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2.
PLoS One ; 18(5): e0284210, 2023.
Article in English | MEDLINE | ID: mdl-37200359

ABSTRACT

Oral antidiabetic agents including the peroxisome proliferator-activated receptor gamma (PPARγ) agonists are available for the clinical management of diabetes mellitus (DM) but most are characterized by many adverse effects. In this study, we explore the antidiabetic properties of phytoconstituents from Trigonellafeonumgraecum (Fabaceae) as potential agonist of PPARγ; using in silico molecular docking, molecular mechanics generalized surface area (MM/GBSA)free binding energy prediction, Pharmacophore modeling experiment, and Pharmacokinetic/ toxicity analysis. One hundred and forty (140) compounds derived from Trigonellafeonumgraecum were screened by molecular docking against protein target PDB 3VI8. Results obtained from binding affinity (BA) and that of binding free energy (BFE) revealed five 5 compounds; arachidonic acid (CID_10467, BA -10.029, BFE -58.9), isoquercetin (CID_5280804, BA -9.507kcal/mol, BFE -56.33), rutin (CID_5280805, BA -9.463kcal/mol, BFE -56.33), quercetin (CID_10121947, BA -11.945kcal/mol, BFE -45.89) and (2S)-2-[[4-methoxy-3-[(pyrene-1-carbonylamino)methyl]phenyl]methyl]butanoic acid (CID_25112371, BA -10.679kcal/mol, BFE -45.73); and were superior to the standard; Rosiglitazone with a docking score of -7.672. Hydrogen bonding was notable in the protein-ligand complex interaction, with hydrophobic bond, polar bond and pipi stacking also observed. Their Pharmacokinetic/ toxicity profile showed varying druggable characteristics, but; arachidonic acid had the most favorable characteristics. These compounds are potential agonists of PPARγ and are considered as antidiabetic agents after successful experimental validation.


Subject(s)
Diabetes Mellitus , Trigonella , Arachidonic Acid , Hypoglycemic Agents/pharmacology , Hypoglycemic Agents/therapeutic use , Hypoglycemic Agents/chemistry , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Pharmacophore , PPAR gamma/metabolism , Trigonella/metabolism , Humans
3.
Science ; 379(6636): 996-1003, 2023 03 10.
Article in English | MEDLINE | ID: mdl-36893255

ABSTRACT

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.


Subject(s)
Carbohydrate Metabolism , L-Lactate Dehydrogenase , Metabolome , Humans , Fatty Acids/metabolism , L-Lactate Dehydrogenase/metabolism , Organ Specificity , Mass Spectrometry/methods , Allosteric Regulation
4.
Biomolecules ; 12(9)2022 09 19.
Article in English | MEDLINE | ID: mdl-36139163

ABSTRACT

Coenzyme A (CoA) is an essential co-factor at the intersection of diverse metabolic pathways. Cellular CoA biosynthesis is regulated at the first committed step-phosphorylation of pantothenic acid-catalyzed by pantothenate kinases (PANK1,2,3 in humans, PANK3 being the most highly expressed). Despite the critical importance of CoA in metabolism, the differential roles of PANK isoforms remain poorly understood. Our investigations of PANK proteins as potential precision oncology collateral lethality targets (PANK1 is co-deleted as part of the PTEN locus in some highly aggressive cancers) were severely hindered by a dearth of commercial antibodies that can reliably detect endogenous PANK3 protein. While we successfully validated commercial antibodies for PANK1 and PANK2 using CRISPR knockout cell lines, we found no commercial antibody that could detect endogenous PANK3. We therefore set out to generate a mouse monoclonal antibody against human PANK3 protein. We demonstrate that a clone (Clone MDA-299-62A) can reliably detect endogenous PANK3 protein in cancer cell lines, with band-specificity confirmed by CRISPR PANK3 knockout and knockdown cell lines. Sub-cellular fractionation shows that PANK3 is overwhelmingly cytosolic and expressed broadly across cancer cell lines. PANK3 monoclonal antibody MDA-299-62A should prove a valuable tool for researchers investigating this understudied family of metabolic enzymes in health and disease.


Subject(s)
Neoplasms , Pantothenic Acid , Animals , Antibodies, Monoclonal , Coenzyme A , Humans , Mice , Precision Medicine , Protein Isoforms
5.
J Med Chem ; 65(3): 2388-2408, 2022 02 10.
Article in English | MEDLINE | ID: mdl-34982556

ABSTRACT

Bromodomain-containing protein 4 (BRD4) is an emerging epigenetic drug target for intractable inflammatory disorders. The lack of highly selective inhibitors among BRD4 family members has stalled the collective understanding of this critical system and the progress toward clinical development of effective therapeutics. Here we report the discovery of a potent BRD4 bromodomain 1 (BD1)-selective inhibitor ZL0590 (52) targeting a unique, previously unreported binding site, while exhibiting significant anti-inflammatory activities in vitro and in vivo. The X-ray crystal structural analysis of ZL0590 in complex with human BRD4 BD1 and the associated mutagenesis study illustrate a first-in-class nonacetylated lysine (KAc) binding site located at the helix αB and αC interface that contains important BRD4 residues (e.g., Glu151) not commonly shared among other family members and is spatially distinct from the classic KAc recognition pocket. This new finding facilitates further elucidation of the complex biology underpinning bromodomain specificity among BRD4 and its protein-protein interaction partners.


Subject(s)
Anti-Inflammatory Agents/pharmacology , Cell Cycle Proteins/antagonists & inhibitors , Nuclear Proteins/antagonists & inhibitors , Phenylurea Compounds/pharmacology , Transcription Factors/antagonists & inhibitors , Animals , Anti-Inflammatory Agents/chemical synthesis , Anti-Inflammatory Agents/metabolism , Anti-Inflammatory Agents/pharmacokinetics , Binding Sites , Cell Cycle Proteins/metabolism , Cell Line , Crystallography, X-Ray , Gene Expression/drug effects , Humans , Interleukin-6/genetics , Interleukin-6/metabolism , Male , Mice, Inbred C57BL , Oxidoreductases Acting on CH-CH Group Donors/genetics , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Phenylurea Compounds/chemical synthesis , Phenylurea Compounds/metabolism , Phenylurea Compounds/pharmacokinetics , Protein Binding , Protein Domains , Rats , Transcription Factors/metabolism
6.
J Med Chem ; 64(20): 15141-15169, 2021 10 28.
Article in English | MEDLINE | ID: mdl-34643390

ABSTRACT

Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2) plays a role in receptor tyrosine kinase (RTK), neurofibromin-1 (NF-1), and Kirsten rat sarcoma virus (KRAS) mutant-driven cancers, as well as in RTK-mediated resistance, making the identification of small-molecule therapeutics that interfere with its function of high interest. Our quest to identify potent, orally bioavailable, and safe SHP2 inhibitors led to the discovery of a promising series of pyrazolopyrimidinones that displayed excellent potency but had a suboptimal in vivo pharmacokinetic (PK) profile. Hypothesis-driven scaffold optimization led us to a series of pyrazolopyrazines with excellent PK properties across species but a narrow human Ether-à-go-go-Related Gene (hERG) window. Subsequent optimization of properties led to the discovery of the pyrimidinone series, in which multiple members possessed excellent potency, optimal in vivo PK across species, and no off-target activities including no hERG liability up to 100 µM. Importantly, compound 30 (IACS-15414) potently suppressed the mitogen-activated protein kinase (MAPK) pathway signaling and tumor growth in RTK-activated and KRASmut xenograft models in vivo.


Subject(s)
Antineoplastic Agents/pharmacology , Drug Discovery , Enzyme Inhibitors/pharmacology , Protein Tyrosine Phosphatase, Non-Receptor Type 11/antagonists & inhibitors , Administration, Oral , Animals , Antineoplastic Agents/administration & dosage , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Enzyme Inhibitors/administration & dosage , Enzyme Inhibitors/chemistry , Humans , Mice , Molecular Structure , Neoplasms, Experimental/drug therapy , Neoplasms, Experimental/metabolism , Neoplasms, Experimental/pathology , Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism , Structure-Activity Relationship
7.
Sci Adv ; 7(32)2021 Aug.
Article in English | MEDLINE | ID: mdl-34348893

ABSTRACT

DNA double-strand break (DSB) repair is initiated by MRE11 nuclease for both homology-directed repair (HDR) and alternative end joining (Alt-EJ). Here, we found that GRB2, crucial to timely proliferative RAS/MAPK pathway activation, unexpectedly forms a biophysically validated GRB2-MRE11 (GM) complex for efficient HDR initiation. GRB2-SH2 domain targets the GM complex to phosphorylated H2AX at DSBs. GRB2 K109 ubiquitination by E3 ubiquitin ligase RBBP6 releases MRE11 promoting HDR. RBBP6 depletion results in prolonged GM complex and HDR defects. GRB2 knockout increased MRE11-XRCC1 complex and Alt-EJ. Reconstitution with separation-of-function GRB2 mutant caused HDR deficiency and synthetic lethality with PARP inhibitor. Cell and cancer genome analyses suggest biomarkers of low GRB2 for noncanonical HDR deficiency and high MRE11 and GRB2 expression for worse survival in HDR-proficient patients. These findings establish GRB2's role in binding, targeting, and releasing MRE11 to promote efficient HDR over Alt-EJ DSB repair, with implications for genome stability and cancer biology.

8.
J Med Chem ; 64(15): 11302-11329, 2021 08 12.
Article in English | MEDLINE | ID: mdl-34292726

ABSTRACT

Indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme that mediates the rate-limiting step in the metabolism of l-tryptophan to kynurenine, has been widely explored as a potential immunotherapeutic target in oncology. We developed a class of inhibitors with a conformationally constrained bicyclo[3.1.0]hexane core. These potently inhibited IDO1 in a cellular context by binding to the apoenzyme, as elucidated by biochemical characterization and X-ray crystallography. A SKOV3 tumor model was instrumental in differentiating compounds, leading to the identification of IACS-9779 (62) and IACS-70465 (71). IACS-70465 has excellent cellular potency, a robust pharmacodynamic response, and in a human whole blood assay was more potent than linrodostat (BMS-986205). IACS-9779 with a predicted human efficacious once daily dose below 1 mg/kg to sustain >90% inhibition of IDO1 displayed an acceptable safety margin in rodent toxicology and dog cardiovascular studies to support advancement into preclinical safety evaluation for human development.


Subject(s)
Drug Discovery , Enzyme Inhibitors/pharmacology , Indoleamine-Pyrrole 2,3,-Dioxygenase/antagonists & inhibitors , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Humans , Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism , Molecular Structure , Structure-Activity Relationship
9.
Dev Med Child Neurol ; 63(9): 1075-1084, 2021 09.
Article in English | MEDLINE | ID: mdl-33929072

ABSTRACT

AIM: To describe the epidemiology and outcomes of convulsive status epilepticus (CSE) since the introduction of buccal midazolam and the change in International League Against Epilepsy definition of CSE to include seizures of at least 5 minutes. METHOD: All children presenting to paediatric emergency departments with CSE (2011-2017) in Lothian, Scotland, were identified. Data, collated from electronic health records, included patient demographics, clinical characteristics, acute seizure management, and adverse outcomes (for example admission to intensive care). RESULTS: Six hundred and sixty-five children were admitted with CSE who had 1228 seizure episodes (381 males, 284 females; median age 3y 8mo; age range 0-20y 11mo). CSE accounted for 0.38% (95% confidence interval 0.34-0.42) of annual attendances at emergency departments. Annual prevalence was 0.8 per 1000 children aged 0 to 14 years. Thirty-four per cent of children had recurrent CSE. Sixty-nine per cent of seizures lasted 5 to 29 minutes (median duration 10min). Buccal midazolam was given to 30% of children with CSE and had no effect on need for ventilatory support. Seventy per cent of children with CSE required hospital admission. Four per cent resulted in adverse outcome and there were only two deaths. Recurrent seizures, longer duration, and unprovoked seizures increased the odds of adverse outcome. INTERPRETATION: Adverse outcomes have decreased and the use of buccal midazolam is promising. Identifying high-risk groups provides an opportunity for early intervention. These data form the basis for an extensive evaluation of acute seizure management and monitoring long-term outcomes. What this paper adds The annual prevalence of convulsive status epilepticus in Lothian, Scotland, was 0.8 per 1000 children. There was a decrease in case-fatality proportion from 3-9% to 0.2%. Use of buccal midazolam has increased, with no increase in adverse outcomes.


Subject(s)
Anticonvulsants/therapeutic use , Midazolam/therapeutic use , Seizures/drug therapy , Seizures/epidemiology , Status Epilepticus/drug therapy , Status Epilepticus/epidemiology , Adolescent , Anticonvulsants/adverse effects , Child , Child, Preschool , Cohort Studies , Emergency Service, Hospital/statistics & numerical data , Female , Humans , Infant , Infant, Newborn , Intubation, Intratracheal , Male , Midazolam/adverse effects , Pediatrics , Scotland/epidemiology , Seizures/etiology , Seizures/physiopathology , Status Epilepticus/physiopathology , Treatment Outcome , Young Adult
10.
Environ Manage ; 67(2): 412-423, 2021 Feb.
Article in English | MEDLINE | ID: mdl-33469694

ABSTRACT

The negative effects of roads on wildlife populations are a growing concern. Movement corridors and road-kill data are typically used to prioritize road segments for mitigation measures. Some research suggests that locations where animals move across roads following corridors coincide with locations where they are often killed by vehicles. Other research indicates that corridors and road-kill rarely occur in the same locations. We compared movement corridor and road mortality models as means of prioritizing road segments for mitigation for five species of felids in Brazil: tiger cats (Leopardus tigrinus and Leopardus guttulus were analyzed together), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi), and puma (Puma concolor). We used occurrence data for each species and applied circuit theory to identify potential movement corridors crossed by roads. We used road-kill records for each species and applied maximum entropy to determine where mortality was most likely to occur on roads. Our findings suggest that movement corridors and high road mortality are not spatially associated. We suggest that differences in the behavioral state of the individuals in the species occurrence and road-kill data may explain these results. We recommend that the road segments for which the results from the two methods agree (~5300 km for all studied species combined at 95th percentile) should be high-priority candidates for mitigation together with road segments identified by at least one method in areas where felids occur in low population densities or are threatened by isolation effects.


Subject(s)
Felidae , Puma , Animals , Animals, Wild , Brazil , Cats , Population Density
12.
Ecol Appl ; 31(1): e2207, 2021 01.
Article in English | MEDLINE | ID: mdl-32632940

ABSTRACT

Migration is common worldwide as species access spatiotemporally varying resources and avoid predators and parasites. However, long-distance migrations are increasingly imperiled due to development and habitat fragmentation. Improved understanding of migratory behavior has implications for conservation and management of migratory species, allowing identification and protection of seasonal ranges and migration corridors. We present a technique that applies circuit theory to predict future effects of development by analyzing season-specific resistance to movement from anthropogenic and natural environmental features across an entire migratory path. We demonstrate the utility of our approach by examining potential effects of a proposed road system on barren ground caribou (Rangifer tarandus granti) and subsistence hunters in northern Alaska. Resource selection functions revealed migratory selection by caribou. We tested five scenarios relating habitat selection to landscape resistance using Circuitscape and GPS telemetry data. To examine the effect of potential roads on connectivity of migrating animals and human hunters, we compared current flow values near communities in the presence of proposed roads. Caribou avoided dense vegetation, rugged terrain, major rivers, and existing roads in both spring and fall. A negative linear relationship between resource selection and landscape resistance was strongly supported for fall migration while spring migration featured a negative logarithmic relationship. Overall patterns of caribou connectivity remained similar in the presence of proposed roads, though reduced current flow was predicted for communities near the center of current migration areas. Such data can inform decisions to allow or disallow projects or to select among alternative development proposals and mitigation measures, though consideration of cumulative effects of development is needed. Our approach is flexible and can easily be adapted to other species, locations and development scenarios to expand understanding of movement behavior and to evaluate proposed developments. Such information is vital to inform policy decisions that balance new development, resource user needs, and preservation of ecosystem function.


Subject(s)
Ecosystem , Reindeer , Alaska , Animal Migration , Animals , Herbivory , Humans
13.
Nat Metab ; 2(12): 1413-1426, 2020 12.
Article in English | MEDLINE | ID: mdl-33230295

ABSTRACT

Inhibiting glycolysis remains an aspirational approach for the treatment of cancer. We have previously identified a subset of cancers harbouring homozygous deletion of the glycolytic enzyme enolase (ENO1) that have exceptional sensitivity to inhibition of its redundant paralogue, ENO2, through a therapeutic strategy known as collateral lethality. Here, we show that a small-molecule enolase inhibitor, POMHEX, can selectively kill ENO1-deleted glioma cells at low-nanomolar concentrations and eradicate intracranial orthotopic ENO1-deleted tumours in mice at doses well-tolerated in non-human primates. Our data provide an in vivo proof of principle of the power of collateral lethality in precision oncology and demonstrate the utility of POMHEX for glycolysis inhibition with potential use across a range of therapeutic settings.


Subject(s)
Antineoplastic Agents/therapeutic use , Biomarkers, Tumor/genetics , DNA-Binding Proteins/genetics , Enzyme Inhibitors/therapeutic use , Neoplasms/drug therapy , Neoplasms/genetics , Phosphopyruvate Hydratase/antagonists & inhibitors , Tumor Suppressor Proteins/genetics , Animals , Cell Line, Tumor , Female , Glioma/drug therapy , Glycolysis/drug effects , Humans , Macaca fascicularis , Male , Mice , Mice, SCID , Phosphopyruvate Hydratase/genetics , Precision Medicine , Sequence Deletion , Structure-Activity Relationship , Xenograft Model Antitumor Assays
14.
J Med Chem ; 63(21): 12957-12977, 2020 11 12.
Article in English | MEDLINE | ID: mdl-33118821

ABSTRACT

Inhibition of glutaminase-1 (GLS-1) hampers the proliferation of tumor cells reliant on glutamine. Known glutaminase inhibitors have potential limitations, and in vivo exposures are potentially limited due to poor physicochemical properties. We initiated a GLS-1 inhibitor discovery program focused on optimizing physicochemical and pharmacokinetic properties, and have developed a new selective inhibitor, compound 27 (IPN60090), which is currently in phase 1 clinical trials. Compound 27 attains high oral exposures in preclinical species, with strong in vivo target engagement, and should robustly inhibit glutaminase in humans.


Subject(s)
Enzyme Inhibitors/chemistry , Glutaminase/antagonists & inhibitors , Triazoles/pharmacokinetics , Administration, Oral , Animals , Cell Line, Tumor , Dogs , Drug Evaluation, Preclinical , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacokinetics , Glutaminase/genetics , Glutaminase/metabolism , Half-Life , Hepatocytes/cytology , Hepatocytes/drug effects , Hepatocytes/metabolism , Humans , Inhibitory Concentration 50 , Male , Mice , Microsomes/metabolism , Protein Binding , Rats , Rats, Sprague-Dawley , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Structure-Activity Relationship , Triazoles/chemistry , Triazoles/metabolism
15.
Cancer Res ; 80(21): 4840-4853, 2020 11 01.
Article in English | MEDLINE | ID: mdl-32928921

ABSTRACT

Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.


Subject(s)
Antineoplastic Agents/pharmacology , Drug Resistance, Neoplasm/drug effects , Neoplasms, Experimental/pathology , Protein Tyrosine Phosphatase, Non-Receptor Type 11/antagonists & inhibitors , Acrylamides/pharmacology , Aniline Compounds/pharmacology , Animals , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Proliferation/drug effects , ErbB Receptors/genetics , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mice , Mutation , Neoplasms, Experimental/genetics , Xenograft Model Antitumor Assays
16.
J Med Chem ; 63(17): 9888-9911, 2020 09 10.
Article in English | MEDLINE | ID: mdl-32787110

ABSTRACT

Tumor-associated macrophages (TAMs) have a significant presence in the tumor stroma across multiple human malignancies and are believed to be beneficial to tumor growth. Targeting CSF1R has been proposed as a potential therapy to reduce TAMs, especially the protumor, immune-suppressive M2 TAMs. Additionally, the high expression of CSF1R on tumor cells has been associated with poor survival in certain cancers, suggesting tumor dependency and therefore a potential therapeutic target. The CSF1-CSF1R signaling pathway modulates the production, differentiation, and function of TAMs; however, the discovery of selective CSF1R inhibitors devoid of type III kinase activity has proven to be challenging. We discovered a potent, highly selective, and orally bioavailable CSF1R inhibitor, IACS-9439 (1). Treatment with 1 led to a dose-dependent reduction in macrophages, promoted macrophage polarization toward the M1 phenotype, and led to tumor growth inhibition in MC38 and PANC02 syngeneic tumor models.


Subject(s)
Antineoplastic Agents/therapeutic use , Benzothiazoles/therapeutic use , Neoplasms/drug therapy , Pyrimidines/therapeutic use , Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/antagonists & inhibitors , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacokinetics , Benzothiazoles/chemical synthesis , Benzothiazoles/pharmacokinetics , Drug Stability , Humans , Microsomes, Liver/metabolism , Molecular Structure , Pyrimidines/chemical synthesis , Pyrimidines/pharmacokinetics , Structure-Activity Relationship , THP-1 Cells , Tumor-Associated Macrophages/drug effects
17.
J Med Chem ; 63(10): 5242-5256, 2020 05 28.
Article in English | MEDLINE | ID: mdl-32255647

ABSTRACT

Bromodomain-containing protein 4 (BRD4) represents a promising drug target for anti-inflammatory therapeutics. Herein, we report the design, synthesis, and pharmacological evaluation of novel chromone derivatives via scaffold hopping to discover a new class of orally bioavailable BRD4-selective inhibitors. Two potent BRD4 bromodomain 1 (BD1)-selective inhibitors 44 (ZL0513) and 45 (ZL0516) have been discovered with high binding affinity (IC50 values of 67-84 nM) and good selectivity over other BRD family proteins and distant BD-containing proteins. Both compounds significantly inhibited the expression of Toll-like receptor-induced inflammatory genes in vitro and airway inflammation in murine models. The cocrystal structure of 45 in complex with human BRD4 BD1 at a high resolution of 2.0 Å has been solved, offering a solid structural basis for its binding validation and further structure-based optimization. These BRD4 BD1 inhibitors demonstrated impressive in vivo efficacy and overall promising pharmacokinetic properties, indicating their therapeutic potential for the treatment of inflammatory diseases.


Subject(s)
Cell Cycle Proteins/antagonists & inhibitors , Chromones/administration & dosage , Chromones/chemistry , Drug Discovery/methods , Transcription Factors/antagonists & inhibitors , Administration, Oral , Animals , Biological Availability , Cell Cycle Proteins/metabolism , Cell Line, Transformed , Chromones/pharmacology , Crystallization/methods , Crystallization/trends , Drug Discovery/trends , Drug Evaluation, Preclinical/methods , Humans , Male , Mice , Mice, Inbred C57BL , Protein Structure, Secondary , Protein Structure, Tertiary , Structure-Activity Relationship , Transcription Factors/metabolism
18.
Molecules ; 24(13)2019 Jul 09.
Article in English | MEDLINE | ID: mdl-31324042

ABSTRACT

We recently reported that SF2312 ((1,5-dihydroxy-2-oxopyrrolidin-3-yl)phosphonic acid), a phosphonate antibiotic with a previously unknown mode of action, is a potent inhibitor of the glycolytic enzyme, Enolase. SF2312 can only be synthesized as a racemic-diastereomeric mixture. However, co-crystal structures with Enolase 2 (ENO2) have consistently shown that only the (3S,5S)-enantiomer binds to the active site. The acidity of the alpha proton at C-3, which deprotonates under mildly alkaline conditions, results in racemization; thus while the separation of four enantiomeric intermediates was achieved via chiral High Performance Liquid Chromatography (HPLC) of the fully protected intermediate, deprotection inevitably nullified enantiopurity. To prevent epimerization of the C-3, we designed and synthesized MethylSF2312, ((1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid), which contains a fully-substituted C-3 alpha carbon. As a racemic-diastereomeric mixture, MethylSF2312 is equipotent to SF2312 in enzymatic and cellular systems against Enolase. Chiral HPLC separation of a protected MethylSF2312 precursor resulted in the efficient separation of the four enantiomers. After deprotection and inevitable re-equilibration of the anomeric C-5, (3S)-MethylSF2312 was up to 2000-fold more potent than (3R)-MethylSF2312 in an isolated enzymatic assay. This observation strongly correlates with biological activity in both human cancer cells and bacteria for the 3S enantiomer of SF2312. Novel X-ray structures of human ENO2 with chiral and racemic MethylSF2312 show that only (3S,5S)-enantiomer occupies the active site. Enolase inhibition is thus a direct result of binding by the (3S,5S)-enantiomer of MethylSF2312. Concurrent with these results for MethylSF2312, we contend that the (3S,5S)-SF2312 is the single active enantiomer of inhibitor SF2312.


Subject(s)
Enzyme Inhibitors/pharmacology , Organophosphonates/pharmacology , Phosphopyruvate Hydratase/antagonists & inhibitors , Phosphopyruvate Hydratase/chemistry , Pyrrolidinones/pharmacology , Binding Sites , Enzyme Activation/drug effects , Enzyme Inhibitors/chemistry , Models, Molecular , Molecular Conformation , Molecular Structure , Organophosphonates/chemistry , Protein Binding , Pyrrolidinones/chemistry , Spectrum Analysis , Stereoisomerism , Structure-Activity Relationship
19.
Cell Rep ; 26(2): 469-482.e5, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30625329

ABSTRACT

The plasticity of a preexisting regulatory circuit compromises the effectiveness of targeted therapies, and leveraging genetic vulnerabilities in cancer cells may overcome such adaptations. Hereditary leiomyomatosis renal cell carcinoma (HLRCC) is characterized by oxidative phosphorylation (OXPHOS) deficiency caused by fumarate hydratase (FH) nullizyogosity. To identify metabolic genes that are synthetically lethal with OXPHOS deficiency, we conducted a genetic loss-of-function screen and found that phosphogluconate dehydrogenase (PGD) inhibition robustly blocks the proliferation of FH mutant cancer cells both in vitro and in vivo. Mechanistically, PGD inhibition blocks glycolysis, suppresses reductive carboxylation of glutamine, and increases the NADP+/NADPH ratio to disrupt redox homeostasis. Furthermore, in the OXPHOS-proficient context, blocking OXPHOS using the small-molecule inhibitor IACS-010759 enhances sensitivity to PGD inhibition in vitro and in vivo. Together, our study reveals a dependency on PGD in OXPHOS-deficient tumors that might inform therapeutic intervention in specific patient populations.


Subject(s)
Oxidative Phosphorylation , Phosphogluconate Dehydrogenase/genetics , Synthetic Lethal Mutations , Animals , Cell Line, Tumor , Female , Fumarate Hydratase/genetics , Genomics/methods , Glycolysis , Humans , Loss of Function Mutation , Mice , Mice, Nude
20.
Conserv Biol ; 33(2): 239-249, 2019 04.
Article in English | MEDLINE | ID: mdl-30311266

ABSTRACT

Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least-cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open-source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat-use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.


Aplicaciones de la Teoría de Circuitos a la Conservación y a la Ciencia de la Conectividad Resumen Quienes practican la conservación han reconocido durante mucho tiempo que la conectividad ecológica es una prioridad mundial para la preservación de la biodiversidad y el funcionamiento del ecosistema. Durante los primeros años de la ciencia de la conservación los ecólogos difundieron los principios de la biografía de islas para evaluar la conectividad con base en la proximidad entre el origen y el fragmento, así como otras medidas derivadas de los mapas binarios de los hábitats. Entre 2006 y 2008 el fallecido Brad McRae introdujo la teoría de circuitos como una estrategia alternativa para modelar el flujo génico y la dispersión o las rutas de movimiento de los organismos. McRae propuso conceptos y medidas de la teoría de circuitos eléctricos como una manera robusta para cuantificar el movimiento a lo largo de múltiples caminos posibles en un paisaje, no solamente a lo largo de un camino o corredor de menor costo. La teoría de circuitos ofrece muchos enlaces teóricos, conceptuales y prácticos con la ciencia de la conservación. Revisamos 459 estudios recientes que citan la teoría de circuitos o el software de fuente abierta Circuitscape. Nos enfocamos en las aplicaciones de la teoría de circuitos a la ciencia y a la práctica de la conservación de la conectividad, incluyendo temas como la genética poblacional y del paisaje, movimiento y caminos de dispersión de los organismos, barreras antropogénicas de la conectividad, comportamiento ante incendios, flujo del agua, y servicios ambientales. La teoría de circuitos probablemente tenga un efecto sobre la ciencia de la conservación y quienes la practican por medio de una percepción mejorada de las dinámicas del paisaje, el movimiento animal, y los estudios de uso de hábitat, y por medio del desarrollo de nuevas herramientas de software para el análisis de datos y su visualización. La influencia de la teoría de circuitos sobre la conservación viene de la base teórica y la elegancia de la estrategia y de las colaboraciones fuertes y la comunidad activa de usuarios que han surgido recientemente. La teoría de circuitos proporciona un trampolín para el entendimiento ecológico y seguirá siendo una importante herramienta de conservación para los investigadores y practicantes en todo el mundo.


Subject(s)
Conservation of Natural Resources , Ecosystem , Animals , Ecology , Gene Flow , Islands
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