Models of HIV-1 protease with peptides representing its natural substrates Irene T. Weber*, David S. Cavanaugh, Robert W. Harrison Department of Pharmacology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA Received 26 June 1996; accepted 23 July 1996 Abstract The substrate specificity of HIV-1 protease has been investigated by molecular modeling of HIV-1 protease with seven peptides representing the naturally occurring cleavage sites in the gag and gag–pol polyprotein precursors. These peptides contain a wide range of amino acids, although only hydrophobic residues are found at either side of the scissile peptide bond. Polar amino acid side chains in each substrate may form hydrogen bond interactions with atoms of HIV protease. HIV-1 protease residues Arg 8, Asp 29, Asp 30, Lys 45, Met 46, Gly 49 and Pro 81 were predicted to form hydrogen bond interactions with polar substrate side chains that may provide sequence specific recognition of the substrates. Several of these protease residues are mutated in inhibitor resistant strains of HIV. Residues equivalent to HIV-1 protease Asp 30 and Pro 81 have been shown to be critical components for substrate recognition. The calculated interaction energy betwen HIV protease and the tetrahedral intermediate of the substrates has a correlation coefficient of 71% with the differences in free energy calculated from kinetic measurements. The implications for the reaction pathway are discussed.  1998 Elsevier Science B.V. Keywords: HIV-1 protease; Molecular modeling; Scissile peptide bond 1. Introduction Human immunodeficiency virus type 1 (HIV-1) protease is essential for production of infectious viral particles (for review see [1,2]. The protease cleaves at a small number of specific sites on the pre- cursor gag and pol polyproteins, releasing itself and the other viral proteins [3,4]. If polyproteins are not cleaved, no infectious viral particles are produced. Therefore, HIV protease has been considered a potential target for anti-viral agents, and several inhi- bitors of HIV protease are currently in clinical trials. However, the therapeutic effectiveness of protease inhibitors is limited by the rapid development of inhibitor resistant variants of the protease [5]. The 99 residue HIV protease is a member of the aspartic proteinase family and is enzymatically active as a dimer. The catalytic mechanism of HIV-1 pro- tease has been studied in different laboratories [6–8]. The substrate specificity of HIV protease has been investigated by a variety of techniques, including kinetic measurements, crystal structures of HIV protease with peptide-like inhibitors and molecular modeling. Retroviral proteases are highly specific Journal of Molecular Structure (Theochem) 423 (1998) 1–12 THEOCH 4869 0166-1280/98/$19.00  1998 Elsevier Science B.V. All rights reserved. PII S0166-1280(96)04869-5 * Corresponding address: Department of Pharmacology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA. Tel.: (215) 503-4575 (I.T. Weber), and (215) 503- 4592 (R.W. Harrison). Fax: (215) 923-2117. e-mail: weber@asterix. jci.tju.edu and harrison@asterix.jci.tju.edu