Biomedical subjects

Scott Lovell

Publications and source records attributed to Scott Lovell.

9 recordsLinked to original sources

PubMed2025

Active- and Allosteric-Site Cyclic Peptide Inhibitors of Secreted M. tuberculosis Chorismate Mutase.

The secreted Chorismate mutase enzyme of Mycobacterium tuberculosis (*MtbCM) is an underexplored potential target for the development of new antitubercular agents that are increasingly needed as antibiotic resistance rises in prevalence. As an enzyme suspected to be involved in virulence and host-pathogen interactions, disruption of its function could circumvent the difficulty of treating tuberculosis-infected granulomas. Drug development, however, is limited by novel ligand discovery. Currently, *MtbCM activity is measured by using a low throughput acid/base-mediated product derivatization absorbance assay. Here, we utilized an RNA-display affinity selection approach enabled by the Random Peptides Integrated Discovery (RaPID) system to screen a vast library of macrocyclic peptides (MCP) for novel *MtbCM ligands. Peptides identified from the RaPID selection, and analogs thereof identified by analyzing the selection population dynamics, produced a new class of *MtbCM inhibiting MCPs. Among these were two noteworthy "chorismides", whose binding modes were elucidated by X-ray crystallography. Both were potent inhibitors of the CM enzyme activity. One was identified as an allosteric binding peptide revealing a novel inhibition approach, while the other is an active-site binding peptide that when conjugated to a fluorescent probe allowed for the development of a series of alternative fluorescence-based ligand-displacement assays that can be utilized for the assessment of potential *MtbCM inhibitors.

Mycobacterium tuberculosis↗

PubMed2006

R406, an orally available spleen tyrosine kinase inhibitor blocks fc receptor signaling and reduces immune complex-mediated inflammation.

Recent compelling evidence has lead to renewed interest in the role of antibodies and immune complexes in the pathogenesis of several autoimmune disorders, such as rheumatoid arthritis. These immune complexes, consisting of autoantibodies to self-antigens, can mediate inflammatory responses largely through binding and activating the immunoglobulin Fc receptors (FcRs). Using cell-based structure activity relationships with cultured human mast cells, we have identified the small molecule R406 [N4-(2,2-dimethyl-3-oxo-4H-pyrid[1,4]oxazin-6-yl)-5-fluoro-N2-(3,4,5-trimethoxyphenyl)-2,4-pyrimidinediamine] as a potent inhibitor of immunoglobulin E (IgE)- and IgG-mediated activation of Fc receptor signaling (EC(50) for degranulation = 56-64 nM). Here we show that the primary target for R406 is the spleen tyrosine kinase (Syk), which plays a key role in the signaling of activating Fc receptors and the B-cell receptor (BCR). R406 inhibited phosphorylation of Syk substrate linker for activation of T cells in mast cells and B-cell linker protein/SLP65 in B cells. R406 bound to the ATP binding pocket of Syk and inhibited its kinase activity as an ATP-competitive inhibitor (K(i) = 30 nM). Furthermore, R406 blocked Syk-dependent FcR-mediated activation of monocytes/macrophages and neutrophils and BCR-mediated activation of B lymphocytes. R406 was selective as assessed using a large panel of Syk-independent cell-based assays representing both specific and general signaling pathways. Consistent with Syk inhibition, oral administration of R406 to mice reduced immune complex-mediated inflammation in a reverse-passive Arthus reaction and two antibody-induced arthritis models. Finally, we report a first-inhuman study showing that R406 is orally bioavailable, achieving exposures capable of inhibiting Syk-dependent IgE-mediated basophil activation. Collectively, the results show R406 potential for modulating Syk activity in human disease.

Animals↗

PubMed2006

What is syncrystallization? States of the pH indicator methyl red in crystals of phthalic acid.

The concept of syncrystallization was reinvestigated by focusing on phthalic acid (PA) grown with methyl red (MR). Crystals are alternately red and yellow in adjacent growth sectors. X-ray structures of MR and its cocrystals, revealing MR in the neutral, zwitterionic, and protonated states, as well as measurements of linear birefringence and linear dichroism of mixed crystals, were used to investigate mechanisms of PA coloring. These experiments were complemented by force field calculations of the lowest energy stable surfaces of expressed facets and energies of MR on and in crystals, as well as molecular orbital calculations of MR. Two MR species were detected in PA having distinct energies, polarizations, and face selectivities. Assignments of structures to these MRs, previously thought to be neutral and protonated, required a nuanced analysis of hydrogen bonds. The essential difference between yellow and red species is whether the MR carboxylic acid proton is inter- or intramolecularly hydrogen bound. Inferences about mixed crystal structure drawn from an examination of cocrystals of PA and MR are inconsistent with polarization spectroscopy signaling caution when using stoichiometric compounds as models of dilute solid solutions. Upon heating mixed crystals, linear dichroism diminishes and oriented, elongated pools of MR separate and pass through the bulk in directions perpendicular to the direction of elongation. These bâtonnets subsequently crystallize leaving macroscopic oriented crystals of a MR-rich phase within PA. No evidence was found for the simultaneous crystallization of MR and PA; however, the MR reorientation on heating as well as the separation and recrystallization of a MR-rich phase are distinct processes that could be embraced by the literal meaning of syncrystallization.

Journal Article↗

PubMed2003

The structural determination of an insect sterol carrier protein-2 with a ligand-bound C16 fatty acid at 1.35-A resolution.

Yellow fever mosquito sterol carrier protein (SCP-2) is known to bind to cholesterol. We report here the three-dimensional structure of the complex of SCP-2 from Aedes aegypti with a C16 fatty acid to 1.35-A resolution. The protein fold is exceedingly similar to the human and rabbit proteins, which consist of a five-stranded beta-sheet that exhibits strand order 3-2-1-4-5 with an accompanying layer of four alpha-helices that cover the beta-sheet. A large cavity exists at the interface of the layer alpha-helices and the beta-sheet, which serves as the fatty acid binding site. The carboxylate moiety of the fatty acid is coordinated by a short loop that connects the first alpha-helix to the first beta-strand, whereas the acyl chain extends deep into the interior of the protein. Interestingly, the orientation of the fatty acid is opposite to the observed orientation for Triton X-100 in the SCP-2-like domain from the peroxisomal multifunctional enzyme (Haapalainen, A. M., van Aalten, D. M., Merilainen, G., Jalonen, J. E., Pirila, P., Wierenga, R. K., Hiltunen, J. K., and Glumoff, T. (2001) J. Mol. Biol. 313, 1127-1138). The present study suggests that the binding pocket in the SCP-2 family of proteins may exhibit conformational flexibility to allow coordination of a variety of lipids.

Acetyl-CoA C-Acetyltransferase↗

PubMed2003

Osmium phosphiniminato complexes: synthesis, protonation, structure, and redox-coupled hydrolytic scission of N-p bonds.

The osmium(VI) nitrido complex TpOs(N)Cl(2) [1, Tp = hydrotris(1-pyrazolyl)borate] reacts with triarylphosphines to afford the Os(IV) phosphiniminato complexes TpOs(NPAr(3))Cl(2) [Ar = p-tolyl (tol) (2a), phenyl (2b), p-CF(3)C(6)H(4) (2c)] in nearly quantitative yield. Protonation of 2a-c with 1 equiv of HOTf in MeCN occurs at the phosphiniminato nitrogen to give [TpOs(IV)(NHPAr(3))Cl(2)]OTf (3a-c) in 68-80% yield. Solutions of 2a-c in CH(2)Cl(2) react with excess H(2)O over 1 week to form the disproportionation products 1 (28%), TpOs(III)(NHPAr(3))Cl(2) (4a-c) (60%), and OPAr(3) (35%). Treatment of solutions of 3a-c with H(2)O also affords 1, 4a-c, and OPAr(3). X-ray structures of 2b, 3b, and 4b are presented. Cyclic voltammograms of compounds 2a-c exhibit Os(V)/Os(IV) and Os(IV)/Os(III) couples at approximately 0.3 and -1 V versus Cp(2)Fe(+/0). Protonation to give 3 makes reduction easier by approximately 1.2 V, so that these compounds show Os(IV)/Os(III) and Os(III)/Os(II) couples. In the hydrolytic disproportionation of 2a-c, labeling studies using (18)O-enriched O(2) and H(2)O establish water as the source of the oxygen atom in the OPAr(3) product. The conversions are accelerated by HOTf and inhibited by NaOD. The relative rates of hydrolytic disproportionation of 2a-c vary in the order tol > Ph > p-CF(3)C(6)H(4). The data indicate that protonation of the phosphiniminato nitrogen is required for hydrolysis. The mechanism of the hydrolytic disproportionation is compared to that of the related reaction of the osmium(IV) acetonitrile complex [TpOs(NCMe)Cl(2)](+).

Journal Article↗

PubMed2002

Evidence for "unseen" transposase--DNA contacts.

In this study, evidence of novel, important interactions between a hyperactive Tn5 transposon recognition end sequence and hyperactive Tn5 transposase (Tnp) are presented. A hyperactive Tn5 end sequence, the mosaic end (ME), was isolated previously. The ME and a wild-type end sequence, the outside end (OE), differ at only three positions, yet transposition on the ME is tenfold higher than on the OE in vivo. Also, transposition on the ME is much more efficient than transposition on the OE in vitro. Here, we show that the decreased activity observed for the OE is caused by a defect in paired ends complex (PEC) formation resulting from the orientation of the A-T base-pair at position 4 of this end. Efficient PEC formation requires an interaction between the C5-methyl group (C5-Me) on the non-transferred strand thymine base at position 4 (T4) and Tnp. PEC formation on nicked substrates is much less affected by the orientation of the A-T base-pair at position 4, indicating that the C5-Me group is important only for steps preceding nicking. A recently determined co-crystal structure of Tn5 Tnp with the ME is discussed and a model explaining possible roles for the base-pair at position 4 is explored.

Bacterial Proteins↗

PubMed2002

Hydrocarbon oxidation by Bis-mu-oxo manganese dimers: electron transfer, hydride transfer, and hydrogen atom transfer mechanisms.

Described here are oxidations of alkylaromatic compounds by dimanganese mu-oxo and mu-hydroxo dimers [(phen)(2)Mn(IV)(mu-O)(2)Mn(IV)(phen)(2)](4+) ([Mn(2)(O)(2)](4+)), [(phen)(2)Mn(IV)(mu-O)(2)Mn(III)(phen)(2)](3+) ([Mn(2)(O)(2)](3+)), and [(phen)(2)Mn(III)(mu-O)(mu-OH)Mn(III)(phen)(2)](3+) ([Mn(2)(O)(OH)](3+)). Dihydroanthracene, xanthene, and fluorene are oxidized by [Mn(2)(O)(2)](3+) to give anthracene, bixanthenyl, and bifluorenyl, respectively. The manganese product is the bis(hydroxide) dimer, [(phen)(2)Mn(III)(mu-OH)(2)Mn(II)(phen)(2)](3+) ([Mn(2)(OH)(2)](3+)). Global analysis of the UV/vis spectral kinetic data shows a consecutive reaction with buildup and decay of [Mn(2)(O)(OH)](3+) as an intermediate. The kinetics and products indicate a mechanism of hydrogen atom transfers from the substrates to oxo groups of [Mn(2)(O)(2)](3+) and [Mn(2)(O)(OH)](3+). [Mn(2)(O)(2)](4+) is a much stronger oxidant, converting toluene to tolyl-phenylmethanes and naphthalene to binaphthyl. Kinetic and mechanistic data indicate a mechanism of initial preequilibrium electron transfer for p-methoxytoluene and naphthalenes because, for instance, the reactions are inhibited by addition of [Mn(2)(O)(2)](3+). The oxidation of toluene by [Mn(2)(O)(2)](4+), however, is not inhibited by [Mn(2)(O)(2)](3+). Oxidation of a mixture of C(6)H(5)CH(3) and C(6)H(5)CD(3) shows a kinetic isotope effect of 4.3 +/- 0.8, consistent with C-H bond cleavage in the rate-determining step. The data indicate a mechanism of initial hydride transfer from toluene to [Mn(2)(O)(2)](4+). Thus, oxidations by manganese oxo dimers occur by three different mechanisms: hydrogen atom transfer, electron transfer, and hydride transfer. The thermodynamics of e(-), H(*), and H(-) transfers have been determined from redox potential and pK(a) measurements. For a particular oxidant and a particular substrate, the choice of mechanism is influenced both by the thermochemistry and by the intrinsic barriers. Rate constants for hydrogen atom abstraction by [Mn(2)(O)(2)](3+) and [Mn(2)(O)(OH)](3+) are consistent with their 79 and 75 kcal mol(-)(1) affinities for H(*). In the oxidation of p-methoxytoluene by [Mn(2)(O)(2)](4+), hydride transfer is thermochemically 24 kcal mol(-)(1) more facile than electron transfer; yet the latter mechanism is preferred. Thus, electron transfer has a substantially smaller intrinsic barrier than does hydride transfer in this system.

Anthracenes↗

PubMed2002

Enhancing reactivity via structural distortion.

To examine how small structural changes influence the reactivity and magnetic properties of biologically relevant metal complexes, the reactivity and magnetic properties of two structurally related five-coordinate Fe(III) thiolate compounds are compared. (Et,Pr)-ligated [Fe(III)(S(2)(Me2)N(3)(Et,Pr))]PF(6) (3) is synthesized via the abstraction of a sulfur from alkyl persulfide ligated [Fe(III)(S(2)(Me2)N(3)(Et,Pr))-S(pers)]PF(6) (2) using PEt(3). (Et,Pr)-3 is structurally related to (Pr,Pr)-ligated [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))]PF(6) (1), a nitrile hydratase model compound previously reported by our group, except it contains one fewer methylene unit in its ligand backbone. Removal of this methylene distorts the geometry, opens a S-Fe-N angle by approximately 10 degrees, alters the magnetic properties by stabilizing the S = 1/2 state relative to the S = 3/2 state, and increases reactivity. Reactivity differences between 3 and 1 were assessed by comparing the thermodynamics and kinetics of azide binding. Azide binds reversibly to both (Et,Pr)-3 and (Pr,Pr)-1 in MeOH solutions. The ambient temperature K(eq) describing the equilibrium between five-coordinate 1 or 3 and azide-bound 1-N(3) or 3-N(3) in MeOH is approximately 10 times larger for the (Et,Pr) system. In CH(2)Cl(2), azide binds approximately 3 times faster to 3 relative to 1, and in MeOH, azide dissociates 1 order of magnitude slower from 3-N(3) relative to 1-N(3). The increased on rates are most likely a consequence of the decreased structural rearrangement required to convert 3 to an approximately octahedral structure, or they reflect differences in the LUMO (vs SOMO) orbital population (i.e., spin-state differences). Dissociation rates from both 3-N(3) and 1-N(3) are much faster than one would expect for low-spin Fe(III). Most likely this is due to the labilizing effect of the thiolate sulfur that is trans to azide in these structures.

Algorithms↗

PubMed2002

Two-metal active site binding of a Tn5 transposase synaptic complex.

A synaptic complex of Tn5 transposase with an extended outside end DNA duplex was prepared and crystallized, and its crystal structure was determined in an effort to reveal the role of metal ions in catalysis. Two Mn2+ ions bound to the active site when a single nucleotide of donor DNA was added to the 3' end of the transferred strand. Marked conformational changes were observed in the DNA bases closest to the active site. The position of the metal ions and the conformational changes of the DNA provide insight into the mechanism of hairpin formation and cleavage, and is consistent with a two-metal model for catalysis.

Binding Sites↗