The crystal structure of Escherchia coli asparaginase II (EC 3.5.1.1), a drug (Elspar) used for the treatment of acute lymphoblastic leukemia, has been determined at 2.3 A resolution by using data from a single heavy atom derivative in combination with molecular replacement. The atomic model was refined to an R factor of 0.143. This enzyme, active as a homotetramer with 222 symmetry, belongs to the class of a/P proteins. Each subunit has two domains with unique topological features. On the basis of present structural evidence consistent with previous biochemical studies, we propose locations for the active sites between the N-and C-terminal domains belonging to different subunits and postulate a catalytic role for Thr-89.

The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-#[CH(OH)CH2N]-Pro-Ile-ValOMe; the K; is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been rermed to an R factor of 0.146 at 2.4A resolution by using restrained least squares with rms deviations in bond lengths of 0.02 A and bond angles of 4'. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.Reverse transcriptase, integrase, and protease are the three virally encoded enzymes necessary for replication of human immunodeficiency virus 1 (HIV-1), so each is a potential target for drug design. Rational design of drugs directed against AIDS would be greatly facilitated by knowledge of the three-dimensional structures of the target molecules, yet the protease is the only one of these enzymes for which the structure of the native form (1-3) or of an inhibitor complex (4) is known. The protease is a member of the wellcharacterized family of aspartic proteases, which also includes mammalian enzymes such as renin, pepsin, and chymosin. Whereas cell-encoded aspartic proteases are monomers with distinct amino and carboxyl domains, the retroviral proteases are dimers of identical subunits that are analogous to these domains (5). The function of the HIV-1 protease is to cleave the translated viral gag-pol polyprotein into discrete components. Without protease activity, the viral particle remains noninfective (6, 7) and this property makes the protease an attractive candidate for therapeutic drug design against AIDS (8)(9)(10)(11)(12)(13)(14).Inhibitors -of aspartic proteases have been developed as potential pharmaceutical agents for modulating the biological processes catalyzed by this class of enzymes (15,16 Herein we report the structure of a synthetic HIV-1 protease complexed with an HEA inhibitor, JG-365, and compare it with a complex structure in which the reduced peptide bond inhibitor MVT-101 was 3000 times less potent (4). The results substantiate a previously proposed mechanism of action for this class of enzymes (23) protease (where Aba is L-a-amino-n-butyric acid) was chemically synthesized as previously described (24,25). The sequence used was that of the SF2 isolate with cysteines replaced by L-a-amino-n-butyric acid (2). The inhibitor JG-365 was synthesized as described (22) The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby...

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Molecular features of ligand binding to MHC class II HLA-DR molecules have been elucidated through a combination of peptide structure-activity studies and structure-based drug design, resulting in analogues with nanomolar affinity in binding assays. Stabilization of lead compounds against cathepsin B cleavage by N-methylation of noncritical backbone NH groups or by dipeptide mimetic substitutions has generated analogues that compete effectively against protein antigens in cellular assays, resulting in inhibition of T-cell proliferation. Crystal structures of four ternary complexes of different peptide mimetics with the rheumatoid arthritis-linked MHC DRB10401 and the bacterial superantigen SEB have been obtained. Peptide-sugar hybrids have also been identified using a structure-based design approach in which the sugar residue replaces a dipeptide. These studies illustrate the complementary roles played by phage display library methods, peptide analogue SAR, peptide mimetics substitutions, and structure-based drug design in the discovery of inhibitors of antigen presentation by MHC class II HLA-DR molecules.

The amino acid sequence and a 2-A-resolution crystallographic structure of Pseudomonas 7A glutaminase-asparaginase (PGA) have been determined. PGA, which belongs to the family of tetrameric bacterial amidohydrolases, deamidates glutamine and asparagine. The amino acid sequence of PGA has a high degree of similarity to the sequences of other members of the family. PGA has the same fold as other bacterial amidohydrolases, with the exception of the position of a 20-residue loop that forms part of the active site. In the PGA structure presented here, the active site loop is observed clearly in only one monomer, in an open position, with a conformation different from that observed for other amidohydrolases. In the other three monomers the loop is disordered and cannot be traced. This phenomenon is probably a direct consequence of a very low occupancy of product(s) of the enzymatic reaction bound in the active sites of PGA in these crystals. The active sites are composed of a rigid part and the flexible loop. The rigid part consists of the residues directly involved in the catalytic reaction as well as residues that assist in orienting the substrate. Two residues that are important for activity reside on the flexible loop. We suggest that the flexible loops actively participate in the transport of substrate and product molecules through the amidohydrolase active sites and participate in orienting the substrate molecules properly in relation to the catalytic residues.Amidohydrolases catalyze the hydrolysis of asparagine and glutamine to their acidic forms. These metabolic enzymes are expressed in large amounts in bacteria and vary in specificity toward their substrates [for review, see Wriston and Yellin (1973)]. Bacterial amidohydrolases are active as tetramers of identical protein chains with molecular weights in the range of 34 000-36 000 per monomer. Some amidohydrolases, such as those from Escherichia coli (EcA)1 and Erwinia chrysanthemi (ErA), have a relatively high specificity for asparagine and are referred to as asparaginases.These enzymes are used clinically in the therapy of certain lymphocytic leukemias (Roberts et al., 1976;Gallagher et al., 1989). Other amidohydrolases can catalyze the hydrolysis of both glutamine and asparagine with comparable efficiency and are, therefore, called glutaminase-asparaginases. These enzymes, examples of which are amidohydrolases from the bacteria Pseudomonas 7A (PGA) and Acinetobacter glutaminasificans (AGA), are not clinically useful against leukemias due to side effects caused by reduction in patient glutamine levels (Benezra et al., 1972;Howard & Carpenter, 1972). Recently, however, PGA has been demonstrated to inhibit retroviral replication (Roberts & McGregor, 1991), and this t This research was sponsored in part by the National Cancer Institute, DHHS, under Contract NO1-CO-74101 with ABL. The contents of this publication do not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products,...

The crystal structure of glutaminase-asparaginase from Acinetobacter glutaminas~'cans has been reinterpreted and refined to an R factor of 0.171 at 2.9 A resolution, using the same X-ray diffraction data that were used to build a preliminary model of this enzyme [Ammon, Weber, Wlodawer, Harrison, Gilliland, Murphy, Sj61in & Roberts (1988). J. Biol. Chem. 263,[150][151][152][153][154][155][156]]. The current model, which does not include solvent, is based in part on the related structure of Escherichia coli asparaginase and is significantly different from the structure of the enzyme from A. glutaminasificans described previously. The reason for the discrepancies has been traced to insufficient phasing power of the original heavyatom derivative data, which could not be compensated for fully by electron-density modification techniques. The corrected structure of A. glutaminasificans glutaminase-asparaginase is presented and compared with the preliminary model and with the structure of E. coli asparaginase.

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