Abstract—The macrophage infectivity potentiator (Mip) from Chlamydia pneumoniae is a major virulence factor. Mip is necessary for optimal intracellular infection and survival within both amoeba and human macrophages. Legionella and Chlamydia is the causative agent responsible for Legionnaires’ disease, Blindness, Sexual Transmitted Disease (STD) and Pneumonia respectively. Mip exhibits peptidyl-prolyl-cis/trans-isomerase (PPIase) activity that is blocked by the immunosuppressant FK506 or rapamycin. The recent significant increase in the number of reported cases of Blindness, STD and Pneumonia, it is necessary to design of new inhibitors directed against Mip proteins of intracellular pathogens. The aim of this study was to construct the 3D model of Chlamydia pneumoniae Mip by homology modeling. Further, pharmacophore model design and molecular docking simulations were carried out to identify Mip inhibitors from a Universal Natural Product Database (UNPD) of over 229358 natural compounds. The virtual screening furnished 2 hit compounds, from which phorbaside C from Marine sponge Phorbas species and emerged as a top candidate. Along with molecular dynamics (MD) simulations will be carried out to analyze the binding affinity for the screened novel lead compounds. Lead compounds will be tested for their ability to inhibit the PPIase activity of Mip proteins in vitro and in vivo.