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1.
Nature ; 629(8010): 184-192, 2024 May.
Article in English | MEDLINE | ID: mdl-38600378

ABSTRACT

Glucocorticoids represent the mainstay of therapy for a broad spectrum of immune-mediated inflammatory diseases. However, the molecular mechanisms underlying their anti-inflammatory mode of action have remained incompletely understood1. Here we show that the anti-inflammatory properties of glucocorticoids involve reprogramming of the mitochondrial metabolism of macrophages, resulting in increased and sustained production of the anti-inflammatory metabolite itaconate and consequent inhibition of the inflammatory response. The glucocorticoid receptor interacts with parts of the pyruvate dehydrogenase complex whereby glucocorticoids provoke an increase in activity and enable an accelerated and paradoxical flux of the tricarboxylic acid (TCA) cycle in otherwise pro-inflammatory macrophages. This glucocorticoid-mediated rewiring of mitochondrial metabolism potentiates TCA-cycle-dependent production of itaconate throughout the inflammatory response, thereby interfering with the production of pro-inflammatory cytokines. By contrast, artificial blocking of the TCA cycle or genetic deficiency in aconitate decarboxylase 1, the rate-limiting enzyme of itaconate synthesis, interferes with the anti-inflammatory effects of glucocorticoids and, accordingly, abrogates their beneficial effects during a diverse range of preclinical models of immune-mediated inflammatory diseases. Our findings provide important insights into the anti-inflammatory properties of glucocorticoids and have substantial implications for the design of new classes of anti-inflammatory drugs.


Subject(s)
Anti-Inflammatory Agents , Glucocorticoids , Inflammation , Macrophages , Mitochondria , Succinates , Animals , Female , Humans , Male , Mice , Anti-Inflammatory Agents/pharmacology , Carboxy-Lyases/metabolism , Carboxy-Lyases/antagonists & inhibitors , Citric Acid Cycle/drug effects , Citric Acid Cycle/genetics , Cytokines/immunology , Cytokines/metabolism , Glucocorticoids/pharmacology , Glucocorticoids/metabolism , Hydro-Lyases/deficiency , Hydro-Lyases/genetics , Inflammation/drug therapy , Inflammation/metabolism , Macrophages/cytology , Macrophages/drug effects , Macrophages/immunology , Macrophages/metabolism , Mice, Inbred C57BL , Mitochondria/metabolism , Mitochondria/drug effects , Pyruvate Dehydrogenase Complex/metabolism , Receptors, Glucocorticoid/metabolism , Succinates/metabolism , Enzyme Activation/drug effects
2.
Diabetes Res Clin Pract ; 206: 111014, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37977551

ABSTRACT

OBJECT: The highly conserved α-amino-ß-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) is the key enzyme that regulates the de novo NAD+ synthesis from tryptophan. NAD+ metabolism in diabetic cardiomyopathy (DCM) was not elucidated yet. METHODS: Mice were assigned to non-diabetic (NDM) group, streptozocin (STZ)-induced diabetic (DM) group, and nicotinamide (NAM) treated (DM + NAM) group. ACMSD mediated NAD+ metabolism were studied both in mice and patients with diabetes. RESULTS: NAD+ level was significantly lower in the heart of DM mice than that of the NDM group. Supplementation with NAM could partially increased myocardial capillary density and ameliorated myocardial fibrosis by increasing NAD+ level through salvage pathway. Compared with NDM mice, the expression of ACMSD in myocardial endothelial cells of DM mice was significantly increased. It was further confirmed that in endothelial cells, high glucose promoted the expression of ACMSD. Inhibition of ACMSD could increase de novo NAD+ synthesis and improve endothelial cell function by increasing Sirt1 activity. Targeted mass spectrometry analysis indicated increased ACMSD enzyme activity in diabetic patients, higher ACMSD activity increased risk of heart diastolic dysfunction. CONCLUSION: In summary, increased expression of ACMSD lead to impaired de novo NAD+ synthesis in diabetic heart. Inhibition of ACMSD could potentially improve DCM.


Subject(s)
Carboxy-Lyases , Diabetic Cardiomyopathies , Animals , Humans , Mice , Diabetic Cardiomyopathies/drug therapy , Endothelial Cells/metabolism , NAD/metabolism , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/metabolism
3.
J Biol Chem ; 299(5): 104659, 2023 05.
Article in English | MEDLINE | ID: mdl-36997087

ABSTRACT

Decarboxylation of phosphatidylserine (PS) to form phosphatidylethanolamine by PS decarboxylases (PSDs) is an essential process in most eukaryotes. Processing of a malarial PSD proenzyme into its active alpha and beta subunits is by an autoendoproteolytic mechanism regulated by anionic phospholipids, with PS serving as an activator and phosphatidylglycerol (PG), phosphatidylinositol, and phosphatidic acid acting as inhibitors. The biophysical mechanism underlying this regulation remains unknown. We used solid phase lipid binding, liposome-binding assays, and surface plasmon resonance to examine the binding specificity of a processing-deficient Plasmodium PSD (PkPSDS308A) mutant enzyme and demonstrated that the PSD proenzyme binds strongly to PS and PG but not to phosphatidylethanolamine and phosphatidylcholine. The equilibrium dissociation constants (Kd) of PkPSD with PS and PG were 80.4 nM and 66.4 nM, respectively. The interaction of PSD with PS is inhibited by calcium, suggesting that the binding mechanism involves ionic interactions. In vitro processing of WT PkPSD proenzyme was also inhibited by calcium, consistent with the conclusion that PS binding to PkPSD through ionic interactions is required for the proenzyme processing. Peptide mapping identified polybasic amino acid motifs in the proenzyme responsible for binding to PS. Altogether, the data demonstrate that malarial PSD maturation is regulated through a strong physical association between PkPSD proenzyme and anionic lipids. Inhibition of the specific interaction between the proenzyme and the lipids can provide a novel mechanism to disrupt PSD enzyme activity, which has been suggested as a target for antimicrobials, and anticancer therapies.


Subject(s)
Carboxy-Lyases , Malaria , Phospholipids , Plasmodium , Amino Acid Motifs , Calcium/metabolism , Calcium/pharmacology , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Enzyme Precursors/metabolism , Liposomes , Phosphatidic Acids/metabolism , Phosphatidic Acids/pharmacology , Phosphatidylcholines/metabolism , Phosphatidylcholines/pharmacology , Phosphatidylethanolamines/metabolism , Phosphatidylethanolamines/pharmacology , Phosphatidylglycerols/metabolism , Phosphatidylglycerols/pharmacology , Phosphatidylinositols/metabolism , Phosphatidylinositols/pharmacology , Phosphatidylserines/metabolism , Phosphatidylserines/pharmacology , Phospholipids/chemistry , Phospholipids/metabolism , Phospholipids/pharmacology , Protein Binding , Malaria/parasitology , Proteolysis/drug effects , Surface Plasmon Resonance , Plasmodium/enzymology
4.
Leukemia ; 36(2): 383-393, 2022 02.
Article in English | MEDLINE | ID: mdl-34344987

ABSTRACT

Acute myeloid leukemia (AML) is a devastating disease, and clinical outcomes are still far from satisfactory. Here, to identify novel targets for AML therapy, we performed a genome-wide CRISPR/Cas9 screen using AML cell lines, followed by a second screen in vivo. We show that PAICS, an enzyme involved in de novo purine biosynthesis, is a potential target for AML therapy. AML cells expressing shRNA-PAICS exhibited a proliferative disadvantage, indicating a toxic effect of shRNA-PAICS. Treatment of human AML cells with a PAICS inhibitor suppressed their proliferation by inhibiting DNA synthesis and promoting apoptosis and had anti-leukemic effects in AML PDX models. Furthermore, CRISPR/Cas9 screens using AML cells in the presence of the inhibitor revealed genes mediating resistance or synthetic lethal to PAICS inhibition. Our findings identify PAICS as a novel therapeutic target for AML and further define components of de novo purine synthesis pathway and its downstream effectors essential for AML cell survival.


Subject(s)
CRISPR-Cas Systems , Carboxy-Lyases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Gene Expression Regulation, Enzymologic/drug effects , Gene Expression Regulation, Leukemic/drug effects , Leukemia, Myeloid, Acute/drug therapy , Purines/metabolism , Animals , Apoptosis , Cell Proliferation , Genome-Wide Association Study , Humans , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/pathology , Mice , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, SCID , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
5.
Cancer Med ; 10(18): 6442-6455, 2021 09.
Article in English | MEDLINE | ID: mdl-34472721

ABSTRACT

Rhabdomyosarcoma exhibits tumor-specific energy metabolic changes that include the Warburg effect. Since targeting cancer metabolism is a promising therapeutic approach, we examined the antitumor effects of suppressing lipid metabolism in rhabdomyosarcoma. We suppressed lipid metabolism in rhabdomyosarcoma cells in vitro by administering an inhibitor of malonyl-CoA decarboxylase, which increases malonyl-CoA and decreases fatty acid oxidation. Suppression of lipid metabolism in rhabdomyosarcoma cells decreased cell proliferation by inducing cell cycle arrest. Metabolomic analysis showed an increase in glycolysis and inactivation of the pentose phosphate pathway. Immunoblotting analysis revealed upregulated expression of the autophagy marker LC3A/B-II due to increased phosphorylation of AMP-activated protein kinase, a nutrient sensor. p21 protein expression level also increased. Inhibition of both lipid metabolism and autophagy suppressed tumor proliferation and increased apoptosis. In vivo studies involved injection of human Rh30 cells into the gastrocnemius muscle of 6-week-old female nude mice, which were divided into normal chow and low-fat diet groups. The mice fed a low-fat diet for 21 days showed reduced tumor growth compared to normal chow diet-fed mice. Suppression of lipid metabolism disrupted the equilibrium of the cancer-specific metabolism in rhabdomyosarcoma, resulting in a tumor growth-inhibition effect. Therefore, the development of treatments focusing on the lipid dependence of rhabdomyosarcoma is highly promising.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Carboxy-Lyases/antagonists & inhibitors , Diet, Fat-Restricted , Lipid Metabolism/drug effects , Rhabdomyosarcoma/drug therapy , Animals , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Apoptosis/drug effects , Autophagy/drug effects , Carboxy-Lyases/metabolism , Cell Cycle Checkpoints/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Combined Modality Therapy/methods , Fatty Acids/metabolism , Female , Humans , Macrolides/pharmacology , Macrolides/therapeutic use , Malonyl Coenzyme A/metabolism , Mice , Muscle, Skeletal/pathology , Oxidation-Reduction/drug effects , Phenylurea Compounds/pharmacology , Phenylurea Compounds/therapeutic use , Rhabdomyosarcoma/pathology , Rhabdomyosarcoma/therapy , Xenograft Model Antitumor Assays
6.
Toxicol Lett ; 349: 115-123, 2021 Oct 01.
Article in English | MEDLINE | ID: mdl-34089817

ABSTRACT

Cisplatin, the most widely used platinum-based anticancer drug, often causes progressive and irreversible sensorineural hearing loss in cancer patients. However, the precise mechanism underlying cisplatin-associated ototoxicity is still unclear. Nicotinamide adenine dinucleotide (NAD+), a co-substrate for the sirtuin family and PARPs, has emerged as a potent therapeutic molecular target in various diseases. In our investigates, we observed that NAD+ level was changed in the cochlear explants of mice treated with cisplatin. Supplementation of a specific inhibitor (TES-1025) of α-amino-ß-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), a rate-limiting enzyme of NAD+de novo synthesis pathway, promoted SIRT1 activity, increased mtDNA contents and enhanced AMPK expression, thus significantly reducing hair cells loss and deformation. The protection was blocked by EX527, a specific SIRT1 inhibitor. Meanwhile, the use of NMN, a precursor of NAD+ salvage synthesis pathway, had shown beneficial effect on hair cell under cisplatin administration, effectively suppressing PARP1. In vivo experiments confirmed the hair cell protection of NAD+ modulators in cisplatin treated mice and zebrafish. In conclusion, we demonstrated that modulation of NAD+ biosynthesis via the de novo synthesis pathway and the salvage synthesis pathway could both prevent ototoxicity of cisplatin. These results suggested that direct modulation of cellular NAD+ levels could be a promising therapeutic approach for protection of hearing from cisplatin-induced ototoxicity.


Subject(s)
Enzyme Inhibitors/pharmacology , Hair Cells, Auditory/drug effects , Hearing Loss/prevention & control , Hearing/drug effects , NAD/biosynthesis , Ototoxicity/prevention & control , Sirtuin 1/metabolism , Animals , Animals, Genetically Modified , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/metabolism , Cisplatin , Disease Models, Animal , Enzyme Activation , Hair Cells, Auditory/enzymology , Hair Cells, Auditory/pathology , Hearing Loss/chemically induced , Hearing Loss/enzymology , Hearing Loss/physiopathology , Lateral Line System/drug effects , Lateral Line System/enzymology , Mice, Inbred C57BL , Mitochondria/drug effects , Mitochondria/enzymology , Mitochondria/pathology , Ototoxicity/enzymology , Ototoxicity/etiology , Ototoxicity/physiopathology , Zebrafish
7.
ACS Chem Biol ; 16(6): 1030-1039, 2021 06 18.
Article in English | MEDLINE | ID: mdl-33984234

ABSTRACT

A common strategy employed in antibacterial drug discovery is the targeting of biosynthetic processes that are essential and specific for the pathogen. Specificity in particular avoids undesirable interactions with potential enzymatic counterparts in the human host, and it ensures on-target toxicity. Synthesis of pantothenate (Vitamine B5), which is a precursor of the acyl carrier coenzyme A, is an example of such a pathway. In Mycobacterium tuberculosis (Mtb), which is the causative agent of tuberculosis (TB), pantothenate is formed by pantothenate synthase, utilizing D-pantoate and ß-Ala as substrates. ß-Ala is mainly formed by the decarboxylation of l-aspartate, generated by the decarboxylase PanD, which is a homo-oliogomer in solution. Pyrazinoic acid (POA), which is the bioactive form of the TB prodrug pyrazinamide, binds and inhibits PanD activity weakly. Here, we generated a library of recombinant Mtb PanD mutants based on structural information and PZA/POA resistance mutants. Alterations in oligomer formation, enzyme activity, and/or POA binding were observed in respective mutants, providing insights into essential amino acids for Mtb PanD's proper structural assembly, decarboxylation activity and drug interaction. This information provided the platform for the design of novel POA analogues with modifications at position 3 of the pyrazine ring. Analogue 2, which incorporates a bulky naphthamido group at this position, displayed a 1000-fold increase in enzyme inhibition, compared to POA, along with moderately improved antimycobacterial activity. The data demonstrate that an improved understanding of mechanistic and enzymatic features of key metabolic enzymes can stimulate design of more-potent PanD inhibitors.


Subject(s)
Antitubercular Agents/pharmacology , Carboxy-Lyases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Mycobacterium tuberculosis/enzymology , Pyrazinamide/analogs & derivatives , Antitubercular Agents/chemistry , Carboxy-Lyases/metabolism , Enzyme Inhibitors/chemistry , Humans , Models, Molecular , Mycobacterium tuberculosis/drug effects , Pyrazinamide/chemistry , Pyrazinamide/pharmacology , Tuberculosis/drug therapy , Tuberculosis/microbiology
8.
Nat Commun ; 12(1): 143, 2021 01 08.
Article in English | MEDLINE | ID: mdl-33420031

ABSTRACT

Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.


Subject(s)
Antitubercular Agents/pharmacology , Bacterial Proteins/antagonists & inhibitors , Carboxy-Lyases/antagonists & inhibitors , Mycobacterium smegmatis/enzymology , Mycobacterium tuberculosis/drug effects , Peptide Synthases/antagonists & inhibitors , Allosteric Regulation/drug effects , Allosteric Site/drug effects , Antitubercular Agents/therapeutic use , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/ultrastructure , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Carboxy-Lyases/ultrastructure , Coenzyme A/biosynthesis , Crystallography, X-Ray , Enzyme Assays , Gene Knockdown Techniques , High-Throughput Screening Assays , Humans , Microbial Sensitivity Tests , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/genetics , Peptide Synthases/genetics , Peptide Synthases/metabolism , Peptide Synthases/ultrastructure , Tuberculosis/drug therapy , Tuberculosis/microbiology
9.
J Med Chem ; 64(1): 797-811, 2021 01 14.
Article in English | MEDLINE | ID: mdl-33369426

ABSTRACT

In the kynurenine pathway for tryptophan degradation, an unstable metabolic intermediate, α-amino-ß-carboxymuconate-ε-semialdehyde (ACMS), can nonenzymatically cyclize to form quinolinic acid, the precursor for de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+). In a competing reaction, ACMS is decarboxylated by ACMS decarboxylase (ACMSD) for further metabolism and energy production. Therefore, the inhibition of ACMSD increases NAD+ levels. In this study, an Food and Drug Administration (FDA)-approved drug, diflunisal, was found to competitively inhibit ACMSD. The complex structure of ACMSD with diflunisal revealed a previously unknown ligand-binding mode and was consistent with the results of inhibition assays, as well as a structure-activity relationship (SAR) study. Moreover, two synthesized diflunisal derivatives showed half-maximal inhibitory concentration (IC50) values 1 order of magnitude better than diflunisal at 1.32 ± 0.07 µM (22) and 3.10 ± 0.11 µM (20), respectively. The results suggest that diflunisal derivatives have the potential to modulate NAD+ levels. The ligand-binding mode revealed here provides a new direction for developing inhibitors of ACMSD.


Subject(s)
Carboxy-Lyases/metabolism , Diflunisal/metabolism , Enzyme Inhibitors/metabolism , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Binding Sites , Biosynthetic Pathways/drug effects , Carboxy-Lyases/antagonists & inhibitors , Catalytic Domain , Crystallography, X-Ray , Diflunisal/analogs & derivatives , Diflunisal/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Inhibitory Concentration 50 , Kynurenine/metabolism , Molecular Docking Simulation , NAD/metabolism , Pseudomonas fluorescens/enzymology , Structure-Activity Relationship , Tryptophan/metabolism
10.
Eur J Clin Invest ; 50(10): e13334, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32594513

ABSTRACT

Nicotinamide adenine dinucleotide (NAD+ ) is an essential metabolite in energy metabolism as well as a co-substrate in biochemical reactions such as protein deacylation, protein ADP-ribosylation and cyclic ADP-ribose synthesis mediated by sirtuins, poly (ADP-ribose) polymerases (PARPs) and CD38. In eukaryotic cells, NAD+ is synthesized through three distinct pathways, which offer different strategies to modulate the bioavailability of NAD+ . The therapeutic potential of dietarily available NAD+ boosters preserving the NAD+ pool has been attracting attention after the discovery of declining NAD+ levels in ageing model organisms as well as in several age-related diseases, including cardiometabolic and neurodegenerative diseases. Here, we review the recent advances in the biology of NAD+ , including the salubrious effects of NAD+ boosters and discuss their future translational strategies.


Subject(s)
Aging/metabolism , Enzyme Inhibitors/therapeutic use , NAD/metabolism , Niacinamide/analogs & derivatives , Nicotinamide Mononucleotide/therapeutic use , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Pyridinium Compounds/therapeutic use , ADP-ribosyl Cyclase/antagonists & inhibitors , ADP-ribosyl Cyclase/metabolism , Animals , Biosynthetic Pathways , Carboxy-Lyases/antagonists & inhibitors , Clinical Trials as Topic , Gastrointestinal Microbiome , Humans , NAD/biosynthesis , Niacinamide/therapeutic use , Poly(ADP-ribose) Polymerases/metabolism , Probiotics , Sirtuins/metabolism , Translational Research, Biomedical
11.
Article in English | MEDLINE | ID: mdl-32373551

ABSTRACT

Current treatments of hepatitis B virus (HBV) are limited to Interferon-alpha or the nucleos(t)ide analogs antiviral therapies, and it is crucial to develop and define new antiviral drugs to cure HBV. In this study, we explored the anti-HBV effect of difluoromethylornithine (DFMO), an irreversibly inhibitor of decarboxylase 1(ODC1) on HBV replication. Firstly, we found that polyamines contributed to HBV DNA replication via increasing levels of the HBV core protein (HBc) and capsids. In contrast, depletion of polyamines either by silencing the expression of ODC1 or DFMO treatment, resulted in decreasing viral DNA replication and levels of HBc protein and capsids. Furthermore, we found that DFMO decreased the stability of the HBc protein without affecting mRNA transcription and protein translation. Taken together, our findings demonstrate that DFMO inhibits HBV replication by reducing HBc stability and this may provide a new approach for HBV therapeutics.


Subject(s)
Carboxy-Lyases , Hepatitis B virus , Virus Replication , Antiviral Agents/pharmacology , Carboxy-Lyases/antagonists & inhibitors , DNA Replication , DNA, Viral , Eflornithine/pharmacology , Hepatitis B virus/drug effects , Hepatitis B virus/physiology , Humans
12.
Nat Commun ; 11(1): 1661, 2020 04 03.
Article in English | MEDLINE | ID: mdl-32245967

ABSTRACT

Pyrazinamide is a sterilizing first-line tuberculosis drug. Genetic, metabolomic and biophysical analyses previously demonstrated that pyrazinoic acid, the bioactive form of the prodrug pyrazinamide (PZA), interrupts biosynthesis of coenzyme A in Mycobacterium tuberculosis by binding to aspartate decarboxylase PanD. While most drugs act by inhibiting protein function upon target binding, we find here that pyrazinoic acid is only a weak enzyme inhibitor. We show that binding of pyrazinoic acid to PanD triggers degradation of the protein by the caseinolytic protease ClpC1-ClpP. Thus, the old tuberculosis drug pyrazinamide exerts antibacterial activity by acting as a target degrader, a mechanism of action that has recently emerged as a successful strategy in drug discovery across disease indications. Our findings provide the basis for the rational discovery of next generation PZA.


Subject(s)
Antitubercular Agents/pharmacology , Carboxy-Lyases/antagonists & inhibitors , Mycobacterium tuberculosis/drug effects , Proteolysis/drug effects , Pyrazinamide/analogs & derivatives , Antitubercular Agents/therapeutic use , Bacterial Proteins/metabolism , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Drug Resistance, Bacterial/genetics , Endopeptidase Clp/metabolism , Heat-Shock Proteins/metabolism , Humans , Microbial Sensitivity Tests , Mutation , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/genetics , Pyrazinamide/pharmacology , Pyrazinamide/therapeutic use , Tuberculosis/drug therapy , Tuberculosis/microbiology
13.
Biomolecules ; 10(3)2020 03 06.
Article in English | MEDLINE | ID: mdl-32155745

ABSTRACT

The biogenic polyamines, spermine, spermidine (Spd) and putrescine (Put) are present at micro-millimolar concentrations in eukaryotic and prokaryotic cells (many prokaryotes have no spermine), participating in the regulation of cellular proliferation and differentiation. In mammalian cells Put is formed exclusively from L-ornithine by ornithine decarboxylase (ODC) and many potent ODC inhibitors are known. In bacteria, plants, and fungi Put is synthesized also from agmatine, which is formed from L-arginine by arginine decarboxylase (ADC). Here we demonstrate that the isosteric hydroxylamine analogue of agmatine (AO-Agm) is a new and very potent (IC50 3•10-8 M) inhibitor of E. coli ADC. It was almost two orders of magnitude less potent towards E. coli ODC. AO-Agm decreased polyamine pools and inhibited the growth of DU145 prostate cancer cells only at high concentration (1 mM). Growth inhibitory analysis of the Acremonium chrysogenum demonstrated that the wild type (WT) strain synthesized Put only from L-ornithine, while the cephalosporin C high-yielding strain, in which the polyamine pool is increased, could use both ODC and ADC to produce Put. Thus, AO-Agm is an important addition to the set of existing inhibitors of the enzymes of polyamine biosynthesis, and an important instrument for investigating polyamine biochemistry.


Subject(s)
Acremonium/chemistry , Agmatine , Carboxy-Lyases , Escherichia coli Proteins , Escherichia coli/enzymology , Agmatine/analogs & derivatives , Agmatine/chemistry , Animals , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/chemistry , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/chemistry , Male , Mice
14.
Int J Mol Sci ; 21(4)2020 Feb 15.
Article in English | MEDLINE | ID: mdl-32075281

ABSTRACT

Doxorubicin (DXR) is a drug widely used in chemotherapy. Its mode of action is based on its intercalation properties, involving the inhibition of topoisomerase II. However, few studies have reported the mitochondrial effects of DXR while investigating cardiac toxicity induced by the treatment, mostly in pediatric cases. Here, we demonstrate that DXR alters the mitochondrial membrane composition associated with bioenergetic impairment and cell death in human cancer cells. The remodeling of the mitochondrial membrane was explained by phosphatidylserine decarboxylase (PSD) inhibition by DXR. PSD catalyzes phosphatidylethanolamine (PE) synthesis from phosphatidylserine (PS), and DXR altered the PS/PE ratio in the mitochondrial membrane. Moreover, we observed that DXR localized to the mitochondrial compartment and drug uptake was rapid. Evaluation of other topoisomerase II inhibitors did not show any impact on the mitochondrial membrane composition, indicating that the DXR effect was specific. Therefore, our findings revealed a side molecular target for DXR and PSD, potentially involved in DXR anti-cancer properties and the associated toxicity.


Subject(s)
Carboxy-Lyases/genetics , Doxorubicin/pharmacology , Mitochondrial Membranes/drug effects , Neoplasms/genetics , Carboxy-Lyases/antagonists & inhibitors , Cardiotoxicity/etiology , Cardiotoxicity/genetics , Cardiotoxicity/pathology , Cell Death/drug effects , Doxorubicin/adverse effects , HeLa Cells , Humans , Mitochondrial Membranes/enzymology , Neoplasms/complications , Neoplasms/drug therapy , Neoplasms/pathology , Phosphatidylethanolamines/metabolism , Phosphatidylserines/metabolism
15.
Chem Pharm Bull (Tokyo) ; 68(1): 34-45, 2020.
Article in English | MEDLINE | ID: mdl-31902900

ABSTRACT

Enzymatic and post-translational modifications (PTMs) such as ubiquitination, acetylation, and methylation occur at lysine residues. The PTMs play critical roles in the regulation of the protein functions, and thus, various cellular processes. In addition, aberrations of the PTMs are associated with various diseases, such as cancer and neurodegenerative disorders. Therefore, we hypothesized that modulation of the PTMs and normalization of the PTM abnormalities could be useful as methods to control various cellular mechanisms and as a therapeutic strategy, respectively. To modulate the PTMs, we have focused on lysine-modifying enzymes and have pursued drug discovery researches on ubiquitination inducers, lysine deacetylase (KDAC) inhibitors, and lysine demethylase (KDM) inhibitors. For the identification of the modulators, we have used not only conventional drug design, such as structure-based drug design (SBDD) and ligand-based drug design (LBDD), but also "strategic chemistry approaches," such as drug design based on enzyme catalytic mechanism. As a result, we have identified several modulators which have pharmacological effects in animal models or in cellular studies. In this review, focusing on the drug design based on enzyme catalytic mechanism, our drug discovery researches have been discussed.


Subject(s)
Carboxy-Lyases/metabolism , Enzyme Inhibitors/chemistry , Histone Demethylases/metabolism , Lysine/chemistry , Carboxy-Lyases/antagonists & inhibitors , Drug Design , Enzyme Inhibitors/chemical synthesis , Histone Demethylases/antagonists & inhibitors , Humans , Lysine/metabolism , Protein Processing, Post-Translational , Ubiquitin-Conjugating Enzymes/antagonists & inhibitors , Ubiquitin-Conjugating Enzymes/metabolism
16.
J Biomol Struct Dyn ; 38(9): 2704-2716, 2020 Jun.
Article in English | MEDLINE | ID: mdl-31304874

ABSTRACT

In the current contribution, a multicomplex-based pharmacophore modeling approach was employed on the structural proteome of Plasmodium falciparum orotidine-5-monophosphate decarboxylase enzyme (PfOMPDC). Among the constructed pharmacophore models, the representative hypotheses were selected as the primary filter to screen the molecules with the complementary features responsible for showing inhibition. Thereafter, auxiliary evaluations were performed on the screened candidates via drug-likeness and molecular docking studies. Subsequently, the stability of the docked protein-ligand complexes was scrutinized by employing molecular dynamics simulations and molecular mechanics-Poisson Boltzmann surface area based free binding energy calculations. The stability the docked candidates was compared with the highly active crystallized inhibitor (3S9Y-FNU) to seek more potential candidates. All the docked molecules displayed stable dynamic behavior and high binding free energy in comparison to 3S9Y-FNU. The employed workflow resulted in the retrieval of five drug-like candidates with diverse scaffolds that may show inhibitory activity against PfOMPDC and could be further used as the novel scaffold to develop novel antimalarials.Communicated by Ramaswamy H. Sarma.


Subject(s)
Antimalarials/pharmacology , Carboxy-Lyases , Enzyme Inhibitors , Carboxy-Lyases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Plasmodium falciparum/drug effects , Uridine/analogs & derivatives
17.
Biochem J ; 476(21): 3125-3139, 2019 11 15.
Article in English | MEDLINE | ID: mdl-31488574

ABSTRACT

CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility-mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.


Subject(s)
Carboxy-Lyases/chemistry , Drug Evaluation, Preclinical/methods , Escherichia coli Proteins/chemistry , Escherichia coli/enzymology , Mass Spectrometry/methods , Multienzyme Complexes/chemistry , Peptide Synthases/chemistry , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/metabolism , Dimerization , Enzyme Inhibitors/chemistry , Escherichia coli/chemistry , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/metabolism , Kinetics , Multienzyme Complexes/antagonists & inhibitors , Multienzyme Complexes/metabolism , Peptide Synthases/antagonists & inhibitors , Peptide Synthases/metabolism , Protein Domains
18.
J Biol Chem ; 294(32): 12146-12156, 2019 08 09.
Article in English | MEDLINE | ID: mdl-31227523

ABSTRACT

Phosphatidylserine decarboxylases (PSDs) catalyze the decarboxylation of phosphatidylserine to generate phosphatidylethanolamine, a critical step in phospholipid metabolism in both prokaryotes and eukaryotes. Most PSDs are membrane-bound, and classical radioisotope-based assays for determining their activity in vitro are not suitable for high-throughput drug screening. The finding that the PkPSD from Plasmodium knowlesi can be purified in a soluble and active form and the recent development of a fluorescence-based distyrylbenzene-bis-aldehyde (DSB-3) assay to measure PSD activity in vitro have laid the groundwork for screening chemical libraries for PSD inhibitors. Using this assay, here we conducted a high-throughput screen of a structurally diverse 130,858-compound library against PkPSD. Further characterization of the hits identified in this screening yielded five PkPSD inhibitors with IC50 values ranging from 3.1 to 42.3 µm Lead compounds were evaluated against the pathogenic yeast Candida albicans in the absence or presence of exogenous ethanolamine, and YU253467 and YU254403 were identified as inhibiting both native C. albicans PSD mitochondrial activity and C. albicans growth, with an MIC50 of 22.5 and 15 µg/ml without ethanolamine and an MIC50 of 75 and 60 µg/ml with ethanolamine, respectively. Together, these results provide the first proof of principle for the application of DSB-3-based fluorescent readouts in high-throughput screening for PSD inhibitors. The data set the stage for future analyses to identify more selective and potent PSD inhibitors with antimicrobial or antitumor activities.


Subject(s)
Carboxy-Lyases/antagonists & inhibitors , Enzyme Inhibitors/analysis , Fluorescent Dyes/chemistry , High-Throughput Screening Assays , Styrenes/chemistry , Candida albicans/drug effects , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Cell Line, Tumor , Cell Survival/drug effects , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Ethanolamine/pharmacology , Humans , Inhibitory Concentration 50 , Phosphatidylserines/metabolism , Plasmodium knowlesi/enzymology , Recombinant Proteins/biosynthesis , Recombinant Proteins/isolation & purification
19.
Biochem Biophys Res Commun ; 512(1): 7-13, 2019 04 23.
Article in English | MEDLINE | ID: mdl-30853184

ABSTRACT

Fibrosis is a serious health problem often leading to accompanying organ failure. During the manifestation of the disease, an accumulation of different extracellular matrix (ECM) molecules, such as proteoglycans, takes place. There is no appropriate therapeutic option available to heal fibrosis to date. Current research focuses primarily on targets such as the cytokine transforming growth factor-ß1 (TGF-ß1), which is assumed to be one of the key mediators of fibrosis. Both xylosyltransferase isoforms, XT-I and XT-II, catalyze the rate-limiting step of the proteoglycan biosynthesis. Consequently, inhibiting XT activity could be a promising approach to treat fibrosis. It was shown in earlier studies that nucleotides and nucleosides have anti-fibrotic properties and decrease XT activity in cell-free systems. In contrast, we evaluated the mechanisms beyond an UDP-mediated induction of intracellular XT-activity in normal human dermal fibroblasts (NHDF). The observed pseudo-fibrotic XT increasement could be attributed to a compensation of decreased UDP-glucuronate decarboxylase 1 (UXS1) mRNA expression as well as a diminished intracellular UDP-xylose concentration. In summary, our results describe a so far unknown XT-inductive pathway and show that UDP could be a promising molecule for the development of an anti-fibrotic therapy. Nevertheless, XT activity has to be inhibited in parallel intracellularly.


Subject(s)
Fibroblasts/drug effects , Fibroblasts/metabolism , Pentosyltransferases/biosynthesis , Uridine Diphosphate/pharmacology , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Cells, Cultured , Drug Development , Enzyme Induction/drug effects , Extracellular Matrix Proteins/genetics , Extracellular Matrix Proteins/metabolism , Fibroblasts/pathology , Fibrosis/drug therapy , Fibrosis/enzymology , Fibrosis/pathology , Gene Expression/drug effects , Gene Knockdown Techniques , Humans , RNA, Messenger/genetics , RNA, Messenger/metabolism , Xylose/metabolism , UDP Xylose-Protein Xylosyltransferase
20.
Nature ; 563(7731): 354-359, 2018 11.
Article in English | MEDLINE | ID: mdl-30356218

ABSTRACT

Nicotinamide adenine dinucleotide (NAD+) is a co-substrate for several enzymes, including the sirtuin family of NAD+-dependent protein deacylases. Beneficial effects of increased NAD+ levels and sirtuin activation on mitochondrial homeostasis, organismal metabolism and lifespan have been established across species. Here we show that α-amino-ß-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), the enzyme that limits spontaneous cyclization of α-amino-ß-carboxymuconate-ε-semialdehyde in the de novo NAD+ synthesis pathway, controls cellular NAD+ levels via an evolutionarily conserved mechanism in Caenorhabditis elegans and mouse. Genetic and pharmacological inhibition of ACMSD boosts de novo NAD+ synthesis and sirtuin 1 activity, ultimately enhancing mitochondrial function. We also characterize two potent and selective inhibitors of ACMSD. Because expression of ACMSD is largely restricted to kidney and liver, these inhibitors may have therapeutic potential for protection of these tissues from injury. In summary, we identify ACMSD as a key modulator of cellular NAD+ levels, sirtuin activity and mitochondrial homeostasis in kidney and liver.


Subject(s)
Carboxy-Lyases/metabolism , Conserved Sequence , Evolution, Molecular , Health , Mitochondria/physiology , NAD/biosynthesis , Animals , Caenorhabditis elegans/cytology , Caenorhabditis elegans/enzymology , Caenorhabditis elegans/metabolism , Carboxy-Lyases/antagonists & inhibitors , Carboxy-Lyases/chemistry , Carboxy-Lyases/deficiency , Cell Line , Choline , Disease Models, Animal , Female , Gene Knockdown Techniques , Hepatocytes/cytology , Hepatocytes/drug effects , Homeostasis/drug effects , Humans , Kidney/cytology , Kidney/drug effects , Liver/cytology , Liver/drug effects , Longevity/drug effects , Male , Methionine/deficiency , Mice , Mice, Inbred C57BL , Non-alcoholic Fatty Liver Disease/physiopathology , Non-alcoholic Fatty Liver Disease/prevention & control , Rats , Sirtuins/metabolism
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