The current study is an effort to discover natural compounds against two RNA viruses: Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV). HCV is responsible for liver cirrhosis and hepatocellular carcinoma, while HIV causes acquired immunodeficiency syndrome, which leads to further opportunistic infections. Both HCV and HIV infection are substantially prevalent worldwide, as well as in Pakistan. The current study comprises of three components. In first part we performed an in silico search to identify natural compounds with inhibitory potential against HCV. In case of HCV, NS3 helicase is responsible for RNA unwinding which is required for efficient viral replication and translation. Using a cheminformatics approach, we searched the natural compounds databases to identify compounds sharing structural similarities with anti-helicase drug fluoroquinolones. We were able to shortlist 20 natural analogs out of 10399 compounds. Effectiveness of most of these shortlisted compounds has been previously reported in multiple disorders, diseases and infections. Molecular docking was performed to get a deeper understanding about interactions of both classes of compounds with NS3. We found significant correlation between interactions of both fluoroquinolones and their natural analogs with amino acids of NS3 helicase. The mean and individual binding affinities of most of the natural analogs, reflected by ACE based score, were found better than fluoroquinolones (mean -55 vs mean -88). Hence, we hypothesize natural analogs to be an effective helicase inhibitors and viable conjugant regimen against HCV in future. In the second part, we optimized a SYBR Green based Real-time PCR technique to quantify helicase activity in real time. High throughput screening of putative drugs is a cumbersome task because of hurdles in executing screening protocols. To test the helicase activity, numerous techniques are in place, each of which has its own limitations, such as involvement of radioactivity, expensive consumables, laborious procedure to set up experiment or instrumental limitations, making these techniques less convenient or inaccessible. We have exploited the capability of ABI thermal cycler 7300 to read fluorescence measures in real time. We used this feature to optimize the temporal time frame (30 minutes) for enzyme activity, and subsequently, plot kinetics of NS3 helicase in a single small reaction mixture.Additionally, using the same system, we were able to demonstrate the anti-helicase activity of ciprofloxacin and EDTA, to be in the range of 11-29%, suggesting that our technique can be efficiently use to test the activity of different inhibitors against enzymes serving as drug targets. Third component of our study deals with a combination of in silico and in vitro approaches to discover HIV entry inhibitors of natural origin. We hypothesized that compounds from natural origin or their derivatives would have better inhibitory potential, while retaining reduced toxicity than their synthetic precursors. HIV viral spike gp160 (gp120+gp41) is indispensible for viral entry into host cell. A synthetic compound DMJII-121 has earlier been reported by other groups to have binding affinity with viral gp120, thereby inhibiting viral entry by blocking viral entry cascades. To accomplish the third aim, we opted for similarity based virtual screening coupled with molecular docking. Using DMJ-II-121 as template, we searched multi-conformer libraries of compounds from 5 different natural compound databases. In the similarity search, we found altogether 4613 conformers having desirable similarity according to the given Tanimoto Combo score threshold. In molecular docking, we were able to shortlist 8 compounds, on the basis of effective drug-protein interaction score and reproducibility, for validation in wet lab experiments. The preliminary gp120 mediated cell-cell fusion assay allowed us to further short list 4 compounds, 1227, 1915, 2064, H-506, out of 8,for more precise viral entry assay. Among these 4 compounds, the most potent inhibition was demonstrated by compound H-506 relative to BMS806, a standard compound known to inhibit viral entry inside the cell.The effectiveness of compound H-506, however, needs to be tested in cell cytotoxicity assay to confirm that the inhibition exhibited by this compound is directed against the virus and not against the host cell. We also speculate that the modest activity exhibited by compounds H-506, 2064 and 516 in cell fusion/ viral entry assays can be improved by making analogs or derivatives of these compounds harboring changes in the structural scaffold.