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1.
PLoS One ; 16(3): e0241738, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33760815

RESUMO

Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain's frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen's high mortality is the lack of sensitivity of N. fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N. fowleri. The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N. fowleri research. In 2017, 178 N. fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.


Assuntos
Descoberta de Drogas , Naegleria fowleri/metabolismo , Proteínas de Protozoários/antagonistas & inibidores , Adenosil-Homocisteinase/antagonistas & inibidores , Adenosil-Homocisteinase/química , Adenosil-Homocisteinase/metabolismo , Sítios de Ligação , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Simulação de Dinâmica Molecular , Naegleria fowleri/genética , Fosfoglicerato Mutase/antagonistas & inibidores , Fosfoglicerato Mutase/química , Fosfoglicerato Mutase/metabolismo , Estrutura Quaternária de Proteína , Proteína-Arginina N-Metiltransferases/antagonistas & inibidores , Proteína-Arginina N-Metiltransferases/química , Proteína-Arginina N-Metiltransferases/metabolismo , Proteoma , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo
2.
Bioorg Med Chem Lett ; 41: 127974, 2021 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-33771585

RESUMO

Lactate dehydrogenase (LDH) is a critical enzyme in the glycolytic metabolism pathway that is used by many tumor cells. Inhibitors of LDH may be expected to inhibit the metabolic processes in cancer cells and thus selectively delay or inhibit growth in transformed versus normal cells. We have previously disclosed a pyrazole-based series of potent LDH inhibitors with long residence times on the enzyme. Here, we report the elaboration of a new subseries of LDH inhibitors based on those leads. These new compounds potently inhibit both LDHA and LDHB enzymes, and inhibit lactate production in cancer cell lines.


Assuntos
Compostos de Anilina/farmacologia , Antineoplásicos/farmacologia , Desenho de Fármacos , Éteres/farmacologia , L-Lactato Desidrogenase/antagonistas & inibidores , L-Lactato Desidrogenase/metabolismo , Compostos de Anilina/química , Antineoplásicos/química , Linhagem Celular Tumoral , Éteres/química , Humanos , L-Lactato Desidrogenase/química
3.
J Med Chem ; 63(19): 10984-11011, 2020 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-32902275

RESUMO

Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of reduced nicotinamide adenine dinucleotide as the final step in the glycolytic pathway. Glycolysis plays an important role in the metabolic plasticity of cancer cells and has long been recognized as a potential therapeutic target. Thus, potent, selective inhibitors of LDH represent an attractive therapeutic approach. However, to date, pharmacological agents have failed to achieve significant target engagement in vivo, possibly because the protein is present in cells at very high concentrations. We report herein a lead optimization campaign focused on a pyrazole-based series of compounds, using structure-based design concepts, coupled with optimization of cellular potency, in vitro drug-target residence times, and in vivo PK properties, to identify first-in-class inhibitors that demonstrate LDH inhibition in vivo. The lead compounds, named NCATS-SM1440 (43) and NCATS-SM1441 (52), possess desirable attributes for further studying the effect of in vivo LDH inhibition.


Assuntos
Inibidores Enzimáticos/farmacologia , L-Lactato Desidrogenase/antagonistas & inibidores , Pirazóis/farmacologia , Animais , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacocinética , Meia-Vida , Humanos , Camundongos , Relação Estrutura-Atividade , Ensaios Antitumorais Modelo de Xenoenxerto
4.
Acta Crystallogr F Struct Biol Commun ; 74(Pt 6): 373-384, 2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29870023

RESUMO

Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.


Assuntos
Difosfato de Adenosina/química , Borrelia burgdorferi/enzimologia , Núcleosídeo-Difosfato Quinase/química , Vanadatos/química , Difosfato de Adenosina/genética , Difosfato de Adenosina/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Borrelia burgdorferi/genética , Feminino , Camundongos , Camundongos Endogâmicos C3H , Núcleosídeo-Difosfato Quinase/genética , Núcleosídeo-Difosfato Quinase/metabolismo , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Vanadatos/metabolismo
5.
J Med Chem ; 60(22): 9184-9204, 2017 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-29120638

RESUMO

We report the discovery and medicinal chemistry optimization of a novel series of pyrazole-based inhibitors of human lactate dehydrogenase (LDH). Utilization of a quantitative high-throughput screening paradigm facilitated hit identification, while structure-based design and multiparameter optimization enabled the development of compounds with potent enzymatic and cell-based inhibition of LDH enzymatic activity. Lead compounds such as 63 exhibit low nM inhibition of both LDHA and LDHB, submicromolar inhibition of lactate production, and inhibition of glycolysis in MiaPaCa2 pancreatic cancer and A673 sarcoma cells. Moreover, robust target engagement of LDHA by lead compounds was demonstrated using the cellular thermal shift assay (CETSA), and drug-target residence time was determined via SPR. Analysis of these data suggests that drug-target residence time (off-rate) may be an important attribute to consider for obtaining potent cell-based inhibition of this cancer metabolism target.


Assuntos
Inibidores Enzimáticos/farmacologia , L-Lactato Desidrogenase/antagonistas & inibidores , Pirazóis/farmacologia , Tiazóis/farmacologia , Animais , Antineoplásicos/síntese química , Antineoplásicos/química , Antineoplásicos/farmacocinética , Antineoplásicos/farmacologia , Linhagem Celular Tumoral , Cristalografia por Raios X , Descoberta de Drogas , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacocinética , Ensaios de Triagem em Larga Escala , Humanos , Masculino , Membranas Artificiais , Camundongos , Microssomos Hepáticos/efeitos dos fármacos , Permeabilidade , Pirazóis/síntese química , Pirazóis/química , Pirazóis/farmacocinética , Ratos , Solubilidade , Relação Estrutura-Atividade , Tiazóis/síntese química , Tiazóis/química , Tiazóis/farmacocinética
7.
PLoS One ; 11(8): e0160350, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27500735

RESUMO

We investigated Brucella melitensis methionyl-tRNA-synthetase (BmMetRS) with molecular, structural and phenotypic methods to learn if BmMetRS is a promising target for brucellosis drug development. Recombinant BmMetRS was expressed, purified from wild type Brucella melitensis biovar Abortus 2308 strain ATCC/CRP #DD-156 and screened by a thermal melt assay against a focused library of one hundred previously classified methionyl-tRNA-synthetase inhibitors of the blood stage form of Trypanosoma brucei. Three compounds showed appreciable shift of denaturation temperature and were selected for further studies on inhibition of the recombinant enzyme activity and cell viability against wild type B. melitensis strain 16M. BmMetRS protein complexed with these three inhibitors resolved into three-dimensional crystal structures and was analyzed. All three selected methionyl-tRNA-synthetase compounds inhibit recombinant BmMetRS enzymatic functions in an aminoacylation assay at varying concentrations. Furthermore, growth inhibition of B. melitensis strain 16M by the compounds was shown. Inhibitor-BmMetRS crystal structure models were used to illustrate the molecular basis of the enzyme inhibition. Our current data suggests that BmMetRS is a promising target for brucellosis drug development. However, further studies are needed to optimize lead compound potency, efficacy and safety as well as determine the pharmacokinetics, optimal dosage, and duration for effective treatment.


Assuntos
Brucella melitensis/efeitos dos fármacos , Brucella melitensis/enzimologia , Brucelose/tratamento farmacológico , Inibidores Enzimáticos/farmacologia , Ensaios de Triagem em Larga Escala/métodos , Metionina tRNA Ligase/antagonistas & inibidores , Sequência de Aminoácidos , Brucella melitensis/crescimento & desenvolvimento , Brucelose/microbiologia , Descoberta de Drogas , Concentração Inibidora 50 , Metionina tRNA Ligase/metabolismo , Conformação Proteica , Homologia de Sequência de Aminoácidos
8.
Curr Opin Struct Biol ; 36: 122-32, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26919170

RESUMO

Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity.


Assuntos
Aptâmeros de Nucleotídeos/química , Modelos Moleculares , Proteínas/química , Aptâmeros de Nucleotídeos/metabolismo , Sítios de Ligação , Interações Hidrofóbicas e Hidrofílicas , Ligantes , Conformação de Ácido Nucleico , Motivos de Nucleotídeos , Ligação Proteica , Conformação Proteica , Proteínas/metabolismo , Relação Estrutura-Atividade
9.
Structure ; 23(7): 1293-304, 2015 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-26027732

RESUMO

Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed essential functions of hydrophobic aromatic side chains in the context of well-known nucleic acid motifs. Here we report a 2.45-Å resolution crystal structure of a SOMAmer complexed with nerve growth factor that lacks any known nucleic acid motifs, instead adopting a configuration akin to a triangular prism. The SOMAmer utilizes extensive hydrophobic stacking interactions, non-canonical base pairing and irregular purine glycosidic bond angles to adopt a completely non-helical, compact S-shaped structure. Aromatic side chains contribute to folding by creating an unprecedented intercalating zipper-like motif and a prominent hydrophobic core. The structure provides compelling rationale for potent inhibitory activity of the SOMAmer and adds entirely novel motifs to the repertoire of structural elements uniquely available to SOMAmers.


Assuntos
DNA/química , Fator de Crescimento Neural/química , Sequência de Aminoácidos , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , Humanos , Interações Hidrofóbicas e Hidrofílicas , Dados de Sequência Molecular , Fator de Crescimento Neural/fisiologia , Ligação Proteica , Estrutura Secundária de Proteína , Técnica de Seleção de Aptâmeros
10.
Acta Crystallogr F Struct Biol Commun ; 71(Pt 5): 615-21, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25961325

RESUMO

Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.


Assuntos
Babesia bovis/enzimologia , Eucariotos/enzimologia , Leishmania major/enzimologia , Superóxido Dismutase/química , Trypanosoma cruzi/enzimologia , Sequência de Aminoácidos , Apicomplexa/química , Apicomplexa/enzimologia , Apicomplexa/genética , Babesia bovis/química , Babesia bovis/genética , Cristalização , Cristalografia por Raios X , Eucariotos/química , Eucariotos/genética , Humanos , Leishmania major/química , Leishmania major/genética , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Superóxido Dismutase/genética , Trypanosoma cruzi/química , Trypanosoma cruzi/genética
11.
Methods Mol Biol ; 1140: 315-23, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24590727

RESUMO

X-ray crystallography is an invaluable technique in structure-based drug discovery, including fragment-based drug discovery, because it is the only technique that can provide a complete three dimensional readout of the interaction between the small molecule and its macromolecular target. X-ray diffraction (XRD) techniques can be employed as the sole method for conducting a screen of a fragment library, or it can be employed as the final technique in a screening campaign to confirm putative "hit" compounds identified by a variety of biochemical and/or biophysical screening techniques. Both approaches require an efficient technique to prepare dozens to hundreds of crystals for data collection, and a reproducible way to deliver ligands to the crystal. Here, a general method for screening cocktails of fragments is described. In cases where X-ray crystallography is employed as a method to verify putative hits, the cocktails of fragments described below would simply be replaced with single fragment solutions.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , Ligantes , Biologia Molecular/métodos , Sítios de Ligação , Biofísica , Cristalografia por Raios X , Descoberta de Drogas , Avaliação Pré-Clínica de Medicamentos , Humanos , Espectroscopia de Ressonância Magnética , Bibliotecas de Moléculas Pequenas/química , Difração de Raios X
12.
J Biol Chem ; 289(12): 8720-34, 2014 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-24415767

RESUMO

IL-6 is a secreted cytokine that functions through binding two cell surface receptors, IL-6Rα and gp130. Because of its involvement in the progression of several chronic inflammatory diseases, IL-6 is a target of pharmacologic interest. We have recently identified a novel class of ligands called SOMAmers (S low Off-rate Modified Aptamers) that bind IL-6 and inhibit its biologic activity. SOMAmers exploit the chemical diversity of protein-like side chains assembled on flexible nucleic acid scaffolds, resulting in an expanded repertoire of intra- and intermolecular interactions not achievable with conventional aptamers. Here, we report the co-crystal structure of a high affinity SOMAmer (Kd = 0.20 nm) modified at the 5-position of deoxyuridine in a complex with IL-6. The SOMAmer, comprised of a G-quartet domain and a stem-loop domain, engages IL-6 in a clamp-like manner over an extended surface exhibiting close shape complementarity with the protein. The interface is characterized by substantial hydrophobic interactions overlapping the binding surfaces of the IL-6Rα and gp130 receptors. The G-quartet domain retains considerable binding activity as a disconnected autonomous fragment (Kd = 270 nm). A single substitution from our diversely modified nucleotide library leads to a 37-fold enhancement in binding affinity of the G-quartet fragment (Kd = 7.4 nm). The ability to probe ligand surfaces in this manner is a powerful tool in the development of new therapeutic reagents with improved pharmacologic properties. The SOMAmer·IL-6 structure also expands our understanding of the diverse structural motifs achievable with modified nucleic acid libraries and elucidates the nature with which these unique ligands interact with their protein targets.


Assuntos
Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/farmacologia , Interleucina-6/química , Interleucina-6/metabolismo , Cristalografia por Raios X , Descoberta de Drogas , Humanos , Ligantes , Modelos Moleculares , Conformação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Técnica de Seleção de Aptâmeros
13.
Proc Natl Acad Sci U S A ; 109(49): 19971-6, 2012 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-23139410

RESUMO

Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.


Assuntos
Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/metabolismo , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Proteínas Proto-Oncogênicas c-sis/metabolismo , Técnica de Seleção de Aptâmeros/métodos , Motivos de Aminoácidos/genética , Becaplermina , Cristalografia por Raios X , Primers do DNA/genética , Dados de Sequência Molecular , Estrutura Molecular , Fosforilação , Ligação Proteica , Proteínas Proto-Oncogênicas c-sis/química , Análise de Sequência de DNA , Temperatura de Transição
14.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 67(Pt 9): 1044-50, 2011 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-21904048

RESUMO

Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.


Assuntos
Burkholderia pseudomallei/enzimologia , Fosfoglicerato Mutase/química , Cristalografia por Raios X , Modelos Moleculares , Fosfoglicerato Mutase/metabolismo , Estrutura Terciária de Proteína , Especificidade por Substrato
15.
Artigo em Inglês | MEDLINE | ID: mdl-21904051

RESUMO

Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.


Assuntos
Burkholderia pseudomallei/enzimologia , Glutaril-CoA Desidrogenase/química , Apoenzimas/química , Domínio Catalítico , Cristalografia por Raios X , Humanos , Modelos Moleculares , Filogenia , Estrutura Quaternária de Proteína , Homologia Estrutural de Proteína
16.
Methods Enzymol ; 493: 91-114, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21371588

RESUMO

Fragment screening using X-ray crystallography is a method that can provide direct three-dimensional readouts of the structures of protein-small molecule complexes for lead development and fragment-based drug discovery. With current technology, an amenable crystal form can be screened crystallographically against a library of 1000-2000 fragments in 1-2 weeks. We have performed over a dozen crystallographic screening campaigns using our own compound collection called Fragments of Life™ (FOL). While the majority of our fragment screening campaigns have generated multiple hits, some unexpectedly turned out to be nonproductive, either yielding no bound ligands, or only those thought to be inadequate for lead development. In this chapter, we have attempted to identify one or more parameters which could be used to predict whether a crystallized protein target would be a good candidate for fragment hit discovery. Here, we describe the parameters of crystals from 18 fragment screening campaigns, including six unsuccessful targets. From this analysis, we have concluded that there are no parameters that are absolutely predictive of fragment screening success. However, we do describe a parameter we have termed pocket factor which provides a statistically significant variance between nonproductive targets and productive targets shown to bind fragments. The pocket factor is calculated using a novel method of consensus scoring from three distinct pocket-finding algorithms, and the results may be used to prioritize targets for fragment screening campaigns based on an initial crystal structure.


Assuntos
Cristalografia por Raios X , Avaliação Pré-Clínica de Medicamentos/métodos , Genômica/métodos , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/química , Algoritmos , Burkholderia pseudomallei/enzimologia , Doenças Transmissíveis , Simulação por Computador , Cristalização , Descoberta de Drogas/métodos , Eritritol/análogos & derivados , Eritritol/biossíntese , Glutaril-CoA Desidrogenase/química , Isoenzimas/química , Ligantes , Modelos Moleculares , Fosfoglicerato Mutase/química , Fósforo-Oxigênio Liases/química , Ligação Proteica , Bibliotecas de Moléculas Pequenas , Solventes
17.
Methods Enzymol ; 493: 533-56, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21371605

RESUMO

Structural genomics efforts have traditionally focused on generating single protein structures of unique and diverse targets. However, a lone structure for a given target is often insufficient to firmly assign function or to drive drug discovery. As part of the Seattle Structural Genomics Center for Infectious Disease (SSGCID), we seek to expand the focus of structural genomics by elucidating ensembles of structures that examine small molecule-protein interactions for selected infectious disease targets. In this chapter, we discuss two applications for small molecule libraries in structural genomics: unbiased fragment screening, to provide inspiration for lead development, and targeted, knowledge-based screening, to confirm or correct the functional annotation of a given gene product. This shift in emphasis results in a structural genomics effort that is more engaged with the infectious disease research community, and one that produces structures of greater utility to researchers interested in both protein function and inhibitor development. We also describe specific methods for conducting high-throughput fragment screening in a structural genomics context by X-ray crystallography.


Assuntos
Doenças Transmissíveis/tratamento farmacológico , Descoberta de Drogas/métodos , Genômica/métodos , Bibliotecas de Moléculas Pequenas , Proteínas de Bactérias/química , Biologia Computacional , Cristalização , Cristalografia por Raios X , Ligantes , Fósforo-Oxigênio Liases/antagonistas & inibidores
18.
J Struct Funct Genomics ; 12(2): 63-76, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21359640

RESUMO

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.


Assuntos
Proteínas de Bactérias/química , Burkholderia pseudomallei/enzimologia , Fósforo-Oxigênio Liases/química , Sítios de Ligação , Domínio Catalítico , Cristalografia por Raios X , Desenho de Fármacos , Ligantes , Espectroscopia de Ressonância Magnética
19.
Nat Chem Biol ; 7(1): 41-50, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21113169

RESUMO

Bruton's tyrosine kinase (Btk) is a therapeutic target for rheumatoid arthritis, but the cellular and molecular mechanisms by which Btk mediates inflammation are poorly understood. Here we describe the discovery of CGI1746, a small-molecule Btk inhibitor chemotype with a new binding mode that stabilizes an inactive nonphosphorylated enzyme conformation. CGI1746 has exquisite selectivity for Btk and inhibits both auto- and transphosphorylation steps necessary for enzyme activation. Using CGI1746, we demonstrate that Btk regulates inflammatory arthritis by two distinct mechanisms. CGI1746 blocks B cell receptor-dependent B cell proliferation and in prophylactic regimens reduces autoantibody levels in collagen-induced arthritis. In macrophages, Btk inhibition abolishes FcγRIII-induced TNFα, IL-1ß and IL-6 production. Accordingly, in myeloid- and FcγR-dependent autoantibody-induced arthritis, CGI1746 decreases cytokine levels within joints and ameliorates disease. These results provide new understanding of the function of Btk in both B cell- or myeloid cell-driven disease processes and provide a compelling rationale for targeting Btk in rheumatoid arthritis.


Assuntos
Artrite Experimental/tratamento farmacológico , Artrite Reumatoide/tratamento farmacológico , Linfócitos B/efeitos dos fármacos , Benzamidas/uso terapêutico , Compostos Bicíclicos Heterocíclicos com Pontes/uso terapêutico , Células Mieloides/efeitos dos fármacos , Inibidores de Proteínas Quinases/uso terapêutico , Tirosina Quinase da Agamaglobulinemia , Animais , Artrite Experimental/imunologia , Artrite Experimental/metabolismo , Artrite Reumatoide/imunologia , Artrite Reumatoide/metabolismo , Autoanticorpos/imunologia , Autoanticorpos/metabolismo , Linfócitos B/imunologia , Linfócitos B/metabolismo , Benzamidas/química , Benzamidas/farmacologia , Compostos Bicíclicos Heterocíclicos com Pontes/química , Compostos Bicíclicos Heterocíclicos com Pontes/farmacologia , Proliferação de Células/efeitos dos fármacos , Ativação Enzimática/efeitos dos fármacos , Interleucina-1beta/imunologia , Interleucina-1beta/metabolismo , Interleucina-6/imunologia , Interleucina-6/metabolismo , Camundongos , Células Mieloides/imunologia , Células Mieloides/metabolismo , Fosforilação/efeitos dos fármacos , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacologia , Proteínas Tirosina Quinases/química , Proteínas Tirosina Quinases/farmacologia , Proteínas Tirosina Quinases/uso terapêutico , Fator de Necrose Tumoral alfa/imunologia , Fator de Necrose Tumoral alfa/metabolismo
20.
PLoS One ; 5(9)2010 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-20824064

RESUMO

BACKGROUND: Ether-à-go-go (EAG) channels are expressed throughout the central nervous system and are also crucial regulators of cell cycle and tumor progression. The large intracellular amino- and carboxy- terminal domains of EAG1 each share similarity with known ligand binding motifs in other proteins, yet EAG1 channels have no known regulatory ligands. METHODOLOGY/PRINCIPAL FINDINGS: Here we screened a library of small biologically relevant molecules against EAG1 channels with a novel two-pronged screen to identify channel regulators. In one arm of the screen we used electrophysiology to assess the functional effects of the library compounds on full-length EAG1 channels. In an orthogonal arm, we used tryptophan fluorescence to screen for binding of the library compounds to the isolated C-terminal region. CONCLUSIONS/SIGNIFICANCE: Several compounds from the flavonoid, indole and benzofuran chemical families emerged as binding partners and/or regulators of EAG1 channels. The two-prong screen can aid ligand and drug discovery for ligand-binding domains of other ion channels.


Assuntos
Eletrofisiologia/métodos , Canais de Potássio Éter-A-Go-Go/química , Canais de Potássio Éter-A-Go-Go/metabolismo , Triptofano/metabolismo , Animais , Avaliação Pré-Clínica de Medicamentos , Canais de Potássio Éter-A-Go-Go/genética , Ligantes , Camundongos , Ligação Proteica , Estrutura Terciária de Proteína , Triptofano/química
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