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1.
Cells ; 9(5)2020 05 09.
Article in English | MEDLINE | ID: mdl-32397494

ABSTRACT

Microbial proteins have recently been found to have more benefits in clinical disease treatment because of their better-developed strategy and properties than traditional medicine. In this study, we investigated the effectiveness of a truncated peptide synthesized from the C-terminal sequence of pneumolysin, i.e., C70PLY4, in Streptococcus pneumoniae, in treating chronic inflammatory conditions. It has been shown that C70PLY4 significantly blocks the transendothelial migration of neutrophils and attenuates the formation of atherosclerotic plaque and the secretion of soluble forms of the intercellular adhesion molecule-1 (ICAM-1), the vascular cell adhesion molecule 1 (VCAM-1), and E-selectin in high-fat-diet/streptozotocin-induced inflammatory rats. The mechanism and the docking simulation analysis further indicated that C70PLY4 might serve as a Toll-like receptor 4 (TLR4) antagonist by competing for the binding site of MD2, an indispensable protein for lipopolysaccharide (LPS)-TLR4 interaction signaling, on the TLR4 structure. Moreover, compared to the full-length PLY, C70PLY4 seems to have no cytotoxicity in human vascular endothelial cells. Our study elucidated a possible therapeutic efficacy of C70PLY4 in reducing chronic inflammatory conditions and clarified the underlying mechanism. Thus, our findings identify a new drug candidate that, by blocking TLR4 activity, could be an effective treatment for patients with chronic inflammatory diseases.


Subject(s)
Inflammation/drug therapy , Mutant Proteins/pharmacology , Mutant Proteins/therapeutic use , Streptococcus pneumoniae/metabolism , Streptolysins/pharmacology , Toll-Like Receptor 4/antagonists & inhibitors , Amino Acid Sequence , Animals , Apoptosis/drug effects , Bacterial Proteins/chemistry , Bacterial Proteins/pharmacology , Binding Sites , Caspase 3/metabolism , Cell Survival/drug effects , Diet, High-Fat , E-Selectin/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Intercellular Adhesion Molecule-1/metabolism , Lipopolysaccharides , Mice , Molecular Docking Simulation , Mutant Proteins/chemistry , NF-kappa B/metabolism , Neutrophils/cytology , Neutrophils/drug effects , Phosphorylation/drug effects , Solubility , Streptolysins/chemistry , Streptozocin , Toll-Like Receptor 4/metabolism , Transendothelial and Transepithelial Migration/drug effects , Vascular Cell Adhesion Molecule-1/metabolism
2.
Article in English | MEDLINE | ID: mdl-32296386

ABSTRACT

Orexin receptors (OXRs) play a critical regulatory role in central control of food intake, maintenance of sleeping states, energy metabolism, and neuroendocrine homeostasis. However, most previous studies have focused on the sleep-promoting functions of OXRs in human beings, while their potential value in enhancing food intake for livestock breeding has not been fully exploited. In this study, we successfully cloned porcine orexin 2 receptor (pOX2R) complementary DNA and constructed four pOX2R mutants (P10S, P11T, V308I, and T401I) by site-directed mutagenesis, and their functional expressions were further confirmed through Western blotting analysis. Pharmacological characteristics of pOX2R and their mutants were further investigated. These results showed that the P10S, P11T, and T401I mutants had decreased cAMP signaling with orexin A, whereas only the P11T mutant decreased under the stimulation of orexin B. Besides, only P10S displayed a decreased calcium release in response to both orexin ligands. Importantly, these mutants exhibited decreased phosphorylation levels of ERK1/2, p38, and CREB to some degree compared with wild-type pOX2R. Collectively, these findings highlight the critical role of these mutations in pOX2R signaling and expand our understanding of molecular and pharmacological characterization of pOX2R.


Subject(s)
Orexin Receptors/metabolism , Orexins/pharmacology , Swine , Animals , Cloning, Molecular , HEK293 Cells , Humans , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutation , Orexin Receptors/chemistry , Orexin Receptors/genetics , Orexins/metabolism , Phylogeny , Protein Conformation , Signal Transduction/drug effects , Swine/genetics , Swine/metabolism
3.
Commun Biol ; 3(1): 97, 2020 03 05.
Article in English | MEDLINE | ID: mdl-32139772

ABSTRACT

Mutations to the gene encoding superoxide dismutase-1 (SOD1) were the first genetic elements discovered that cause motor neuron disease (MND). These mutations result in compromised SOD1 dimer stability, with one of the severest and most common mutations Ala4Val (A4V) displaying a propensity to monomerise and aggregate leading to neuronal death. We show that the clinically used ebselen and related analogues promote thermal stability of A4V SOD1 when binding to Cys111 only. We have developed a A4V SOD1 differential scanning fluorescence-based assay on a C6S mutation background that is effective in assessing suitability of compounds. Crystallographic data show that the selenium atom of these compounds binds covalently to A4V SOD1 at Cys111 at the dimer interface, resulting in stabilisation. This together with chemical amenability for hit expansion of ebselen and its on-target SOD1 pharmacological chaperone activity holds remarkable promise for structure-based therapeutics for MND using ebselen as a template.


Subject(s)
Azoles/chemistry , Azoles/pharmacology , Drug Design , Motor Neuron Disease/drug therapy , Organoselenium Compounds/chemistry , Organoselenium Compounds/pharmacology , Superoxide Dismutase-1 , Amino Acid Substitution/genetics , Azoles/chemical synthesis , Azoles/therapeutic use , Crystallography, X-Ray , Drug Discovery/methods , Drug Evaluation, Preclinical/methods , Humans , Isoindoles , Models, Molecular , Molecular Chaperones/chemical synthesis , Molecular Chaperones/chemistry , Molecular Chaperones/therapeutic use , Molecular Docking Simulation , Motor Neuron Disease/genetics , Motor Neuron Disease/metabolism , Motor Neuron Disease/pathology , Mutant Proteins/chemistry , Mutant Proteins/drug effects , Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutation, Missense , Organoselenium Compounds/chemical synthesis , Organoselenium Compounds/isolation & purification , Organoselenium Compounds/therapeutic use , Protein Folding/drug effects , Protein Multimerization/drug effects , Protein Stability/drug effects , Protein Structure, Tertiary , Sulfur Compounds/chemical synthesis , Sulfur Compounds/chemistry , Superoxide Dismutase-1/chemistry , Superoxide Dismutase-1/drug effects , Superoxide Dismutase-1/genetics , Superoxide Dismutase-1/metabolism , Thermodynamics
4.
FEBS Lett ; 594(3): 424-438, 2020 02.
Article in English | MEDLINE | ID: mdl-31605637

ABSTRACT

NAD(P)H:quinone oxidoreductase 1 (NQO1) is a human FAD-dependent enzyme that plays a crucial role in the antioxidant defense system. A naturally occurring single-nucleotide polymorphism (NQO1*2) in the NQO1 gene leads to an amino acid substitution (P187S), which severely compromises the activity and stability of the enzyme. The NQO1*2 genotype has been linked to a higher risk for several types of cancer and poor survival rate after anthracycline-based chemotherapy. In this study, we show that a small molecular chaperone (N-(2-bromophenyl)pyrrolidine-1-sulfonamide) repopulates the native wild-type conformation. As a consequence of the stabilizing effect, the enzymatic activity of the P187S variant protein is strongly improved in the presence of the molecular chaperone in vitro.


Subject(s)
Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutation , NAD(P)H Dehydrogenase (Quinone)/genetics , NAD(P)H Dehydrogenase (Quinone)/metabolism , Neoplasms/genetics , Amino Acid Sequence , Drug Evaluation, Preclinical , Enzyme Activation/drug effects , Enzyme Stability/drug effects , Ligands , Molecular Docking Simulation , Mutant Proteins/antagonists & inhibitors , Mutant Proteins/chemistry , NAD(P)H Dehydrogenase (Quinone)/antagonists & inhibitors , NAD(P)H Dehydrogenase (Quinone)/chemistry , Protein Conformation
5.
J Plant Physiol ; 245: 153091, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31887556

ABSTRACT

Potato (Solanum tuberosum) mutant (ST) lacking one isoform of manganese-stabilizing protein (MSPI) of photosystem II exhibited besides spontaneous tuberization also growth changes with strongly impaired root system development. Previous studies revealed marked changes in carbohydrate levels and allocation within ST plant body. To verify causal relationship between changed carbohydrate balance and root growth restriction we engaged dark grown sucrose-supplied root organ-cultures of ST plants to exclude/confirm shoot effects. Unexpectedly, in ST root cultures we observed large alterations in growth and architecture as well as saccharide status similar to those found in the intact plant roots. The gene expression analysis, however, proved PsbO1 transcript (coding MSPI protein) neither in ST nor in WT root-organ cultures. Therefore, the results point to indirect effects of PsbO1 allele absence connected possibly with some epigenetic modulations.


Subject(s)
Photosynthesis/genetics , Photosystem II Protein Complex/metabolism , Plant Proteins/genetics , Plant Roots/metabolism , Solanum tuberosum/genetics , Alleles , Carbohydrate Metabolism/genetics , Cells, Cultured , Gene Expression Regulation, Plant/genetics , Gene Expression Regulation, Plant/physiology , Manganese/metabolism , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutation , Photosynthesis/radiation effects , Photosystem II Protein Complex/genetics , Plant Proteins/metabolism , Plant Roots/growth & development , Plant Tubers/genetics , Plant Tubers/growth & development , Protein Isoforms/genetics , Protein Isoforms/metabolism , Solanum tuberosum/growth & development , Sucrose/metabolism
6.
J Biomol Struct Dyn ; 38(3): 807-826, 2020 02.
Article in English | MEDLINE | ID: mdl-30836878

ABSTRACT

Aryl Hydrocarbon Receptor (AhR) is a key player to regulate the expression of a group of enzymes known as cytochrome P450s (CYPs) super family (CYP1A1, CYP1B1, CYP2B6, and CYP2E1) which metabolites diverse endogenous as well as toxic compounds such as Benzo[a] Pyrene (B[a] P) and TCDD. B[a] P induces oxidative stress and causes degeneration of dopaminergic neurons in the midbrain, may leads to Parkinson's disease (PD). The metabolism of B[a] P through the expression of CYPs is mainly triggered after binding of B[a] P within ligand binding domain of AhR. But, the molecular mechanism of AhR mediated xenobiotic metabolism in presence of diverse phytochemicals is yet to be studied. The solved AhR (PDB ID: 5NJ8, 23-273aa) structure lacks information for ligand binding domain therefore both wild type and mutant models were predicted and screened virtually against sixty one natural compounds. The result proposed withaferin A, withanolide A, withanolide B, withanolide D and withanone of plant Withania Somnifera as efficient ligand against both wild type and mutants (V381A and V381D) AhR models. However, in silico studies hypothesised withanolide A as a potent phytochemical to trigger the AhR mediated gene regulation activity of CYPs. The in vivo study in zebra fish model proposed about the neuro protective role of W. Somnifera leaf extract in presence of B[a]P. The present study would throw lights on the molecular mechanism of phytochemicals mediated AhR activity which may be useful in treatment of PD. [Formula: see text] Communicated by Ramaswamy H. Sarma.


Subject(s)
Computer Simulation , Mutant Proteins/metabolism , Parkinson Disease/drug therapy , Phytochemicals/therapeutic use , Receptors, Aryl Hydrocarbon/metabolism , Amino Acid Sequence , Animals , Brain/drug effects , Brain/enzymology , Cytochrome P-450 CYP1A1/metabolism , Drug Evaluation, Preclinical , Humans , Hydrogen Bonding , Ligands , Molecular Docking Simulation , Mutant Proteins/chemistry , Phytochemicals/chemistry , Phytochemicals/pharmacology , Protein Binding , Protein Domains , Protein Interaction Maps , Protein Stability , Protein Structure, Secondary , Receptors, Aryl Hydrocarbon/chemistry , Zebrafish
7.
Nature ; 575(7781): 203-209, 2019 11.
Article in English | MEDLINE | ID: mdl-31666698

ABSTRACT

Accumulation of mutant proteins is a major cause of many diseases (collectively called proteopathies), and lowering the level of these proteins can be useful for treatment of these diseases. We hypothesized that compounds that interact with both the autophagosome protein microtubule-associated protein 1A/1B light chain 3 (LC3)1 and the disease-causing protein may target the latter for autophagic clearance. Mutant huntingtin protein (mHTT) contains an expanded polyglutamine (polyQ) tract and causes Huntington's disease, an incurable neurodegenerative disorder2. Here, using small-molecule-microarray-based screening, we identified four compounds that interact with both LC3 and mHTT, but not with the wild-type HTT protein. Some of these compounds targeted mHTT to autophagosomes, reduced mHTT levels in an allele-selective manner, and rescued disease-relevant phenotypes in cells and in vivo in fly and mouse models of Huntington's disease. We further show that these compounds interact with the expanded polyQ stretch and could lower the level of mutant ataxin-3 (ATXN3), another disease-causing protein with an expanded polyQ tract3. This study presents candidate compounds for lowering mHTT and potentially other disease-causing proteins with polyQ expansions, demonstrating the concept of lowering levels of disease-causing proteins using autophagosome-tethering compounds.


Subject(s)
Alleles , Drug Evaluation, Preclinical/methods , Huntingtin Protein/antagonists & inhibitors , Huntingtin Protein/genetics , Mutant Proteins/antagonists & inhibitors , Mutant Proteins/genetics , Mutation/genetics , Animals , Ataxin-3/genetics , Autophagosomes/metabolism , Autophagy , Disease Models, Animal , Drosophila Proteins/antagonists & inhibitors , Drosophila Proteins/chemistry , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Female , Humans , Huntingtin Protein/chemistry , Huntingtin Protein/metabolism , Male , Mice , Microtubule-Associated Proteins/genetics , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Mutation/drug effects , Neurons/cytology , Peptides/genetics , Phenotype , Reproducibility of Results
8.
Sci Rep ; 9(1): 6915, 2019 05 06.
Article in English | MEDLINE | ID: mdl-31061434

ABSTRACT

Limb-girdle muscular dystrophy type 2D (LGMD2D) is characterized by a progressive proximal muscle weakness. LGMD2D is caused by mutations in the gene encoding α-sarcoglycan (α-SG), a dystrophin-associated glycoprotein that plays a key role in the maintenance of sarcolemma integrity in striated muscles. We report here on the development of a new in vitro high-throughput screening assay that allows the monitoring of the proper localization of the most prevalent mutant form of α-SG (R77C substitution). Using this assay, we screened a library of 2560 FDA-approved drugs and bioactive compounds and identified thiostrepton, a cyclic antibiotic, as a potential drug to repurpose for LGMD2D treatment. Characterization of the thiostrepton effect revealed a positive impact on R77C-α-SG and other missense mutant protein localization (R34H, I124T, V247M) in fibroblasts overexpressing these proteins. Finally, further investigations of the molecular mechanisms of action of the compound revealed an inhibition of the chymotrypsin-like activity of the proteasome 24 h after thiostrepton treatment and a synergistic effect with bortezomib, an FDA-approved proteasome inhibitor. This study reports on the first in vitro model for LGMD2D that is compatible with high-throughput screening and proposes a new therapeutic option for LGMD2D caused by missense mutations of α-SG.


Subject(s)
Mutant Proteins/chemistry , Mutant Proteins/metabolism , Protein Folding/drug effects , Proteolysis/drug effects , Sarcoglycans/chemistry , Sarcoglycans/metabolism , Thiostrepton/pharmacology , Cell Line , Cell Membrane/drug effects , Cell Membrane/metabolism , Drug Evaluation, Preclinical , Humans , Induced Pluripotent Stem Cells/cytology , Mutant Proteins/genetics , Myoblasts/cytology , Myoblasts/drug effects , Sarcoglycans/genetics
9.
Nucleic Acids Res ; 47(4): 1637-1652, 2019 02 28.
Article in English | MEDLINE | ID: mdl-30649466

ABSTRACT

The DNA binding domain (DBD) of the tumor suppressor p53 is the site of several oncogenic mutations. A subset of these mutations lowers the unfolding temperature of the DBD. Unfolding leads to the exposure of a hydrophobic ß-strand and nucleates aggregation which results in pathologies through loss of function and dominant negative/gain of function effects. Inspired by the hypothesis that structural changes that are associated with events initiating unfolding in DBD are likely to present opportunities for inhibition, we investigate the dynamics of the wild type (WT) and some aggregating mutants through extensive all atom explicit solvent MD simulations. Simulations reveal differential conformational sampling between the WT and the mutants of a turn region (S6-S7) that is contiguous to a known aggregation-prone region (APR). The conformational properties of the S6-S7 turn appear to be modulated by a network of interacting residues. We speculate that changes that take place in this network as a result of the mutational stress result in the events that destabilize the DBD and initiate unfolding. These perturbations also result in the emergence of a novel pocket that appears to have druggable characteristics. FDA approved drugs are computationally screened against this pocket.


Subject(s)
DNA-Binding Proteins/chemistry , Mutant Proteins/chemistry , Small Molecule Libraries/chemistry , Tumor Suppressor Protein p53/chemistry , DNA-Binding Proteins/genetics , Drug Evaluation, Preclinical/methods , Humans , Hydrophobic and Hydrophilic Interactions/drug effects , Models, Molecular , Molecular Dynamics Simulation , Mutant Proteins/genetics , Mutation/genetics , Protein Conformation/drug effects , Protein Domains/drug effects , Protein Domains/genetics , Protein Unfolding/drug effects , Tumor Suppressor Protein p53/genetics
10.
Elife ; 62017 10 24.
Article in English | MEDLINE | ID: mdl-29063836

ABSTRACT

Mutations in the human BEST1 gene lead to retinal degenerative diseases displaying progressive vision loss and even blindness. BESTROPHIN1, encoded by BEST1, is predominantly expressed in retinal pigment epithelium (RPE), but its physiological role has been a mystery for the last two decades. Using a patient-specific iPSC-based disease model and interdisciplinary approaches, we comprehensively analyzed two distinct BEST1 patient mutations, and discovered mechanistic correlations between patient clinical phenotypes, electrophysiology in their RPEs, and the structure and function of BESTROPHIN1 mutant channels. Our results revealed that the disease-causing mechanism of BEST1 mutations is centered on the indispensable role of BESTROPHIN1 in mediating the long speculated Ca2+-dependent Cl- current in RPE, and demonstrate that the pathological potential of BEST1 mutations can be evaluated and predicted with our iPSC-based 'disease-in-a-dish' approach. Moreover, we demonstrated that patient RPE is rescuable with viral gene supplementation, providing a proof-of-concept for curing BEST1-associated diseases.


Subject(s)
Bestrophins/genetics , Bestrophins/metabolism , Calcium/metabolism , Chlorides/metabolism , Mutation, Missense , Retinal Diseases/physiopathology , Retinal Pigment Epithelium/physiology , Aged , Bestrophins/chemistry , Cells, Cultured , Child , Crystallography, X-Ray , Humans , Ions/metabolism , Male , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Protein Conformation , Retinal Diseases/genetics
11.
Biochem Pharmacol ; 142: 204-215, 2017 10 15.
Article in English | MEDLINE | ID: mdl-28734777

ABSTRACT

Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints. Understanding the molecular mechanisms governing the pharmacological inhibition of DAT is therefore key for understanding the requisite interactions for behavioral modulation and addiction. Previously, we leveraged complementary computational docking, mutagenesis, peptide mapping, and substituted cysteine accessibility strategies to identify the specific adduction site and binding pose for the crosslinkable, photoactive cocaine analog, RTI 82, which contains a photoactive azide attached at the 2ß position of the tropane pharmacophore. Here, we utilize similar methodology with a different cocaine analog N-[4-(4-azido-3-I-iodophenyl)-butyl]-2-carbomethoxy-3-(4-chlorophenyl)tropane, MFZ 2-24, where the photoactive azide is attached to the tropane nitrogen. In contrast to RTI 82, which crosslinked into residue Phe319 of transmembrane domain (TM) 6, our findings show that MFZ 2-24 adducts to Leu80 in TM1 with modeling and biochemical data indicating that MFZ 2-24, like RTI 82, occupies the central S1 binding pocket with the (+)-charged tropane ring nitrogen coordinating with the (-)-charged carboxyl side chain of Asp79. The superimposition of the tropane ring in the three-dimensional binding poses of these two distinct ligands provides strong experimental evidence for cocaine binding to DAT in the S1 site and the importance of the tropane moiety in competitive mechanisms of DA uptake inhibition. These findings set a structure-function baseline for comparison of typical and atypical DAT inhibitors and how their interactions with DAT could lead to the loss of cocaine-like behaviors.


Subject(s)
Cocaine/analogs & derivatives , Dopamine Plasma Membrane Transport Proteins/antagonists & inhibitors , Substance-Related Disorders/metabolism , Tropanes/metabolism , Animals , Azides/chemistry , Azides/metabolism , Binding Sites , Cocaine/chemistry , Cocaine/metabolism , Cross-Linking Reagents/chemistry , Cross-Linking Reagents/metabolism , Dopamine Plasma Membrane Transport Proteins/chemistry , Iodine Radioisotopes , LLC-PK1 Cells , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Molecular Structure , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Peptide Mapping , Photoaffinity Labels , Protein Binding , Structure-Activity Relationship , Substance-Related Disorders/psychology , Swine , Tropanes/chemistry
12.
PLoS One ; 12(1): e0170163, 2017.
Article in English | MEDLINE | ID: mdl-28095457

ABSTRACT

Lysine decarboxylase (LDC) catalyzes the decarboxylation of l-lysine to produce cadaverine, an important industrial platform chemical for bio-based polyamides. However, due to high flexibility at the pyridoxal 5-phosphate (PLP) binding site, use of the enzyme for cadaverine production requires continuous supplement of large amounts of PLP. In order to develop an LDC enzyme from Selenomonas ruminantium (SrLDC) with an enhanced affinity for PLP, we introduced an internal disulfide bond between Ala225 and Thr302 residues with a desire to retain the PLP binding site in a closed conformation. The SrLDCA225C/T302C mutant showed a yellow color and the characteristic UV/Vis absorption peaks for enzymes with bound PLP, and exhibited three-fold enhanced PLP affinity compared with the wild-type SrLDC. The mutant also exhibited a dramatically enhanced LDC activity and cadaverine conversion particularly under no or low PLP concentrations. Moreover, introduction of the disulfide bond rendered SrLDC more resistant to high pH and temperature. The formation of the introduced disulfide bond and the maintenance of the PLP binding site in the closed conformation were confirmed by determination of the crystal structure of the mutant. This study shows that disulfide bond-mediated spatial reconstitution can be a platform technology for development of enzymes with enhanced PLP affinity.


Subject(s)
Cadaverine/metabolism , Carboxy-Lyases/metabolism , Disulfides/metabolism , Lysine/metabolism , Mutant Proteins/metabolism , Pyridoxal Phosphate/metabolism , Selenomonas/enzymology , Binding Sites , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Catalytic Domain , Disulfides/chemistry , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutation/genetics , Protein Conformation , Structure-Activity Relationship , Substrate Specificity
13.
J Cell Sci ; 129(21): 4118-4129, 2016 11 01.
Article in English | MEDLINE | ID: mdl-27656112

ABSTRACT

A number of genes have been linked to familial forms of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). Over 150 mutations within the gene encoding superoxide dismutase 1 (SOD1) have been implicated in ALS, but why such mutations lead to ALS-associated cellular dysfunction is unclear. In this study, we identify how ALS-linked SOD1 mutations lead to changes in the cellular health of the yeast Saccharomyces cerevisiae We find that it is not the accumulation of aggregates but the loss of Sod1 protein stability that drives cellular dysfunction. The toxic effect of Sod1 instability does not correlate with a loss of mitochondrial function or increased production of reactive oxygen species, but instead prevents acidification of the vacuole, perturbs metabolic regulation and promotes senescence. Central to the toxic gain-of-function seen with the SOD1 mutants examined was an inability to regulate amino acid biosynthesis. We also report that leucine supplementation results in an improvement in motor function in a Caenorhabditis elegans model of ALS. Our data suggest that metabolic dysfunction plays an important role in Sod1-mediated toxicity in both the yeast and worm models of ALS.


Subject(s)
Amyotrophic Lateral Sclerosis/metabolism , Models, Biological , Saccharomyces cerevisiae/enzymology , Superoxide Dismutase-1/metabolism , Alleles , Amino Acid Sequence , Amino Acids/biosynthesis , Amyotrophic Lateral Sclerosis/pathology , Animals , Caenorhabditis elegans/metabolism , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Magnetic Resonance Spectroscopy , Metabolome , Microbial Viability , Mitochondria/metabolism , Motor Neurons/metabolism , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Mutation/genetics , Protein Aggregates , Reactive Oxygen Species/metabolism , Saccharomyces cerevisiae/growth & development , Solubility , Stress, Physiological , Superoxide Dismutase-1/chemistry , Superoxide Dismutase-1/genetics , Vacuoles/metabolism
14.
J Mol Graph Model ; 68: 128-139, 2016 07.
Article in English | MEDLINE | ID: mdl-27434826

ABSTRACT

Dot1-like protein (DOT1L) is a histone methyltransferase that has become a novel and promising target for acute leukemias bearing mixed lineage leukemia (MLL) gene rearrangements. In this study, a hierarchical docking-based virtual screening combined with molecular dynamic (MD) simulation was performed to identify DOT1L inhibitors with novel scaffolds. Consequently, 8 top-ranked hits were eventually identified and were further subjected to MD simulation. It was indicated that all hits could reach equilibrium with DOT1L in the MD simulation and further binding free energy calculations suggested that phenoxyacetamide-derived hits such as L01, L03, L04 and L05 exhibited remarkably higher binding affinity compared to other hits. Among them, L03 showed both the lowest glide score (-12.281) and the most favorable binding free energy (-303.9+/-16.5kJ/mol), thereby making it a promising lead for further optimization.


Subject(s)
Acetamides/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Methyltransferases/antagonists & inhibitors , Molecular Docking Simulation , Molecular Dynamics Simulation , Acetamides/chemistry , Drug Evaluation, Preclinical , Methyltransferases/chemistry , Mutant Proteins/chemistry , ROC Curve , Thermodynamics , User-Computer Interface
15.
Cell Death Differ ; 23(10): 1615-27, 2016 10.
Article in English | MEDLINE | ID: mdl-27258787

ABSTRACT

Mutations in the p53 tumor-suppressor gene are prevalent in human cancers. The majority of p53 mutations are missense, which can be classified into contact mutations (that directly disrupts the DNA-binding activity of p53) and structural mutations (that disrupts the conformation of p53). Both of the mutations can disable the normal wild-type (WT) p53 activities. Nevertheless, it has been amply documented that small molecules can rescue activity from mutant p53 by restoring WT tumor-suppressive functions. These compounds hold promise for cancer therapy and have now entered clinical trials. In this study, we show that cruciferous-vegetable-derived phenethyl isothiocyanate (PEITC) can reactivate p53 mutant under in vitro and in vivo conditions, revealing a new mechanism of action for a dietary-related compound. PEITC exhibits growth-inhibitory activity in cells expressing p53 mutants with preferential activity toward p53(R175), one of the most frequent 'hotspot' mutations within the p53 sequence. Mechanistic studies revealed that PEITC induces apoptosis in a p53(R175) mutant-dependent manner by restoring p53 WT conformation and transactivation functions. Accordingly, in PEITC-treated cells the reactivated p53(R175) mutant induces apoptosis by activating canonical WT p53 targets, inducing a delay in S and G2/M phase, and by phosphorylating ATM/CHK2. Interestingly, the growth-inhibitory effects of PEITC depend on the redox state of the cell. Further, PEITC treatments render the p53(R175) mutant sensitive to degradation by the proteasome and autophagy in a concentration-dependent manner. PEITC-induced reactivation of p53(R175) and its subsequent sensitivity to the degradation pathways likely contribute to its anticancer activities. We further show that dietary supplementation of PEITC is able to reactivate WT activity in vivo as well, inhibiting tumor growth in xenograft mouse model. These findings provide the first example of mutant p53 reactivation by a dietary compound and have important implications for cancer prevention and therapy.


Subject(s)
Diet , Isothiocyanates/pharmacology , Mutation/genetics , Neoplasms/genetics , Neoplasms/pathology , Tumor Suppressor Protein p53/genetics , Apoptosis/drug effects , Ataxia Telangiectasia Mutated Proteins/metabolism , Autophagy/drug effects , Cell Cycle/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Checkpoint Kinase 2/metabolism , Histones/metabolism , Humans , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Oxidation-Reduction , Proteasome Endopeptidase Complex/metabolism , Protein Conformation , Proteolysis/drug effects , Transcriptional Activation/genetics , Xenograft Model Antitumor Assays , Zinc/pharmacology
16.
FEBS Lett ; 590(6): 838-47, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26910132

ABSTRACT

This work focuses on the pathogenic missense mutation in YY1 protein correlated with insulinomas. Based on in vitro studies, we demonstrate that the mutation does not affect the secondary structure of either zinc fingers or the N-terminal fragment (NTF) of the protein. Apart from a slight increase in the protein's compactness, no changes in the tertiary structure were observed. The introduced mutation significantly alters DNA-binding properties, both the affinity and enthalpy-entropy contribution of the process, which are highly dependent on the recognized sequence. Obtained results indicate concerted rather than a modular mode of sequence recognition by YY1 with the significant impact of a disordered NTF.


Subject(s)
Mutant Proteins/chemistry , Mutant Proteins/genetics , YY1 Transcription Factor/chemistry , YY1 Transcription Factor/genetics , Amino Acid Substitution , Binding Sites/genetics , Circular Dichroism , DNA/chemistry , DNA/genetics , DNA/metabolism , Fluorescence Polarization , Humans , Insulinoma/genetics , Insulinoma/metabolism , Mutant Proteins/metabolism , Mutation, Missense , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/metabolism , Peptide Fragments/chemistry , Peptide Fragments/genetics , Peptide Fragments/metabolism , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thermodynamics , YY1 Transcription Factor/metabolism , Zinc Fingers
17.
Elife ; 5: e12814, 2016 Jan 08.
Article in English | MEDLINE | ID: mdl-26744778

ABSTRACT

Many driver mutations in cancer are specific in that they occur at significantly higher rates than - presumably - functionally alternative mutations. For example, V600E in the BRAF hydrophobic activation segment (AS) pocket accounts for >95% of all kinase mutations. While many hypotheses tried to explain such significant mutation patterns, conclusive explanations are lacking. Here, we use experimental and in silico structure-energy statistical analyses, to elucidate why the V600E mutation, but no other mutation at this, or any other positions in BRAF's hydrophobic pocket, is predominant. We find that BRAF mutation frequencies depend on the equilibrium between the destabilization of the hydrophobic pocket, the overall folding energy, the activation of the kinase and the number of bases required to change the corresponding amino acid. Using a random forest classifier, we quantitatively dissected the parameters contributing to BRAF AS cancer frequencies. These findings can be applied to genome-wide association studies and prediction models.


Subject(s)
Amino Acid Substitution , Enzyme Activation , Point Mutation , Protein Folding , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/metabolism , Cells, Cultured , Computational Biology , Humans , Models, Molecular , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Mutation Rate , Protein Conformation , Protein Stability , Proto-Oncogene Proteins B-raf/chemistry
18.
PLoS One ; 10(8): e0133969, 2015.
Article in English | MEDLINE | ID: mdl-26252490

ABSTRACT

The cyclin-dependent kinase 4 (CDK4)-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1) and protein-ligand (CDK4-flavopiridol) interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL) _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.


Subject(s)
Cyclin-Dependent Kinase 4/antagonists & inhibitors , Cyclin-Dependent Kinase 4/genetics , Molecular Dynamics Simulation , Mutation/genetics , Cyclin D1/metabolism , Cyclin-Dependent Kinase 4/chemistry , Drug Evaluation, Preclinical , Flavonoids/chemistry , Flavonoids/pharmacology , Humans , Hydrogen Bonding , Mutant Proteins/chemistry , Piperidines/chemistry , Piperidines/pharmacology , Polymorphism, Single Nucleotide/genetics , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Protein Structure, Secondary , Software , Thermodynamics
19.
J Biol Chem ; 290(28): 17611-27, 2015 Jul 10.
Article in English | MEDLINE | ID: mdl-26028650

ABSTRACT

ERα has a ligand-dependent transactivation function in the ligand binding domain of ERα C terminus (AF-2) and a ligand-independent activation function in the N terminus (AF-1). It is still not fully understood how AF-1 and AF-2 activities are regulated cooperatively by ligands. To evaluate the AF-1 involvement in the estrogenic activities of various compounds, we analyzed these transactivation functions using AF-1-truncated and AF-2-mutated ERα mutants. AF-2 is composed of two domains with flexible and static regions. We used an AF-2 flexible region mutant and an AF-2 static region mutant. Both mutants have been reported as non-E2 responsive due to disruption of E2-mediated coactivator recruitment to the AF-2. The AF-2 mutants were not activated by agonists, but surprisingly antagonists and selective estrogen receptor modulators (SERMs) activated the AF-2 mutants. This antagonist reversal activity was derived from AF-1. Furthermore, we demonstrated that the AF-2 contains an AF-1 suppression function using C-terminal-truncated ERα mutants. From these findings we hypothesized that the mutation of AF-2 disrupted its ability to suppress AF-1, causing the antagonist reversal. To assess the AF-2-mediated AF-1 suppression, we analyzed the transcription activity of physically separated AF-1 and AF-2 using a novel hybrid reporter assay. We observed that the AF-1 activity was not suppressed by the physically separated AF-2. Furthermore, SERMs did not induce the AF-1-mediated activity from the separated mutant AF-2, which differed from the intact protein. These results imply that SERM activity is dependent on a conformational change of the full-length ERα molecule, which allows for AF-1 activation.


Subject(s)
Estrogen Receptor alpha/chemistry , Estrogen Receptor alpha/metabolism , Animals , Endocrine Disruptors/pharmacology , Estrogen Receptor alpha/genetics , Hep G2 Cells , Humans , Ligands , Mice , Mutagenesis, Site-Directed , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Phytoestrogens/pharmacology , Protein Conformation , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Selective Estrogen Receptor Modulators/pharmacology , Sequence Deletion , Trans-Activators/chemistry , Trans-Activators/genetics , Trans-Activators/metabolism
20.
Plant Mol Biol ; 88(4-5): 503-14, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26105828

ABSTRACT

The nitrogen-fixing cyanobacterium, Anabaena PCC7120 encodes for a membrane-targeted 30 kDa Mn-superoxide dismutase (MnSOD) and a cytosolic FeSOD. The MnSOD is post-translationally processed to 27 and 24 kDa forms in the cytosol and periplasm/thylakoid lumen. The extent of cleavage of signal and linker peptides at the N-terminus is dependent on the availability of combined nitrogen during growth. While the 24 and 27 kDa forms are present in near equal proportions under nitrogen-fixing conditions, the 24 kDa form is predominant under nitrogen-supplemented conditions. Individual contribution of these forms of MnSOD to total oxidative stress tolerance was analysed using recombinant Anabaena strains overexpressing either different molecular forms of MnSOD or MnSOD defective in the cleavage of signal/linker peptide. Targeting of MnSOD to the membrane and subsequent cleavage to release both the 24 and 27 kDa forms was essential for oxidative stress tolerance under nitrogen-fixing conditions. On the other hand, the cleavage of linker peptide was absolutely essential and the release of cytosolic 24 kDa form of MnSOD was obligatory for developing oxidative stress tolerance under nitrogen-supplemented conditions. Thus, a single MnSOD caters to the reduction of superoxide radical in both cytosol and thylakoid lumen/periplasm irrespective of the N-status of growth by regulating its cleavage. This is the first report on the physiological advantage of membrane-targeting and processing of MnSOD in either bacteria or plants. The higher oxidative stress tolerance offered by the cytosolic form of MnSOD has possibly resulted in retention of only the cytosolic form in bacterial non-nitrogen-fixers during evolution.


Subject(s)
Anabaena/metabolism , Bacterial Proteins/metabolism , Superoxide Dismutase/metabolism , Anabaena/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cell Membrane/metabolism , Cytosol/metabolism , Genes, Bacterial , Molecular Weight , Mutant Proteins/chemistry , Mutant Proteins/genetics , Mutant Proteins/metabolism , Nitrogen/metabolism , Nitrogen Fixation , Oxidative Stress , Phylogeny , Protein Processing, Post-Translational , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Superoxide Dismutase/chemistry , Superoxide Dismutase/genetics
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