Our goal for this project is to design, synthesize and test novel antiviral chemotherapeutic agents, specifically targeted against HIV-1 reverse transcriptase and HIV-1 ribonuclease H, which are vital enzymes to the life cycle of HIV-1. We have designed and synthesized a wide variety of chemical compounds which include: nucleotide and deoxynucleotide analog inhibitors, pyrophosphate analog inhibitors, heteroaromatic inhibitors, unnatural amino acids, peptide-based and petidomimetic inhibitors. Mass spectrometry has played an important role in association with 1H NMR, 13C NMR, 19F NMR and 31P NMR in characterizing these lead compounds of diverse chemical nature and background. Mass spectrometry will remain an integral part of our research in analyzing the next generation of inhibitors.