available chemotherapeutic options are not fully effective in curbing the menace of disease in all patients. The deprived experimental traceability of the pathogen, lack of a suitable in-vivo model are few factors that hindered the development of reliable chemotherapeutic options despite continuous efforts. The underway COVID-19 pandemic widens this gap as most of the scientific resources and researches shifted priority. The genome sequencing of the Cryptosporidium parvum (C. parvum) has discovered many new targets, such as Inosine 5′-Monophosphate Dehydrogenase (IMPDH), Lactate Dehydrogenase and many more. The parasite uses the host adenosine pool to synthesize guanine nucleotide in a streamlined pathway, where IMPDH catalyzes the first rate-limiting step. The present study aims to discover new anti-cryptosporidial agents that work against the IMPDH of the parasite. Methodology and results: In this study, The PharmaGist (https://bioinfo3d.cs.tau.ac.il/PharmaGist/) tool was deployed for the pharmacophore model generation employing previously reported Cryptosporidium parvum IMPDH (CpIMPDH) inhibitors having IC50 values ranging from 0.009 μM to 0.028 μM. The model having the highest scores was used as a 3D query for high throughput screening of the Zinc database via ZINC pharmer (http://zincpharmer.csb.pitt.edu/) tool. The screened 'hits' were further subjected to molecular docking in the active site of CpIMPDH (PDB ID:4IXH), Lipinski's rule of 5, and SwissADME (http://www.swissadme.ch/) filter. Finally, the best three 'hits' or proposed leads (ZINC09672610, ZINC16511373, and ZINC39780256) docked CpIMPDH were further subjected to 50 ns molecular dynamic simulation (MDL) analysis for stability analysis. Conclusion and significance: The ZINC09672610 and ZINC39780256 compounds show excellent in-silico inhibitory efficacy against CpIMPDH. These compounds were used as a starting point for the discovery and development of new anti-cryptosporidial compounds. Future anti-cryptosporidial agents could be designed by utilizing these three molecules.