We have identified unique chemical and biological properties of a cationic monofunctional platinum(II) complex, cis-diammine(pyridine)chloroplatinum(II), cis-[Pt(NH 3)2(py)Cl]؉ or cDPCP, a coordination compound previously identified to have significant anticancer activity in a mouse tumor model. This compound is an excellent substrate for organic cation transporters 1 and 2, also designated SLC22A1 and SLC22A2, respectively. These transporters are abundantly expressed in human colorectal cancers, where they mediate uptake of oxaliplatin, cis-[Pt(DACH)(oxalate)] (DACH ‫؍‬ trans-R,R-1,2-diaminocyclohexane), an FDA-approved first-line therapy for colorectal cancer. Unlike oxaliplatin, however, cDPCP binds DNA monofunctionally, as revealed by an x-ray crystal structure of cis-{Pt(NH 3)2(py)} 2؉ bound to the N7 atom of a single guanosine residue in a DNA dodecamer duplex. Although the quaternary structure resembles that of B-form DNA, there is a base-pair step to the 5 side of the Pt adduct with abnormally large shift and slide values, features characteristic of cisplatin intrastrand cross-links. cDPCP effectively blocks transcription from DNA templates carrying adducts of the complex, unlike DNA lesions of other monofunctional platinum(II) compounds like {Pt(dien)} 2؉ . cDPCP-DNA adducts are removed by the nucleotide excision repair apparatus, albeit much less efficiently than bifunctional platinum-DNA intrastrand cross-links. These exceptional characteristics indicate that cDPCP and related complexes merit consideration as therapeutic options for treating colorectal and other cancers bearing appropriate cation transporters.cancer therapy ͉ nucleotide excision repair ͉ organic cation transporter ͉ RNA polymerase II inhibition ͉ x-ray crystal structure

The magnitude of the conformational entropy change experienced by the peptide backbone upon protein folding was investigated experimentally and by computational analysis. Experimentally, two different pairs of mutants of a 33 amino acid peptide corresponding to the leucine zipper region of GCN4 were used for high‐sensitivity microcalorimetric analysis. Each pair of mutants differed only by having alanine or glycine at a specific solvent‐exposed position under conditions in which the differences in stability could be attributed to differences in the conformational entropy of the unfolded state. The mutants studied were characterized by different stabilities but had identical heat capacity changes of unfolding (ΔCp), identical solvent‐related entropies of unfolding (ΔSsolv), and identical enthalpies of unfolding (ΔH) at equivalent temperatures. Accordingly, the differences in stability between the different mutants could be attributed to differences in conformational entropy. The computational studies were aimed at generating the energy profile of backbone conformations as a function of the main chain dihedral angles ϕ and ϱ. The energy profiles permit a direct calculation of the probability distribution of different conformers and therefore of the conformational entropy of the backbone. The experimental results presented in this paper indicate that the presence of the methyl group in alanine reduces the conformational entropy of the peptide backbone by 2.46 ± 0.2 cal/K · mol with respect to that of glycine, consistent with a 3.4‐fold reduction in the number of allowed conformations in the alanine‐containing peptides. Similar results were obtained from the energy profiles. The computational analysis also indicates that the addition of further carbon atoms to the side chain had only a small effect as long as the side chains were unbranched at position β. A further reduction with respect to Ala of only 0.61 and 0.81 cal/K · mol in the backbone entropy was obtained for leucine and lysine, respectively. β‐branching (Val) produces the largest decrease in conformational entropy (1.92 cal/K · mol less than Ala). Finally, the backbone entropy change associated with the unfolding of an α‐helix is 6.51 cal/K · mol for glycine. These and previous results have allowed a complete estimation of the conformational entropy changes associated with protein folding. © 1996 Wiley‐Liss, Inc.

We present a docking scheme that utilizes both a surface complementarity screen as well as an energetic criterion based on surface area burial. Twenty rigid enzyme/inhibitor complexes with known coordinate sets are arbitrarily separated and reassembled to an average all-atom rms (root mean square) deviation of 1.0 A from the native complexes. Docking is accomplished by a hierarchical search of geometrically compatible triplets of surface normals on each molecule. A pruned tree of possible bound configurations is built up using successive consideration of larger and larger triplets. The best scoring configurations are then passed through a free-energy screen where the lowest energy member is selected as the predicted native state. The free energy approximation is derived from observations of surface burial by atom pairs across the interface of known enzyme/inhibitor complexes. The occurrence of specific atom-atom surface burial, for a set of complexes with well-defined secondary structure both in the bound and unbound states, is parameterized to mimic the free energy of binding. The docking procedure guides the inhibitor into its native state using orientation and distance-dependent functions that reproduce the ideal model of free energies with an average rms deviation of 0.9 kcal/mol. For all systems studied, this docking procedure identifies a single, unique minimum energy configuration that is highly compatible with the native state.

Human lysosomal enzymes acid-β-glucosidase (GCase) and acid-α-galactosidase (α-Gal A) hydrolyze, respectively, the sphingolipids glucosyl- and globotriaosyl- ceramide, and mutations in these enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease. We have investigated the structure and stability of GCase and α-Gal A at the neutral-pH environment reflective of the endoplasmic reticulum and the acidic-pH environment reflective of the lysosome. These details are important for the development of pharmacological chaperone therapy for Gaucher and Fabry disease, in which small molecules bind mutant enzymes in the ER to enable the mutant enzyme to meet quality control requirements for lysosomal trafficking. We report crystal structures of apo GCase at pH 4.5, pH 5.5, and in complex with the pharmacological chaperone isofagomine (IFG) at pH 7.5. We also present thermostability analysis of GCase at pH 7.4 and pH 5.2 using differential scanning calorimetry. We compare our results with analogous experiments using α-Gal A and the chaperone 1-deoxygalactonijirimycin (DGJ), including the first structure of α-Gal A with DGJ. Both GCase and α-Gal A are more stable at lysosomal pH with and without their respective iminosugars bound, and notably, the GCase/IFG complex stability is pH sensitive. We show that the conformations of the active site loops in GCase are sensitive to ligand binding but not pH, whereas analogous galactose- or DGJ- dependent conformational changes in α-Gal A are not seen. Thermodynamic parameters obtained from α-Gal A unfolding indicate two-state, van't-Hoff unfolding in the absence of the iminosugar at neutral and lysosomal pH, and non two-state unfolding in the presence of DGJ. Taken together, these results provide insight into how GCase and α-Gal A are thermodynamically stabilized by iminosugars, and suggest strategies for the development of new pharmacological chaperones for lysosomal storage disorders.

Cryptosporidium parvum is a potential biowarfare agent, an important AIDS pathogen, and a major cause of diarrhea and malnutrition. No vaccines or effective drug treatment exist to combat Cryptosporidium infection. This parasite relies on inosine 5'-monophosphate dehydrogenase (IMPDH) to obtain guanine nucleotides, and inhibition of this enzyme blocks parasite proliferation. Here, we report the first crystal structures of CpIMPDH. These structures reveal the structural basis of inhibitor selectivity and suggest a strategy for further optimization. Using this information, we have synthesized low-nanomolar inhibitors that display 10(3) selectivity for the parasite enzyme over human IMPDH2.