Structural insights into HDAC6 tubulin deacetylation and its selective inhibition

Features and development of Coot

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Phaser crystallographic software

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XDS

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Towards automated crystallographic structure refinement with phenix.refine

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HDAC6 is a microtubule-associated deacetylase

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Data processing and analysis with the autoPROC toolbox

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Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A.

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The Buccaneer software for automated model building. 1. Tracing protein chains

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Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors

Sandrone, G., Cukier, C. D., Źrubek, K., Marchini, M., Vergani, B., Caprini, G., Fossati, G., Steinkühler, C., & Stevenazzi, A. (2021) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.1c00425 · Cited by 31

Multi-Targeting Anticancer Agents: Rational Approaches, Synthetic Routes and Structure Activity Relationship

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Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype

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Hydroxyl Ketone-Based Histone Deacetylase Inhibitors To Gain Insight into Class I HDAC Selectivity versus That of HDAC6

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Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10

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Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

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Photochromic histone deacetylase inhibitors based on dithienylethenes and fulgimides

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Microtubule damage shapes the acetylation gradient

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Deficiency of RITA results in multiple mitotic defects by affecting microtubule dynamics

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Design, Synthesis, and Biological Evaluation of 2,4-Imidazolinedione Derivatives as HDAC6 Isoform-Selective Inhibitors

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Microtubule acetylation: A reading key to neural physiology and degeneration

Cappelletti, G., Calogero, A. M., & Rolando, C. (2021) · Neuroscience Letters · doi:10.1016/j.neulet.2021.135900 · Cited by 29

Targeting Histone Deacetylases 6 in Dual-Target Therapy of Cancer

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Synthesis and Pharmacological Evaluation of Selective Histone Deacetylase 6 Inhibitors in Melanoma Models

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Multitarget Inhibition of Histone Deacetylase (HDAC) and Phosphatidylinositol‐3‐kinase (PI3K): Current and Future Prospects

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A highly HDAC6-selective inhibitor acts as a fluorescent probe

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Methods for the expression, purification, and crystallization of histone deacetylase 6–inhibitor complexes

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The emerging role of tubulin posttranslational modifications in cilia and ciliopathies

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SKLB-23bb, A HDAC6-Selective Inhibitor, Exhibits Superior and Broad-Spectrum Antitumor Activity via Additionally Targeting Microtubules

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Development of Potent Inhibitors of Fatty Acid Amide Hydrolase Useful for the Treatment of Neuropathic Pain

Brindisi, M., Borrelli, G., Brogi, S., Grillo, A., Maramai, S., Paolino, M., Benedusi, M., Pecorelli, A., Valacchi, G., Mannelli, L. D. C., et al. (2018) · ChemMedChem · doi:10.1002/cmdc.201800397 · Cited by 27

Advances in the Design and Development of PROTAC-mediated HDAC Degradation

Rodrigues, D. A., Roe, A. J., Griffith, D. M., & Chonghaile, T. N. (2021) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026621666211015092047 · Cited by 27

Emerging therapeutic strategies in cancer therapy by HDAC inhibition as the chemotherapeutic potent and epigenetic regulator

Karati, D., Mukherjee, S., & Roy, S. (2024) · Medical Oncology · doi:10.1007/s12032-024-02303-x · Cited by 25

Tubulin Acetylation Mediates Bisphenol A Effects on the Microtubule Arrays of Allium cepa and Triticum turgidum

Adamakis, I. S., Panteris, E., & Eleftheriou, E. P. (2019) · Biomolecules · doi:10.3390/biom9050185 · Cited by 25

Novel alkoxyamide-based histone deacetylase inhibitors reverse cisplatin resistance in chemoresistant cancer cells

Asfaha, Y., Schrenk, C., Avelar, L. A. A., Lange, F., Wang, C., Bandolik, J. J., Hamacher, A., Kassack, M. U., & Kurz, T. (2019) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2019.115108 · Cited by 25

Highly fluorescent and HDAC6 selective scriptaid analogues

Fleming, C. L., Natoli, A. L., Schreuders, J., Devlin, M. G., Yoganantharajah, P., Gibert, Y., Leslie, K. G., New, E. J., Ashton, T. D., & Pfeffer, F. M. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.11.020 · Cited by 24

Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6

Sixto‐López, Y., Bello, M., & Correa‐Basurto, J. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1557560 · Cited by 23

Inhibition of Class IIa HDACs improves endothelial barrier function in endotoxin‐induced acute lung injury

Kovács‐Kása, A., Kovács, L., Cherian‐Shaw, M., Patel, V. S., Meadows, M. L., Fulton, D. J., Su, Y., & Verin, A. D. (2020) · Journal of Cellular Physiology · doi:10.1002/jcp.30053 · Cited by 25

X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10

Herbst‐Gervasoni, C. J., & Christianson, D. W. (2021) · Biochemistry · doi:10.1021/acs.biochem.0c00936 · Cited by 22

Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition

Winkler, R., Mägdefrau, A.-S., Piskor, E.-M., Kleemann, M., Beyer, M., Linke, K., Hansen, L., Schaffer, A.-M., Hoffmann, M. E., Poepsel, S., et al. (2022) · Oncogene · doi:10.1038/s41388-022-02450-3 · Cited by 23

Role of HDAC6 and Its Selective Inhibitors in Gastrointestinal Cancer

Zhou, B., Liu, D., & Tan, Y. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.719390 · Cited by 23

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement**

Herp, D., Ridinger, J., Robaa, D., Shinsky, S. A., Schmidtkunz, K., Yesiloglu, T. Z., Bayer, T., Steimbach, R. R., Herbst‐Gervasoni, C. J., Merz, A., et al. (2022) · ChemBioChem · doi:10.1002/cbic.202200180 · Cited by 22

HDAC6 Degrades nsp8 of Porcine Deltacoronavirus through Deacetylation and Ubiquitination to Inhibit Viral Replication

Li, Z., Duan, P., Qiu, R., Fang, L., Fang, P., & Xiao, S. (2023) · Journal of Virology · doi:10.1128/jvi.00375-23 · Cited by 22

Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors

Reddy, D. R., Ballante, F., Zhou, N., & Marshall, G. R. (2016) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2016.12.032 · Cited by 22

Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies

Uba, A. İ., & Yelekçi, K. (2018) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2018.05.004 · Cited by 22

Acoustic mist ionization mass spectrometry (AMI-MS) as a drug discovery platform

Sinclair, I., Davies, G. M., & Semple, H. (2019) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2019.1613369 · Cited by 22

Synthesis and biological evaluation of selective histone deacetylase 6 inhibitors as multifunctional agents against Alzheimer's disease

Wang, X.-X., Xie, F., Jia, C.-C., Yan, N., Zeng, Y.-L., Wu, J.-D., & Liu, Z.-P. (2021) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2021.113821 · Cited by 23

Structure of Arabidopsis HISTONE DEACETYLASE15

Chen, C., Tu, Y., Hsu, J.-C., Hung, H.-C., Liu, T.-C., Lee, Y., Chou, C., Cheng, Y., & Wu, K. (2020) · PLANT PHYSIOLOGY · doi:10.1104/pp.20.00604 · Cited by 19

Loss of Deacetylation Enzymes Hdac6 and Sirt2 Promotes Acetylation of Cytoplasmic Tubulin, but Suppresses Axonemal Acetylation in Zebrafish Cilia

Lysyganicz, P. K., Pooranachandran, N., Liu, X., Adamson, K. I., Zielonka, K., Elworthy, S., van Eeden, F. J., Grierson, A. J., & Malicki, J. J. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.676214 · Cited by 19

Glutamylation is a negative regulator of microtubule growth

Chen, J., & Roll‐Mecak, A. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e23-01-0030 · Cited by 23

Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6)

Motlová, L., Šnajdr, I., Kutil, Z., Andris, E., Ptacek, J., Novotná, A., Nováková, Z., Havlínová, B., Tueckmantel, W., Dráberová, H., et al. (2023) · ACS Chemical Biology · doi:10.1021/acschembio.3c00212 · Cited by 14

Recent advances in epigenetic proteolysis targeting chimeras (Epi-PROTACs)

Tomaselli, D., Mautone, N., Mai, A., & Rotili, D. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112750 · Cited by 21

Structure-activity relationship study of thiazolyl-hydroxamate derivatives as selective histone deacetylase 6 inhibitors

Nam, G., Jung, J. M., Park, H., Baek, S. Y., Baek, K. S., Mok, H. Y., Kim, D. E., & Jung, Y. H. (2019) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2019.06.036 · Cited by 21

Novel pyrrolo[2,1-c][1,4]benzodiazepine-3,11-dione (PBD) derivatives as selective HDAC6 inhibitors to suppress tumor metastasis and invasion in vitro and in vivo

Li, Y., Quan, J., Song, H., Li, D., Ma, E., Wang, Y., & Ma, C. (2021) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2021.105081 · Cited by 20

HDAC6 finally crystal clear

Liu, Y., Li, L., & Min, J. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2158 · Cited by 20

Recent Advances in Small Molecular Modulators Targeting Histone Deacetylase 6

Xiao, Y., & Zhang, X. (2020) · Future Drug Discovery · doi:10.4155/fdd-2020-0023 · Cited by 20

Design of Selective Histone Deacetylase Inhibitors: Rethinking Classical Pharmacophore

Melesina, J., Praetorius, L., Simoben, C. V., Robaa, D., & Sippl, W. (2018) · Future Medicinal Chemistry · doi:10.4155/fmc-2018-0125 · Cited by 21

Structure-activity relationship and mechanistic studies for a series of cinnamyl hydroxamate histone deacetylase inhibitors

Tavares, M. T., de Almeida, L. C., Kronenberger, T., Ferreira, G. M., de Divitiis, T. F., Toledo, M. F. Z. J., Hassimotto, N. M. A., Machado‐Neto, J. A., Costa-Lotufo, L. V., & Parise‐Filho, R. (2021) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2021.116085 · Cited by 19

A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism

Lage‐Rupprecht, V., Schultz, B. T., Dick, J., Namysł, M., Zaliani, A., Gebel, S., Pleß, O., Reinshagen, J., Ellinger, B., Ebeling, C., et al. (2022) · Patterns · doi:10.1016/j.patter.2021.100433 · Cited by 19

Synthesis of aminophenylhydroxamate and aminobenzylhydroxamate derivatives and in vitro screening for antiparasitic and histone deacetylase inhibitory activity

Loeuillet, C., Touquet, B., Oury, B., Eddaikra, N., Pons, J.-L., Guichou, J., Labesse, G., & Séréno, D. (2018) · International Journal for Parasitology Drugs and Drug Resistance · doi:10.1016/j.ijpddr.2018.01.002 · Cited by 20

The histone deacetylase class I, II inhibitor trichostatin A delays peripheral neurodegeneration

Kim, M., Park, C., Jung, J., & Yeo, S. G. (2019) · Journal of Molecular Histology · doi:10.1007/s10735-019-09815-1 · Cited by 19

Design and Synthesis of sEH/HDAC6 Dual-Targeting Inhibitors for the Treatment of Inflammatory Pain

Xu, H., Chen, Y., Tong, H., Chen, L., Morisseau, C. H. P., Zhou, Z., Zhuang, J., Song, C., Cai, P., Liu, Z., et al. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c00847 · Cited by 18

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Simoben, C. V., Ghazy, E., Zeyen, P., Darwish, S., Schmidt, M., Romier, C., Robaa, D., & Sippl, W. (2021) · Molecules · doi:10.3390/molecules26092584 · Cited by 17

Molecular design, synthesis and in vitro biological evaluation of thienopyrimidine–hydroxamic acids as chimeric kinase HDAC inhibitors: a challenging approach to combat cancer

Abdel-Atty, M. M., Farag, N. A., Serya, R. A. T., Abouzid, K. A. M., & Mowafy, S. (2021) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2021.1933465 · Cited by 17

Histone deacetylase 6 inhibitors with blood-brain barrier penetration as a potential strategy for CNS-Disorders therapy

Gu, X. Q., Zhang, H., Jiao, M.-R., Han, B. R., Zhang, Z., Li, J., & Zhang, Q. (2021) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2021.114090 · Cited by 18

Discovery of BRAF/HDAC Dual Inhibitors Suppressing Proliferation of Human Colorectal Cancer Cells

Li, Y., Huang, Y., Cheng, H., Xu, F. L., Qi, R., Dai, B., Yang, Y., Tu, Z., Peng, L., & Zhang, Z. (2022) · Frontiers in Chemistry · doi:10.3389/fchem.2022.910353 · Cited by 17

Discovery of 1-Benzhydryl-Piperazine-Based HDAC Inhibitors with Anti-Breast Cancer Activity: Synthesis, Molecular Modeling, In Vitro and In Vivo Biological Evaluation

Ružić, D., Petkovic, M., Djoković, N., Santibanez, J. F., Ellinger, B., Beljkaš, M., Gul, S., Djuric, A., Ganesan, A., Pavić, A., et al. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14122600 · Cited by 17

Discovery of specific HDAC6 inhibitor with anti-metastatic effects in pancreatic cancer cells through virtual screening and biological evaluation

Song, H., Niu, X., Quan, J., Li, Y., Yuan, L., Wang, J., Ma, C., & Ma, E. (2020) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2020.103679 · Cited by 17

Aggresome–Autophagy Associated Gene HDAC6 Is a Potential Biomarker in Pan-Cancer, Especially in Colon Adenocarcinoma

Zhang, Z., Zhang, X., & Huang, A. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.718589 · Cited by 17

Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2

Marek, M., Ramos‐Morales, E., Picchi, G. F. A., Bayer, T., Norström, C., Herp, D., Sales-Junior, P. A., Guerra-Slompo, E. P., Hausmann, K., Chakrabarti, A., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110129 · Cited by 18

Constitutive β-Catenin Overexpression Represses Lncrna MIR100HG Transcription via HDAC6-Mediated Histone Modification in Colorectal Cancer

Peng, J., Ma, Y., Zhao, X., Yang, X., & Wang, H. (2022) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-21-0923 · Cited by 17

Development of Hydrazide-Based HDAC6 Selective Inhibitors for Treating NLRP3 Inflammasome-Related Diseases

Yue, K., Sun, S., Yin, Z., Liu, E., Jia, G., Jiang, Y., Duan, Y., Chen, Y., & Li, X. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c02883 · Cited by 16

Structure-based design generated novel hydroxamic acid based preferential HDAC6 lead inhibitor with on-target cytotoxic activity against primary choroid plexus carcinoma

Kassab, S. E., Mowafy, S., Alserw, A. M., Seliem, J. A., El‐Naggar, S., Omar, N. N., & Awad, M. M. (2019) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2019.1613987 · Cited by 16

Up-regulation of HDAC6 Results in Poor Prognosis and Chemoresistance in Patients With Advanced Ovarian High-grade Serous Carcinoma

Yano, M., Miyazawa, M., Ogane, N., Ogasawara, A., Hasegawa, K., Narahara, H., & Yasuda, M. (2021) · Anticancer Research · doi:10.21873/anticanres.14927 · Cited by 16

Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6

Watson, P. R., Bai, P., Wang, C., Cragin, A. D., Hooker, J. M., & Christianson, D. W. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00332 · Cited by 15

Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6

Harding, R., Franzoni, I., Mann, M. K., Szewczyk, M. M., Mirabi, B., de Freitas, R. F., Owens, D. D. G., Ackloo, S. Z., Scheremetjew, A., Juárez‐Ornelas, K. A., et al. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.3c00314 · Cited by 15

Rethinking tubulin acetylation: From regulation to cellular adaptation

Donker, L., & Godinho, S. A. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102512 · Cited by 14

Carbamates as Potential Prodrugs and a New Warhead for HDAC Inhibition

King, K., Hauser, A., Melesina, J., Sippl, W., & Jung, M. (2018) · Molecules · doi:10.3390/molecules23020321 · Cited by 15

Crystal Structure of a Histone Deacetylase Homologue from Pseudomonas aeruginosa

Krämer, A., Wagner, T., Yıldız, Ö., & Meyer‐Almes, F. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00613 · Cited by 14

Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6

Cellupica, E., Gaiassi, A., Rocchio, I., Rovelli, G., Pomarico, R., Sandrone, G., Caprini, G., Cordella, P., Cukier, C. D., Fossati, G., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25115885 · Cited by 14

Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations

Prejanò, M., Vidossich, P., Russo, N., Vivo, M. D., & Marino, T. (2021) · ACS Catalysis · doi:10.1021/acscatal.0c04729 · Cited by 15

Acetylated α-Tubulin and α-Synuclein: Physiological Interplay and Contribution to α-Synuclein Oligomerization

Calogero, A. M., Basellini, M. J., Isilgan, H. B., Longhena, F., Bellucci, A., Mazzetti, S., Rolando, C., Pezzoli, G., & Cappelletti, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241512287 · Cited by 13

Exploring new histone deacetylase 6 inhibitors and their effects on reversing the α-tubulin deacetylation and cell morphology changes caused by methamphetamine

Gupta, S., Ali, K. H., Lee, S., & Seo, Y. H. (2023) · Archives of Pharmacal Research · doi:10.1007/s12272-023-01467-w · Cited by 12

Preferential HDAC6 inhibitors derived from HPOB exhibit synergistic antileukemia activity in combination with decitabine

Tretbar, M., Schliehe‐Diecks, J., von Bredow, L., Tan, K., Roatsch, M., Tu, J., Kemkes, M., Sönnichsen, M., Schöler, A., Borkhardt, A., et al. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116447 · Cited by 11

Discovery of Janus Kinase and Histone Deacetylase Dual Inhibitors as a New Strategy to Treat Psoriasis

Hu, W., Shen, J., Zhou, C., Tai, Z., Zhu, Q., Chen, Z., Huang, Y., & Sheng, C. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c01681 · Cited by 13

Histone deacetylases and their inhibitors in kidney diseases

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Small-molecule compounds boost genome-editing efficiency of cytosine base editor

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