ABSTRACT This is an exploratory proposal to develop new anti-HIV compounds that will inhibit entry of the virus into human host cells by targeting gp41, the protein responsible for fusion of viral and host cell membranes. The project utilizes synthetic organic chemistry, NMR structure determination, computational docking and energy minimization, X-ray crystallography of protein – ligand complexes and biophysical and biological evaluation of potency and mechanism. The specific focus of the proposal is development of molecules with chemical reactive groups that can form covalent links with residues in the binding site. Recent research in this area has revealed the propensity for covalent association to dramatically increase the potency of small molecule inhibitors by extending the lifetime of the complexes formed with protein targets. The specific target on gp41 is a highly conserved hydrophobic pocket that is exposed during the process of fusion and plays a key role in stabilizing the post-fusion structure required for a successful fusion event. The hydrophobic pocket contains lysine, glutamine and threonine residues that will be the target of the covalent inhibitors. Boron chemistry will be used to generate reversible covalent bonds that stabilize the complexes but will avoid off-target effects and consequently potential toxicity. Development of low molecular weight fusion inhibitors has been an elusive but attractive goal, because of the potential to obtain orally available drugs that can prevent the initial infection of cells and are likely to have a high barrier to resistance. Thus the work proposed represents an important new direction towards developing nM small molecule inhibitors of fusion.