Natural products have proven to be effective in fighting various human diseases. The identification of bioactive natural products is an efficient method of finding new drug leads. Screening of natural product extracts on therapeutic targets for the presence of active compounds is a rapid and effective strategy to identify noncovalent interactions between active ligands from natural product extracts and their therapeutic protein targets. This thesis presents an effort of exploring a novel approach to screen natural product extracts using bioaffinity mass spectrometry against malarial targets and studies the relationship between HPLC retention time and Log P values of natural products. With an aim to identify noncovalent complexes and to obtain chemical information of active compounds at the screening stage as well as exploit the connection between HPLC retention time and Log P values of chemical constituents isolated from the active extracts, a research plan containing four major steps has been undertaken in this study. Step one includes understanding of mass spectrometry technique and its approaches in drug discovery screening, understanding of physicochemical properties of antimalarial natural products and using ChemGPS to assess drug potential of reported anti-malarial natural products.