The majority of current pharmaceuticals are derived from traditional plants; one of these, Azadirachta indica, also known as neem, has a variety of therapeutic applications ranging from simple infections to cancer. All of these pharmacological effects are due to the secondary metabolites present in the various plant parts. Diverse researchers made numerous attempts to identify the active ingredients using techniques such as Gas Chromatography-Mass Spectrometry (GC-MS), High-performance liquid chromatography (HPLC), and High performance thin-layer chromatography (HPTLC), among others. The GC-MS technique is used to isolate various secondary metabolites from the leaves of an aqueous extract of A.indica. The isolated compounds were analysed for their pharmacokinetics and pharmacodynamics properties using software such as SWISSADME, OPENBABEL, Swiss target prediction, etc. The aqueous extract of A.indica yielded 13 compounds, but only 5 compounds showed the highest number of hits; those with the highest concentration were chosen to obtain the pharmacodynamic, pharmacokinetic, and toxicological profiles. All five compounds are non-toxic and can be administered orally, and molecules with specific properties are capable of modulating a variety of proteins, including some enzymes. Based on this information, we can assume that these molecules can be used as "hit" or "lead" molecules in preclinical studies.