Robin J. Rosenfeld

Deciphering the fluorescence signature of daunomycin and doxorubicin.

The fluorescence characteristics of daunomycin (DNM), doxorubicin (DXR), and other anthracycline drugs are often used to monitor localization of the drug within lipid bilayers and liposomal delivery systems and to assess interaction of the drug with DNA and other macromolecules. However, the binding of DNM and DXR to proteins and membrane systems has been observed to exhibit variable effects on the anthracyclines fluorescence. We have delineated the spectroscopic response of DXR and DNM to their surroundings in several systems, including solvents of differing dielectric constant, aqueous solutions of varying pH or fluorophore concentration, and the reverse micellar system of AOT/heptane/water with a range of doxorubicin concentrations. We have observed that the ratio of fluorescence intestinal at the two principal lambda max values shows a parabolic dependence on solvent dielectric constant, i.e. inverted solvatochromism. This behavior has been overlooked by previous investigators and, together with the appearance of a long-wavelength band near 630 nm in solvents of low dielectric strength (also previously not reported), is key to understanding the partitioning of anthracyclines in membrane systems as well as resolving the conflicting interpretation of data in the literature.

Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase

Nitric oxide synthase (NOS) enzymes synthesize nitric oxide, a signal for vasodilatation and neurotransmission at low levels, and a defensive cytotoxin at higher levels. The high active-site conservation among all three NOS isozymes hinders the design of selective NOS inhibitors to treat inflammation, arthritis, stroke, septic shock, and cancer. Our structural and mutagenesis results identified an isozyme-specific induced-fit binding mode linking a cascade of conformational changes to a novel specificity pocket. Plasticity of an isozyme-specific triad of distant second- and third-shell residues modulates conformational changes of invariant first-shell residues to determine inhibitor selectivity. To design potent and selective NOS inhibitors, we developed the anchored plasticity approach: anchor an inhibitor core in a conserved binding pocket, then extend rigid bulky substituents towards remote specificity pockets, accessible upon conformational changes of flexible residues. This approach exemplifies general principles for the design of selective enzyme inhibitors that overcome strong active-site conservation.

N-Terminal Domain Swapping and Metal Ion Binding in Nitric Oxide Synthase Dimerization

Nitric oxide synthase oxygenase domains (NOSox) must bind tetrahydrobiopterin and dimerize to be active. New crystallographic structures of inducible NOSox reveal that conformational changes in a switch region (residues 103–111) preceding a pterin‐binding segment exchange N‐terminal β‐hairpin hooks between subunits of the dimer. N‐terminal hooks interact primarily with their own subunits in the ‘unswapped’ structure, and two switch region cysteines (104 and 109) from each subunit ligate a single zinc ion at the dimer interface. N‐terminal hooks rearrange from intra‐ to intersubunit interactions in the ‘swapped structure’, and Cys109 forms a self‐symmetric disulfide bond across the dimer interface. Subunit association and activity are adversely affected by mutations in the N‐terminal hook that disrupt interactions across the dimer interface only in the swapped structure. Residue conservation and electrostatic potential at the NOSox molecular surface suggest likely interfaces outside the switch region for electron transfer from the NOS reductase domain. The correlation between three‐dimensional domain swapping of the N‐terminal hook and metal ion release with disulfide formation may impact inducible nitric oxide synthase (i)NOS stability and regulation in vivo.

Fragment-based screen against HIV protease.

We have employed a fragment‐based screen against wild‐type (NL4‐3) HIV protease (PR) using the Active Sight fragment library and X‐ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co‐crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3–1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL‐3 inhibited PR during co‐crystallization. One fragment, 2‐methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly 16 Gly 17 Gln 18 loop where the amide of Gly 17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys 14 and Leu 63 . Another fragment, indole‐6‐carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp 42 , Pro 44 , Met 46 , and Lys 55 , a hydrogen bond with Val 56 , and a salt‐bridge with Arg 57 . 2‐acetyl‐benzothiophene also binds at this site. This study is the first fragment‐based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor‐bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

Molecular modeling and crystal structure of ERK2-hypothemycin complexes.

Resorcylic acid lactones containing a cis-enone-such as hypothemycin-are susceptible to Michael addition reactions and are potent and specific inhibitors of about 45 of the known Ser/Thr/Tyr protein kinases. These inhibitors bind reversibly, and then form a covalent adduct with a completely conserved cysteine in the ATP binding site of their target kinases. As a paradigm for the structures of the cis-enone resorcylic acid lactone complexes with this subset of kinases, we have modeled the structure of ERK2-hypothemycin reversible and covalent complexes using docking and extended molecular dynamics simulations. Subsequently, we determined the 2.5A resolution crystal structure of the complex that was in excellent accord with the modeled structure. The results were used to discuss structure-activity relationships, and provide a structural template for the development of irreversible inhibitors that complement the ATP binding site of kinases.

Nitric-oxide Synthase Forms N-NO-pterin and S-NO-Cys: IMPLICATIONS FOR ACTIVITY, ALLOSTERY, AND REGULATION*

Inducible nitric-oxide synthase (iNOS) produces biologically stressful levels of nitric oxide (NO) as a potent mediator of cellular cytotoxicity or signaling. Yet, how this nitrosative stress affects iNOS function in vivo is poorly understood. Here we define two specific non-heme iNOS nitrosation sites discovered by combining UV-visible spectroscopy, chemiluminescence, mass spectrometry, and x-ray crystallography. We detected auto-S-nitrosylation during enzymatic turnover by using chemiluminescence. Selective S-nitrosylation of the ZnS4 site, which bridges the dimer interface, promoted a dimer-destabilizing order-to-disorder transition. The nitrosated iNOS crystal structure revealed an unexpected N-NO modification on the pterin cofactor. Furthermore, the structurally defined N-NO moiety is solvent-exposed and available to transfer NO to a partner. We investigated glutathione (GSH) as a potential transnitrosation partner because the intracellular GSH concentration is high and NOS can form S-nitrosoglutathione. Our computational results predicted a GSH binding site adjacent to the N-NO-pterin. Moreover, we detected GSH binding to iNOS with saturation transfer difference NMR spectroscopy. Collectively, these observations resolve previous paradoxes regarding this uncommon pterin cofactor in NOS and suggest means for regulating iNOS activity via N-NO-pterin and S-NO-Cys modifications. The iNOS self-nitrosation characterized here appears appropriate to help control NO production in response to cellular conditions.

Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand‐binding channel

A previously proposed electron transfer (ET) pathway in the heme enzyme cytochrome c peroxidase has been excised from the structure, leaving an open ligand‐binding channel in its place. Earlier studies on cavity mutants of this enzyme have revealed structural plasticity in this region of the molecule. Analysis of these structures has allowed the design of a variant in which the specific section of protein backbone representing a previously proposed ET pathway is accurately extracted from the protein. A crystal structure verified the creation of an open channel that overlays the removed segment, extending from the surface of the protein to the heme at the core of the protein. A number of heterocyclic cations were found to bind to the proximal‐channel mutant with affinities that can be rationalized based on the structures. It is proposed that small ligands bind more weakly to the proximal‐channel mutant than to the W191G cavity due to an increased off rate of the open channel, whereas larger ligands are able to bind to the channel mutant without inducing large conformational changes. The structure of benzimidazole bound to the proximal‐channel mutant shows that the ligand accurately overlays the position of the tryptophan radical center that was removed from the wild‐type enzyme and displaces four of the eight ordered solvent molecules seen in the empty cavity. Ligand binding also caused a small rearrangement of the redesigned protein loop, perhaps as a result of improved electrostatic interactions with the ligand. The engineered channel offers the potential for introducing synthetic replacements for the removed structure, such as sensitizer‐linked substrates. These installed “molecular wires” could be used to rapidly initiate reactions, trap reactive intermediates, or answer unresolved questions about ET pathways.