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Elbatrawy OR, Hagras M, El Deeb MA, Agili F, Hegazy M, El-Husseiny AA, Mokhtar MM, Elkhawaga SY, Eissa IH, El-Kalyoubi S. Discovery of New Uracil and Thiouracil Derivatives as Potential HDAC Inhibitors. Pharmaceuticals (Basel) 2023; 16:966. [PMID: 37513878 PMCID: PMC10384246 DOI: 10.3390/ph16070966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Background: Histone deacetylase inhibitors (HDACIs) are a relatively new class of potential drugs for treating cancer. Aim: Discovery of new anticancer agents targeting HDAC. Methods: New uracil and thiouracil derivatives panels were designed and synthesized as HDAC inhibitors. The synthesized compounds were tested against MCF-7, HepG2, and HCT-116. HDAC1 and HDAC4 inhibitory activities of these compounds were tested. The most active member was tested for its potential against cell cycle, apoptosis, caspase-3, and caspase-8. Docking studies were carried out against HDAC1. Results: Compounds 5a, 5b, 5f, 5i, 5k, and 5m exhibited promising cytotoxic activities. HDAC1 and HDAC4 inhibitory activities of these compounds were tested. Regarding the HDAC1 inhibitory activity, compound 5m was the most potent member (IC50 = 0.05 µg/mL) compared to trichostatin A (IC50 = 0.0349 µg/mL). For HDAC4, compound 5m showed superior activity (IC50 = 2.83 µg/mL) than trichostatin A (IC50 = 3.349 µg/mL). Compound 5m showed a high potential to arrest the HCT116 cell cycle at the G0-G1 phase. In addition, it showed an almost 17 times apoptotic effect (37.59%) compared to the control cells (2.17%). Furthermore, Compound 5m showed significant increases in the levels of caspase-3 and caspase-8. Finally, the uracil and thiouracil derivatives showed accepted binding mods against HDAC. Conclusions: Compound 5m has potential anticancer activity targeting HDAC with a significant apoptotic effect.
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Affiliation(s)
- Omnia R Elbatrawy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11823, Egypt
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Moshira A El Deeb
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11823, Egypt
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia
| | - Maghawry Hegazy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Mahmoud Mohamed Mokhtar
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42511, Egypt
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2
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Kamimura S, Inoue K, Mizutani E, Kim JM, Inoue H, Ogonuki N, Miyamoto K, Ihashi S, Itami N, Wakayama T, Ito A, Nishino N, Yoshida M, Ogura A. Improved development of mouse somatic cell nuclear transfer embryos by chlamydocin analogues, class I and IIa histone deacetylase inhibitors†. Biol Reprod 2021; 105:543-553. [PMID: 33982061 PMCID: PMC8335354 DOI: 10.1093/biolre/ioab096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/29/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
In mammalian cloning by somatic cell nuclear transfer (SCNT), the treatment of reconstructed embryos with histone deacetylase (HDAC) inhibitors improves efficiency. So far, most of those used for SCNT are hydroxamic acid derivatives-such as trichostatin A-characterized by their broad inhibitory spectrum. Here, we examined whether mouse SCNT efficiency could be improved using chlamydocin analogues, a family of newly designed agents that specifically inhibit class I and IIa HDACs. Development of SCNT-derived embryos in vitro and in vivo revealed that four out of five chlamydocin analogues tested could promote the development of cloned embryos. The highest pup rates (7.1-7.2%) were obtained with Ky-9, similar to those achieved with trichostatin A (7.2-7.3%). Thus, inhibition of class I and/or IIa HDACs in SCNT-derived embryos is enough for significant improvements in full-term development. In mouse SCNT, the exposure of reconstructed oocytes to HDAC inhibitors is limited to 8-10 h because longer inhibition with class I inhibitors causes a two-cell developmental block. Therefore, we used Ky-29, with higher selectivity for class IIa than class I HDACs for longer treatment of SCNT-derived embryos. As expected, 24-h treatment with Ky-29 up to the two-cell stage did not induce a developmental block, but the pup rate was not improved. This suggests that the one-cell stage is a critical period for improving SCNT cloning using HDAC inhibitors. Thus, chlamydocin analogues appear promising for understanding and improving the epigenetic status of mammalian SCNT-derived embryos through their specific inhibitory effects on HDACs.
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Affiliation(s)
- Satoshi Kamimura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan.,Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Kimiko Inoue
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Eiji Mizutani
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan.,Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jin-Moon Kim
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Hiroki Inoue
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Narumi Ogonuki
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Kei Miyamoto
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa-shi, Wakayama-ken, Japan
| | - Shunya Ihashi
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa-shi, Wakayama-ken, Japan
| | - Nobuhiko Itami
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Teruhiko Wakayama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan
| | - Akihiro Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Norikazu Nishino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Atsuo Ogura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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3
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Ahangarzadeh S, Kanafi MM, Hosseinzadeh S, Mokhtarzadeh A, Barati M, Ranjbari J, Tayebi L. Bicyclic peptides: types, synthesis and applications. Drug Discov Today 2019; 24:1311-1319. [PMID: 31102732 DOI: 10.1016/j.drudis.2019.05.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/19/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
Bicyclic peptides form one of the most promising platforms for drug development owing to their biocompatibility, similarity and chemical diversity to proteins, and they are considered as a possible practical tool in various therapeutic and diagnostic applications. Bicyclic peptides are known to have the capability of being employed as an effective alternative to complex molecules, such as antibodies, or small molecules. This review provides a summary of the recent progress on the types, synthesis and applications of bicyclic peptides. More specifically, natural and synthetic bicyclic peptides are introduced with their different production methods and relevant applications, including drug targeting, imaging and diagnosis. Their uses as antimicrobial agents, as well as the therapeutic functions of different bicyclic peptides, are also discussed.
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Affiliation(s)
- Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad M Kanafi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Simzar Hosseinzadeh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahmood Barati
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javad Ranjbari
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA.
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4
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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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5
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6
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An efficient synthesis of SK-658 and its analogs as potent histone deacetylase inhibitors. Bioorg Chem 2015; 59:145-50. [DOI: 10.1016/j.bioorg.2015.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/03/2015] [Accepted: 02/08/2015] [Indexed: 11/18/2022]
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7
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Islam MN, Islam MS, Hoque MA, Kato T, Nishino N, Ito A, Yoshida M. Bicyclic tetrapeptide histone deacetylase inhibitors with methoxymethyl ketone and boronic acid zinc-binding groups. Bioorg Chem 2014; 57:121-126. [DOI: 10.1016/j.bioorg.2014.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/11/2014] [Accepted: 10/13/2014] [Indexed: 11/28/2022]
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8
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RETRACTED: Design and synthesis of CHAP31, trapoxin B and HC-toxin based bicyclic tetrapeptides disulfide as potent histone deacetylase inhibitors. Bioorg Med Chem 2014; 22:3850-5. [DOI: 10.1016/j.bmc.2014.06.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 11/18/2022]
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9
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Hoque MA, Islam MS, Islam MN, Kato T, Nishino N, Ito A, Yoshida M. Design and synthesis of mono and bicyclic tetrapeptides thioester as potent inhibitor of histone deacetylases. Amino Acids 2014; 46:2435-44. [PMID: 25048030 DOI: 10.1007/s00726-014-1800-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 06/26/2014] [Indexed: 11/30/2022]
Abstract
Inhibitors of histone deacetylases (HDACs) are a promising class of anticancer agents that have an effect on gene regulation. The naturally occurring cyclic depsipeptide FK228 containing disulfide and Largazole possessing thioester functionalities act as pro-drugs and share the same HDAC inhibition mechanism in cell. Inspired from these facts, we have reported bicyclic tetrapeptide disulfide HDAC inhibitors resembling FK228 with potent activity and enhanced selectivity. In the present study, we report the design and synthesis of several mono and bicyclic tetrapeptide thioester HDAC inhibitors that share the inhibition mechanism similar to Largazole. Most of the compounds showed HDAC1 and HDAC4 inhibition and p21 promoting activity in nanomolar ranges. Among these the monocyclic peptides 1, 2 and bicyclic peptide, 4 are notable demanding more advanced research to be promising anticancer drug candidates.
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Affiliation(s)
- Md Ashraful Hoque
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Malaysia,
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10
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Islam MN, Islam MS, Hoque MA, Kato T, Nishino N, Ito A, Yoshida M. Bicyclic tetrapeptides as potent HDAC inhibitors: effect of aliphatic loop position and hydrophobicity on inhibitory activity. Bioorg Med Chem 2014; 22:3862-70. [PMID: 25022972 DOI: 10.1016/j.bmc.2014.06.031] [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: 04/16/2014] [Revised: 06/15/2014] [Accepted: 06/17/2014] [Indexed: 11/17/2022]
Abstract
Several histone deacetylase (HDAC) inhibiting bicyclic tetrapeptides have been designed and synthesized through intramolecular ring-closing metathesis (RCM) reaction and peptide cyclization. We designed bicyclic tetrapeptides based on CHAP31, trapoxin B and HC-toxin I. The HDAC inhibitory and p21 promoter assay results showed that the aliphatic loop position as well as the hydrophobicity plays an important role toward the activity of the bicyclic tetrapeptide HDAC inhibitors.
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Affiliation(s)
- Md Nurul Islam
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan; Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Md Shahidul Islam
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan; Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Ashraful Hoque
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan; Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tamaki Kato
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | - Norikazu Nishino
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | - Akihiro Ito
- Chemical Genetics Laboratory/Chemical Genomics Research Group, RIKEN Advanced Science Institute, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory/Chemical Genomics Research Group, RIKEN Advanced Science Institute, Saitama 351-0198, Japan
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11
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Li XH, Huang ML, Wang SM, Wang Q. Selective Inhibition of Bicyclic Tetrapeptide Histone Deacetylase Inhibitor on HDAC4 and K562 Leukemia Cell. Asian Pac J Cancer Prev 2013; 14:7095-100. [DOI: 10.7314/apjcp.2013.14.12.7095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Amin J, Puglisi A, Clarke J, Milton J, Wang M, Paranal RM, Bradner JE, Spencer J. A cyclodextrin-capped histone deacetylase inhibitor. Bioorg Med Chem Lett 2013; 23:3346-8. [DOI: 10.1016/j.bmcl.2013.03.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 11/30/2022]
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13
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A novel two-step QSAR modeling work flow to predict selectivity and activity of HDAC inhibitors. Bioorg Med Chem Lett 2013; 23:929-33. [PMID: 23321563 DOI: 10.1016/j.bmcl.2012.12.067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/22/2022]
Abstract
A two-step modeling approach was employed to study the selectivity and activity of histone deacetylase inhibitors. First, according to the activity difference against HDAC1 and HDAC6, a binary classification model was established to classify two kinds of inhibitors. Then two continuous models were built for each subclass to predict the activity value of HDAC1 and HDAC6 inhibitors. The three models were all built with the GA-kNN method combined with dragon descriptors. They were external validated by using external prediction set and Y-randomization test. The highly predictive models were generated for all three data sets. For the classification model, the classification accuracies of the models were as high as 100% for the external test set. For HDAC1 and HDAC6 inhibitor consecutive models, external R(2) values are 0.947 and 0.911, respectively. The results proved the reliability of these models. All models were used to screen 1000 compounds included in PubMed dataset. Virtual screening resulted in 8 and 13 structurally unique consensus hits that were considered novel putative HDAC1 and HDAC6 inhibitors, respectively.
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14
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Herndon JW. The chemistry of the carbon–transition metal double and triple bond: Annual survey covering the year 2010. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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