Webster L. Santos

Structure of a DNA glycosylase searching for lesions.

DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.

Lysophosphatidic Acid-induced Mitogenesis Is Regulated by Lipid Phosphate Phosphatases and Is Edg-receptor Independent

Lysophosphatidic acid (LPA) is an extracellular signaling mediator with a broad range of cellular responses. Three G-protein-coupled receptors (Edg-2, -4, and -7) have been identified as receptors for LPA. In this study, the ectophosphatase lipid phosphate phosphatase 1 (LPP1) has been shown to down-regulate LPA-mediated mitogenesis. Furthermore, using degradation-resistant phosphonate analogs of LPA and stereoselective agonists of the Edg receptors we have demonstrated that the mitogenic and platelet aggregation responses to LPA are independent of Edg-2, -4, and -7. Specifically, we found that LPA degradation is insufficient to account for the decrease in LPA potency in mitogenic assays, and the stereoselectivity observed at the Edg receptors is not reflected in mitogenesis. Additionally, RH7777 cells, which are devoid of Edg-2, -4, and -7 receptor mRNA, have a mitogenic response to LPA and LPA analogs. Finally, we have determined that the ligand selectivity of the platelet aggregation response is consistent with that of mitogenesis, but not with Edg-2, -4, and -7.

sp2−sp3 Hybridized Mixed Diboron: Synthesis, Characterization, and Copper-Catalyzed β-Boration of α,β-Unsaturated Conjugated Compounds

A novel sp(2)-sp(3) hybridized mixed diboron and its reactivity on the copper-catalyzed beta-boration of alpha,beta-unsaturated conjugated compounds to afford the corresponding beta-borated compounds is reported. The presence of sp(3)-hybridized boron provides a mild beta-boration condition in the absence of phosphine and base additives. Finally, our investigations demonstrate that the sp(2)-hybridized boron of the mixed diboron is selectively transferred to the beta-carbon of conjugated substrates.

Structure and reactivity of a preactivated sp2-sp3 diboron reagent: catalytic regioselective boration of α,β-unsaturated conjugated compounds.

A novel sp(2)-sp(3) diboron reagent has been developed for the copper-catalyzed β-boration of α,β-unsaturated conjugated compounds. The reaction proceeds under mild conditions with various substrates, i.e., α,β-unsaturated esters, ketones, nitriles, ynones, amides, and aldehydes, in the absence of additives such as phosphine and sodium tert-butoxide to provide β-borylhomoenolates in good to excellent yields. The presence of an sp(3)-hybridized boron center, unambigously confirmed by X-ray crystallography, sufficiently activates the unsymmetrical pinacolato diisopropanolaminato diboron (PDIPA diboron, 2) to transfer the sp(2)-hybridized boron moiety chemoselectively. These observations suggest that the activation of one of the boron atoms is an essential step in the Cu-catalyzed β-boration catalytic cycle.

Integration Requires a Specific Interaction of the Donor DNA Terminal 5′-Cytosine with Glutamine 148 of the HIV-1 Integrase Flexible Loop

Integration is essential for retroviral replication and gene therapy using retroviral vectors. Human immunodeficiency virus, type 1 (HIV-1), integrase specifically recognizes the terminal sequences of each long terminal repeat (LTR) and cleaves the 3′-end terminal dinucleotide 5′-GT. The exposed 3′-hydroxyl is then positioned for nucleophilic attack and subsequent strand transfer into another DNA duplex (target or chromosomal DNA). We report that both the terminal cytosine at the protruding 5′-end of the long terminal repeats (5′-C) and the integrase residue Gln-148 are critical for strand transfer. Proximity of the 5′-C and Gln-148 was demonstrated by disulfide cross-linking. Cross-linking is inhibited by the inhibitor 5CITEP 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone. We propose that strand transfer requires a conformational change of the integrase-viral (donor) DNA complex with formation of an H-bond between the N-3 of the 5′-C and the amine group of Gln-148. These findings have implications for the molecular mechanisms coupling 3′-processing and strand transfer as well as for the molecular pharmacology of integrase inhibitors.

Sphingosine kinase type 2 inhibition elevates circulating sphingosine 1-phosphate.

S1P (sphingosine 1-phosphate) is a pleiotropic lipid mediator involved in numerous cellular and physiological functions. Of note among these are cell survival and migration, as well as lymphocyte trafficking. S1P, which exerts its effects via five GPCRs (G-protein-coupled receptors) (S1P1-S1P5), is formed by the action of two SphKs (sphingosine kinases). Although SphK1 is the more intensively studied isotype, SphK2 is unique in it nuclear localization and has been reported to oppose some of the actions ascribed to SphK1. Although several scaffolds of SphK1 inhibitors have been described, there is a scarcity of selective SphK2 inhibitors that are necessary to evaluate the downstream effects of inhibition of this isotype. In the present paper we report a cationic amphiphilic small molecule that is a selective SphK2 inhibitor. In the course of characterizing this compound in wild-type and SphK-null mice, we discovered that administration of the inhibitor to wild-type mice resulted in a rapid increase in blood S1P, which is in contrast with our SphK1 inhibitor that drives circulating S1P levels down. Using a cohort of F2 hybrid mice, we confirmed, compared with wild-type mice, that circulating S1P levels were higher in SphK2-null mice and lower in SphK1-null mice. Thus both SphK1 and SphK2 inhibitors recapitulate the blood S1P levels observed in the corresponding null mice. Moreover, circulating S1P levels mirror SphK2 inhibitor levels, providing a convenient biomarker of target engagement.

Subunit-specific Protein Footprinting Reveals Significant Structural Rearrangements and a Role for N-terminal Lys-14 of HIV-1 Integrase during Viral DNA Binding

To identify functional contacts between HIV-1 integrase (IN) and its viral DNA substrate, we devised a new experimental strategy combining the following two methodologies. First, disulfide-mediated cross-linking was used to site-specifically link select core and C-terminal domain amino acids to respective positions in viral DNA. Next, surface topologies of free IN and IN-DNA complexes were compared using Lys- and Arg-selective small chemical modifiers and mass spectrometric analysis. This approach enabled us to dissect specific contacts made by different monomers within the multimeric complex. The foot-printing studies for the first time revealed the importance of a specific N-terminal domain residue, Lys-14, in viral DNA binding. In addition, a DNA-induced conformational change involving the connection between the core and C-terminal domains was observed. Site-directed mutagenesis experiments confirmed the importance of the identified contacts for recombinant IN activities and virus infection. These new findings provided major constraints, enabling us to identify the viral DNA binding channel in the active full-length IN multimer. The experimental approach described here has general application to mapping interactions within functional nucleoprotein complexes.

Unexpected Copper(II) Catalysis: Catalytic Amine Base Promoted β-Borylation of α,β-Unsaturated Carbonyl Compounds in Water

Using bis(pinacolato)diboron, catalytic amounts of Cu(II), and various amine bases in water under atmospheric conditions at rt, acyclic and cyclic α,β-unsaturated ketones and esters are β-borylated in up to 98% yield. Mechanistic investigations using UV-vis spectroscopy, (11)B NMR, and solvent kinetic isotope effect suggest that the role of the amine is not only to coordinate to Cu(II) but also to activate a nucleophilic water molecule to form the reactive sp(2)-sp(3) diboron complex.

Drugging sphingosine kinases.

The transfer of the gamma phosphate from ATP to sphingosine (Sph) to generate a small signaling molecule, sphingosine 1-phosphate (S1P), is catalyzed by sphingosine kinases (SphK), which exist as two isoforms, SphK1 and SphK2. SphK is a key regulator of S1P and the S1P:Sph/ceramide ratio. Increases in S1P levels have been linked to diseases including sickle cell disease, cancer, and fibrosis. Therefore, SphKs are potential targets for drug discovery. However, the current chemical biology toolkit needed to validate these enzymes as drug targets is inadequate. With this review, we survey in vivo active SphK inhibitors and highlight the need for developing more potent and selective inhibitors.

Copper(II)‐Catalyzed Silylation of Activated Alkynes in Water: Diastereodivergent Access to E‐ or Z‐β‐Silyl‐α,β‐Unsaturated Carbonyl and Carboxyl Compounds

Copper(II)-catalyzed silylation of substituted alkynylcarbonyl compounds was investigated. Through the activation of Me2 PhSiBpin in water at room temperature and open atmosphere, vinylsilanes conjugated to carbonyl groups are synthesized in high yield. A surprising diastereodivergent access to olefin geometry was discovered using a silyl conjugate addition strategy: aldehydes and ketones were Z selective while esters and amides were exclusively transformed into the E products.