Recently many chemical drugs are capable of causing the side effects to the humans , in order to prevent this side effects herbal based drugs is necessary for the better alternative. Most promisingly the algal based drug molecules have been explored for their interesting physicochemical and biological properties. The amine functionality is present in many natural products and due to its interesting physiological activity it is an extremely important, pharmacophore in many biologically active compounds. Same time HIV is an inevitable one of the most studied and unsolved human diseases. So far six million HIV positive people are on treatment, a majority of them in countries like India, Brazil, Thailand and South Africa. Thus Patents on lifesaving drugs can end access for them and so activists across the world are fighting against multinationals from stopping the production of generics recently most of the scientist and doctors are continuously working to resolve this diseases by new effective drugs for this Anti HIV treatment. At present study we have isolated a natural compound from Gracilaria corticata and another compound from its associated endophytic fungus . Most of the compounds reveal that some Pharmacophores are indeed essential to impact desired therapeutic effect in the molecules. The significant Pharmacophores like halogen, Phenolic –NH2,-CH2OH,-CH=N-,-C6H5 and chiral centre in the molecules could exhibit broad spectrum activities. Some of the FDA approved Anti-HIV active compounds are lopinavir, Ampenavir and Indinavir etc.