1
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Liu P, Shi C, Qiu L, Shang D, Lu Z, Tu Z, Liu H. Menin signaling and therapeutic targeting in breast cancer. Curr Probl Cancer 2024; 51:101118. [PMID: 38968834 DOI: 10.1016/j.currproblcancer.2024.101118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
To date, mounting evidence have shown that patients with multiple endocrine neoplasia type 1 (MEN1) may face an increased risk for breast carcinogenesis. The product of the MEN1 gene, menin, was also indicated to be an important regulator in breast cancer signaling network. Menin directly interacts with MLL, EZH2, JunD, NF-κB, PPARγ, VDR, Smad3, β-catenin and ERα to modulate gene transcriptions leading to cell proliferation inhibition. Moreover, interaction of menin-FANCD2 contributes to the enhancement of BRCA1-mediated DNA repair mechanism. Ectopic expression of menin causes Bax-, Bak- and Caspase-8-dependent apoptosis. However, despite numbers of menin inhibitors were exploited in other cancers, data on the usage of menin inhibitors in breast cancer treatment remain limited. In this review, we focused on the menin associated signaling pathways and gene transcription regulations, with the aim of elucidating its molecular mechanisms and of guiding the development of novel menin targeted drugs in breast cancer therapy.
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Affiliation(s)
- Peng Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Chaowen Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Lipeng Qiu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Dongsheng Shang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Ziwen Lu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Zhigang Tu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China.
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2
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Bai H, Yang Z, Lei H, Wu Y, Liu J, Yuan B, Ma M, Gao L, Zhang SQ, Xin M. Discovery of novel pyrrolo[2,3-d]pyrimidines as potent menin-mixed lineage leukemia interaction inhibitors. Eur J Med Chem 2024; 268:116226. [PMID: 38367493 DOI: 10.1016/j.ejmech.2024.116226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024]
Abstract
To interfere the Menin-MLL interaction using small molecular inhibitors has been shown as new treatment of several special hematological malignancies. Herein, a series of Menin-MLL interaction inhibitors with pyrrolo[2,3-d]pyrimidine scaffold were designed, synthesized and evaluated. Among them, compound A6 exhibited potent binding affinity with an IC50 value of 0.38 μM, and strong anti-proliferative activity against MV4-11 cells with an IC50 value of 1.07 μM. Further study showed A6 reduced the transcriptional levels of HOXA9 and MEIS1 genes. Moreover, A6 induced cellular apoptosis, arrested the cell cycle in G0/G1 phase, and reversed the differentiation arrest in a concentration-dependent manner. This study suggested compound A6 was as a novel potent Menin-MLL interaction inhibitor, and it proved that introduction of 4-amino pyrrolo[2,3-d]pyrimidine to occupy the P10 hydrophobic pocket was new idea for design of novel Menin-MLL interaction inhibitors.
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Affiliation(s)
- Huanrong Bai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Zhe Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Hao Lei
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yujie Wu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Jiaxin Liu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Bo Yuan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Mengyan Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Li Gao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - San-Qi Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Minhang Xin
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China.
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3
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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4
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Thomas X. Small Molecule Menin Inhibitors: Novel Therapeutic Agents Targeting Acute Myeloid Leukemia with KMT2A Rearrangement or NPM1 Mutation. Oncol Ther 2024; 12:57-72. [PMID: 38300432 PMCID: PMC10881917 DOI: 10.1007/s40487-024-00262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Recent advances have included insights into the clinical value of genomic abnormalities in acute myeloid leukemia (AML) and consequently the development of numerous targeted therapeutic agents that have improved clinical outcome. In this setting, various clinical trials have recently explored novel therapeutic agents either used alone or in combination with intensive chemotherapy or low-intensity treatments. Among them, menin inhibitors could represent a novel group of targeted therapies in AML driven by rearrangement of the lysine methyltransferase 2A (KMT2A) gene, previously known as mixed-lineage leukemia (MLL), or by mutation of the nucleophosmin 1 (NPM1) gene. Recent phase 1/2 clinical trials confirmed the efficacy of SNDX-5613 (revumenib) and KO-539 (ziftomenib) and their acceptable tolerability. Several small molecule menin inhibitors are currently being evaluated as a combination therapy with standard of care treatments. The current paper reviews the recent progress in exploring the inhibitors of menin-KMT2A interactions and their application prospects in the treatment of acute leukemias.
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Affiliation(s)
- Xavier Thomas
- Department of Clinical Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Bâtiment 1G, 165 Chemin du Grand Revoyet, 69495, Pierre-Bénite Cedex, France.
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5
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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6
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Lei H, Zhang SQ, Bai H, Zhao HY, Sun J, Chuai H, Xin M. Discovery of Novel, Potent, and Selective Small-Molecule Menin-Mixed Lineage Leukemia Interaction Inhibitors through Attempting Introduction of Hydrophilic Groups. J Med Chem 2022; 65:13413-13435. [PMID: 36173787 DOI: 10.1021/acs.jmedchem.2c01313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Introduction of the N,N-dimethylaminoethoxy group to pyrido[3,2-d]pyrimidine led to the discovery of menin-mixed lineage leukemia (MLL) interaction inhibitor C20. C20 showed strong binding affinity to menin protein and achieved sub-micromolar potency in cell growth inhibition. C20 had good selectivity for the inhibition of the interaction between menin and MLL in the kinase profile evaluation. Pharmacokinetic studies demonstrated that C20 possessed good stability and low clearance rate in liver microsomes and acceptable bioavailability in rats. Subsequent oral administration of C20 showed potent antitumor activity in the MV4;11 subcutaneous xenograft models of MLL-rearranged leukemia. The docking study showed that C20 bound highly with menin, and the N,N-dimethylaminoethoxy group occupied the F9 pocket of menin. This study proved that introducing a hydrophilic group into the F9 pocket of menin would be a new strategy for the design of menin-MLL interaction inhibitors with potent binding affinity and improved physical properties.
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Affiliation(s)
- Hao Lei
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - Huanrong Bai
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - Jiajia Sun
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - Hongyan Chuai
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi710061, P. R. China
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7
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Bai H, Zhang SQ, Lei H, Wang F, Ma M, Xin M. Menin-MLL protein-protein interaction inhibitors: a patent review (2014-2021). Expert Opin Ther Pat 2022; 32:507-522. [PMID: 35202550 DOI: 10.1080/13543776.2022.2045947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Chromosomal translocations involving the mixed-lineage leukemia (MLL, KMT2A, MLL1) genes result in the production of MLL fusion proteins, which cause abnormal transcriptional regulation leading to acute leukemia (AL). Menin (MEN1) protein is essential for MLL to regulate the expression of related target genes. High affinity interactions between the amino terminus of MLL proteins and Menin proteins are required to mediate the oncogenic transformation of MLL fusion proteins. Therefore, inhibition of Menin and MLL interaction is a potential therapeutic strategy for MLL rearrangement (MLL-r) leukemia and can provide a new choice for treatment of other diseases. Therefore, researchers have made great efforts to explore small molecule Menin-MLL interaction inhibitors. AREAS COVERED This review is to provide an overview of the patented Menin-MLL protein protein interaction inhibitors from 2014 to 2021. EXPERT OPINION Menin-MLL interaction inhibitors have therapeutic potential in the treatment of acute leukemia, such as acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Nowadays, SNDX-5613 and KO-539 have been granted orphan drug designation by the FDA for treatment of refractory/relapsed leukemia and AML, respectively. In addition, they are undergoing clinical evaluation for other indications. It is clear that Menin-MLL interaction inhibitors have promising benefits in the clinical treatment of acute leukemia and other diseases.
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Affiliation(s)
- Huanrong Bai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - San-Qi Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Hao Lei
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Fang Wang
- Hebei Chemical & Pharmaceutical College, Shijiazhuang 050000, P.R. China
| | - Mengyan Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Minhang Xin
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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8
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Lei H, Zhang SQ, Fan S, Bai HR, Zhao HY, Mao S, Xin M. Recent Progress of Small Molecule Menin-MLL Interaction Inhibitors as Therapeutic Agents for Acute Leukemia. J Med Chem 2021; 64:15519-15533. [PMID: 34726905 DOI: 10.1021/acs.jmedchem.1c00872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mixed lineage leukemia (MLL) gene rearrangements are associated with acute leukemia. The protein menin is regarded as a critical oncogenic cofactor of the resulting MLL fusion proteins in acute leukemia. A direct interaction between menin and the MLL amino terminal sequences is necessary for MLL fusion protein-mediated leukemogenesis. Thus, inhibition of the interaction between menin and MLL has emerged as a novel therapeutic strategy. Recent improvements in structural biology and chemical reactivity have promoted the design and development of selective and potent menin-MLL interaction inhibitors. In this Perspective, different classes of menin-MLL interaction inhibitors are comprehensively summarized. Further research potential, challenges, and opportunities in the field are also discussed.
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Affiliation(s)
- Hao Lei
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Shu Fan
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Huan-Rong Bai
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Shuai Mao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, PR China
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9
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Zhang M, Aguilar A, Xu S, Huang L, Chinnaswamy K, Sleger T, Wang B, Gross S, Nicolay BN, Ronseaux S, Harvey K, Wang Y, McEachern D, Kirchhoff PD, Liu Z, Stuckey J, Tron AE, Liu T, Wang S. Discovery of M-1121 as an Orally Active Covalent Inhibitor of Menin-MLL Interaction Capable of Achieving Complete and Long-Lasting Tumor Regression. J Med Chem 2021; 64:10333-10349. [PMID: 34196551 DOI: 10.1021/acs.jmedchem.1c00789] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the menin-MLL protein-protein interaction is being pursued as a new therapeutic strategy for the treatment of acute leukemia carrying MLL-rearrangements (MLLr leukemia). Herein, we report M-1121, a covalent and orally active inhibitor of the menin-MLL interaction capable of achieving complete and persistent tumor regression. M-1121 establishes covalent interactions with Cysteine 329 located in the MLL binding pocket of menin and potently inhibits growth of acute leukemia cell lines carrying MLL translocations with no activity in cell lines with wild-type MLL. Consistent with the mechanism of action, M-1121 drives dose-dependent down-regulation of HOXA9 and MEIS1 gene expression in the MLL-rearranged MV4;11 leukemia cell line. M-1121 is orally bioavailable and shows potent antitumor activity in vivo with tumor regressions observed at tolerated doses in the MV4;11 subcutaneous and disseminated models of MLL-rearranged leukemia. Together, our findings support development of an orally active covalent menin inhibitor as a new therapy for MLLr leukemia.
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Affiliation(s)
- Meng Zhang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Angelo Aguilar
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shilin Xu
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Liyue Huang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Taryn Sleger
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Bo Wang
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Stefan Gross
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Brandon N Nicolay
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Sebastien Ronseaux
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Kaitlin Harvey
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yu Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul D Kirchhoff
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhaomin Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Adriana E Tron
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Tao Liu
- Agios Pharmaceuticals, Inc., Cambridge, Massachusetts 02139, United States
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Medicinal Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Histone H3K4 Methyltransferases as Targets for Drug-Resistant Cancers. BIOLOGY 2021; 10:biology10070581. [PMID: 34201935 PMCID: PMC8301125 DOI: 10.3390/biology10070581] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022]
Abstract
The KMT2 (MLL) family of proteins, including the major histone H3K4 methyltransferase found in mammals, exists as large complexes with common subunit proteins and exhibits enzymatic activity. SMYD, another H3K4 methyltransferase, and SET7/9 proteins catalyze the methylation of several non-histone targets, in addition to histone H3K4 residues. Despite these structural and functional commonalities, H3K4 methyltransferase proteins have specificity for their target genes and play a role in the development of various cancers as well as in drug resistance. In this review, we examine the overall role of histone H3K4 methyltransferase in the development of various cancers and in the progression of drug resistance. Compounds that inhibit protein-protein interactions between KMT2 family proteins and their common subunits or the activity of SMYD and SET7/9 are continuously being developed for the treatment of acute leukemia, triple-negative breast cancer, and castration-resistant prostate cancer. These H3K4 methyltransferase inhibitors, either alone or in combination with other drugs, are expected to play a role in overcoming drug resistance in leukemia and various solid cancers.
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11
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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12
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Ozyerli‐Goknar E, Nizamuddin S, Timmers HTM. A Box of Chemistry to Inhibit the MEN1 Tumor Suppressor Gene Promoting Leukemia. ChemMedChem 2021; 16:1391-1402. [PMID: 33534953 PMCID: PMC8252030 DOI: 10.1002/cmdc.202000972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 12/30/2022]
Abstract
Targeting protein-protein interactions (PPIs) with small-molecule inhibitors has become a hotbed of modern drug development. In this review, we describe a new class of PPI inhibitors that block menin from binding to MLL proteins. Menin is encoded by the MEN1 tumor suppressor, but acts as an essential cofactor for MLL/KMT2A-rearranged leukemias. The most promising menin-MLL inhibitors belong to the thienopyrimidine class and have recently entered phase I/II clinical trials for treating acute leukemias characterized by MLL/KMT2A translocations or NPM1 mutations. As single agents, thienopyrimidine compounds eradicate leukemia in a xenograft models of primary leukemic cells belonging to the MLL-rearranged or NPM1-mutant subtypes. These compounds are well tolerated with few or no side effects, which is remarkable given the tumor-suppressor function of menin. The menin-MLL inhibitors highlight how leukemia patients could benefit from a targeted epigenetic therapy with novel PPI inhibitors obtained by directed chemical evolution.
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Affiliation(s)
- Ezgi Ozyerli‐Goknar
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
| | - H. T. Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg German Cancer Research Center (DKFZ) Medical Center-University of Freiburg, Department of UrologyBreisacherstrasse 6679016FreiburgGermany
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13
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Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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14
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Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. J Am Chem Soc 2021; 143:3779-3793. [DOI: 10.1021/jacs.0c09799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Nakadai M, Tomida S. Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein-Protein Interactions. J Chem Inf Model 2020; 60:4785-4790. [PMID: 32808775 DOI: 10.1021/acs.jcim.0c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional (3D) molecular descriptors, including physicochemical and shape properties, for protein-protein interaction (PPI) interface inhibitors have become a topic of discussion. However, the relationships between such properties and binding free energy have not been adequately investigated. In this study, we focused on identifying key 3D molecular descriptors related to the binding free energy and/or the ligand efficiency (LE) of PPI interface inhibitors. A positive correlation was found between the binding free energy and the diameter (D) of cylindrical 3D molecules, in addition to a correlation between LE and D/heavy atom count (HAC). In addition, we showed a correlation between LE and D/HAC for macrocyclic compounds, suggesting that the present findings could be applied during assessments of the potential of macrocyclic PPI interface inhibitors in drug discovery processes.
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Affiliation(s)
- Masakazu Nakadai
- Genome Pharmaceutical Institute Company, Ltd., 1-27-8-1207 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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16
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Covalent and noncovalent constraints yield a figure eight-like conformation of a peptide inhibiting the menin-MLL interaction. Eur J Med Chem 2020; 207:112748. [PMID: 32882610 DOI: 10.1016/j.ejmech.2020.112748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 11/21/2022]
Abstract
The interaction between menin and mixed lineage leukemia (MLL) was identified as an interesting target for treating some cancers including acute leukemia. On the basis of the known crystal structure of the MBM1-menin complex (MBM - menin binding motif), several cyclic peptides were designed. Elaboration of the effective cyclization strategy using a metathesis reaction allowed for a successfully large number of derivatives to be obtained. Subsequent optimization of the loop size, as well as N-terminal, central and C-terminal parts of the studied peptides resulted in structures exhibiting low nanomolar activities. A crystal structure of an inhibitor-menin complex revealed a compact conformation of the ligand molecule, which is stabilized not only by the introduction of a covalent linker but also three intramolecular hydrogen bonds. The inhibitor adopts a figure eight-like conformation, which perfectly fits the cleft of menin. We demonstrated that the development of compact, miniprotein-like structures is a highly effective approach for inhibition of protein-protein interactions.
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17
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Xu S, Aguilar A, Huang L, Xu T, Zheng K, McEachern D, Przybranowski S, Foster C, Zawacki K, Liu Z, Chinnaswamy K, Stuckey J, Wang S. Discovery of M-808 as a Highly Potent, Covalent, Small-Molecule Inhibitor of the Menin-MLL Interaction with Strong In Vivo Antitumor Activity. J Med Chem 2020; 63:4997-5010. [PMID: 32338903 PMCID: PMC7981784 DOI: 10.1021/acs.jmedchem.0c00547] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Targeting the menin-MLL protein-protein interaction is a new therapeutic strategy for the treatment of acute leukemia carrying MLL fusion (MLL leukemia). We describe herein the structure-based optimization of a class of covalent menin inhibitors, which led to the discovery of M-808 (16) as a highly potent and efficacious covalent menin inhibitor. M-808 effectively inhibits leukemia cell growth at low nanomolar concentrations and is capable of achieving partial tumor regression in an MV4;11 xenograft tumor model in mice at a well-tolerated dose schedule. Determination of the co-crystal structure of M-808 in complex with menin provides a structural basis for their high-affinity, covalent interactions. M-808 represents a promising, covalent menin inhibitor for further optimization and evaluation toward developing a new therapy for the treatment of MLL leukemia.
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Affiliation(s)
- Shilin Xu
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Angelo Aguilar
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Liyue Huang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tianfeng Xu
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ke Zheng
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sally Przybranowski
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Caroline Foster
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kaitlin Zawacki
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhaomin Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States,Department of Medicinal Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States,Corresponding Author Phone: 1-734-615-0362;
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18
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Takahashi S, Yokoyama A. The molecular functions of common and atypical MLL fusion protein complexes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194548. [PMID: 32320750 DOI: 10.1016/j.bbagrm.2020.194548] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/19/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
Abstract
Mixed-lineage leukemia (MLL) fuses with a variety of partners to produce a functionally altered MLL complex that is not expressed in normal cells, which transforms normal hematopoietic progenitors into leukemia cells. Because more than 80 fusion partners have been identified to date, the molecular functions of MLL fusion protein complexes appear diverse. However, over the past decade, the common functions utilized for leukemic transformation have begun to be elucidated. It appears that most (if not all) MLL fusion protein complexes utilize the AF4/ENL/P-TEFb and DOT1L complexes to some extent. Based on an understanding of the underlying molecular mechanisms, several molecular targeting drugs are being developed, opening paths to novel therapies. Here, we review the recent progress made in identifying the molecular functions of various MLL fusions and categorize the numerous fusion partners into several functionally-distinct groups to help discern commonalities and differences among various MLL fusion protein complexes.
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Affiliation(s)
- Satoshi Takahashi
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan; Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan; National Cancer Center Research Institute, Tokyo, Japan.
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19
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Structure-Based Design, Synthesis and Bioactivity of a New Anti-TNFα Cyclopeptide. Molecules 2020; 25:molecules25040922. [PMID: 32093030 PMCID: PMC7071015 DOI: 10.3390/molecules25040922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
As opposed to small molecules, macrocyclic peptides possess a large surface area and are recognised as promising candidates to selectively treat diseases by disrupting specific protein–protein interactions (PPIs). Due to the difficulty in predicting cyclopeptide conformations in solution, the de novo design of bioactive cyclopeptides remains significantly challenging. In this study, we used the combination of conformational analyses and molecular docking studies to design a new cyclopeptide inhibitor of the interaction between the human tumour necrosis factor alpha (TNFα) and its receptor TNFR-1. This interaction is a key in mediating the inflammatory response to tissue injury and infection in humans, and it is also an important causative factor of rheumatoid arthritis, psoriasis and inflammatory bowel disease. The solution state NMR structure of the cyclopeptide was determined, which helped to deduce its mode of interaction with TNFα. TNFα sensor cells were used to evaluate the biological activity of the peptide.
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20
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Caswell RC, Owens MM, Gunning AC, Ellard S, Wright CF. Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1. J Endocr Soc 2019; 3:2258-2275. [PMID: 31737856 PMCID: PMC6846327 DOI: 10.1210/js.2019-00260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022] Open
Abstract
Despite the rapid expansion in recent years of databases reporting either benign or pathogenic genetic variations, the interpretation of novel missense variants remains challenging, particularly for clinical or genetic testing laboratories where functional analysis is often unfeasible. Previous studies have shown that thermodynamic analysis of protein structure in silico can discriminate between groups of benign and pathogenic missense variants. However, although structures exist for many human disease‒associated proteins, such analysis remains largely unexploited in clinical laboratories. Here, we analyzed the predicted effect of 338 known missense variants on the structure of menin, the MEN1 gene product. Results provided strong discrimination between pathogenic and benign variants, with a threshold of >4 kcal/mol for the predicted change in stability, providing a strong indicator of pathogenicity. Subsequent analysis of seven novel missense variants identified during clinical testing of patients with MEN1 showed that all seven were predicted to destabilize menin by >4 kcal/mol. We conclude that structural analysis provides a useful tool in understanding the effect of missense variants in MEN1 and that integration of proteomic with genomic data could potentially contribute to the classification of novel variants in this disease.
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Affiliation(s)
- Richard C Caswell
- Institute of Biomedical and Clinical Science, University of Exeter School of Medicine, Exeter, United Kingdom
| | - Martina M Owens
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Adam C Gunning
- Institute of Biomedical and Clinical Science, University of Exeter School of Medicine, Exeter, United Kingdom
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
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21
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Ye F, Huang J, Wang H, Luo C, Zhao K. Targeting epigenetic machinery: Emerging novel allosteric inhibitors. Pharmacol Ther 2019; 204:107406. [PMID: 31521697 DOI: 10.1016/j.pharmthera.2019.107406] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Epigenetics has emerged as an extremely exciting fast-growing area of biomedical research in post genome era. Epigenetic dysfunction is tightly related with various diseases such as cancer and aging related degeneration, potentiating epigenetics modulators as important therapeutics targets. Indeed, inhibitors of histone deacetylase and DNA methyltransferase have been approved for treating blood tumor malignancies, whereas inhibitors of histone methyltransferase and histone acetyl-lysine recognizer bromodomain are in clinical stage. However, it remains a great challenge to discover potent and selective inhibitors by targeting catalytic site, as the same subfamily of epigenetic enzymes often share high sequence identity and very conserved catalytic core pocket. It is well known that epigenetic modifications are usually carried out by multi-protein complexes, and activation of catalytic subunit is often tightly regulated by other interactive protein component, especially in disease conditions. Therefore, it is not unusual that epigenetic complex machinery may exhibit allosteric regulation site induced by protein-protein interactions. Targeting allosteric site emerges as a compelling alternative strategy to develop epigenetic drugs with enhanced druggability and pharmacological profiles. In this review, we highlight recent progress in the development of allosteric inhibitors for epigenetic complexes through targeting protein-protein interactions. We also summarized the status of clinical applications of those inhibitors. Finally, we provide perspectives of future novel allosteric epigenetic machinery modulators emerging from otherwise undruggable single protein target.
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Affiliation(s)
- Fei Ye
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jing Huang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Cheng Luo
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, South Dong Qing Road, Guizhou 550025, China.
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
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22
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Cicaloni V, Trezza A, Pettini F, Spiga O. Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019; 19:534-554. [PMID: 30836920 DOI: 10.2174/1568026619666190304153901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/02/2019] [Accepted: 01/25/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Identification of Protein-Protein Interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. OBJECTIVE Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. METHODS Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. RESULTS In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/ inhibitor molecules. CONCLUSION A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention.
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Affiliation(s)
- Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy.,Toscana Life Sciences Foundation, via Fiorentina 1, 53100 Siena, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Francesco Pettini
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
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23
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Micewicz ED, Nguyen C, Micewicz A, Waring AJ, McBride WH, Ruchala P. Position of lipidation influences anticancer activity of Smac analogs. Bioorg Med Chem Lett 2019; 29:1628-1635. [PMID: 31047753 PMCID: PMC6625762 DOI: 10.1016/j.bmcl.2019.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 10/26/2022]
Abstract
A small group of lipid-conjugated Smac mimetics was synthesized to probe the influence of the position of lipidation on overall anti-cancer activity. Specifically, new compounds were modified with lipid(s) in position 3 and C-terminus. Previously described position 2 lipidated analog M11 was also synthesized. The resulting mini library of Smacs lipidated in positions 2, 3 and C-terminus was screened extensively in vitro against a total number of 50 diverse cancer cell lines revealing that both the position of lipidation as well as the type of lipid, influence their anti-cancer activity and cancer type specificity. Moreover, when used in combination therapy with inhibitor of menin-MLL1 protein interactions, position 2 modified analog SM2 showed strong synergistic anti-cancer properties. The most promising lipid-conjugated analogs SM2 and SM6, showed favorable pharmacokinetics and in vivo activity while administered subcutaneously in the preclinical mouse model. Collectively, our findings suggest that lipid modification of Smacs may be a viable approach in the development of anti-cancer therapeutic leads.
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Affiliation(s)
- Ewa D Micewicz
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Christine Nguyen
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alina Micewicz
- David Geffen School of Medicine at UCLA, Volunteering Program, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alan J Waring
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1000 West Carson Street, Torrance, CA 90502, USA
| | - William H McBride
- Department of Radiation Oncology, University of California at Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Piotr Ruchala
- Department of Psychiatry and Biobehavioral Sciences, University of California at Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90024, USA; The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, 760 Westwood Plaza, Los Angeles, CA 90024, USA.
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24
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Aguilar A, Zheng K, Xu T, Xu S, Huang L, Fernandez-Salas E, Liu L, Bernard D, Harvey KP, Foster C, McEachern D, Stuckey J, Chinnaswamy K, Delproposto J, Kampf JW, Wang S. Structure-Based Discovery of M-89 as a Highly Potent Inhibitor of the Menin-Mixed Lineage Leukemia (Menin-MLL) Protein-Protein Interaction. J Med Chem 2019; 62:6015-6034. [PMID: 31244110 DOI: 10.1021/acs.jmedchem.9b00021] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Inhibition of the menin-mixed lineage leukemia (MLL) protein-protein interaction is a promising new therapeutic strategy for the treatment of acute leukemia carrying MLL fusion (MLL leukemia). We describe herein our structure-based design, synthesis, and evaluation of a new class of small-molecule inhibitors of the menin-MLL interaction (hereafter called menin inhibitors). Our efforts have resulted in the discovery of highly potent menin inhibitors, as exemplified by compound 42 (M-89). M-89 binds to menin with a Kd value of 1.4 nM and effectively engages cellular menin protein at low nanomolar concentrations. M-89 inhibits cell growth in the MV4;11 and MOLM-13 leukemia cell lines carrying MLL fusion with IC50 values of 25 and 55 nM, respectively, and demonstrates >100-fold selectivity over the HL-60 leukemia cell line lacking MLL fusion. The determination of a co-crystal structure of M-89 in a complex with menin provides the structural basis for their high-affinity interaction. Further optimization of M-89 may lead to a new class of therapy for the treatment of MLL leukemia.
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25
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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26
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In-solution enrichment identifies peptide inhibitors of protein-protein interactions. Nat Chem Biol 2019; 15:410-418. [PMID: 30886434 DOI: 10.1038/s41589-019-0245-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
The use of competitive inhibitors to disrupt protein-protein interactions (PPIs) holds great promise for the treatment of disease. However, the discovery of high-affinity inhibitors can be a challenge. Here we report a platform for improving the affinity of peptide-based PPI inhibitors using non-canonical amino acids. The platform utilizes size exclusion-based enrichment from pools of synthetic peptides (1.5-4 kDa) and liquid chromatography-tandem mass spectrometry-based peptide sequencing to identify high-affinity binders to protein targets, without the need for 'reporter' or 'encoding' tags. Using this approach-which is inherently selective for high-affinity binders-we realized gains in affinity of up to ~100- or ~30-fold for binders to the oncogenic ubiquitin ligase MDM2 or HIV capsid protein C-terminal domain, which inhibit MDM2-p53 interaction or HIV capsid protein C-terminal domain dimerization, respectively. Subsequent macrocyclization of select MDM2 inhibitors rendered them cell permeable and cytotoxic toward cancer cells, demonstrating the utility of the identified compounds as functional PPI inhibitors.
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Chen QB, Gao J, Zou GA, Xin XL, Aisa HA. Piperidine Alkaloids with Diverse Skeletons from Anacyclus pyrethrum. JOURNAL OF NATURAL PRODUCTS 2018; 81:1474-1482. [PMID: 29775308 DOI: 10.1021/acs.jnatprod.8b00239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fifteen new piperidine derivatives, pyracyclumines A-J (1-10), including five pairs of enantiomers, (+)-1/(-)-1 to (+)-5/(-)-5, together with three known compounds, agrocybenine (11), 4,6,6-trimethyl-5,6-dihydro-2(1 H)-pyridone (12), and 3,5,5-trimethyl-1,5-dihydro-2 H-pyrrol-2-one (13), were isolated from the roots of Anacyclus pyrethrum. Pyracyclumines A, B, and H (1, 2, and 8) possess a novel 6/5/6/6 dimeric piperidine skeleton, a unique 6/5/6 dimeric piperidine skeleton, and a 1,4,6-triazaindan skeleton, respectively. Pyracyclumine C (3) is based on a rare cyclopentane-piperidine framework. The structures of the isolated compounds were established by analysis of their NMR and HRESIMS data. The racemic pyracyclumines A-E (1-5) were further separated by chiral HPLC to give the enantiomers (+)-1/(-)-1 to (+)-5/(-)-5, for which the absolute configurations were determined by comparison of their experimental and calculated ECD spectra. The plausible biogenetic pathways of these piperidine alkaloids were proposed starting from the basic units of compounds 12 and 13. All of the isolated compounds were tested for their inhibitory effects on menin-mixed lineage leukemia 1 protein-protein interaction.
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Affiliation(s)
- Qi-Bin Chen
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , People's Republic of China
| | - Jie Gao
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , People's Republic of China
| | - Guo-An Zou
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , People's Republic of China
| | - Xue-Lei Xin
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , People's Republic of China
| | - Haji Akber Aisa
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Urumqi 830011 , People's Republic of China
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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Bedewy W, Liao H, Abou-Taleb NA, Hammad SF, Nasr T, Pei D. Generation of a cell-permeable cycloheptapeptidyl inhibitor against the peptidyl-prolyl isomerase Pin1. Org Biomol Chem 2018; 15:4540-4543. [PMID: 28517007 DOI: 10.1039/c7ob00430c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cyclic peptides are capable of binding and modulating challenging drug targets including protein-protein interactions. However, their lack of membrane permeability prevents their application against intracellular targets. In this study, we show that it is possible to design a cell-permeable and biologically active cycloheptapeptide inhibitor against the intracellular enzyme peptidyl-prolyl isomerase Pin1 by integrating cell-penetrating and target-binding sequences.
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Affiliation(s)
- Walaa Bedewy
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
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Munikumar M, Krishna VS, Reddy VS, Rajeswari B, Sriram D, Rao MV. In silico design of small peptides antagonist against leptin receptor for the treatment of obesity and its associated immune-mediated diseases. J Mol Graph Model 2018; 82:20-36. [PMID: 29649778 DOI: 10.1016/j.jmgm.2018.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Excess adiposity in obese inhibits negatively impacts immune function and host defence. Obesity is characterized by a state of low-grade, chronic inflammation in addition to disturbed levels of circulating nutrients and metabolic hormones. The impact of metabolic abnormalities on obesity-related co-morbidities has undergone intense scrutiny over the past decades. Thus, treatment of obesity and its associated immune-mediated diseases is challenging due to impaired function of leptin system. These disorders are managed through antibiotics and by cytokines replacement. However, the effectiveness of cytokines coupled to the complexity of the cytokine network leads to severe side-effects, which can still occur after careful preclinical evaluation. In addition, synthetic immunotherapeutics carry a degree of risk, time-consuming and expensive. Hence, the complexity of existing therapy and adverse effects emphasizes the need for an alternative approach for the management of immune dysfunction associated with obesity. Computer-aided small molecule antibody technology has been successful in the design of novel biologicals for the diagnosis of diseases and therapeutic interventions. In this study, the crystal structure of leptin receptor (LEPR) complex with monoclonal antibody (9F8 Fab) was explored to predict Ag-Ab interactions using bioinformatics tools. The LEPR of complementarity-determining region (CDR) loops were mutated with published positive control residues of Ser, Thr, Tyr, Trp, and Phe to design a set of 678 peptides which were evaluated through Ag-peptide docking, binding free-energies, and interaction energies. Thus, hypothesized novel peptides can be explored as clinically applicable antagonists for the treatment of obesity and associated immune-mediated diseases.
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Affiliation(s)
- Manne Munikumar
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India.
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | | | - Bolla Rajeswari
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | - Mendu Vishnuvardhana Rao
- National Institute of Medical Statistics, Indian Council of Medical Research, (ICMR), Ansari Nagar, New Delhi, 110029, India
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Xu S, Aguilar A, Xu T, Zheng K, Huang L, Stuckey J, Chinnaswamy K, Bernard D, Fernández‐Salas E, Liu L, Wang M, McEachern D, Przybranowski S, Foster C, Wang S. Design of the First‐in‐Class, Highly Potent Irreversible Inhibitor Targeting the Menin‐MLL Protein–Protein Interaction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shilin Xu
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Angelo Aguilar
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Tianfeng Xu
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Ke Zheng
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Liyue Huang
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Jeanne Stuckey
- Life Sciences Institute University of Michigan 210 Washtenaw Ann Arbor MI 48109 USA
| | | | - Denzil Bernard
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Ester Fernández‐Salas
- Department of Pathology University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Liu Liu
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Mi Wang
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Donna McEachern
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Sally Przybranowski
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Caroline Foster
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Shaomeng Wang
- Comprehensive Cancer and Departments of Internal Medicine Pharmacology and Medicinal Chemistry University of Michigan 1600 Huron Parkway Ann Arbor MI 48109 USA
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Xu S, Aguilar A, Xu T, Zheng K, Huang L, Stuckey J, Chinnaswamy K, Bernard D, Fernández-Salas E, Liu L, Wang M, McEachern D, Przybranowski S, Foster C, Wang S. Design of the First-in-Class, Highly Potent Irreversible Inhibitor Targeting the Menin-MLL Protein-Protein Interaction. Angew Chem Int Ed Engl 2018; 57:1601-1605. [PMID: 29284071 DOI: 10.1002/anie.201711828] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Indexed: 01/03/2023]
Abstract
The structure-based design of M-525 as the first-in-class, highly potent, irreversible small-molecule inhibitor of the menin-MLL interaction is presented. M-525 targets cellular menin protein at sub-nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL-regulated gene expression in MLL leukemia cells. M-525 demonstrates high cellular specificity over non-MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co-crystal structure of M-525 in complex with menin firmly establish its mode of action. A single administration of M-525 effectively suppresses MLL-regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M-525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.
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Affiliation(s)
- Shilin Xu
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Angelo Aguilar
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Tianfeng Xu
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Ke Zheng
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Liyue Huang
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, 210 Washtenaw, Ann Arbor, MI, 48109, USA
| | | | - Denzil Bernard
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Ester Fernández-Salas
- Department of Pathology, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Liu Liu
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Mi Wang
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Donna McEachern
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Sally Przybranowski
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Caroline Foster
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
| | - Shaomeng Wang
- Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA
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Castelli G, Pelosi E, Testa U. Targeting histone methyltransferase and demethylase in acute myeloid leukemia therapy. Onco Targets Ther 2017; 11:131-155. [PMID: 29343972 PMCID: PMC5749389 DOI: 10.2147/ott.s145971] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome. In fact, genes involved in DNA demethylation (such as DNMT3A, TET2, IDH1, and IDH2) or histone methylation and demethylation (EZH2, MLL, DOT1L) are frequently mutated in primary and secondary AML. Furthermore, some histone demethylases, such as LSD1, are frequently overexpressed in AML. These observations have strongly supported a major role of dysregulated epigenetic regulatory processes in leukemia onset and development. This conclusion was further supported by the observation that mutations in genes encoding epigenetic modifiers, such as DMT3A, ASXL1, TET2, IDH1, and IDH2, are usually acquired early and are present in the founding leukemic clone. These observations have contributed to development of the idea that targeting epigenetic abnormalities could represent a potentially promising strategy for the development of innovative treatments of AML. In this review, we analyze those proteins and their inhibitors that have already reached the first stages of clinical trials in AML, namely the histone methyltransferase DOT1L, the demethylase LSD1, and the MLL-interacting protein menin.
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Affiliation(s)
- Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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Chen QB, Aisa HA. Alkaloid constituents from Viola tianschanica. PHYTOCHEMISTRY 2017; 144:233-242. [PMID: 28985571 DOI: 10.1016/j.phytochem.2017.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/11/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Eighteen previously undescribed alkaloids, tishaviolamines A-J, including eight pairs of enantiomers, together with two known benzylisoquinoline alkaloids, (-)-bicuculline and (-)-corlumine, were isolated from Viola tianschanica. Among them, tishaviolamine A-E were demonstrated to possess three types of unpresented skeletons. The structures of these alkaloids were established by comprehensive analyses of the 1D, 2D-NMR and (+)HRESIMS data. The absolute configurations of enantiomers were determined by comparing their calculated ECD spectra with the experimental ones. The menin-mixed lineage leukemia 1 protein-protein interaction inhibitory effect of the isolated compounds were also measured.
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Affiliation(s)
- Qi-Bin Chen
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Haji Akber Aisa
- Key Laboratory of Plant Resources and Chemistry in Arid Zone and State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, PR China.
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Wang ZH, Li DD, Chen WL, You QD, Guo XK. Targeting protein-protein interaction between MLL1 and reciprocal proteins for leukemia therapy. Bioorg Med Chem 2017; 26:356-365. [PMID: 29254892 DOI: 10.1016/j.bmc.2017.11.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022]
Abstract
The mixed lineage leukemia protein-1 (MLL1), as a lysine methyltransferase, predominantly regulates the methylation of histone H3 lysine 4 (H3K4) and functions in hematopoietic stem cell (HSC) self-renewal. MLL1 gene fuses with partner genes that results in the generation of MLL1 fusion proteins (MLL1-FPs), which are frequently detected in acute leukemia. In the progress of leukemogenesis, a great deal of proteins cooperate with MLL1 to form multiprotein complexes serving for the dysregulation of H3K4 methylation, the overexpression of homeobox (HOX) cluster genes, and the consequent generation of leukemia. Hence, disrupting the interactions between MLL1 and the reciprocal proteins has been considered to be a new treatment strategy for leukemia. Here, we reviewed potential protein-protein interactions (PPIs) between MLL1 and its reciprocal proteins, and summarized the inhibitors to target MLL1 PPIs. The druggability of MLL1 PPIs for leukemia were also discussed.
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Affiliation(s)
- Zhi-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Dong-Dong Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Wei-Lin Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiao-Ke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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36
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Qian Z, Dougherty PG, Pei D. Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides. Curr Opin Chem Biol 2017; 38:80-86. [PMID: 28388463 DOI: 10.1016/j.cbpa.2017.03.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for conventional drug modalities, because small molecules generally do not bind to their large, flat binding sites with high affinity, whereas monoclonal antibodies cannot cross the cell membrane to reach the targets. Cyclic peptides in the 700-2000 molecular-weight range have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat PPI interfaces with antibody-like affinity and specificity. Several powerful cyclic peptide library technologies were developed over the past decade to rapidly discover potent, specific cyclic peptide ligands against proteins of interest including those involved in PPIs. Methods are also being developed to enhance the membrane permeability of cyclic peptides through both passive diffusion and active transport mechanisms. Integration of the permeability-enhancing elements into cyclic peptide design has led to an increasing number of cell-permeable and biologically active cyclic peptides against intracellular PPIs. In this account, we review the recent developments in the design and synthesis of cell-permeable cyclic peptides.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Patrick G Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States.
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Vedadi M, Blazer L, Eram MS, Barsyte-Lovejoy D, Arrowsmith CH, Hajian T. Targeting human SET1/MLL family of proteins. Protein Sci 2017; 26:662-676. [PMID: 28160335 PMCID: PMC5368065 DOI: 10.1002/pro.3129] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 12/15/2022]
Abstract
The SET1 family of proteins, and in particular MLL1, are essential regulators of transcription and key mediators of normal development and disease. Here, we summarize the detailed characterization of the methyltransferase activity of SET1 complexes and the role of the key subunits, WDR5, RbBP5, ASH2L, and DPY30. We present new data on full kinetic characterization of human MLL1, MLL3, SET1A, and SET1B trimeric, tetrameric, and pentameric complexes to elaborate on substrate specificities and compare our findings with what has been reported before. We also review exciting recent work identifying potent inhibitors of oncogenic MLL1 function through disruption of protein–protein interactions within the MLL1 complex.
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Affiliation(s)
- Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
| | | | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7
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Lin W, Francis JM, Li H, Gao X, Pedamallu CS, Ernst P, Meyerson M. Kmt2a cooperates with menin to suppress tumorigenesis in mouse pancreatic islets. Cancer Biol Ther 2016; 17:1274-1281. [PMID: 27801610 PMCID: PMC5199165 DOI: 10.1080/15384047.2016.1250986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The reported incidence of pancreatic neuroendocrine tumors (PanNETs) has increased, due in large part to improvements in detection and awareness. However, therapeutic options are limited and a critical need exists for understanding a more thorough characterization of the molecular pathology underlying this disease. The Men1 knockout mouse model recapitulates the early stage of human PanNET development and can serve as a foundation for the development of advanced mouse models that are necessary for preclinical testing. Menin, the product of the MEN1 gene, has been shown to physically interact with the KMT2A and KMT2B histone methyltransferases. Both the KMT2A and MEN1 genes are located on chromosome 11q, which frequently undergoes loss of heterozygosity (LOH) in PanNETs. We report herein that inactivation of Kmt2a in Men1-deficient mice accelerated pancreatic islet tumorigenesis and shortened the average life span. Increases in cell proliferation were observed in mouse pancreatic islet tumors upon inactivation of both Kmt2a and Men1. The Kmt2a/Men1 double knockout mouse model can be used as a mouse model to study advanced PanNETs.
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Affiliation(s)
- Wenchu Lin
- a High Magnetic Field Laboratory, Chinese Academy of Sciences , Hefei , Anhui , P.R. China.,b Department of Medical Oncology & Center for Cancer Genome Discovery , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA
| | - Joshua M Francis
- b Department of Medical Oncology & Center for Cancer Genome Discovery , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA.,c Cancer Program, Broad Institute of Harvard and MIT , Cambridge , MA , USA
| | - Hong Li
- a High Magnetic Field Laboratory, Chinese Academy of Sciences , Hefei , Anhui , P.R. China
| | - Xiaoping Gao
- a High Magnetic Field Laboratory, Chinese Academy of Sciences , Hefei , Anhui , P.R. China
| | - Chandra Sekhar Pedamallu
- b Department of Medical Oncology & Center for Cancer Genome Discovery , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA.,c Cancer Program, Broad Institute of Harvard and MIT , Cambridge , MA , USA
| | - Patricia Ernst
- d Department of Pediatrics , The University of Colorado Anschutz Medical Campus , Aurora , USA
| | - Matthew Meyerson
- b Department of Medical Oncology & Center for Cancer Genome Discovery , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA.,c Cancer Program, Broad Institute of Harvard and MIT , Cambridge , MA , USA
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39
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Wang L, Li L, Fu WT, Jiang ZY, You QD, Xu XL. Optimization and bioevaluation of Cdc37-derived peptides: An insight into Hsp90-Cdc37 protein-protein interaction modulators. Bioorg Med Chem 2016; 25:233-240. [PMID: 27818030 DOI: 10.1016/j.bmc.2016.10.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/22/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
Targeting Hsp90-Cdc37 protein-protein interaction (PPI) is becoming an alternative approach for future anti-cancer drug development. We previously reported the discovery of an eleven-residue peptide (Pep-1) with micromolar activity for the disruption of Hsp90-Cdc37 PPI. Efforts to improve upon the Pep-1 led to the discovery of more potent modulators for Hsp90-Cdc37 PPI. Through the analysis of peptides binding patterns, more peptides were designed for further verification which resulted in Pep-5, the shortest peptide targeting Hsp90-Cdc37, exerting the optimal structure and the most efficient binding mode. Subsequent MD simulation analysis also confirmed that Pep-5 could perform more stable binding ability and better ligand properties than Pep-1. Under the premise of retentive binding capacity, Pep-5 exhibited lower molecular weight and higher ligand efficiency with a Kd value of 5.99μM (Pep-1 Kd=6.90μM) in both direct binding determination and biological evaluation. The optimal and shortest Pep-5 might provide a breakthrough and a better model for the future design of small molecule inhibitors targeting Hsp90-Cdc37 PPI.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li Li
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wei-Tao Fu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiao-Li Xu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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40
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Xu Y, Yue L, Wang Y, Xing J, Chen Z, Shi Z, Liu R, Liu YC, Luo X, Jiang H, Chen K, Luo C, Zheng M. Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening. J Chem Inf Model 2016; 56:1847-55. [PMID: 27513308 DOI: 10.1021/acs.jcim.6b00185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disrupting the interaction between mixed lineage leukemia (MLL) fusion protein and menin provides a therapeutic approach for MLL-mediated leukemia. Here, we aim to discover novel inhibitors targeting the menin-MLL interface with virtual screening. Both structure-based molecular docking and ligand-based pharmacophore models were established, and the models used for compound screening show a remarkable ability to retrieve known active ligands from decoy molecules. Verified by a fluorescence polarization assay, five hits with novel scaffolds were identified. Among them, DCZ_M123 exhibited potent inhibitory activity with an IC50 of 4.71 ± 0.12 μM and a KD of 14.70 ± 2.13 μM, and it can effectively inhibit the human MLL-rearranged leukemia cells MV4;11 and KOPN8 with GI50 values of 0.84 μM and 0.54 μM, respectively.
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Affiliation(s)
- Yuan Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Liyan Yue
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yulan Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jing Xing
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhifeng Chen
- School of Life Science and Technology, Shanghai Tech University , Shanghai 200031, China
| | - Zhe Shi
- Shanghai ChemPartner LifeScience Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Rongfeng Liu
- Shanghai ChemPartner LifeScience Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Yu-Chih Liu
- Shanghai ChemPartner LifeScience Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University , Shanghai 200031, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University , Shanghai 200031, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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41
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Ren J, Xu W, Tang L, Su M, Chen D, Chen YL, Zang Y, Li J, Shen J, Zhou Y, Xiong B. Design and synthesis of benzylpiperidine inhibitors targeting the menin-MLL1 interface. Bioorg Med Chem Lett 2016; 26:4472-4476. [PMID: 27528435 DOI: 10.1016/j.bmcl.2016.07.074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/07/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022]
Abstract
Menin is an essential oncogenic cofactor for mixed lineage leukemia (MLL)-mediated leukemogenesis, functioning through its direct interaction with MLL1 protein. Therefore, targeting the menin-MLL1 protein-protein interface represents a promising strategy to block MLL-mediated leukemogenesis. On the basis of co-crystal structure analysis, starting from thienopyrimidine chemotype, we have investigated the detailed structure-activity relationship of the piperazinyl-dihydrothiazole moiety. Several compounds were found with potent inhibitory activity against menin and better activities in cell-based experiments than MI-2-2. Molecular docking analysis revealed a less explored subpocket, which could be used for the design of new menin-MLL1 inhibitors.
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Affiliation(s)
- Jing Ren
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Wei Xu
- The National Center for Drug Screening, 189 Guoshoujing Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Le Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China
| | - Minbo Su
- The National Center for Drug Screening, 189 Guoshoujing Road, Shanghai 201203, PR China
| | - Danqi Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China
| | - Yue-Lei Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Yi Zang
- The National Center for Drug Screening, 189 Guoshoujing Road, Shanghai 201203, PR China
| | - Jia Li
- The National Center for Drug Screening, 189 Guoshoujing Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Jingkang Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Yubo Zhou
- The National Center for Drug Screening, 189 Guoshoujing Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China.
| | - Bing Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China.
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42
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Gao M, Cheng K, Yin H. Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 2016; 104:310-6. [PMID: 25664609 DOI: 10.1002/bip.22625] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) are critical in numerous biological processes including signaling transduction, function regulations, and disease development. To regulate PPIs has been thought to be challenging due to their highly dynamic and expansive interfacial areas. Nonetheless, successful examples have been reported of targeting PPIs using small molecules, peptides, and proteins. Peptides, especially macrocyclic peptides have proven to be a particularly useful tool to inhibit PPIs for their exquisite potency, stability and selectivity. Herein we review the recent developments of this area of research, focusing on the macrocyclic peptides isolated from natural products, identified from library screening, and rationally designed based on structures, as PPI regulators.
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Affiliation(s)
- Meng Gao
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Kui Cheng
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Hang Yin
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309-0596
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43
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Cai SF, Chen CW, Armstrong SA. Drugging Chromatin in Cancer: Recent Advances and Novel Approaches. Mol Cell 2016; 60:561-70. [PMID: 26590715 DOI: 10.1016/j.molcel.2015.10.042] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromatin regulatory mechanisms play a major role in the control of gene expression programs during normal development and are disrupted in specific disease states, particularly in cancer. Important mediators of chromatin regulatory processes can broadly be classified into writers, erasers, and readers of covalent chromatin modifications that modulate eukaryotic gene transcription and maintain the integrity of the genome. The reversibility and disease-specific nature of these chromatin states make these regulators attractive therapeutic targets. As such, there is an ever-increasing number of candidate therapies aimed at targeting cancer-associated chromatin states that are in various stages of preclinical and clinical development. In this review, we discuss recent advances that have been made in the rational therapeutic targeting of chromatin regulatory mechanisms and highlight certain cancers where there is a specific rationale to assess these therapeutic approaches.
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Affiliation(s)
- Sheng F Cai
- Cancer Biology and Genetics Program, Departments of Medicine and Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Wei Chen
- Cancer Biology and Genetics Program, Departments of Medicine and Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Departments of Medicine and Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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44
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Julian LM, Carpenedo RL, Rothberg JLM, Stanford WL. Formula G1: Cell cycle in the driver's seat of stem cell fate determination. Bioessays 2016; 38:325-32. [DOI: 10.1002/bies.201500187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lisa M. Julian
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
| | - Richard L. Carpenedo
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
| | - Janet L. Manias Rothberg
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
- Department of Cellular and Molecular Medicine; University of Ottawa; Ottawa ON Canada
| | - William L. Stanford
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
- Department of Cellular and Molecular Medicine; University of Ottawa; Ottawa ON Canada
- Department of Biochemistry; Microbiology and Immunology; University of Ottawa; Ottawa ON Canada
- Ottawa Institute of Systems Biology; Ottawa; Ontario Canada
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45
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Peptide-based inhibitors of protein–protein interactions. Bioorg Med Chem Lett 2016; 26:707-713. [DOI: 10.1016/j.bmcl.2015.12.084] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 12/22/2022]
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46
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Yue L, Du J, Ye F, Chen Z, Li L, Lian F, Zhang B, Zhang Y, Jiang H, Chen K, Li Y, Zhou B, Zhang N, Yang Y, Luo C. Identification of novel small-molecule inhibitors targeting menin–MLL interaction, repurposing the antidiarrheal loperamide. Org Biomol Chem 2016; 14:8503-19. [DOI: 10.1039/c6ob01248e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Scaffold hopping combines with biochemical studies and medicinal chemistry optimizations, leading to potent inhibitors of the menin–MLL interaction.
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47
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Singh S, Singh H, Tuknait A, Chaudhary K, Singh B, Kumaran S, Raghava GPS. PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct 2015; 10:73. [PMID: 26690490 PMCID: PMC4687368 DOI: 10.1186/s13062-015-0103-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/18/2015] [Indexed: 12/16/2022] Open
Abstract
Background In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natural and non-natural/modified residues. Results PEPstrMOD integrates Forcefield_NCAA and Forcefield_PTM force field libraries to handle 147 non-natural residues and 32 types of post-translational modifications respectively by performing molecular dynamics using AMBER. AMBER was also used to handle other modifications like peptide cyclization, use of D-amino acids and capping of terminal residues. In addition, GROMACS was used to implement 210 non-natural side-chains in peptides using SwissSideChain force field library. We evaluated the performance of PEPstrMOD on three datasets generated from Protein Data Bank; i) ModPep dataset contains 501 non-natural peptides, ii) ModPep16, a subset of ModPep, and iii) CyclicPep contains 34 cyclic peptides. We achieved backbone Root Mean Square Deviation between the actual and predicted structure of peptides in the range of 3.81–4.05 Å. Conclusions In summary, the method PEPstrMOD has been developed that predicts the structure of modified peptide from the sequence/structure given as input. We validated the PEPstrMOD application using a dataset of peptides having non-natural/modified residues. PEPstrMOD offers unique advantages that allow the users to predict the structures of peptides having i) natural residues, ii) non-naturally modified residues, iii) terminal modifications, iv) post-translational modifications, v) D-amino acids, and also allows extended simulation of predicted peptides. This will help the researchers to have prior structural information of modified peptides to further design the peptides for desired therapeutic property. PEPstrMOD is freely available at http://osddlinux.osdd.net/raghava/pepstrmod/. Reviewers This article was reviewed by Prof Michael Gromiha, Dr. Bojan Zagrovic and Dr. Zoltan Gaspari. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0103-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandeep Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - Harinder Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - Abhishek Tuknait
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - Kumardeep Chaudhary
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - Balvinder Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - S Kumaran
- CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
| | - Gajendra P S Raghava
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sec 39-A, Chandigarh, 160036, India.
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48
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Nguyen GKT, Kam A, Loo S, Jansson AE, Pan LX, Tam JP. Butelase 1: A Versatile Ligase for Peptide and Protein Macrocyclization. J Am Chem Soc 2015; 137:15398-401. [PMID: 26633100 DOI: 10.1021/jacs.5b11014] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Macrocyclization is a valuable tool for drug design and protein engineering. Although various methods have been developed to prepare macrocycles, a general and efficient strategy is needed. Here we report a highly efficient method using butelase 1 to macrocyclize peptides and proteins ranging in sizes from 26 to >200 residues. We achieved cyclizations that are 20,000 times faster than sortase A, the most widely used ligase for protein cyclization. The reactions completed within minutes with up to 95% yields.
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Affiliation(s)
- Giang K T Nguyen
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Antony Kam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Shining Loo
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Anna E Jansson
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Lucy X Pan
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
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49
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Pollock J, Borkin D, Lund G, Purohit T, Dyguda-Kazimierowicz E, Grembecka J, Cierpicki T. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J Med Chem 2015; 58:7465-74. [PMID: 26288158 PMCID: PMC4584387 DOI: 10.1021/acs.jmedchem.5b00975] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions.
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Affiliation(s)
- Jonathan Pollock
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dmitry Borkin
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - George Lund
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Trupta Purohit
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Edyta Dyguda-Kazimierowicz
- Molecular Modeling and Quantum Chemistry Group, Department of Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
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50
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Cierpicki T, Grembecka J. Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies? Immunol Rev 2015; 263:279-301. [PMID: 25510283 DOI: 10.1111/imr.12244] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Over the past several years, there has been an increasing research effort focused on inhibition of protein-protein interactions (PPIs) to develop novel therapeutic approaches for cancer, including hematologic malignancies. These efforts have led to development of small molecule inhibitors of PPIs, some of which already advanced to the stage of clinical trials while others are at different stages of preclinical optimization, emphasizing PPIs as an emerging and attractive class of drug targets. Here, we review several examples of recently developed inhibitors of PPIs highly relevant to hematologic cancers. We address the existing skepticism about feasibility of targeting PPIs and emphasize potential therapeutic benefit from blocking PPIs in hematologic malignancies. We then use these examples to discuss the approaches for successful identification of PPI inhibitors and provide analysis of the protein-protein interfaces, with the goal to address 'druggability' of new PPIs relevant to hematology. We discuss lessons learned to improve the success of targeting new PPIs and evaluate prospects and limits of the research in this field. We conclude that not all PPIs are equally tractable for blocking by small molecules, and detailed analysis of PPI interfaces is critical for selection of those with the highest chance of success. Together, our analysis uncovers patterns that should help to advance drug discovery in hematologic malignancies by successful targeting of new PPIs.
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Affiliation(s)
- Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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