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1.
Cancers (Basel) ; 15(21)2023 Nov 03.
Article in English | MEDLINE | ID: mdl-37958457

ABSTRACT

Chromosomal translocations involving the mixed lineage leukemia (MLL) gene cause 5-10% acute leukemias with poor clinical outcomes. Protein-protein interactions (PPI) between the most frequent MLL fusion partner proteins AF9/ENL and AF4 or histone methyltransferase DOT1L are drug targets for MLL-rearranged (MLL-r) leukemia. Several benzothiophene-carboxamide compounds were identified as novel inhibitors of these PPIs with IC50 values as low as 1.6 µM. Structure-activity relationship studies of 77 benzothiophene and related indole and benzofuran compounds show that a 4-piperidin-1-ylphenyl or 4-pyrrolidin-1-ylphenyl substituent is essential for the activity. The inhibitors suppressed expression of MLL target genes HoxA9, Meis1 and Myc, and selectively inhibited proliferation of MLL-r and other acute myeloid leukemia cells with EC50 values as low as 4.7 µM. These inhibitors are useful chemical probes for biological studies of AF9/ENL, as well as pharmacological leads for further drug development against MLL-r and other leukemias.

2.
Eur J Med Chem ; 237: 114407, 2022 Jul 05.
Article in English | MEDLINE | ID: mdl-35512565

ABSTRACT

Acetylation of histone lysine residues by histone acetyltransferase (HAT) p300 and its paralog CBP play important roles in gene regulation in health and diseases. The HAT domain of p300/CBP has been found to be a potential drug target for cancer. Compound screening followed by structure-activity relationship studies yielded a novel series of 1,4-pyrazine-containing inhibitors of p300/CBP HAT with their IC50s as low as 1.4 µM. Enzyme kinetics and other studies support the most potent compound 29 is a competitive inhibitor of p300 HAT against the substrate histone. It exhibited a high selectivity for p300 and CBP, with negligible activity on other classes of HATs in human. Compound 29 inhibited cellular acetylation of several histone lysine residues and showed strong activity against proliferation of a panel of solid and blood cancer cells. These results indicate it is a novel pharmacological lead for drug development targeting these cancers as well as a useful chemical probe for biological studies of p300/CBP.


Subject(s)
Histones , Neoplasms , Acetylation , Acetyltransferases/metabolism , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Histone Acetyltransferases/metabolism , Histones/metabolism , Humans , Lysine , Pyrazines/pharmacology , Structure-Activity Relationship
3.
J Hematol Oncol ; 15(1): 41, 2022 04 08.
Article in English | MEDLINE | ID: mdl-35395864

ABSTRACT

BACKGROUND: Chromosome translocations involving mixed lineage leukemia 1 (MLL1) cause acute leukemia in most infants and 5-10% children/adults with dismal clinical outcomes. Most frequent MLL1-fusion partners AF4/AFF4, AF9/ENL and ELL, together with CDK9/cyclin-T1, constitute super elongation complexes (SEC), which promote aberrant gene transcription, oncogenesis and maintenance of MLL1-rearranged (MLL1-r) leukemia. Notably, ENL, but not its paralog AF9, is essential for MLL1-r leukemia (and several other cancers) and therefore a drug target. Moreover, recurrent ENL mutations are found in Wilms tumor, the most common pediatric kidney cancer, and play critical roles in oncogenesis. METHODS: Proteolysis-Targeting Chimera (PROTAC) molecules were designed and synthesized to degrade ENL. Biological activities of these compounds were characterized in cell and mouse models of MLL1-r leukemia and other cancers. RESULTS: Compound 1 efficiently degraded ENL with DC50 of 37 nM and almost depleted it at ~ 500 nM in blood and solid tumor cells. AF9 (as well as other proteins in SEC) was not significantly decreased. Compound 1-mediated ENL reduction significantly suppressed malignant gene signatures, selectively inhibited cell proliferation of MLL1-r leukemia and Myc-driven cancer cells with EC50s as low as 320 nM, and induced cell differentiation and apoptosis. It exhibited significant antitumor activity in a mouse model of MLL1-r leukemia. Compound 1 can also degrade a mutant ENL in Wilms tumor and suppress its mediated gene transcription. CONCLUSION: Compound 1 is a novel chemical probe for cellular and in vivo studies of ENL (including its oncogenic mutants) and a lead compound for further anticancer drug development.


Subject(s)
Kidney Neoplasms , Leukemia, Myeloid, Acute , Wilms Tumor , Animals , Humans , Mice , Carcinogenesis , Gene Expression , Kidney Neoplasms/drug therapy , Kidney Neoplasms/genetics , Leukemia, Myeloid, Acute/genetics , Myeloid-Lymphoid Leukemia Protein/genetics , Myeloid-Lymphoid Leukemia Protein/metabolism , Proteolysis , Transcriptional Elongation Factors/chemistry , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/metabolism , Wilms Tumor/drug therapy , Wilms Tumor/genetics
4.
IEEE Trans Image Process ; 30: 9442-9455, 2021.
Article in English | MEDLINE | ID: mdl-34780325

ABSTRACT

Many state-of-the-art stereo matching algorithms based on deep learning have been proposed in recent years, which usually construct a cost volume and adopt cost filtering by a series of 3D convolutions. In essence, the possibility of all the disparities is exhaustively represented in the cost volume, and the estimated disparity holds the maximal possibility. The cost filtering could learn contextual information and reduce mismatches in ill-posed regions. However, this kind of methods has two main disadvantages: 1) cost filtering is very time-consuming, and it is thus difficult to simultaneously satisfy the requirements for both speed and accuracy; 2) thickness of the cost volume determines the disparity range which can be estimated, and the pre-defined disparity range may not meet the demand of practical application. This paper proposes a novel real-time stereo matching method called RLStereo, which is based on reinforcement learning and abandons the cost volume or the routine of exhaustive search. The trained RLStereo makes only a few actions iteratively to search the value of the disparity for each pair of stereo images. Experimental results show the effectiveness of the proposed method, which achieves comparable performances to state-of-the-art algorithms with real-time speed on the public large-scale testset, i.e., Scene Flow.

5.
Theranostics ; 11(17): 8172-8184, 2021.
Article in English | MEDLINE | ID: mdl-34373735

ABSTRACT

Chromosome translocations involving mixed lineage leukemia (MLL) gene cause acute leukemia with a poor prognosis. MLL is frequently fused with transcription cofactors AF4 (~35%), AF9 (25%) or its paralog ENL (10%). The AHD domain of AF9/ENL binds to AF4, its paralog AFF4, or histone-H3 lysine-79 (H3K79) methyltransferase DOT1L. Formation of AF9/ENL/AF4/AFF4-containing super elongation complexes (SEC) and the catalytic activity of DOT1L are essential for MLL-rearranged leukemia. Protein-protein interactions (PPI) between AF9/ENL and DOT1L/AF4/AFF4 are therefore a potential drug target. Methods: Compound screening followed by medicinal chemistry was used to find inhibitors of such PPIs, which were examined for their biological activities against MLL-rearranged leukemia and other cancer cells. Results: Compound-1 was identified to be a novel small-molecule inhibitor of the AF9/ENL-DOT1L/AF4/AFF4 interaction with IC50s of 0.9-3.5 µM. Pharmacological inhibition of the PPIs significantly reduced SEC and DOT1L-mediated H3K79 methylation in the leukemia cells. Gene profiling shows compound-1 significantly suppressed the gene signatures related to onco-MLL, DOT1L, HoxA9 and Myc. It selectively inhibited proliferation of onco-MLL- or Myc-driven cancer cells and induced cell differentiation and apoptosis. Compound-1 exhibited strong antitumor activity in a mouse model of MLL-rearranged leukemia. Conclusions: The AF9/ENL-DOT1L/AF4/AFF4 interactions are validated to be an anticancer target and compound-1 is a useful in vivo probe for biological studies as well as a pharmacological lead for further drug development.


Subject(s)
Antineoplastic Agents/pharmacology , Leukemia, Myeloid, Acute , Oncogene Proteins, Fusion , Animals , Gene Expression/drug effects , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/drug effects , Histone-Lysine N-Methyltransferase/genetics , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Mice , Oncogene Proteins, Fusion/chemistry , Oncogene Proteins, Fusion/drug effects , Oncogene Proteins, Fusion/genetics , Oncogenes/drug effects , Protein Interaction Domains and Motifs , Transcriptional Elongation Factors/chemistry , Transcriptional Elongation Factors/drug effects , Transcriptional Elongation Factors/genetics
6.
Eur J Med Chem ; 225: 113767, 2021 Dec 05.
Article in English | MEDLINE | ID: mdl-34450494

ABSTRACT

Zika virus belongs to the Flavivirus family of RNA viruses, which include other important human pathogens such as dengue and West Nile virus. There are no approved antiviral drugs for these viruses. The highly conserved NS2B-NS3 protease of Flavivirus is essential for the replication of these viruses and it is therefore a drug target. Compound screen followed by medicinal chemistry optimization yielded a novel series of 2,6-disubstituted indole compounds that are potent inhibitors of Zika virus protease (ZVpro) with IC50 values as low as 320 nM. The structure-activity relationships of these and related compounds are discussed. Enzyme kinetics studies show the inhibitor 66 most likely exhibited a non-competitive mode of inhibition. In addition, this series of ZVpro inhibitors also inhibit the NS2B-NS3 protease of dengue and West Nile virus with reduced potencies. The most potent compounds 66 and 67 strongly inhibited Zika virus replication in cells with EC68 values of 1-3 µM. These compounds are novel pharmacological leads for further drug development targeting Zika virus.


Subject(s)
Antiviral Agents/pharmacology , Indoles/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Zika Virus/drug effects , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Dose-Response Relationship, Drug , Indoles/chemical synthesis , Indoles/chemistry , Microbial Sensitivity Tests , Molecular Structure , RNA Helicases/antagonists & inhibitors , RNA Helicases/metabolism , Serine Endopeptidases/metabolism , Structure-Activity Relationship , Viral Nonstructural Proteins/metabolism
7.
J Med Chem ; 64(5): 2777-2800, 2021 03 11.
Article in English | MEDLINE | ID: mdl-33596380

ABSTRACT

Flaviviruses, including Zika, dengue, and West Nile viruses, are important human pathogens. The highly conserved NS2B-NS3 protease of Flavivirus is essential for viral replication and therefore a promising drug target. Through compound screening, followed by medicinal chemistry studies, a novel series of 2,5,6-trisubstituted pyrazine compounds are found to be potent, allosteric inhibitors of Zika virus protease (ZVpro) with IC50 values as low as 130 nM. Their structure-activity relationships are discussed. The ZVpro inhibitors also inhibit homologous proteases of dengue and West Nile viruses, and their inhibitory activities are correlated. The most potent compounds 47 and 103 potently inhibited Zika virus replication in cells with EC68 values of 300-600 nM and in a mouse model of Zika infection. These compounds represent novel pharmacological leads for drug development against Flavivirus infections.


Subject(s)
Antiviral Agents/therapeutic use , Pyrazines/therapeutic use , Serine Endopeptidases/metabolism , Serine Proteinase Inhibitors/therapeutic use , Viral Proteins/metabolism , Zika Virus Infection/drug therapy , Allosteric Regulation/drug effects , Animals , Antiviral Agents/chemical synthesis , Cell Line, Tumor , Dengue Virus/enzymology , Humans , Mice , Molecular Structure , Pyrazines/chemical synthesis , Serine Proteinase Inhibitors/chemical synthesis , Structure-Activity Relationship , Viral Nonstructural Proteins/antagonists & inhibitors , Virus Replication/drug effects , West Nile virus/enzymology , Zika Virus/enzymology
8.
Commun Biol ; 3(1): 165, 2020 04 07.
Article in English | MEDLINE | ID: mdl-32265480

ABSTRACT

As approximately 70% of human breast tumors are estrogen receptor α (ERα)-positive, estrogen and ERα play essential roles in breast cancer development. By interrupting the ERα signaling pathway, endocrine therapy has been proven to be an effective therapeutic strategy. In this study, we identified a mechanism by which Transcription Start Site (TSS)-associated histone H3K27 acetylation signals the Super Elongation Complex (SEC) to regulate transcriptional elongation of the ESR1 (ERα) gene. SEC interacts with H3K27ac on ESR1 TSS through its scaffold protein AFF4. Depletion of AFF4 by siRNA or CRISPR/Cas9 dramatically reduces expression of ESR1 and its target genes, consequently inhibiting breast cancer cell growth. More importantly, a AFF4 mutant which lacks H3K27ac interaction failed to rescue ESR1 gene expression, suggesting H3K27 acetylation at TSS region is a key mark bridging the transition from transcriptional initiation to elongation, and perturbing SEC function can be an alternative strategy for targeting ERα signaling pathway at chromatin level.


Subject(s)
Breast Neoplasms/metabolism , Estrogen Receptor alpha/metabolism , Histones/metabolism , Protein Processing, Post-Translational , Transcription Elongation, Genetic , Acetylation , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Proliferation , Estrogen Receptor alpha/genetics , Female , Gene Expression Regulation, Neoplastic , HEK293 Cells , Histones/genetics , Humans , MCF-7 Cells , RNA Polymerase II/genetics , RNA Polymerase II/metabolism , Signal Transduction , Transcription Factor AP-2/genetics , Transcription Factor AP-2/metabolism , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/metabolism
9.
J Med Chem ; 63(9): 4716-4731, 2020 05 14.
Article in English | MEDLINE | ID: mdl-32314924

ABSTRACT

Histone acetyltransferase (HAT) p300 and its paralog CBP acetylate histone lysine side chains and play critical roles in regulating gene transcription. The HAT domain of p300/CBP is a potential drug target for cancer. Through compound screening and medicinal chemistry, novel inhibitors of p300/CBP HAT with their IC50 values as low as 620 nM were discovered. The most potent inhibitor is competitive against histone substrates and exhibits a high selectivity for p300/CBP. It inhibited cellular acetylation and had strong activity with EC50 of 1-3 µM against proliferation of several tumor cell lines. Gene expression profiling in estrogen receptor (ER)-positive breast cancer MCF-7 cells showed that inhibitor treatment recapitulated siRNA-mediated p300 knockdown, inhibited ER-mediated gene transcription, and suppressed expression of numerous cancer-related gene signatures. These results demonstrate that the inhibitor is not only a useful probe for biological studies of p300/CBP HAT but also a pharmacological lead for further drug development targeting cancer.


Subject(s)
Antineoplastic Agents/pharmacology , Enzyme Inhibitors/pharmacology , Thiophenes/pharmacology , p300-CBP Transcription Factors/antagonists & inhibitors , Acetylation/drug effects , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Drug Discovery , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/metabolism , Gene Expression Regulation, Neoplastic/drug effects , Humans , Molecular Docking Simulation , Molecular Structure , Structure-Activity Relationship , Thiophenes/chemical synthesis , Thiophenes/metabolism , p300-CBP Transcription Factors/metabolism
10.
Mol Genet Genomic Med ; 8(2): e1101, 2020 02.
Article in English | MEDLINE | ID: mdl-31876398

ABSTRACT

BACKGROUND: VAC14 is a component of a trimolecular complex that tightly regulates the level of phosphatidylinositol 3,5-bisphosphate [PI (3,5) P2]. VAC14 pathogenic variants cause prominent vacuolation of neurons in basal ganglia of patients with childhood-onset striatonigral degeneration (SNDC). METHODS: We identified two siblings with SNDC. Whole-exome sequencing was performed for genetic molecular analysis in these probands. RESULTS: The patients were compound heterozygotes for two novel variants in the VAC14 gene, p.Ala582Thr and p.Arg681His. The pathogenicity of these variants was indicated by a bioinformatic study and protein three-dimensional modeling. Eight previously reported SNDC cases and a Yunis-Varón syndrome caused by VAC14 mutations were summarized and compared. CONCLUSION: We present novel compound heterozygous variants (c.1744G>A/c.2042G>A) in our proband, and these novel variants were predicted to be likely pathogenic. The affected siblings were clinically severe and lethal; their phenotypes were similar to the majority of previously reported SNDC cases, with the exception of two cases that showed mild clinical manifestations. VAC14 pathogenic variants may be associated with various phenotypes. Herein, we report the Chinese siblings with SNDC, they are the first Asian cases. Our results expanded the spectrum of VAC14 pathogenic variants and the ethnic backgrounds of the affected cases.


Subject(s)
Intracellular Signaling Peptides and Proteins/genetics , Membrane Proteins/genetics , Mutation , Striatonigral Degeneration/genetics , Adult , Child , Child, Preschool , Female , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Male , Membrane Proteins/chemistry , Pedigree , Protein Domains , Striatonigral Degeneration/pathology
11.
Medicine (Baltimore) ; 98(44): e17749, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31689829

ABSTRACT

RATIONALE: Early infantile epileptic encephalopathy (EIEE) 65 was recently shown to be caused by the cytoplasmic FMRP interacting protein 2 (CYFIP2) mutation. To date, only 5 cases have been reported in two articles, and all the outcomes in all cases were poor. PATIENT CONCERNS: In this study, we reported an 8-month-old girl with a 1 month-long history of seizures and developmental delay. Over 1 month later, she developed epileptic spasms in clusters with hypsarrhythmia on electroencephalography. DIAGNOSIS: The patient was diagnosed with EIEE 65 and trio-based whole-exome sequencing revealed a causative de novo CYFIP2 mutation c.260G >T (p.Arg87Leu). INTERVENTIONS: The proband was successively treated with multiple antiepileptic drugs, including levetiracetam, phenobarbital, VitB6, topiramate, methylprednisolone, prednisone, valproic acid and vigabatrin. OUTCOMES: After resistance to multiple anti-epileptic drugs over 2 months of treatment, she finally achieved seizure-free several days after vigabatrin administration and her developmental delay steadily improved. LESSONS: OUR: case confirmed that CYFIP2 was the pathogenic gene of EIEE 65. We also first demonstrated vigabatrin might be effective for control of seizures and helpful for the improved outcomes of these patients.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Mutation/genetics , Spasms, Infantile/genetics , Anticonvulsants/therapeutic use , Early Diagnosis , Female , Humans , Infant , Spasms, Infantile/diagnosis , Spasms, Infantile/drug therapy , Treatment Outcome
12.
Mol Med Rep ; 20(6): 5145-5151, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31638258

ABSTRACT

To the best of our knowledge, the present study reported the case of the first Chinese patient with microcephaly­capillary malformation (MIC­CAP) syndrome caused by a novel compound heterozygous mutation in the STAMBP gene, which encodes STAM binding protein. The present study also provides a review of relevant previously published studies. A boy with MIC­CAP syndrome with developmental delay, intractable epilepsy and prominent dyskinesia was examined. A pathogenic mutation was identified by whole­exome sequencing, and the protein structure and function affected by this mutation were predicted using bioinformatics analysis. Finally, the clinical features of 16 other cases reported in previous studies were reviewed and compared. A novel compound heterozygous mutation of the STAMBP (c.1119­1G>T, c.968A>G) was identified in the present study and epilepsy was refractory, consistent with previously reported cases. The present study also highlighted the fact that STAMBP mutation­associated MIC­CAP often presents as intractable early­life epilepsy, which may lead to mortality.


Subject(s)
Capillaries/abnormalities , Endosomal Sorting Complexes Required for Transport/genetics , Epilepsy/genetics , Genetic Predisposition to Disease , Microcephaly/genetics , Mutation , Ubiquitin Thiolesterase/genetics , Vascular Malformations/genetics , Age of Onset , Child , DNA Mutational Analysis , Epilepsy/diagnosis , Genetic Association Studies , Humans , Male , Microcephaly/diagnosis , Pedigree , Sequence Analysis, DNA , Syndrome , Vascular Malformations/diagnosis
13.
PLoS One ; 14(5): e0216203, 2019.
Article in English | MEDLINE | ID: mdl-31048839

ABSTRACT

Transcription factor RUNX1 and its binding partner CBFß play a critical role in gene regulation for hematopoiesis. Mutations of RUNX1 cause ~10% of acute myeloid leukemia (AML) with a particularly poor prognosis. The current paradigm for the leukemogenesis is that insufficient activity of wild-type (WT) RUNX1 impairs hematopoietic differentiation. The majority of mutant RUNX1 proteins lose the DNA-binding affinity and inhibit WT RUNX1 by depletion of CBFß. Here, isothermal titration calorimetry (ITC) was used to quantitatively study the interactions of WT and three clinical mutant RUNX1, CBFß and DNA. Our data show that the binding of RUNX1 to DNA is enthalpy-driven, and the affinity decreases in the order of WT > S114L > R139Q >> K83E, which support previous observations and conclusion. To find potentially beneficial RUNX1 mutations that could increase the overall RUNX1 activity, K83R and H179K mutations of RUNX1 were designed, using structure-based computational modeling, and found to possess significantly higher DNA-binding affinities than does WT RUNX1. K83R and H179K mutant RUNX1 could therefore be protein-based RUNX1 activators.


Subject(s)
Core Binding Factor Alpha 2 Subunit/genetics , Core Binding Factor Alpha 2 Subunit/metabolism , Calorimetry/methods , Cell Differentiation/genetics , Core Binding Factor beta Subunit/genetics , Core Binding Factor beta Subunit/metabolism , DNA/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Hematopoiesis/genetics , Hematopoietic Stem Cells/metabolism , Humans , Leukemia, Myeloid, Acute/genetics , Mutation , Thermodynamics , Transcription Factors/genetics , Transcription Factors/metabolism
14.
J Am Chem Soc ; 141(17): 6832-6836, 2019 05 01.
Article in English | MEDLINE | ID: mdl-31017399

ABSTRACT

Flaviviruses, including dengue, West Nile and recently emerged Zika virus, are important human pathogens, but there are no drugs to prevent or treat these viral infections. The highly conserved Flavivirus NS2B-NS3 protease is essential for viral replication and therefore a drug target. Compound screening followed by medicinal chemistry yielded a series of drug-like, broadly active inhibitors of Flavivirus proteases with IC50 as low as 120 nM. The inhibitor exhibited significant antiviral activities in cells (EC68: 300-600 nM) and in a mouse model of Zika virus infection. X-ray studies reveal that the inhibitors bind to an allosteric, mostly hydrophobic pocket of dengue NS3 and hold the protease in an open, catalytically inactive conformation. The inhibitors and their binding structures would be useful for rational drug development targeting Zika, dengue and other Flaviviruses.


Subject(s)
Antiviral Agents/therapeutic use , Protease Inhibitors/therapeutic use , Serine Endopeptidases/metabolism , Viral Nonstructural Proteins/antagonists & inhibitors , Zika Virus Infection/drug therapy , Allosteric Site , Aminopyridines/chemical synthesis , Aminopyridines/metabolism , Aminopyridines/therapeutic use , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/metabolism , Cell Line, Tumor , Chlorocebus aethiops , Crystallography, X-Ray , Dengue Virus/enzymology , Drug Discovery , Female , Humans , Male , Mice, Inbred C57BL , Protease Inhibitors/chemical synthesis , Protease Inhibitors/metabolism , Protein Binding , Pyrazines/chemical synthesis , Pyrazines/metabolism , Pyrazines/therapeutic use , Serine Endopeptidases/chemistry , Vero Cells , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism , West Nile virus/enzymology , Zika Virus/enzymology
15.
Theranostics ; 8(8): 2189-2201, 2018.
Article in English | MEDLINE | ID: mdl-29721072

ABSTRACT

Acute myeloid leukemia (AML) is a major blood cancer with poor prognosis. New therapies are needed to target oncogene-driven leukemia stem cells, which account for relapse and resistance. Chromosome translocation t(8;21), which produces RUNX1-ETO (R-E) fusion oncoprotein, is found in ~13% AML. R-E dominance negatively inhibits global gene expression regulated by RUNX1, a master transcription factor for hematopoiesis, causing increased self-renewal and blocked cell differentiation of hematopoietic progenitor cells, and eventually leukemia initiation. Methods: Connectivity-Map followed by biological activity testing were used to identify candidate compounds that can inhibit R-E-mediated gene transcription. Molecular mechanistic studies were also performed. Results: Glucocorticoid drugs, such as betamethasone and dexamethasone, were found to exhibit potent and selective in vitro and in vivo activities against R-E leukemia, as well as strong synergy when combined with chemotherapeutics. Microarray analysis showed that treatment with glucocorticoids significantly inhibited R-E's activity and reactivated that of RUNX1. Such gene expression changes caused differentiation and apoptosis of R-E leukemia cells. Our studies also show a possible molecular mechanism for the targeted therapy. Upon treatment with a glucocorticoid drug, more glucocorticoid receptor (GR) was translocated into the nucleus and bound to DNA, including promoters of RUNX1 target genes. GR was found to associate with RUNX1, but not R-E. This interaction increased binding of RUNX1 to DNA and reduced that of R-E, shifting to a RUNX1 dominance. Conclusion: Glucocorticoid drugs represent a targeted therapy for AML with chromosome translocation t(8:21). Given their high activity, favorable human pharmacokinetics as well as synergy with chemotherapeutics, glucocorticoids could be clinically useful to treat R-E AML.


Subject(s)
Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 8/genetics , Glucocorticoids/pharmacology , Leukemia, Myeloid, Acute/genetics , Oncogene Proteins, Fusion/metabolism , Translocation, Genetic , Animals , Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Cell Differentiation/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , DNA/metabolism , Dexamethasone/pharmacology , Gene Expression Regulation, Leukemic/drug effects , Humans , Leukemia, Myeloid, Acute/pathology , Mice, Inbred NOD , Mice, SCID , Neoplastic Stem Cells/drug effects , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , Oncogene Proteins, Fusion/antagonists & inhibitors , RNA, Long Noncoding , Receptors, Glucocorticoid/metabolism , Transcriptome/genetics
16.
Med Chem ; 14(7): 715-724, 2018.
Article in English | MEDLINE | ID: mdl-29792149

ABSTRACT

BACKGROUND: R132H mutation of isocitrate dehydrogenase 1 (IDH1) is found in ~75% of low-grade gliomas and secondary glioblastomas as well as in several other types of cancer. More chemotypes of inhibitors of IDH1(R132H) are therefore needed. OBJECTIVE: The study aimed to develop a new class of IDH1(R132H) inhibitors as potent antitumor agents. METHOD: A biochemical assay was developed to find inhibitors of IDH1(R132H) mutant enzyme. Chemical synthesis and structure-activity relationship studies were used to find compounds with improved potency. Antitumor activities of selected compounds were evaluated. RESULTS: A series of aromatic sulfonamide compounds was found to be novel, potent inhibitors of IDH1(R132H) with Ki values as low as 0.6 µM. Structure-activity relationships of these compounds are discussed. Enzyme kinetics studies showed that one compound is a competitive inhibitor against the substrate α-KG and a non-competitive inhibitor against the cofactor NADPH. Several inhibitors were found to have no activity against wild-type IDH1, showing a high selectivity. Two potent inhibitors exhibited strong activity against proliferation of BT142 glioma cells with IDH1 R132H mutation, while these compounds did not significantly affect the growth of glioma cells without IDH1 mutation. CONCLUSION: This novel series of IDH1(R132H) inhibitors have potential to be further developed for the treatment of glioma with IDH1 mutation.


Subject(s)
Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Isocitrate Dehydrogenase/antagonists & inhibitors , Isocitrate Dehydrogenase/genetics , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Survival/drug effects , Enzyme Inhibitors , Gene Expression Regulation, Enzymologic/drug effects , Humans , Molecular Structure , Mutation , Structure-Activity Relationship
17.
PLoS One ; 12(2): e0170301, 2017.
Article in English | MEDLINE | ID: mdl-28158205

ABSTRACT

Post-translational modifications of histone play important roles in gene transcription. Aberrant methylation of histone lysine sidechains have been often found in cancer. Lysine specific demethylase 1 (LSD1), which can demethylate histone H3 lysine 4 (H3K4) and other proteins, has recently been found to be a drug target for acute myeloid leukemia. To understand structure activity/selectivity relationships of LSD1 inhibitors, several series of cyclopropylamine and related compounds were synthesized and tested for their activities against LSD1 and related monoamine oxidase (MAO) A and B. Several cyclopropylamine containing compounds were found to be highly potent and selective inhibitors of LSD1. A novel series cyclopropylimine compounds also exhibited strong inhibitory activity against LSD1. Structure activity relationships (SAR) of these compounds are discussed. Docking studies were performed to provide possible binding models of a representative compound in LSD1 and MAO-A. Moreover, these modeling studies can rationalize the observed SARs and selectivity.


Subject(s)
Histone Demethylases/antagonists & inhibitors , Histone Demethylases/metabolism , Monoamine Oxidase Inhibitors/chemistry , Cyclopropanes/chemistry , Cyclopropanes/pharmacology , Histone Demethylases/chemistry , Histones/metabolism , Humans , Kinetics , Monoamine Oxidase/chemistry , Monoamine Oxidase/metabolism , Monoamine Oxidase Inhibitors/pharmacology , Protein Processing, Post-Translational , Structure-Activity Relationship
18.
J Hematol Oncol ; 9(1): 49, 2016 06 17.
Article in English | MEDLINE | ID: mdl-27316347

ABSTRACT

Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.


Subject(s)
DNA Methylation , Histones/genetics , Neoplasms/drug therapy , DNA Methylation/drug effects , Enzyme Inhibitors/therapeutic use , Epigenesis, Genetic , Histones/metabolism , Methyltransferases/antagonists & inhibitors
19.
J Hematol Oncol ; 9: 24, 2016 Mar 12.
Article in English | MEDLINE | ID: mdl-26970896

ABSTRACT

BACKGROUND: Mixed lineage leukemia (MLL) gene translocations are found in ~75% infant and 10% adult acute leukemia, showing a poor prognosis. Lysine-specific demethylase 1 (LSD1) has recently been implicated to be a drug target for this subtype of leukemia. More studies using potent LSD1 inhibitors against MLL-rearranged leukemia are needed. METHODS: LSD1 inhibitors were examined for their biochemical and biological activities against LSD1 and MLL-rearranged leukemia as well as other cancer cells. RESULTS: Potent LSD1 inhibitors with biochemical IC50 values of 9.8-77 nM were found to strongly inhibit proliferation of MLL-rearranged leukemia cells with EC50 of 10-320 nM, while these compounds are generally non-cytotoxic to several other tumor cells. LSD1 inhibition increased histone H3 lysine 4 (H3K4) methylation, downregulated expression of several leukemia-relevant genes, induced apoptosis and differentiation, and inhibited self-renewal of stem-like leukemia cells. Moreover, LSD1 inhibitors worked synergistically with inhibition of DOT1L, a histone H3 lysine 79 (H3K79) methyltransferase, against MLL-rearranged leukemia. The most potent LSD1 inhibitor showed significant in vivo activity in a systemic mouse model of MLL-rearranged leukemia without overt toxicities. Mechanistically, LSD1 inhibitors caused significant upregulation of several pathways that promote hematopoietic differentiation and apoptosis. CONCLUSIONS: LSD1 is a drug target for MLL-rearranged leukemia, and LSD1 inhibitors are potential therapeutics for the malignancy.


Subject(s)
Enzyme Inhibitors/pharmacology , Gene Rearrangement , Histone Demethylases/antagonists & inhibitors , Histone-Lysine N-Methyltransferase/genetics , Leukemia/drug therapy , Myeloid-Lymphoid Leukemia Protein/genetics , Animals , Blotting, Western , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , Child , Drug Synergism , Enzyme Inhibitors/chemistry , Gene Expression Regulation, Leukemic/drug effects , Histone Demethylases/genetics , Histone Demethylases/metabolism , Histones/metabolism , Humans , Leukemia/genetics , Leukemia/metabolism , Lysine/metabolism , MCF-7 Cells , Methylation/drug effects , Methyltransferases/antagonists & inhibitors , Methyltransferases/genetics , Methyltransferases/metabolism , Mice, Inbred NOD , Mice, SCID , Molecular Structure , Monoamine Oxidase Inhibitors/chemistry , Monoamine Oxidase Inhibitors/pharmacology , Reverse Transcriptase Polymerase Chain Reaction , U937 Cells , Xenograft Model Antitumor Assays
20.
Alkaloids Chem Biol ; 76: 1-61, 2016.
Article in English | MEDLINE | ID: mdl-26827882

ABSTRACT

The biosynthetic pathway of the monoterpenoid indole alkaloid ajmaline in the genus Rauvolfia, in particular Rauvolfia serpentina Benth. ex Kurz, is one of the few pathways that have been comprehensively uncovered. Every step in the progress of plant alkaloid biosynthesis research is due to the endeavors of several generations of scientists and the advancement of technologies. The tissue and cell suspension cultures developed in the 1970s by M.H. Zenk enabled the extraction of alkaloids and crude enzymes for use as experimental materials, thus establishing the foundation for further research on enzymatic reaction networks. In vivo NMR technology was first used in biosynthetic investigations in the 1990s following the invention of high-field cryo-NMR, which allowed the rapid and reliable detection of bioconversion processes within living plant cells. Shortly before, in 1988, a milestone was reached with the heterologous expression of the strictosidine synthase cDNA, which paved the way for the application of "reverse genetics" and "macromolecular crystallography." Both methods allowed the structural analysis of several Rauvolfia enzymes involved in ajmaline biosynthesis and expanded our knowledge of the enzyme mechanisms, substrate specificities, and structure-activity relationships. It also opened the door for rational enzyme engineering and metabolic steering. Today, the research focus of ajmaline biosynthesis is shifting from "delineation" to "utilization." The Pictet-Spenglerase strictosidine synthase, strictosidine glucosidase, together with raucaffricine glucosidase, as pioneers in this area, have become useful tools to generate "privileged structures" and "diversity oriented" syntheses, which may help to construct novel scaffolds and to set up libraries of sarpagan-ajmalan-type alkaloids in chemo-enzymatic approaches.


Subject(s)
Ajmaline/biosynthesis , Indole Alkaloids/metabolism , Ajmaline/chemistry , Glucosidases/metabolism , Indole Alkaloids/chemistry , Magnetic Resonance Spectroscopy , Secologanin Tryptamine Alkaloids/chemistry , Secologanin Tryptamine Alkaloids/metabolism
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