1
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Zhan MM, Xing Y, Li Z, Yin F. A GSH-resistant FK228 analogue containing a stable disulfide bond. Bioorg Chem 2024; 144:107119. [PMID: 38219481 DOI: 10.1016/j.bioorg.2024.107119] [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] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
FK228 is a potent natural pan HDAC inhibitor approved by the FDA for the treatment of cutaneous T-cell lymphoma as well as peripheral T-cell lymphoma. It is generally believed that the mechanism of FK228 acting on HDACs is by reducing its disulfide bond after entering the cell, and the dithiol group may chelate with Zn2+ and form a weak reversible covalent bond with cysteine in the catalytic pocket of HDACs, therefore inhibiting the activity of HDACs. However, due to the weak stability of the disulfide bond in FK228, it has been difficult to obtain direct evidence for the above conjecture. Thus, improving the stability of the FK228 disulfide bond will help to explore the exact mechanism of FK228. In this study, based on the stability and target-induced covalent properties of the Cysteine-Penicillamine (Cys-Pen) disulfide bond reported previously, the Pen was introduced into the modification of FK228. Specifically, the d-Cys in FK228 was replaced by d-Pen, the total synthetic pathway was optimized, and the novel synthetic FK228 analogue (FK-P) stability was verified. FK-P can also be used as a new drug molecule in the future to participate in the research of related biological mechanisms or the treatment of diseases.
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Affiliation(s)
- Mei-Miao Zhan
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Yun Xing
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China.
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China.
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2
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Wahi A, Jain P, Sinhari A, Jadhav HR. Progress in discovery and development of natural inhibitors of histone deacetylases (HDACs) as anti-cancer agents. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:675-702. [PMID: 37615708 DOI: 10.1007/s00210-023-02674-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
The study of epigenetic translational modifications had drawn great interest for the last few decades. These processes play a vital role in many diseases and cancer is one of them. Histone acetyltransferase (HAT) and histone deacetylases (HDACs) are key enzymes involved in the acetylation and deacetylation of histones and ultimately in post-translational modifications. Cancer frequently exhibits epigenetic changes, particularly disruption in the expression and activity of HDACs. It includes the capacity to regulate proliferative signalling, circumvent growth inhibitors, escape cell death, enable replicative immortality, promote angiogenesis, stimulate invasion and metastasis, prevent immunological destruction, and genomic instability. The majority of tumours develop and spread as a result of HDAC dysregulation. As a result, HDAC inhibitors (HDACis) were developed, and they today stand as a very promising therapeutic approach. One of the most well-known and efficient therapies for practically all cancer types is chemotherapy. However, the efficiency and safety of treatment are constrained by higher toxicity. The same has been observed with the synthetic HDACi. Natural products, owing to many advantages over synthetic compounds for cancer treatment have always been a choice for therapy. Hence, naturally available molecules are of particular interest for HDAC inhibition and HDAC has drawn the attention of the research fraternity due to their potential to offer a diverse array of chemical structures and bioactive compounds. This diversity opens up new avenues for exploring less toxic HDAC inhibitors to reduce side effects associated with conventional synthetic inhibitors. The review presents comprehensive details on natural product HDACi, their mechanism of action and their biological effects. Moreover, this review provides a brief discussion on the structure activity relationship of selected natural HDAC inhibitors and their analogues which can guide future research to discover selective, more potent HDACi with minimal toxicity.
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Affiliation(s)
- Abhishek Wahi
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India.
| | - Apurba Sinhari
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
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3
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Kumar S, Arora A, Sapra S, Kumar R, Singh BK, Singh SK. Recent advances in the synthesis and utility of thiazoline and its derivatives. RSC Adv 2024; 14:902-953. [PMID: 38174252 PMCID: PMC10759189 DOI: 10.1039/d3ra06444a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Thiazolines and their derivatives hold significant importance in the field of medicinal chemistry due to their promising potential as pharmaceutical agents. These molecular entities serve as critical scaffolds within numerous natural products, including curacin A, thiangazole, and mirabazole, and play a vital role in a wide array of physiological reactions. Their pharmacological versatility encompasses anti-HIV, neurological, anti-cancer, and antibiotic activities. Over the course of recent decades, researchers have extensively explored and developed analogs of these compounds, uncovering compelling therapeutic properties such as antioxidant, anti-tumor, anti-microbial, and anti-inflammatory effects. Consequently, thiazoline-based compounds have emerged as noteworthy targets for synthetic endeavors. In this review, we provide a comprehensive summary of recent advancements in the synthesis of thiazolines and thiazoline-based derivatives, along with an exploration of their diverse potential applications across various scientific domains.
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Affiliation(s)
- Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Shivani Sapra
- Bioorganic Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Rajesh Kumar
- Department of Chemistry, R. D. S College, B. R. A. Bihar University Muzaffarpur 842002 India
| | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Sunil K Singh
- Department of Chemistry, Kirori Mal College, University of Delhi Delhi-110007 India
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4
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Novel histone deacetylase inhibitor CT-101 induces γ-globin gene expression in sickle erythroid progenitors with targeted epigenetic effects. Blood Cells Mol Dis 2022; 93:102626. [PMID: 34856533 PMCID: PMC9733664 DOI: 10.1016/j.bcmd.2021.102626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Induction of fetal hemoglobin (HbF) expression ameliorates the clinical severity and prolong survival in persons with sickle cell disease (SCD). Hydroxyurea (HU) is the only FDA-approved HbF inducer however, additional therapeutics that produce an additive effect in SCD are needed. To this end, development of potent Class I histone deacetylase inhibitors (HDACi) for HbF induction represents a rational molecularly targeted approach. In studies here, we evaluated CT-101, a novel Class I-restricted HDACi, a Largazole derivative, for pharmacodynamics, cytotoxicity, and targeted epigenetic effects. In SCD-derived erythroid progenitors, CT-101 induced HbF expression with additive activity in combination with HU. CT-101 preferentially activated γ-globin gene transcription, increased acetylated histone H3 levels, and conferred an open chromatin conformation in the γ-globin promoter. These data indicate CT-101 represents a strong potential candidate as a molecularly targeted inducer of HbF.
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5
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Zhu Y, Zhou B, Hu X, Ying S, Zhou Q, Xu W, Feng L, Hou T, Wang X, Zhu L, Jin H. LncRNA LINC00942 promotes chemoresistance in gastric cancer by suppressing MSI2 degradation to enhance c-Myc mRNA stability. Clin Transl Med 2022; 12:e703. [PMID: 35073459 PMCID: PMC8785984 DOI: 10.1002/ctm2.703] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chemoresistance to cisplatin (DDP) remains a major challenge in advanced gastric cancer (GC) treatment. Although accumulating evidence suggests an association between dysregulation of long non-coding RNAs (lncRNAs) and chemoresistance, the regulatory functions and complexities of lncRNAs in modulating DDP-based chemotherapy in GC remain under-investigated. This study was designed to explore the critical chemoresistance-related lncRNAs in GC and identify novel therapeutic targets for patients with chemoresistant GC. METHODS Chemoresistance-related lncRNAs were identified through microarray and verified through a quantitative real-time polymerase chain reaction (qRT-PCR). Proteins bound by lncRNAs were identified through a human proteome array and validated through RNA immunoprecipitation (RIP) and RNA pull-down assays. Co-immunoprecipitation and ubiquitination assays were performed to explore the molecular mechanisms of the Musashi2 (MSI2) post-modification. The effects of LINC00942 (LNC942) and MSI2 on DDP-based chemotherapy were investigated through MTS, apoptosis assays and xenograft tumour formation in vivo. RESULTS LNC942 was found to be up-regulated in chemoresistant GC cells, and its high expression was positively correlated with the poor prognosis of patients with GC. Functional studies indicated that LNC942 confers chemoresistance to GC cells by impairing apoptosis and inducing stemness. Mechanically, LNC942 up-regulated the MSI2 expression by preventing its interaction with SCFβ-TRCP E3 ubiquitin ligase, eventually inhibiting ubiquitination. Then, LNC942 stabilized c-Myc mRNA in an N6-methyladenosine (m6 A)-dependent manner. As a potential m6 A recognition protein, MSI2 stabilized c-Myc mRNA with m6 A modifications. Moreover, inhibition of the LNC942-MSI2-c-Myc axis was found to restore chemosensitivity both in vitro and in vivo. CONCLUSIONS These results uncover a chemoresistant accelerating function of LNC942 in GC, and disrupting the LNC942-MSI2-c-Myc axis could be a novel therapeutic strategy for GC patients undergoing chemoresistance.
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Affiliation(s)
- Yiran Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Bingluo Zhou
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Xinyang Hu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Shilong Ying
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Qiyin Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of MedicineZhejiang UniversityHangzhouChina
| | - Wenxia Xu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Lifeng Feng
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Tianlun Hou
- Department of Clinical MedicineWenzhou Medical UniversityWenzhouChina
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of MedicineZhejiang UniversityHangzhouChina
| | - Liyuan Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang ProvinceCancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
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6
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Wang TC, Zhu L, Luo S, Nong ZS, Wang PS, Gong LZ. Palladium-Catalyzed Enantioselective C(sp 3)-H/C(sp 3)-H Umpolung Coupling of N-Allylimine and α-Aryl Ketones. J Am Chem Soc 2021; 143:20454-20461. [PMID: 34817997 DOI: 10.1021/jacs.1c10721] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Asymmetric functionalization of the C(sp3)-H bond is an attractive yet challenging strategy to achieve versatile bond-forming events, enabling the precise assembly of molecular complexity with minimal manipulation of functional groups. Here, we report an asymmetric C(sp3)-H/C(sp3)-H umpolung coupling of N-allylimine and coordinating α-aryl carbonyls by using chiral phosphoramidite-palladium catalysis. A wide variety of α-heteroaryl ketones and 2-acylimidazoles are nicely tolerated to open a convenient and tunable avenue for efficient synthesis of enantioenriched β-amino-γ,δ-unsaturated carbonyl derivatives with high levels of regio- and stereoselectivities, capable of providing a key intermediate for asymmetric synthesis of Focalin. This protocol showcases an umpolung reactivity of the N-allylimines through a concerted proton and two-electron transfer process to cleave the allylic C-H bond, effectively complementing established methodology for allylic C-H functionalization. An inner-sphere allylation pathway for both α-heteroaryl carbonyls and 2-acylimidazoles to attack the π-allylpalladium species is suggested by computational studies and experimental facts, wherein the nitrogen coordination to the palladium center enables the preference of branched regioselectivity.
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Affiliation(s)
- Tian-Ci Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Ling Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Shiwei Luo
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Zhong-Sheng Nong
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Pu-Sheng Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Liu-Zhu Gong
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.,Center for Excellence in Molecular Synthesis of CAS, University of Science and Technology of China, Hefei 230026, China
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7
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Cruz DL, Pipalia N, Mao S, Gadi D, Liu G, Grigalunas M, O'Neill M, Quinn TR, Kipper A, Ekebergh A, Dimmling A, Gartner C, Melancon BJ, Wagner FF, Holson E, Helquist P, Wiest O, Maxfield FR. Inhibition of Histone Deacetylases 1, 2, and 3 Enhances Clearance of Cholesterol Accumulation in Niemann-Pick C1 Fibroblasts. ACS Pharmacol Transl Sci 2021; 4:1136-1148. [PMID: 34151204 PMCID: PMC8204796 DOI: 10.1021/acsptsci.1c00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Indexed: 11/29/2022]
Abstract
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Niemann-Pick disease type C1 (NPC1) is a rare genetic cholesterol storage disorder
caused by mutations in the NPC1 gene. Mutations in this transmembrane
late endosome protein lead to loss of normal cholesterol efflux from late endosomes and
lysosomes. It has been shown that broad spectrum histone deacetylase inhibitors
(HDACi's) such as Vorinostat correct the cholesterol accumulation phenotype in the
majority of NPC1 mutants tested in cultured cells. In order to determine the optimal
specificity for HDACi correction of the mutant NPC1s, we screened 76 HDACi's of varying
specificity. We tested the ability of these HDACi's to correct the excess accumulation
of cholesterol in patient fibroblast cells that homozygously express
NPC1I1061T, the most common mutation. We
determined that inhibition of HDACs 1, 2, and 3 is important for correcting the defect,
and combined inhibition of all three is needed to achieve the greatest effect,
suggesting a need for multiple effects of the HDACi treatments. Identifying the specific
HDACs involved in the process of regulating cholesterol trafficking in NPC1 will help to
focus the search for more specific druggable targets.
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Affiliation(s)
- Dana L Cruz
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Nina Pipalia
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Shu Mao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Deepti Gadi
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Gang Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Michael Grigalunas
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Matthew O'Neill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Taylor R Quinn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andi Kipper
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andreas Ekebergh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Alexander Dimmling
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carlos Gartner
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bruce J Melancon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Florence F Wagner
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Edward Holson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,KDAc Therapeutics, Cambridge, Massachusetts 02142, United States
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University, Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Frederick R Maxfield
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
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8
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Su M, Gong X, Liu F. An update on the emerging approaches for histone deacetylase (HDAC) inhibitor drug discovery and future perspectives. Expert Opin Drug Discov 2021; 16:745-761. [PMID: 33530771 DOI: 10.1080/17460441.2021.1877656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION HDACs catalyze the removal of acetyl groups from the ε-N-acetylated lysine residues of various protein substrates including both histone and nonhistone proteins. Different HDACs have distinct biological functions and are recruited to specific regions of the genome. HDAC inhibitors have attracted much attention in recent decades; indeed, there have been more than thirty HDAC inhibitors investigated in clinic trials with five approvals being achieved. AREAS COVERED This review covers the emerging approaches for HDAC inhibitor drug discovery from the past five years and includes discussion of structure-based rational design, isoform selectivity, and dual mechanism/multi-targeting. Chemical structures in addition to the in vitro and in vivo inhibiting activity of these compounds have also been discussed. EXPERT OPINION The exact role and biological functions of HDACs is still under investigation with a variety of HDAC inhibitors having been designed and evaluated. HDAC inhibitors have shown promise in treating cancer, AD, metabolic disease, viral infection, and multiple sclerosis, but there is still a lot of room for clinical improvement. In the future, more efforts should be put into (i) HDAC isoform identification (ii) the optimization of selectivity, activity, and pharmacokinetics; and (iii) unconventional approaches for discovering different effective scaffolds and pharmacophores.
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Affiliation(s)
- Ma Su
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
| | - Xingyu Gong
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
| | - Feng Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, PR China
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9
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Zang X, Peraro L, Davison RT, Blum TR, Vallabhaneni D, Fennell CE, Cramer SL, Shah HK, Wholly DM, Fink EA, Sivak JT, Ingalls KM, Herr CT, Lawson VE, Burnett MR, Slade DJ, Cole KE, Carle SA, Miller JS. Synthesis and Biological Evaluation of a Depsipeptidic Histone Deacetylase Inhibitor via a Generalizable Approach Using an Optimized Latent Thioester Solid-Phase Linker. J Org Chem 2020; 85:8253-8260. [DOI: 10.1021/acs.joc.0c00854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiaoyu Zang
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Leila Peraro
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Ryan T. Davison
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Travis R. Blum
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Deepak Vallabhaneni
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Caitlyn E. Fennell
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Stephanie L. Cramer
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Heli K. Shah
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Deirdre M. Wholly
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Elissa A. Fink
- Department of Molecular Biology and Chemistry, Christopher Newport University, Newport News, Virginia 23606, United States
| | - Jacob T. Sivak
- Department of Molecular Biology and Chemistry, Christopher Newport University, Newport News, Virginia 23606, United States
| | - Kathryn M. Ingalls
- Department of Molecular Biology and Chemistry, Christopher Newport University, Newport News, Virginia 23606, United States
| | - Chelsea T. Herr
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Vernon E. Lawson
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Matthew R. Burnett
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - David J. Slade
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Kathryn E. Cole
- Department of Molecular Biology and Chemistry, Christopher Newport University, Newport News, Virginia 23606, United States
| | - Sigrid A. Carle
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Justin S. Miller
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
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10
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Owens DK, Bajsa-Hirschel J, Duke SO, Carbonari CA, Gomes GLGC, Asolkar R, Boddy L, Dayan FE. The Contribution of Romidepsin to the Herbicidal Activity of Burkholderia rinojensis Biopesticide. JOURNAL OF NATURAL PRODUCTS 2020; 83:843-851. [PMID: 32091209 DOI: 10.1021/acs.jnatprod.9b00405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The culture broth of Burkholderia rinojensis strain A396 is herbicidal to a number of weed species with greater observed efficacy against broadleaf than grass weeds. A portion of this activity is attributed to romidepsin, a 16-membered cyclic depsipeptide bridged by a 15-membered macrocyclic disulfide. Romidepsin, which is present in small amounts in the broth (18 to 25 μg mL-1), was isolated and purified using standard chromatographic techniques. It was established that romidepsin is a natural proherbicide that targets the activity of plant histone deacetylases (HDAC). Assays to measure plant HDAC activity were optimized by testing a number of HDAC substrates. The activity of romidepsin was greater when its macrocyclic-forming disulfide bridge was reduced to liberate a highly reactive free butenyl thiol side chain. Reduction was achieved using 200 mM tris(2-carboxyethyl)phosphine hydrochloride. A similar bioactivation of the proherbicide via reduction of the disulfide bridge of romidepsin was observed in plant-cell-free extracts. Molecular dynamic simulation of the binding of romidepsin to Arabidopsis thaliana HDAC19 indicated the reduced form of the compound could reach deep inside the catalytic domain and interact with an associated zinc atom required for enzyme activity.
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Affiliation(s)
- Daniel K Owens
- Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, USDA-ARS, Thad Cochran Center, University Avenue, University, Mississippi 38677 United States
| | - Stephen O Duke
- Natural Products Utilization Research Unit, USDA-ARS, Thad Cochran Center, University Avenue, University, Mississippi 38677 United States
| | - Caio A Carbonari
- Faculty of Agronomic Sciences, São Paulo State University, Botucatu, 01049-010, SP, Brazil
| | - Giovanna L G C Gomes
- Faculty of Agronomic Sciences, São Paulo State University, Botucatu, 01049-010, SP, Brazil
| | - Ratnakar Asolkar
- Marrone Bio Innovations, 1540 Drew Avenue, Davis, California 95618, United States
| | - Louis Boddy
- Marrone Bio Innovations, 1540 Drew Avenue, Davis, California 95618, United States
| | - Franck E Dayan
- Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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11
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Discovery of class I histone deacetylase inhibitors based on romidpesin with promising selectivity for cancer cells. Future Med Chem 2020; 12:311-323. [DOI: 10.4155/fmc-2019-0290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: Class I histone deacetylases (HDACs) are considered to be promising anticancer targets, but selective inhibition of class I HDAC isoforms remains a challenge. Methods & results: Previously, we obtained a selective class I HDAC inhibitor 9 based on a macrocyclic HDAC inhibitor Romidpesin. As our continuous efforts, a library of novel cyclicdepsipeptides based on 9 was established using a convergent synthesis strategy. The most active compounds 10, 16 and 19 selectively inhibit class I HDACs and exhibit promising nanomolar antiproliferative activities against several cancer cell lines with excellent selectivity toward cancer cells over normal cells. Besides, compound 10 demonstrates excellent antitumor effects in human prostate carcinoma PC3 xenograft models with no observed toxicity. Conclusion: These cyclicdepsipeptides show great therapeutic potential as novel anticancer agents for clinical translation.
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12
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Conformational analysis of macrocycles: comparing general and specialized methods. J Comput Aided Mol Des 2020; 34:231-252. [PMID: 31965404 PMCID: PMC7036058 DOI: 10.1007/s10822-020-00277-2] [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: 07/29/2019] [Accepted: 01/03/2020] [Indexed: 11/24/2022]
Abstract
Abstract Macrocycles represent an important class of medicinally relevant small molecules due to their interesting biological properties. Therefore, a firm understanding of their conformational preferences is important for drug design. Given the importance of macrocycle-protein modelling in drug discovery, we envisaged that a systematic study of both classical and recent specialized methods would provide guidance for other practitioners within the field. In this study we compare the performance of the general, well established conformational analysis methods Monte Carlo Multiple Minimum (MCMM) and Mixed Torsional/Low-Mode sampling (MTLMOD) with two more recent and specialized macrocycle sampling techniques: MacroModel macrocycle Baseline Search (MD/LLMOD) and Prime macrocycle conformational sampling (PRIME-MCS). Using macrocycles extracted from 44 macrocycle-protein X-ray crystallography complexes, we evaluated each method based on their ability to (i) generate unique conformers, (ii) generate unique macrocycle ring conformations, (iii) identify the global energy minimum, (iv) identify conformers similar to the X-ray ligand conformation after Protein Preparation Wizard treatment (X-rayppw), and (v) to the X-rayppw ring conformation. Computational speed was also considered. In addition, conformational coverage, as defined by the number of conformations identified, was studied. In order to study the relative energies of the bioactive conformations, the energy differences between the global energy minima and the energy minimized X-rayppw structures and, the global energy minima and the MCMM-Exhaustive (1,000,000 search steps) generated conformers closest to the X-rayppw structure, were calculated and analysed. All searches were performed using relatively short run times (10,000 steps for MCMM, MTLMOD and MD/LLMOD). To assess the performance of the methods, they were compared to an exhaustive MCMM search using 1,000,000 search steps for each of the 44 macrocycles (requiring ca 200 times more CPU time). Prior to our analysis, we also investigated if the general search methods MCMM and MTLMOD could also be optimized for macrocycle conformational sampling. Taken together, our work concludes that the more general methods can be optimized for macrocycle modelling by slightly adjusting the settings around the ring closure bond. In most cases, MCMM and MTLMOD with either standard or enhanced settings performed well in comparison to the more specialized macrocycle sampling methods MD/LLMOD and PRIME-MCS. When using enhanced settings for MCMM and MTLMOD, the X-rayppw conformation was regenerated with the greatest accuracy. The, MD/LLMOD emerged as the most efficient method for generating the global energy minima. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10822-020-00277-2) contains supplementary material, which is available to authorized users.
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13
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Zhang B, Liu J, Gao D, Yu X, Wang J, Lei X. A fluorine scan on the Zn2+-binding thiolate side chain of HDAC inhibitor largazole: Synthesis, biological evaluation, and molecular modeling. Eur J Med Chem 2019; 182:111672. [DOI: 10.1016/j.ejmech.2019.111672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/31/2019] [Accepted: 08/31/2019] [Indexed: 10/26/2022]
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14
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Dewaker V, Srivastava PN, Verma S, Prabhakar YS. Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds. J Biomol Struct Dyn 2019; 38:1197-1213. [DOI: 10.1080/07391102.2019.1598497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Pratik Narain Srivastava
- Parasitology Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Saroj Verma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Yenamandra S. Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
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15
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Itoh H, Inoue M. Comprehensive Structure–Activity Relationship Studies of Macrocyclic Natural Products Enabled by Their Total Syntheses. Chem Rev 2019; 119:10002-10031. [DOI: 10.1021/acs.chemrev.9b00063] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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16
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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17
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Létévé M, Gonzalez C, Moroy G, Martinez A, Jeanblanc J, Legastelois R, Naassila M, Sapi J, Bourguet E. Unexpected effect of cyclodepsipeptides bearing a sulfonylhydrazide moiety towards histone deacetylase activity. Bioorg Chem 2018; 81:222-233. [PMID: 30153587 DOI: 10.1016/j.bioorg.2018.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Mathieu Létévé
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Céline Gonzalez
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Gautier Moroy
- INSERM UMR-S 973, Molécules Thérapeutiques In Silico, Université de Paris Diderot, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris Cedex, France
| | - Agathe Martinez
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Jérôme Jeanblanc
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Rémi Legastelois
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Mickaël Naassila
- INSERM U1247, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP), Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé), Chemin du Thil, 80000 Amiens, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Janos Sapi
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France
| | - Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé), France.
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18
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Poli G, Di Fabio R, Ferrante L, Summa V, Botta M. Largazole Analogues as Histone Deacetylase Inhibitors and Anticancer Agents: An Overview of Structure-Activity Relationships. ChemMedChem 2017; 12:1917-1926. [PMID: 29117473 DOI: 10.1002/cmdc.201700563] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/31/2017] [Indexed: 12/18/2022]
Abstract
Since the time of its identification, the natural compound largazole rapidly caught the attention of the medicinal chemistry community for its impressive potency as an inhibitor of histone deacetylases (HDACs) and its strong antiproliferative activity against a broad panel of cancer cell lines. The design of largazole analogues is an expanding field of study, due to their remarkable potential as novel anticancer therapeutics. At present, a large ensemble of largazole analogues has been reported, allowing the identification of important structure-activity relationships (SAR) that can guide the design of novel compounds with improved HDAC inhibitory profiles, anticancer activity, and pharmacokinetic properties. The aim of this review is to concisely summarize the information obtained by biological evaluations of the various largazole analogues reported to date, with particular attention given to the latest analogues, as well as to analyze the various SAR obtained from this data, with the purpose of providing useful guidelines for the development of novel potent and selective HDAC inhibitors to be used as anticancer agents.
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Affiliation(s)
- Giulio Poli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Romano Di Fabio
- Promidis, Via Olgettina 60, 20132, Milano, Italy.,IRBM Science Park, Via Pontina Km 30 600, 00070, Pomezia, Italy
| | | | - Vincenzo Summa
- IRBM Science Park, Via Pontina Km 30 600, 00070, Pomezia, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
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19
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Gabr MT, El-Gohary NS, El-Bendary ER, El-Kerdawy MM, Ni N. Microwave-assisted synthesis and antitumor evaluation of a new series of thiazolylcoumarin derivatives. EXCLI JOURNAL 2017; 16:1114-1131. [PMID: 29285008 PMCID: PMC5735336 DOI: 10.17179/excli2017-208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/31/2017] [Indexed: 12/22/2022]
Abstract
A new series of thiazolylcoumarin derivatives was synthesized. The designed strategy embraced a molecular hybridization approach which involves the combination of the thiazole and coumarin pharmacophores together. The new hybrid compounds were tested for in vitro antitumor efficacy over cervical (Hela) and kidney fibroblast (COS-7) cancer cells. Compounds 5f, 5h, 5m and 5r displayed promising efficacy toward Hela cell line. In addition, 5h and 5r were found to be the most active candidates toward COS-7 cell line. The four active analogs, 5f, 5h, 5m and 5r were screened for in vivo antitumor activity over EAC cells in mice, as well as in vitro cytotoxicity toward W138 normal cells. Results illustrated that 5r has the highest in vivo activity, and that the four analogs are less cytotoxic than 5-FU toward W138 normal cells. In this study, 3D pharmacophore analysis was performed to investigate the matching pharmacophoric features of the synthesized compounds with trichostatin A. In silico studies showed that the investigated compounds meet the optimal needs for good oral absorption with no expected toxicity hazards.
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Affiliation(s)
- Moustafa T Gabr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
| | - Nadia S El-Gohary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Eman R El-Bendary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed M El-Kerdawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nanting Ni
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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20
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Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP. Orally Absorbed Cyclic Peptides. Chem Rev 2017; 117:8094-8128. [PMID: 28541045 DOI: 10.1021/acs.chemrev.6b00838] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailability are analyzed, including molecular weight, octanol-water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.
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Affiliation(s)
- Daniel S Nielsen
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Nicholas E Shepherd
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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21
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Garza I, Wallace MJ, Fernando D, Singh A, Lee RE, Gerding JS, Franklin C, Yendapally R. Synthesis and Evaluation of Thiazolidine Amide and N-Thiazolyl Amide Fluoroquinolone Derivatives. Arch Pharm (Weinheim) 2017; 350. [PMID: 28429393 DOI: 10.1002/ardp.201700029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 11/11/2022]
Abstract
In an effort to develop new fluoroquinolones, we synthesized eight compounds and tested them against a panel of bacteria. The design of these compounds was guided by the introduction of the isothiazoloquinolone motif. The three most active compounds in this series, 8-10, demonstrated good antibacterial activity against methicillin-sensitive Staphylococcus aureus and healthcare-acquired methicillin-resistant Staphylococcus aureus (MIC 0.62-6.3 µg/mL). Further, when these three active compounds were tested for their inhibitory effects on bacterial enzymes, compound 9 was the most effective agent exhibiting IC50 values of 33.9 and 116.5 μM in the S. aureus deoxyribonucleic acid (DNA) gyrase supercoiling and topoisomerase IV decatenation assays, respectively.
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Affiliation(s)
- Isaac Garza
- University of the Incarnate Word Feik School of Pharmacy, San Antonio, TX, USA
| | - Miranda J Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dinesh Fernando
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aman Singh
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason S Gerding
- University of the Incarnate Word Feik School of Pharmacy, San Antonio, TX, USA
| | - Cynthia Franklin
- University of the Incarnate Word Feik School of Pharmacy, San Antonio, TX, USA
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22
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Zhao L, Dunne CE, Clausen DJ, Roberts JM, Paulk J, Liu H, Wiest OG, Bradner JE, Williams RM. Synthesis and Biochemical Evaluation of Biotinylated Conjugates of Largazole Analogues: Selective Class I Histone Deacetylase Inhibitors. Isr J Chem 2017; 57:319-330. [PMID: 30760938 PMCID: PMC6370329 DOI: 10.1002/ijch.201600130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of biotinylated conjugates of synthetic analogues of the potent and selective histone deacetylase (HDAC) inhibitor largazole is reported. The thiazole moiety of the parent compound's cap group was derivatized to allow the chemical conjugation to biotin. The derivatized largazole analogues were assayed across a panel of HDACs 1-9 and retained potent and selective inhibitory activity towards the class I HDAC isoforms. The biotinylated conjugate was further shown to pull down HDACs 1, 2, and 3.
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Affiliation(s)
- Le Zhao
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 (USA)
| | - Christine E. Dunne
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 (USA)
| | - Dane J. Clausen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 (USA)
| | - Justin M. Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115 (USA)
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115 (USA)
| | - Haining Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670 (USA)
| | - Olaf G. Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670 (USA)
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115 (USA)
| | - Robert M. Williams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 (USA)
- University of Colorado Cancer Center, Aurora, Colorado 80045 (USA)
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23
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Alogheli H, Olanders G, Schaal W, Brandt P, Karlén A. Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide. J Chem Inf Model 2017; 57:190-202. [PMID: 28079375 DOI: 10.1021/acs.jcim.6b00443] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In recent years, there has been an increased interest in using macrocyclic compounds for drug discovery and development. For docking of these commonly large and flexible compounds to be addressed, a screening and a validation set were assembled from the PDB consisting of 16 and 31 macrocycle-containing protein complexes, respectively. The macrocycles were docked in Glide by rigid docking of pregenerated conformational ensembles produced by the macrocycle conformational sampling method (MCS) in Schrödinger Release 2015-3 or by direct Glide flexible docking after performing ring-templating. The two protocols were compared to rigid docking of pregenerated conformational ensembles produced by an exhaustive Monte Carlo multiple minimum (MCMM) conformational search and a shorter MCMM conformational search (MCMM-short). The docking accuracy was evaluated and expressed as the RMSD between the heavy atoms of the ligand as found in the X-ray structure after refinement and the poses obtained by the docking protocols. The median RMSD values for top-scored poses of the screening set were 0.83, 0.80, 0.88, and 0.58 Å for MCMM, MCMM-short, MCS, and Glide flexible docking, respectively. There was no statistically significant difference in the performance between rigid docking of pregenerated conformations produced by the MCS and direct docking using Glide flexible docking. However, the flexible docking protocol was 2-times faster in docking the screening set compared to that of the MCS protocol. In a final study, the new Prime-MCS method was evaluated in Schrödinger Release 2016-3. This method is faster compared that of to MCS; however, the conformations generated were found to be suboptimal for rigid docking. Therefore, on the basis of timing, accuracy, and ease of set up, standard Glide flexible docking with prior ring-templating is recommended over current gold standard protocols using rigid docking of pregenerated conformational ensembles.
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Affiliation(s)
- Hiba Alogheli
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC , Box 574, SE-751 23 Uppsala, Sweden
| | - Gustav Olanders
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC , Box 574, SE-751 23 Uppsala, Sweden
| | - Wesley Schaal
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC , Box 574, SE-751 23 Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC , Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC , Box 574, SE-751 23 Uppsala, Sweden
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Qin HT, Li HQ, Liu F. Selective histone deacetylase small molecule inhibitors: recent progress and perspectives. Expert Opin Ther Pat 2016; 27:621-636. [PMID: 28033734 DOI: 10.1080/13543776.2017.1276565] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Since the first pan-HDAC inhibitor SAHA was approved by U.S. FDA 10 years ago, HDACs including SIRT1-7 have received significant attention due to the fact that aberrant histone deacetylase activtiy has been implicated in a variety of human diseases, such as cancers, virus infection, and neurodegenerative diseases. During the past years, a considerable achievement of development of isoform- or class-selective HDAC inhibitors has been made, yielding many drug candidates for further clinical studies, which represents a state-of-the-art technology in the drug discovery arena. Areas covered: This review covers new patents and articles about isoform- or class-selective HDAC inhibitors during the last four years, as well as the therapeutic potential of these compounds. Expert opinion: HDACs represent one of the most promising therapeutic targets, particularly for tumor therapy though their roles in cancer are still blurry. From 2012 to present, along with the advances of structural biology and homology models, lots of isoform- or class-selective HDAC inhibitors, such as hydroxamic acids and benzamides with various capping groups were found, providing a promising way to circumvent drug toxicity and side-effect issues, as well as providing chemical probes for further better understanding of the biological process related to specific isoform.
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Affiliation(s)
- Hai-Tao Qin
- a Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry , College of Pharmaceutical Sciences, Soochow University , Suzhou , PR China
| | - Huan-Qiu Li
- b Department of Medicinal Chemistry , College of Pharmaceutical Sciences, Soochow University , Suzhou , PR China
| | - Feng Liu
- a Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry , College of Pharmaceutical Sciences, Soochow University , Suzhou , PR China
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25
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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26
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Narita K, Matsuhara K, Itoh J, Akiyama Y, Dan S, Yamori T, Ito A, Yoshida M, Katoh T. Synthesis and biological evaluation of novel FK228 analogues as potential isoform selective HDAC inhibitors. Eur J Med Chem 2016; 121:592-609. [DOI: 10.1016/j.ejmech.2016.05.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 11/25/2022]
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27
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Mukherjee JP, Sil S, Chattopadhyay SK. A modular approach to cyclic tetrapeptides related to histone deacetylase inhibition: synthesis of epi-microsporin A. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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28
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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29
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Reddy DN, Ballante F, Chuang T, Pirolli A, Marrocco B, Marshall GR. Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors. J Med Chem 2016; 59:1613-33. [PMID: 26681404 DOI: 10.1021/acs.jmedchem.5b01632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Selective inhibition of KDAC isoforms while maintaining potency remains a challenge. Using the largazole macrocyclic depsipeptide structure as a starting point for developing new KDACIs with increased selectivity, a combination of four different simplified largazole analogue (SLA) scaffolds with diverse zinc-binding groups (for a total of 60 compounds) were designed, synthesized, and evaluated against class I KDACs 1, 3, and 8, and class II KDAC6. Experimental evidence as well as molecular docking poses converged to establish the cyclic tetrapeptides (CTPs) as the primary determinant of both potency and selectivity by influencing the correct alignment of the zinc-binding group in the KDAC active site, providing a further basis for developing new KDACIs of higher isoform selectivity and potency.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Timothy Chuang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Adele Pirolli
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
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30
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Abstract
The ubiquitin–proteasome system has been recognized as fundamental toward protein turnover in eukaryotic cells. The system comprises the ubiquitin conjugation machinery consisting of an enzyme cascade of E1, E2, and E3 enzymes, the deubiquitinases (DUBs) and the proteasome, a multisubunit protease complex acting through an N-terminal threonine protease mechanism. A number of natural product inhibitors of the proteasome have been studied in detail and these inhibitors and their derivatives have been highly valuable in developing our understanding of this system. These efforts culminated in the successful development of bortezomib as a pharmacological agent used clinically as a cancer therapeutic in the treatment of multiple myeloma. This review is focused on natural product inhibitors of the enzymes involved in intracellular ubiquitin conjugation (ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, ubiquitin ligase E3) and ubiquitin deconjugation (DUBs). Members of both of these enzyme systems have been proposed as pharmacological targets for cancer therapy and several other diseases. Furthermore compounds with activities toward enzymes from the analogous ubiquitin-like (Ubl) protein families have been identified for SUMO and NEDD8. To date natural product inhibitors have been described for members of each of these protein families and were isolated from plant, fungal, animal, and microbial sources. Insights into the mechanism of action of natural products and their derivatives will enhance our understanding of this complex system and will improve our ability to rationally design novel inhibitors. The increased availability of assays and research tools for the study of protein ubiquitination, deubiquitination, and Ubl proteins will contribute to the discovery of more potent and selective compounds. We expect that these studies will stimulate development of further potential pharmacological agents in this area.
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New macrocyclic analogs of the natural histone deacetylase inhibitor FK228; design, synthesis and preliminary biological evaluation. Bioorg Med Chem 2015; 23:6785-93. [PMID: 26481659 DOI: 10.1016/j.bmc.2015.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/08/2015] [Accepted: 10/05/2015] [Indexed: 11/23/2022]
Abstract
Among the natural histone deacetylase inhibitors (HDACi), the bicyclic depsipeptide macrolactone FK228 stands out for its unique chemical structure and mechanism of action. In order to expand the chemical diversity, exploiting the FK228 peculiar structure, we have synthesized a collection of 24 simplified novel analogs. A first series consists of bicyclic macrolactones, where the carboxy terminus of the natural compound was substituted by peptidomimetic aminomethylphenylacetic acid derivatives. These analogs, 7a-i, showed submicromolar cytotoxic activity, even though very low inhibitory activity against HDAC enzymes, suggesting that most probably they behave with a mechanism different from the natural compound. One of the most active members in the group, 7g, was evaluated in vivo and exhibited significant antitumor activity. This evidence supports that the activity is unrelated to HDAC inhibition and these compounds represent a novel series of promising active agents. Another analog series consists of monocyclic macrolactones, 9a-c and 10a-d which lack the disulfide bridge and bear the protected sulfur on the linear external chain; they showed similar cytotoxic activities compared to the natural compound, but proved to be very sensitive to the nature of the sulfur protection. In fact, when the sulfur was protected by an 1-octanoyl residue, like in 9b, the product displayed a one digit nanomolar activity. The results provide evidence that our approach may be followed to develop novel series of FK228 analogs.
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32
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Yao Y, Tu Z, Liao C, Wang Z, Li S, Yao H, Li Z, Jiang S. Discovery of Novel Class I Histone Deacetylase Inhibitors with Promising in Vitro and in Vivo Antitumor Activities. J Med Chem 2015; 58:7672-80. [DOI: 10.1021/acs.jmedchem.5b01044] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yiwu Yao
- Laboratory of
Medicinal Chemistry, Guangzhou Institute of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhengchao Tu
- Laboratory of
Medicinal Chemistry, Guangzhou Institute of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chenzhong Liao
- School
of Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhen Wang
- Laboratory of
Medicinal Chemistry, Guangzhou Institute of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shang Li
- Laboratory of
Medicinal Chemistry, Guangzhou Institute of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hequan Yao
- State
Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Zheng Li
- Department
of Nanomedicine, Houston Methodist Hospital Research Institute, Houston, Texas 77030, United States
| | - Sheng Jiang
- Laboratory of
Medicinal Chemistry, Guangzhou Institute of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
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33
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Kim B, Hong J. An overview of naturally occurring histone deacetylase inhibitors. Curr Top Med Chem 2015; 14:2759-82. [PMID: 25487010 DOI: 10.2174/1568026615666141208105614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/26/2014] [Accepted: 11/29/2014] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) have recently emerged as key elements in epigenetic control of gene expression. Due to the implication of HDACs in a variety of diseases ranging from cancer to neurodegenerative disorder, HDAC inhibitors have received increased attention in recent years. Over the last few decades, a myriad of HDAC inhibitors containing a wide variety of structural features have been identified from natural sources. Here, we review the discovery, synthesis, biological properties, and modes of action of these naturally occurring HDAC inhibitors and consider their implications for future research.
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Affiliation(s)
| | - Jiyong Hong
- Duke University, Department of Chemistry, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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34
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Predicting the unpredictable: Recent structure–activity studies on peptide-based macrocycles. Bioorg Chem 2015; 60:74-97. [DOI: 10.1016/j.bioorg.2015.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 11/18/2022]
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Clausen DJ, Smith WB, Haines BE, Wiest O, Bradner JE, Williams RM. Modular synthesis and biological activity of pyridyl-based analogs of the potent Class I Histone Deacetylase Inhibitor Largazole. Bioorg Med Chem 2015; 23:5061-5074. [PMID: 26054247 DOI: 10.1016/j.bmc.2015.03.063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 11/26/2022]
Abstract
The formation of a series of analogs containing a pyridine moiety in place of the natural thiazole heterocycle, based on the potent, naturally occurring HDAC inhibitor Largazole has been accomplished. The synthetic strategy was designed modularly to access multiple inhibitors with different aryl functionalities containing both the natural depsipeptide and peptide isostere variant of the macrocycle. The cytotoxicity and biochemical activity of the library of HDAC inhibitors is described herein.
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Affiliation(s)
- Dane J Clausen
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - William B Smith
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Brandon E Haines
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Olaf Wiest
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; University of Colorado Cancer Center, Aurora, CO 80045, USA.
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Decroos C, Clausen DJ, Haines BE, Wiest O, Williams RM, Christianson DW. Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8. Biochemistry 2015; 54:2126-35. [PMID: 25793284 DOI: 10.1021/acs.biochem.5b00010] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The macrocyclic depsipeptide Largazole is a potent inhibitor of metal-dependent histone deacetylases (HDACs), some of which are drug targets for cancer chemotherapy. Indeed, Largazole partially resembles Romidepsin (FK228), a macrocyclic depsipeptide already approved for clinical use. Each inhibitor contains a pendant side chain thiol that coordinates to the active site Zn(2+) ion, as observed in the X-ray crystal structure of the HDAC8-Largazole complex [Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., and Christianson, D. W. (2011) J. Am. Chem. Soc. 133, 12474]. Here, we report the X-ray crystal structures of HDAC8 complexed with three synthetic analogues of Largazole in which the depsipeptide ester is replaced with a rigid amide linkage. In two of these analogues, a six-membered pyridine ring is also substituted (with two different orientations) for the five-membered thiazole ring in the macrocycle skeleton. The side chain thiol group of each analogue coordinates to the active site Zn(2+) ion with nearly ideal geometry, thereby preserving the hallmark structural feature of inhibition by Largazole. Surprisingly, in comparison with the binding of Largazole, these analogues trigger alternative conformational changes in loops L1 and L2 flanking the active site. However, despite these structural differences, inhibitory potency is generally comparable to, or just moderately less than, the inhibitory potency of Largazole. Thus, this study reveals important new structure-affinity relationships for the binding of macrocyclic inhibitors to HDAC8.
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Affiliation(s)
- Christophe Decroos
- †Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Dane J Clausen
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brandon E Haines
- §Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Olaf Wiest
- §Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,∥Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Robert M Williams
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States.,⊥University of Colorado Cancer Center, Aurora, Colorado 80045, United States
| | - David W Christianson
- †Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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37
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Pilon JL, Clausen DJ, Hansen RJ, Lunghofer PJ, Charles B, Rose BJ, Thamm DH, Gustafson DL, Bradner JE, Williams RM. Comparative pharmacokinetic properties and antitumor activity of the marine HDACi Largazole and Largazole peptide isostere. Cancer Chemother Pharmacol 2015; 75:671-82. [PMID: 25616967 DOI: 10.1007/s00280-015-2675-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 01/03/2015] [Indexed: 12/12/2022]
Abstract
PURPOSE Largazole is a potent class I-selective HDACi natural product isolated from the marine cyanobacteria Symploca sp. The purpose of this study was to test synthetic analogs of Largazole to identify potential scaffold structural modifications that would improve the drug-like properties of this clinically relevant natural product. METHODS The impact of Largazole scaffold replacements on in vitro growth inhibition, cell cycle arrest, induction of apoptosis, pharmacokinetic properties, and in vivo activity using a xenograft model was investigated. RESULTS In vitro studies in colon, lung, and pancreatic cancer cell lines showed that pyridyl-substituted Largazole analogs had low-nanomolar/high-picomolar antiproliferative activity, and induced apoptosis and cell cycle arrest at concentrations equivalent to or lower than the parent compound Largazole. Using IV bolus delivery at 5 mg/kg, two compartmental pharmacokinetic modeling on the peptide isostere analog of Largazole indicated improved pharmacokinetic parameters. In an A549 non-small cell lung carcinoma xenograft model using a dosage of 5 mg/kg administered intraperitoneally every other day, Largazole, Largazole thiol, and Largazole peptide isostere demonstrated tumor growth inhibition (TGI%) of 32, 44, and 66%, respectively. Largazole peptide isostere treatment was statistically superior to control (p = 0.002) and to Largazole (p = 0.006). Surprisingly, tumor growth inhibition was not observed with the potent pyridyl-based analogs. CONCLUSIONS These results establish that replacing the depsipeptide linkage in Largazole with an amide may impart pharmacokinetic and therapeutic advantage and that alternative prodrug forms of Largazole are feasible.
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Affiliation(s)
- John L Pilon
- Cetya Therapeutics, 1301 Center Avenue, Fort Collins, CO, 80523, USA
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38
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Maolanon AR, Villadsen JS, Christensen NJ, Hoeck C, Friis T, Harris P, Gotfredsen CH, Fristrup P, Olsen CA. Methyl Effect in Azumamides Provides Insight Into Histone Deacetylase Inhibition by Macrocycles. J Med Chem 2014; 57:9644-57. [DOI: 10.1021/jm501399d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alex R. Maolanon
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jesper S. Villadsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Niels J. Christensen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Casper Hoeck
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Tina Friis
- Department
of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte H. Gotfredsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Christian A. Olsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
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39
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Design, synthesis, and biological evaluation of largazole derivatives: alteration of the zinc-binding domain. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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40
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Bhansali P, Hanigan CL, Perera L, Casero RA, Tillekeratne LMV. Synthesis and biological evaluation of largazole analogues with modified surface recognition cap groups. Eur J Med Chem 2014; 86:528-41. [PMID: 25203782 DOI: 10.1016/j.ejmech.2014.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/25/2014] [Accepted: 09/03/2014] [Indexed: 01/02/2023]
Abstract
Several largazole analogues with modified surface recognition cap groups were synthesized and their HDAC inhibitory activities were determined. The C7-epimer 12 caused negligible inhibition of HDAC activity, failed to induce global histone 3 (H3) acetylation in the HCT116 colorectal cancer cell line and demonstrated minimal effect on growth. Although previous studies have shown some degree of tolerance of structural changes at C7 position of largazole, these data show the negative effect of conformational change accompanying change of configuration at this position. Similarly, analogue 16a with D-1-naphthylmethyl side chain at C2 too had negligible inhibition of HDAC activity, failed to induce global histone 3 (H3) acetylation in the HCT116 colorectal cancer cell line and demonstrated minimal effect on growth. In contrast, the L-allyl analogue 16b and the L-1-naphthylmethyl analogue 16c were potent HDAC inhibitors, showing robust induction of global H3 acetylation and significant effect on cell growth. The data suggest that even bulky substituents are tolerated at this position, provided the stereochemistry at C2 is retained. With bulky substituents, inversion of configuration at C2 results in loss of inhibitory activity. The activity profiles of 16b and 16c on Class I HDAC1 vs Class II HDAC6 are similar to those of largazole and, taken together with x-ray crystallography information of HDAC8-largazole complex, may suggest that the C2 position of largazole is not a suitable target for structural optimization to achieve isoform selectivity. The results of these studies may guide the synthesis of more potent and selective HDAC inhibitors.
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Affiliation(s)
- Pravin Bhansali
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801, W. Bancroft Street, Toledo, OH 43606, United States
| | - Christin L Hanigan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Bunting/Blaustein Cancer Research Building 1, 1650 Orleans Street, Room 551, Baltimore, MD 21231, United States
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - Robert A Casero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Bunting/Blaustein Cancer Research Building 1, 1650 Orleans Street, Room 551, Baltimore, MD 21231, United States
| | - L M Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801, W. Bancroft Street, Toledo, OH 43606, United States.
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41
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Schnekenburger M, Dicato M, Diederich M. Epigenetic modulators from “The Big Blue”: A treasure to fight against cancer. Cancer Lett 2014; 351:182-97. [DOI: 10.1016/j.canlet.2014.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 01/14/2023]
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Abstract
Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.
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Affiliation(s)
- Kai Chen
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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43
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Tumminakatti S, Reddy DN, Lakshmi AN, Prabhakaran EN. Synthesis of 5,6-dihydro-4H-1,3-thiazine containing peptide mimics from N-(3-hydroxypropyl)thioamides and epimerization studies. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.06.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Kim B, Park H, Salvador LA, Serrano PE, Kwan JC, Zeller SL, Chen QY, Ryu S, Liu Y, Byeon S, Luesch H, Hong J. Evaluation of class I HDAC isoform selectivity of largazole analogues. Bioorg Med Chem Lett 2014; 24:3728-31. [PMID: 25070421 DOI: 10.1016/j.bmcl.2014.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 10/25/2022]
Abstract
Largazole is a potent class I selective histone deacetylase (HDAC) inhibitor. The majority of largazole analogues to date have modified the thiazole-thiazoline and the warhead moiety. In order to elucidate class I-specific structure-activity relationships, a series of analogues with modifications in the valine or the linker region were prepared and evaluated for their class I isoform selectivity. The inhibition profile showed that the C2 position of largazole has an optimal steric requirement for efficient HDAC inhibition and that substitution of the trans-alkene in the linker with an aromatic group results in complete loss of activity. This data will aid the design of class I isoform selective HDAC inhibitors.
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Affiliation(s)
- Bumki Kim
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Heekwang Park
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Lilibeth A Salvador
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States; Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City 1100, Philippines
| | - Patrick E Serrano
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Jason C Kwan
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Sabrina L Zeller
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Qi-Yin Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States; Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Soyoung Ryu
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Yanxia Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States; Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Seongrim Byeon
- Department of Chemistry, Duke University, Durham, NC 27708, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States; Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, United States; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, United States.
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45
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Chen F, Chai H, Su MB, Zhang YM, Li J, Xie X, Nan FJ. Potent and orally efficacious bisthiazole-based histone deacetylase inhibitors. ACS Med Chem Lett 2014; 5:628-33. [PMID: 24944733 DOI: 10.1021/ml400470s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 04/04/2014] [Indexed: 01/18/2023] Open
Abstract
Inspired by the thiazole-thiazoline cap group in natural product largazole, a series of structurally simplified bisthiazole-based histone deacetylase inhibitors were prepared and evaluated. Compound 8f was evaluated in vivo in an experimental autoimmune encephalomyelitis (EAE) model and found to be orally efficacious in ameliorating clinical symptoms of EAE mice.
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Affiliation(s)
- Fei Chen
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Hui Chai
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Ming-Bo Su
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Yang-Ming Zhang
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Jia Li
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Xin Xie
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Fa-Jun Nan
- Chinese National Center for
Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, 189 Guoshoujing Road, Shanghai, 201203, China
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46
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Wender PA, Donnelly AC, Loy BA, Near KE, Staveness D. Rethinking the Role of Natural Products: Function-Oriented Synthesis, Bryostatin, and Bryologs. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Schotes C, Ostrovskyi D, Senger J, Schmidtkunz K, Jung M, Breit B. Total synthesis of (18S)- and (18R)-homolargazole by rhodium-catalyzed hydrocarboxylation. Chemistry 2014; 20:2164-8. [PMID: 24478039 DOI: 10.1002/chem.201303300] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Indexed: 11/05/2022]
Abstract
Homolargazole derivatives, in which the macrocycle of natural largazole is extended by one methylene group, were prepared by the recently developed rhodium-catalyzed hydrocarboxylation reaction onto allenes. This strategy gives access to both the (18S)- and (18R)-stereoisomers in high stereoselectivity under ligand control.
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Affiliation(s)
- Christoph Schotes
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg i. Bg. (Germany), Fax: (+49) 761-203-8715
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48
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Microbial natural products: molecular blueprints for antitumor drugs. J Ind Microbiol Biotechnol 2013; 40:1181-210. [PMID: 23999966 DOI: 10.1007/s10295-013-1331-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.
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49
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Guerra-Bubb JM, Bowers AA, Smith WB, Paranal R, Estiu G, Wiest O, Bradner JE, Williams RM. Synthesis and HDAC inhibitory activity of isosteric thiazoline-oxazole largazole analogs. Bioorg Med Chem Lett 2013; 23:6025-8. [PMID: 24035339 DOI: 10.1016/j.bmcl.2013.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 06/03/2013] [Indexed: 11/15/2022]
Abstract
The synthesis of an isosteric analog of the natural product and HDAC inhibitor largazole is described. The sulfur atom in the thizaole ring of the natural product has been replaced with an oxygen atom, constituting an oxazole ring. The biochemical activity and cytotoxicity of this species is described.
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Affiliation(s)
- Jennifer M Guerra-Bubb
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States
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50
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Abstract
Histone deacetylases (HDACs) have emerged as important drug targets in epigenetics. The most common HDAC inhibitors use hydroxamic acids as zinc binding groups despite unfavorable pharmacokinetic properties. A two-stage protocol of M05-2X calculations of a library of 48 fragments in a small model active site, followed by QM/MM hybrid calculations of the full enzyme with selected binders, is used to prospectively select potential bidentate zinc binders. The energetics and interaction patterns of several zinc binders not previously used for the inhibition of HDACs are discussed.
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Affiliation(s)
- Kai Chen
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Liping Xu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Olaf Wiest
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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