ABSTRACT
The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6-Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S-S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I). The results of this comparison are reported. Graphical abstract Conformations of PheB25 and PheD25 in three insulin structures: implications for biological activity? Insulin residues PheB25 and PheD25 are considered to be important for insulin receptor binding and changes in biological activity occur when these residues are modified. In porcine insulin and Intergen (II) PheB25 adopts conformation B and PheD25 conformation D. However, unexpectedly PheB25 in Insugen (I) human recombinant insulin adopts two distinct conformations corresponding to B and D, Figure 1 and PheD25 adopts a single conformation corresponding to B not D, Figure 2. Conformations of this residue in the ultra-high resolution structure of Insugen (I) are therefore unique within this set. Figures were produced with Biovia, Discovery Studio 2016.
ABSTRACT
Mycobacterium tuberculosis (MTb) is the causative agent of pulmonary tuberculosis (TB). MTb colonizes the human lung, often entering a non-replicating state before progressing to life-threatening active infections. Transcriptional reprogramming is essential for TB pathogenesis. In vitro, Cmr (a member of the CRP/FNR super-family of transcription regulators) bound at a single DNA site to act as a dual regulator of cmr transcription and an activator of the divergent rv1676 gene. Transcriptional profiling and DNA-binding assays suggested that Cmr directly represses dosR expression. The DosR regulon is thought to be involved in establishing latent tuberculosis infections in response to hypoxia and nitric oxide. Accordingly, DNA-binding by Cmr was severely impaired by nitrosation. A cmr mutant was better able to survive a nitrosative stress challenge but was attenuated in a mouse aerosol infection model. The complemented mutant exhibited a â¼2-fold increase in cmr expression, which led to increased sensitivity to nitrosative stress. This, and the inability to restore wild-type behaviour in the infection model, suggests that precise regulation of the cmr locus, which is associated with Region of Difference 150 in hypervirulent Beijing strains of Mtb, is important for TB pathogenesis.
Subject(s)
Bacterial Proteins/genetics , Mycobacterium tuberculosis/metabolism , Protein Kinases/genetics , Transcription Factors/physiology , Tuberculosis/microbiology , Animals , Bacterial Proteins/metabolism , Cells, Cultured , DNA-Binding Proteins , Escherichia coli , Female , Gene Expression Regulation, Bacterial , Macrophages/microbiology , Mice, Inbred BALB C , Mycobacterium smegmatis , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/pathogenicity , Oxidation-Reduction , Protein Binding , Protein Kinases/metabolism , Transcription, Genetic , Virulence , Virulence Factors/genetics , Virulence Factors/metabolismABSTRACT
BACKGROUND: TRNT1 (CCA-adding transfer RNA nucleotidyl transferase) enzyme deficiency is a new metabolic disease caused by defective post-transcriptional modification of mitochondrial and cytosolic transfer RNAs (tRNAs). RESULTS: We investigated four patients from two families with infantile-onset cyclical, aseptic febrile episodes with vomiting and diarrhoea, global electrolyte imbalance during these episodes, sideroblastic anaemia, B lymphocyte immunodeficiency, retinitis pigmentosa, hepatosplenomegaly, exocrine pancreatic insufficiency and renal tubulopathy. Other clinical features found in children include sensorineural deafness, cerebellar atrophy, brittle hair, partial villous atrophy and nephrocalcinosis. Whole exome sequencing and bioinformatic filtering were utilised to identify recessive compound heterozygous TRNT1 mutations (missense mutation c.668T>C, p.Ile223Thr and a novel splice mutation c.342+5G>T) segregating with disease in the first family. The second family was found to have a homozygous TRNT1 mutation (c.569G>T), p.Arg190Ile, (previously published). We found normal mitochondrial translation products using passage matched controls and functional perturbation of 3' CCA addition to mitochondrial tRNAs (tRNA(Cys), tRNA(LeuUUR) and tRNA(His)) in fibroblasts from two patients, demonstrating a pathomechanism affecting the CCA addition to mt-tRNAs. Acute management of these patients included transfusion for anaemia, fluid and electrolyte replacement and immunoglobulin therapy. We also describe three-year follow-up findings after treatment by bone marrow transplantation in one patient, with resolution of fever and reversal of the abnormal metabolic profile. CONCLUSIONS: Our report highlights that TRNT1 mutations cause a spectrum of disease ranging from a childhood-onset complex disease with manifestations in most organs to an adult-onset isolated retinitis pigmentosa presentation. Systematic review of all TRNT1 cases and mutations reported to date revealed a distinctive phenotypic spectrum and metabolic and other investigative findings, which will facilitate rapid clinical recognition of future cases.
Subject(s)
Mitochondrial Diseases/genetics , Nucleotidyltransferases/deficiency , Anemia, Sideroblastic/genetics , Developmental Disabilities/genetics , Humans , Mutation/genetics , Nucleotidyltransferases/genetics , Protein Biosynthesis/genetics , RNA, Transfer/geneticsABSTRACT
Adprhl1, a member of the ADP-ribosylhydrolase protein family, is expressed exclusively in the developing heart of all vertebrates. In the amphibian Xenopus laevis, distribution of its mRNA is biased towards actively growing chamber myocardium. Morpholino oligonucleotide-mediated knockdown of all Adprhl1 variants inhibits striated myofibril assembly and prevents outgrowth of the ventricle. The resulting ventricles retain normal electrical conduction and express markers of chamber muscle differentiation but are functionally inert. Using a cardiac-specific Gal4 binary expression system, we show that the abundance of Adprhl1 protein in tadpole hearts is tightly controlled through a negative regulatory mechanism targeting the 5'-coding sequence of Xenopus adprhl1. Over-expression of full length (40kDa) Adprhl1 variants modified to escape such repression, also disrupts cardiac myofibrillogenesis. Disarrayed myofibrils persist that show extensive branching, with sarcomere division occurring at the actin-Z-disc boundary. Ultimately, Adprhl1-positive cells contain thin actin threads, connected to numerous circular branch points. Recombinant Adprhl1 can localize to stripes adjacent to the Z-disc, suggesting a direct role for Adprhl1 in modifying Z-disc and actin dynamics as heart chambers grow. Modelling the structure of Adprhl1 suggests this cardiac-specific protein is a pseudoenzyme, lacking key residues necessary for ADP-ribosylhydrolase catalytic activity.
Subject(s)
Actin Cytoskeleton/physiology , Gene Expression Regulation, Developmental , Myocardium/cytology , N-Glycosyl Hydrolases/physiology , Xenopus Proteins/physiology , Animals , Animals, Genetically Modified , Gene Knockdown Techniques , Heart/embryology , Heart/growth & development , Heart Ventricles/embryology , Heart Ventricles/growth & development , Humans , Larva , Luminescent Proteins/analysis , Luminescent Proteins/genetics , Mice , Models, Molecular , Molecular Dynamics Simulation , Morpholinos/pharmacology , Mutation , Myocardium/metabolism , N-Glycosyl Hydrolases/biosynthesis , N-Glycosyl Hydrolases/genetics , Organogenesis , Protein Conformation , RNA, Messenger/biosynthesis , Recombinant Fusion Proteins/metabolism , Xenopus Proteins/biosynthesis , Xenopus Proteins/genetics , Xenopus laevis/embryology , Xenopus laevis/growth & developmentABSTRACT
KAL1 is implicated in 5% of Kallmann syndrome cases, a disorder which genotypically overlaps with septo-optic dysplasia (SOD). To date, a reporter-based assay to assess the functional consequences of KAL1 mutations is lacking. We aimed to develop a luciferase assay for novel application to functional assessment of rare KAL1 mutations detected in a screen of 422 patients with SOD. Quantitative analysis was performed using L6-myoblasts stably expressing FGFR1, transfected with a luciferase-reporter vector containing elements of the FGF-responsive osteocalcin promoter. The two variants assayed [p.K185N, p.P291T], were detected in three females with SOD (presenting with optic nerve hypoplasia, midline and pituitary defects). Our novel assay revealed significant decreases in transcriptional activity [p.K185N: 21% (p < 0.01); p.P291T: 40% (p < 0.001)]. Our luciferase-reporter assay, developed for assessment of KAL1 mutations, determined that two variants in females with hypopituitarism/SOD are loss-of-function; demonstrating that this assay is suitable for quantitative assessment of mutations in this gene.
Subject(s)
Extracellular Matrix Proteins/genetics , Extracellular Matrix Proteins/metabolism , Luciferases/metabolism , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Polymorphism, Single Nucleotide , Septo-Optic Dysplasia/genetics , Animals , COS Cells , Chlorocebus aethiops , Female , Humans , In Vitro Techniques , Models, Molecular , Pedigree , Pituitary Gland/metabolism , Septo-Optic Dysplasia/metabolism , Septo-Optic Dysplasia/pathologyABSTRACT
Whole exome sequencing was used to investigate the genetic cause of mitochondrial disease in two siblings with a syndrome of congenital lamellar cataracts associated with nephrocalcinosis, medullary cysts and 3-methylglutaconic aciduria. Autosomal recessive inheritance in a gene encoding a mitochondrially targeted protein was assumed; the only variants which satisfied these criteria were c.1882C>T (p.Arg628Cys) and c.1915G>A (p.Glu639Lys) in the CLPB gene, encoding a heat shock protein/chaperonin responsible for disaggregating mitochondrial and cytosolic proteins. Functional studies, including quantitative PCR (qPCR) and Western blot, support pathogenicity of these mutations. Furthermore, molecular modelling suggests that the mutations disrupt interactions between subunits so that the CLPB hexamer cannot form or is unstable, thus impairing its role as a protein disaggregase. We conclude that accumulation of protein aggregates underlies the development of cataracts and nephrocalcinosis in CLPB deficiency, which is a novel genetic cause of 3-methylglutaconic aciduria. A common mitochondrial cause for 3-methylglutaconic aciduria appears to be disruption of the architecture of the mitochondrial membranes, as in Barth syndrome (tafazzin deficiency), Sengers syndrome (acylglycerol kinase deficiency) and MEGDEL syndrome (impaired remodelling of the mitochondrial membrane lipids because of SERAC1 mutations). We now propose that perturbation of the mitochondrial membranes by abnormal protein aggregates leads to 3-methylglutaconic aciduria in CLPB deficiency.
Subject(s)
Cataract/genetics , Endopeptidase Clp/genetics , Kidney Diseases, Cystic/genetics , Metabolism, Inborn Errors/genetics , Mitochondrial Diseases/genetics , Mutation , Nephrocalcinosis/genetics , Cataract/diagnosis , Cataract/enzymology , Cells, Cultured , DNA Mutational Analysis , Endopeptidase Clp/chemistry , Endopeptidase Clp/deficiency , Exome , Female , Genetic Predisposition to Disease , Heredity , Humans , Kidney Diseases, Cystic/diagnosis , Kidney Diseases, Cystic/enzymology , Male , Metabolism, Inborn Errors/diagnosis , Metabolism, Inborn Errors/enzymology , Mitochondrial Diseases/diagnosis , Mitochondrial Diseases/enzymology , Mitochondrial Membranes/pathology , Models, Molecular , Nephrocalcinosis/diagnosis , Nephrocalcinosis/enzymology , Pedigree , Phenotype , Protein Aggregation, Pathological , Protein Conformation , Risk Factors , Siblings , Structure-Activity RelationshipABSTRACT
INTRODUCTION: Immunotherapy targeting amyloid-ß peptide is under active clinical investigation for treatment of Alzheimer's disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-ß to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-ß1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD. METHODS: To gain further insight into the epitope conformation, we interrogated structural details of amino-terminal epitopes in amyloid-ß using x-ray crystallography of 3D6Fab:amyloid-ß complexes. Humanization of 3D6 was carried out using standard procedures integrating recombinant methods, sequence informatics, and homology modeling predictions to identify important mouse framework residues for retention in the finished humanized product. RESULTS: Here we report the crystal structure of a recombinant Fab fragment of 3D6 in complex with amyloid-ß1-7 solved at 2.0 Å resolution. The N-terminus of amyloid-ß is bound to 3D6 as a 310 helix. The amino-terminal Asp residue is buried deepest in the antibody binding pocket, with the Cß atom of residue 6 visible at the entrance to the binding pocket near the surface of the antibody. We further evaluate homology model based predictions used to guide humanization of 3D6 to bapineuzumab, with actual structure of the Fab. The structure of the Fab:amyloid-ß complex validates design of the humanized antibody, and confirms the amyloid-ß epitope recognized by 3D6 as previously mapped by ELISA. CONCLUSIONS: The conformation of amyloid-ß antigen recognized by 3D6 is novel and distinct from other antibodies recognizing N-terminal epitopes. Our result provides the first report demonstrating structural conservation of antigen contact residues, and conformation of antigen recognized, between the parent murine antibody and its humanized version.
ABSTRACT
The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
ABSTRACT
Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
ABSTRACT
FAN1 is a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. It is the only eukaryotic protein with a virus-type replication-repair nuclease ("VRR-Nuc") "module" that commonly occurs as a standalone domain in many bacteria and viruses. Crystal structures of three representatives show that they structurally resemble Holliday junction resolvases (HJRs), are dimeric in solution, and are able to cleave symmetric four-way junctions. In contrast, FAN1 orthologs are monomeric and cleave 5' flap structures in vitro, but not Holliday junctions. Modeling of the VRR-Nuc domain of FAN1 reveals that it has an insertion, which packs against the dimerization interface observed in the structures of the viral/bacterial VRR-Nuc proteins. We propose that these additional structural elements in FAN1 prevent dimerization and bias specificity toward flap structures.
Subject(s)
Bacterial Proteins/chemistry , DNA, Cruciform/metabolism , Endodeoxyribonucleases/chemistry , Exodeoxyribonucleases/chemistry , Holliday Junction Resolvases/chemistry , Amino Acid Sequence , Animals , Bacterial Proteins/metabolism , DNA Repair , Endodeoxyribonucleases/metabolism , Exodeoxyribonucleases/metabolism , Holliday Junction Resolvases/metabolism , Humans , Mice , Molecular Sequence Data , Multifunctional Enzymes , Protein Binding , Protein Multimerization , Protein Structure, Tertiary , Pseudomonas aeruginosa/enzymologyABSTRACT
We have used alanine-scanning mutagenesis followed by functional expression and molecular modeling to analyze the roles of the 14 residues, Asn422 to Cys435, C-terminal to transmembrane (TM) helix 7 of the M(1) muscarinic acetylcholine receptor. The results suggest that they form an eighth (H8) helix, associated with the cytoplasmic surface of the cell membrane in the active state of the receptor. We suggest that the amide side chain of Asn422 may act as a cap to the C terminus of TM7, stabilizing its junction with H8, whereas the side chain of Phe429 may restrict the relative movements of H8 and the C terminus of TM7 in the inactive ground state of the receptor. We have identified four residues, Phe425, Arg426, Thr428, and Leu432, which are important for G protein binding and signaling. These may form a docking site for the C-terminal helix of the G protein α subunit, and collaborate with G protein recognition residues elsewhere in the cytoplasmic domain of the receptor to form a coherent surface for G protein binding in the activated state of the receptor.
Subject(s)
GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Mutagenesis/genetics , Receptor, Muscarinic M1/genetics , Receptor, Muscarinic M1/metabolism , Alanine/genetics , Animals , Binding Sites/genetics , COS Cells , Chlorocebus aethiops , Dose-Response Relationship, Drug , GTP-Binding Proteins/chemistry , Protein Structure, Secondary/genetics , Protein Structure, Tertiary/genetics , Rats , Receptor, Muscarinic M1/chemistryABSTRACT
Coenzyme Q (CoQ) or ubiquinone is a lipid component of the electron transport chain required for ATP generation in mitochondria. Mutations in CoQ biosynthetic genes are associated with rare but severe infantile multisystemic diseases. CoQ itself is a popular over-the-counter dietary supplement that some clinical and rodent studies suggest might be beneficial for neurodegenerative diseases. Here, we identify mutations in the Drosophila qless gene, which encodes an orthologue of the human PDSS1 prenyl transferase that synthesizes the isoprenoid side chain of CoQ. We show that neurons lacking qless activity upregulate markers of mitochondrial stress and undergo caspase-dependent apoptosis. Surprisingly, even though experimental inhibition of caspase activity did not prevent mitochondrial disruption, it was sufficient to rescue the size of neural progenitor clones. This demonstrates that, within the developing larval CNS, qless activity is required primarily for cell survival rather than for cell growth and proliferation. Full rescue of the qless neural phenotype was achieved by dietary supplementation with CoQ4, CoQ9 or CoQ10, indicating that a side chain as short as four isoprenoid units can provide in vivo activity. Together, these findings show that Drosophila qless provides a useful model for studying the neural effects of CoQ deficiency and dietary supplementation.
Subject(s)
Dietary Supplements , Disease Models, Animal , Drosophila melanogaster/metabolism , Nervous System/growth & development , Nervous System/pathology , Ubiquinone/deficiency , Alkyl and Aryl Transferases/metabolism , Amino Acid Sequence , Animals , Caspases/metabolism , Cell Proliferation , Cell Survival , Conserved Sequence/genetics , Cytoprotection , Drosophila Proteins/chemistry , Drosophila Proteins/metabolism , Enzyme Activation , Humans , Mitochondria/pathology , Molecular Sequence Data , Nervous System/metabolism , Neurons/enzymology , Neurons/pathology , Stress, Physiological , Ubiquinone/metabolismABSTRACT
Cross-talk of BMP and Wnt signaling pathways has been implicated in many aspects of biological events during embryogenesis and in adulthood. A secreted protein Wise and its orthologs (Sostdc1, USAG-1, and Ectodin) have been shown to modulate Wnt signaling and also inhibit BMP signals. Modulation of Wnt signaling activity by Wise is brought about by an interaction with the Wnt co-receptor LRP6, whereas BMP inhibition is by binding to BMP ligands. Here we have investigated the mode of action of Wise on Wnt and BMP signals. It was found that Wise binds LRP6 through one of three loops formed by the cystine knot. The Wise deletion construct lacking the LRP6-interacting loop domain nevertheless binds BMP4 and inhibits BMP signals. Moreover, BMP4 does not interfere with Wise-LRP6 binding, suggesting separate domains for the physical interaction. Functional assays also show that the ability of Wise to block Wnt1 activity through LRP6 is not impeded by BMP4. In contrast, the ability of Wise to inhibit BMP4 is prevented by additional LRP6, implying a preference of Wise in binding LRP6 over BMP4. In addition to the interaction of Wise with BMP4 and LRP6, the molecular characteristics of Wise, such as glycosylation and association with heparan sulfate proteoglycans on the cell surface, are suggested. This study helps to understand the multiple functions of Wise at the molecular level and suggests a possible role for Wise in balancing Wnt and BMP signals.
Subject(s)
Bone Morphogenetic Proteins/chemistry , Bone Morphogenetic Proteins/metabolism , Wnt Proteins/metabolism , Animals , Blotting, Western , Bone Morphogenetic Protein 4/genetics , Bone Morphogenetic Protein 4/metabolism , Bone Morphogenetic Proteins/genetics , Cell Line , Chickens , Glycosylation , Humans , Immunoprecipitation , LDL-Receptor Related Proteins/genetics , LDL-Receptor Related Proteins/metabolism , Mice , Models, Molecular , Mutation , Protein Binding , Protein Structure, Tertiary , Proteoglycans/metabolism , Signal Transduction , Wnt Proteins/geneticsABSTRACT
BACKGROUND: Prostate cancer is a common disease in men and at present there is no effective therapy available due to its recurrence despite androgen deprivation therapy. The epidermal growth factor receptor family (EGFR/HER1, HER2/neu and HER3)/PI3K/Akt signaling axis has been implicated in prostate cancer development and progression. However, Erlotinib, an EGFR tyrosine kinase inhibitor, has less effect on proliferation and apoptosis in prostate cancer cell lines. In this study, we evaluate whether MP470, a novel receptor tyrosine kinase inhibitor alone or in combination with Erlotinib has inhibitory effect on prostate cancer in vitro and in vivo. METHODS: The efficacy of MP470 or MP470 plus Erlotinib was evaluated in vitro using three prostate cancer cell lines by MTS and apoptosis assays. The molecular mechanism study was carried out by phosphorylation antibody array, immunoblotting and immunohistochemistry. A LNCaP mouse xenograft model was also used to determine the tumor growth inhibition by MP470, Erlotinib or the combination treatments. RESULTS: MP470 exhibits low microM IC50 in prostate cancer cell lines. Additive effects on both cytotoxicity and induction of apoptosis were observed when LNCaP were treated with MP470 in combination with Erlotinib. This combination treatment completely inhibited phosphorylation of the HER family members (HER1, 2, 3), binding of PI3K regulatory unit p85 to HER3 and downstream Akt activity even after androgen depletion. Furthermore, in a LNCaP mouse xenograft model, the MP470-Erlotinib combination produced 30-65% dose-dependent tumor growth inhibition (TGI). CONCLUSION: We propose that MP470-Erlotinib targets the HER family/PI3K/Akt pathway and may represent a novel therapeutic strategy for prostate cancer.
Subject(s)
Antineoplastic Agents/pharmacology , Cell Proliferation/drug effects , Prostatic Neoplasms/drug therapy , Protein Kinase Inhibitors/pharmacology , Pyrimidines/pharmacology , Quinazolines/therapeutic use , Signal Transduction/drug effects , Animals , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Drug Therapy, Combination , ErbB Receptors/metabolism , Erlotinib Hydrochloride , Humans , Male , Mice , Mice, SCID , Multigene Family , Phosphatidylinositol 3-Kinases/metabolism , Phosphorylation/drug effects , Piperazines , Prostatic Neoplasms/metabolism , Protein Binding/drug effects , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins c-akt/metabolism , Pyrimidines/therapeutic use , Receptor Protein-Tyrosine Kinases/antagonists & inhibitors , Receptor Protein-Tyrosine Kinases/metabolism , ThioureaABSTRACT
Pancreatic ductal adenocarcinoma (PDA) is a lethal disease, with surgery being the only curative modality for localized disease, and gemcitabine with or without erlotinib remains the standard of therapy for unresectable or metastatic disease. CEACAM6 is overexpressed in human PDA independent of stage or grade and causes anoikis resistance when dysregulated. Because murine monoclonal antibody 13-1 possesses target-specific cytotoxicity in human PDA cell lines, we designed a humanized anti-CEACAM6 single-chain variable fragment (scFv) based on monoclonal antibody 13-1. PEGylation of the glycine-serine linker was used to enhance plasma half-life. These scFvs bound CEACAM6 with high affinity, exhibited cytotoxic activity, and induced dose-dependent poly(ADP-ribose) polymerase cleavage. Murine PDA xenograft models treated with humanized scFv alone elicited tumor growth inhibition, which was enhanced in combination with gemcitabine. Immunohistochemistry showed significant apoptosis, with inhibition of angiogenesis and proliferation, and preservation of the target. Collectively, our results have important implications for the development of novel antibody-based therapies against CEACAM6 in PDA.
Subject(s)
Adenocarcinoma/therapy , Antibodies, Monoclonal/therapeutic use , Antigens, CD/immunology , Carcinoma, Pancreatic Ductal/therapy , Cell Adhesion Molecules/immunology , Immunoglobulin Fragments/therapeutic use , Pancreatic Neoplasms/therapy , Animals , Antigens, CD/analysis , Cell Adhesion Molecules/analysis , Cell Line, Tumor , Complementarity Determining Regions , Dimerization , GPI-Linked Proteins , Humans , MiceABSTRACT
Recently published X-ray structures of three common forms, A, B and C, of oligomycin, including absolute configurations, are investigated to examine their binding to ATP Synthase. The X-ray studies reveal regions with differences in three-dimensional structure and hydrogen bonding propensity between the oligomycins, which may be associated with their potential to bind to sites on ATP Synthase. Computational docking studies carried out using MOE with the X-ray structures and an homology model of the F(O) domain of ATP Synthase from Escherichia coli, are used to derive an induced fit pocket. Docking of all oligomycins to this pocket indicate that the B and C forms bind more tightly than the A form. Consideration of the single crystal X-ray data alone indicate the B form may be the best inhibitor and that O(24) is the most important ligating group for binding, this is supported by the docking data. The latter reveals Asn214 and other key proton translocating residues to be the main residues contacted by the inhibitor. These data allow the binding modes of different forms of oligomycin to be deduced from X-ray single crystal data supported by molecular modelling and computational docking studies.
Subject(s)
Anti-Bacterial Agents/chemistry , Bacterial Proton-Translocating ATPases/chemistry , Crystallography, X-Ray , Escherichia coli/enzymology , Oligomycins/chemistry , Anti-Bacterial Agents/metabolism , Bacterial Proton-Translocating ATPases/metabolism , Binding Sites , Computer Simulation , Models, Molecular , Molecular Conformation , Oligomycins/metabolism , Protein Binding , ThermodynamicsABSTRACT
Single nucleotide polymorphisms (SNPs) are present in the global transcriptional regulator cyclic AMP (cAMP) receptor protein (CRP) of the attenuated vaccine strain Mycobacterium bovis, bacillus Calmette-Guérin (BCG). We have found that these SNPs resulted in small but significant changes in the expression of a number of genes in M. tuberculosis when a deletion of the Rv3676 CRP was complemented by the BCG allele, compared to complementation by the M. tuberculosis allele. We can explain these changes in gene expression by modeling the structure of the mycobacterial protein on the known structure of CRP from Escherichia coli. Thus, the SNP change in the DNA-binding domain, Lys178, is predicted to form a hydrogen bond with the phosphate backbone of the DNA, as does the equivalent residue in E. coli, whereas Glu178 in M. tuberculosis/M. bovis does not, thus explaining the stronger binding reported for CRP of BCG to CRP-binding sites in mycobacterial DNA. In contrast, the SNP change in the nucleotide binding domain (Leu47Pro) is predicted to result in the loss of one hydrogen bond, which is accommodated by the structure, and would not therefore be expected to cause any change in function relating to cAMP binding. The BCG allele fully complemented the growth defect caused by the deletion of the Rv3676 protein in M. tuberculosis, both in vitro and in macrophage and mouse infections, suggesting that these SNPs do not play any role in the attenuation of BCG. However, they may have allowed BCG to grow better under the in vitro-selective conditions used in its derivation from the M. bovis wild type.
Subject(s)
Cyclic AMP Receptor Protein/genetics , Cyclic AMP Receptor Protein/metabolism , Gene Expression Regulation, Bacterial , Mycobacterium bovis/physiology , Mycobacterium bovis/pathogenicity , Polymorphism, Single Nucleotide , Amino Acid Sequence , Amino Acid Substitution/genetics , Animals , Cells, Cultured , Cyclic AMP/metabolism , Cyclic AMP Receptor Protein/chemistry , DNA, Bacterial/metabolism , Female , Gene Deletion , Gene Expression Profiling , Genetic Complementation Test , Macrophages/microbiology , Mice , Mice, Inbred BALB C , Models, Molecular , Molecular Sequence Data , Mycobacterium Infections/microbiology , Mycobacterium bovis/genetics , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/growth & development , Protein Binding , Protein Structure, Tertiary , Sequence Alignment , VirulenceABSTRACT
Human glutamate carboxypeptidase II [GCPII (EC 3.4.17.21)] is recognized as a promising pharmacological target for the treatment and imaging of various pathologies, including neurological disorders and prostate cancer. Recently reported crystal structures of GCPII provide structural insight into the organization of the substrate binding cavity and highlight residues implicated in substrate/inhibitor binding in the S1' site of the enzyme. To complement and extend the structural studies, we constructed a model of GCPII in complex with its substrate, N-acetyl-l-aspartyl-l-glutamate, which enabled us to predict additional amino acid residues interacting with the bound substrate, and used site-directed mutagenesis to assess the contribution of individual residues for substrate/inhibitor binding and enzymatic activity of GCPII. We prepared and characterized 12 GCPII mutants targeting the amino acids in the vicinity of substrate/inhibitor binding pockets. The experimental results, together with the molecular modeling, suggest that the amino acid residues delineating the S1' pocket of the enzyme (namely Arg210) contribute primarily to the high affinity binding of GCPII substrates/inhibitors, whereas the residues forming the S1 pocket might be more important for the 'fine-tuning' of GCPII substrate specificity.
Subject(s)
Antigens, Surface/chemistry , Antigens, Surface/metabolism , Glutamate Carboxypeptidase II/chemistry , Glutamate Carboxypeptidase II/metabolism , Mutagenesis, Site-Directed , Animals , Antigens, Surface/genetics , Binding Sites , Glutamate Carboxypeptidase II/antagonists & inhibitors , Glutamate Carboxypeptidase II/genetics , Glutamic Acid/metabolism , Humans , Kinetics , Mice , Models, Molecular , Rats , Sequence Alignment , Structure-Activity Relationship , Substrate SpecificityABSTRACT
The chemokine receptor CCR1 and its principal ligand, CCL3/MIP-1alpha, have been implicated in the pathology of several inflammatory diseases including rheumatoid arthritis, multiple sclerosis, and asthma. As such, these molecules are the focus of much research with the ultimate aim of developing novel therapies. We have described previously a non-competitive small molecule antagonist of CCR1 (UCB 35625), which we hypothesized interacted with amino acids located within the receptor transmembrane (TM) helices (Sabroe, I., Peck, M. J., Jan Van Keulen, B., Jorritsma, A., Simmons, G., Clapham, P. R., Williams, T. J., and Pease, J. E. (2000) J. Biol. Chem. 275, 25985-25992). Here we describe an approach to identifying the mechanism by which the molecule antagonizes CCR1. Thirty-three point mutants of CCR1 were expressed transiently in L1.2 cells, and the cells were assessed for their capacity to migrate in response to CCL3 in the presence or absence of UCB 35625. Cells expressing the mutant constructs Y41A (TM helix 1, or TM1), Y113A (TM3), and E287A (TM7) were responsive to CCL3 but resistant to the antagonist, consistent with a role for the TM helices in CCR1 interactions with UCB 35625. Subsequent molecular modeling successfully docked the compound with CCR1 and suggests that the antagonist ligates TM1, 2, and 7 of CCR1 and severely impedes access to TM2 and TM3, a region thought to be perturbed by the chemokine amino terminus during the process of receptor activation. Insights into the mechanism of action of these compounds may facilitate the development of more potent antagonists that show promise as future therapeutic agents in the treatment of inflammatory disease.
Subject(s)
Receptors, Chemokine/chemistry , Receptors, Chemokine/genetics , Xanthenes/pharmacology , Amino Acid Sequence , Binding Sites , Binding, Competitive , Cell Membrane/metabolism , Cell Movement , Chemotaxis , Dose-Response Relationship, Drug , Glutamic Acid/chemistry , Humans , Inflammation , Models, Chemical , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Mutation , Point Mutation , Protein Binding , Protein Conformation , Protein Structure, Secondary , Protein Structure, Tertiary , Receptors, CCR1 , Sequence Homology, Amino Acid , Signal Transduction , Software , Stereoisomerism , TransfectionABSTRACT
A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; alpha-[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C17H23NO3) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo Kalpha radiation, lambda=0.71073A at 150K. The compound crystallises in space group Fdd2 with Z=16 molecules per unit cell.