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Mondal P, Bai P, Gomm A, Bakiasi G, Lin CJ, Wang Y, Choi SH, Tanzi RE, Wang C, Zhang C. Structure-Based Discovery of A Small Molecule Inhibitor of Histone Deacetylase 6 (HDAC6) that Significantly Reduces Alzheimer's Disease Neuropathology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304545. [PMID: 37990786 PMCID: PMC10767396 DOI: 10.1002/advs.202304545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/27/2023] [Indexed: 11/23/2023]
Abstract
Histone deacetylase 6 (HDAC6) is one of the key histone deacetylases (HDACs) that regulates various cellular functions including clearance of misfolded protein and immunological responses. Considerable evidence suggests that HDAC6 is closely related to amyloid and tau pathology, the two primary hallmarks of Alzheimer's disease (AD). It is still unclear whether HDAC6 expression changes with amyloid deposition in AD during disease progression or HDAC6 may be regulating amyloid phagocytosis or neuroinflammation or other neuropathological changes in AD. In this work, the pathological accumulation of HDAC6 in AD brains over age as well as the relationship of its regulatory activity - with amyloid pathogenesis and pathophysiological alterations is aimed to be enlightened using the newly developed HDAC6 inhibitor (HDAC6i) PB118 in microglia BV2 cell and 3D-AD human neural culture model. Results suggest that the structure-based rational design led to biologically compelling HDAC6i PB118 with multiple mechanisms that clear Aβ deposits by upregulating phagocytosis, improve tubulin/microtubule network by enhancing acetyl α-tubulin levels, regulate different cytokines and chemokines responsible for inflammation, and significantly reduce phospho-tau (p-tau) levels associated with AD. These findings indicate that HDAC6 plays key roles in the pathophysiology of AD and potentially serves as a suitable pharmacological target through chemical biology-based drug discovery in AD.
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Affiliation(s)
- Prasenjit Mondal
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Ashley Gomm
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Grisilda Bakiasi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Chih‐Chung Jerry Lin
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Yanli Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Se Hoon Choi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General HospitalHarvard Medical SchoolBuilding 149, CharlestownBostonMA02129USA
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General HospitalHarvard Medical School BostonCharlestownBostonMA02114USA
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Mondal P, Chowdhury R, Nandi S, Amin MA, Bhattacharyya K, Ghosh S. Probing Deviation of Adhered Membrane Dynamics between Reconstituted Liposome and Cellular System. Chem Asian J 2019; 14:4616-4624. [PMID: 31210021 DOI: 10.1002/asia.201900588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/10/2019] [Indexed: 01/22/2023]
Abstract
The dynamics of cell-cell adhesion are complicated due to complexities in cellular interactions and intra-membrane interactions. In the present work, we have reconstituted a liposome-based model system to mimic the cell-cell adhesion process. Our model liposome system consists of one fluorescein-tagged and one TRITC (tetramethyl-rhodamine isothiocyanate)-tagged liposome, adhered through biotin-neutravidin interaction. We monitored the adhesion process in liposomes using Förster Resonance Energy Transfer (FRET) between fluorescein (donor) and TRITC (acceptor). Occurrence of FRET is confirmed by the decrease in donor lifetime as well as distinct rise time of the acceptor fluorescence. Interestingly, the acceptor's emission exhibits fluctuations in the range of ≈3±1 s. This may be attributed to structural oscillations associated in two adhered liposomes arising from the flexible nature of biotin-neutravidin interaction. We have compared the dynamics in a cell-mimicking liposome system with that in an in vitro live cell system. In the adhered live cell system, we used CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin, donor) and nile red (acceptor), which are known to stain the membrane of CHO (Chinese Hamster Ovary) cells. The dynamics of the adhered membranes of two live CHO cells were observed through FRET between CPM and nile red. The acceptor fluorescence intensity exhibits an oscillation in the time-scale of ≈1±0.75 s, which is faster compared to the reconstituted liposome system, indicating the contributions and involvement of multiple dynamic protein complexes around the cell membrane. This study offers simple reconstituted model systems to understand the complex membrane dynamics using a FRET-based physical chemistry approach.
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Affiliation(s)
- Prasenjit Mondal
- Organic & Medicinal Chemistry Division, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-, 700032, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-, 201002, India
| | - Rajdeep Chowdhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India.,Present Address: Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
| | - Somen Nandi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Md Asif Amin
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | | | - Surajit Ghosh
- Organic & Medicinal Chemistry Division, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-, 700032, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-, 201002, India
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Mondal P, Khan J, Gupta V, Ghosh S. In Silico Approach for Designing Potent Neuroprotective Hexapeptide. ACS Chem Neurosci 2019; 10:3018-3030. [PMID: 31117343 DOI: 10.1021/acschemneuro.9b00251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a constantly recurring neurodegenerative disease that deteriorates over a period of time. In this pathology, connections between neurons become extremely damaged due to the deposition of senile plaques in the membrane region, which results in abnormal signal transduction processes. Also, the intracellular microtubule networks are disrupted in the hyperphosphorylated tau cascade of AD. Therefore, design and development of potent neuroprotective molecules that can instantaneously target multiple facets of AD pathogenesis are greatly needed to tackle this unmet medical need. Here, we have implemented a pharmacophore based in silico analysis of various neuroprotective peptides known for neurotherapeutic application in AD. Fascinatingly, we have identified an active core of these peptides and designed a library of hexapeptides. We observed that peptide "LETVNQ" (LE6) has shown significant protection ability against degeneration of neurons. Experimental evidence suggests that this peptide immensely reduced the aggregation rate of amyloid-β (Aβ) and helped in microtubule polymerization. Intriguingly, this newly designed peptide does not have any cytotoxicity toward differentiated PC12 neurons; rather it helps in neurite outgrowth. Further, LE6 helps to maintain the complex microtubule network in cells by promoting the polymerization rate of intracellular microtubules and mediates excellent protection of neurons even after removal of nerve growth factor (NGF). Finally, we observed that this LE6 peptide has substantial stability under physiological conditions and helps to retain healthy morphology of primary rat cortical neurons. This excellent piece of work identifies a potent hexapeptide, which has exceptional ability to protect neurons as well as microtubule from degeneration and may become potent therapeutics against AD pathogenesis in the future.
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Affiliation(s)
- Prasenjit Mondal
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Juhee Khan
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
| | - Varsha Gupta
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700 032 WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Mondal P, Gupta V, Das G, Pradhan K, Khan J, Gharai PK, Ghosh S. Peptide-Based Acetylcholinesterase Inhibitor Crosses the Blood-Brain Barrier and Promotes Neuroprotection. ACS Chem Neurosci 2018; 9:2838-2848. [PMID: 30015476 DOI: 10.1021/acschemneuro.8b00253] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Design and development of acetylcholinesterase (AChE) inhibitor has tremendous implications in the treatment of Alzheimer's disease (AD). Here, we have adopted a computational approach for the design of a peptide based AChE inhibitor from its active site. We identified an octapeptide, which interacts with the catalytic anionic site (CAS) of AChE enzyme and inhibits its activity. Interestingly, this peptide also inhibits amyloid aggregation through its interaction at the 17-21 region of amyloid-beta (Aβ) and stabilizes microtubules by interacting with tubulin as well. Eventually, in the PC12 derived neurons, it shows noncytotoxicity, promotes neurite out-growth, stabilizes intracellular microtubules, and confers significant neuroprotection even upon withdrawal of nerve growth factor (NGF). Further, results reveal that this peptide possesses good serum stability, crosses the blood-brain barrier (BBB), and maintains the healthy architecture of the primary cortical neurons. This work shows discovery of an excellent peptide-based AChE inhibitor with additional potential as a microtubule stabilizer, which will pave the way for the development of potential anti-AD therapeutics in the near future.
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Affiliation(s)
- Prasenjit Mondal
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Varsha Gupta
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Gaurav Das
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnangsu Pradhan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Juhee Khan
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Prabir Kumar Gharai
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology Campus, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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Nandi S, Ghosh S, Bhattacharyya K. Live Cell Microscopy: A Physical Chemistry Approach. J Phys Chem B 2018; 122:3023-3036. [PMID: 29389140 DOI: 10.1021/acs.jpcb.7b11689] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing dynamics of intracellular components using physical chemistry techniques is a remarkable bottom-up approach for understanding the structures and functions of a biological cell. In this "Feature Article", we give an overview on local polarity, solvation, viscosity, acid-base property, red-ox processes (thiol-disulfide exchange), and gene silencing at selected intracellular components inside a live cell. Significant differences have been observed between cancer cells and their noncancer counterparts. We demonstrate that thiol-disulfide exchange, calcium oscillation, and gene silencing are manifested in time dependence of fluorescence intensity. We show that fluorescent gold nanoclusters may be used in drug delivery (e.g., doxorubicin) and selective killing of cancer cells. Further, we discuss dynamics and structural changes of DNA quadruplexes and i-motifs, induced by different external conditions (e.g., pH) and additives (e.g., K+ and other target specific small molecules). We demonstrate that peptidomimetic analogues have high specificity over double-stranded DNA for binding with i-motifs and G-quadruplexes. These results may have significant biological implications.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Jadavpur, Kolkata , 700 032 West Bengal , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-Indian Institute of Chemical Biology Campus , 4 Raja S. C. Mullick Road , Jadavpur, Kolkata 700 032 , India
| | - Kankan Bhattacharyya
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal , 462 066 Madhya Pradesh , India
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Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. NANOSCALE 2016; 8:19928-19944. [PMID: 27883140 PMCID: PMC5145784 DOI: 10.1039/c6nr06794h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.
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Affiliation(s)
- Dibyendu K Sasmal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura E Pulido
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Shan Kasal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Jun Huang
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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Chattoraj S, Bhattacharyya K. Biological oscillations: Fluorescence monitoring by confocal microscopy. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bhunia D, Chowdhury R, Bhattacharyya K, Ghosh S. Fluorescence fluctuation of an antigen-antibody complex: circular dichroism, FCS and smFRET of enhanced GFP and its antibody. Phys Chem Chem Phys 2016; 17:25250-9. [PMID: 26353083 DOI: 10.1039/c5cp04908c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure and dynamics of an antigen-antibody complex are monitored by circular dichroism (CD) spectroscopy, fluorescence correlation spectroscopy (FCS) and single molecule FRET (smFRET). In this work, the antigen is enhanced GFP (EGFP) and the antibody is anti-EGFP VHH-His6. From FCS measurements, the hydrodynamic radius (rH) of EGFP and its antibody (VHH-His6) is found to be 24 ± 2 Å and 18 ± 2 Å, respectively. For the antigen-antibody complex (EGFP:anti-EGFP VHH-His6), rH is 41 ± 3 Å. CD spectra indicate that the addition of guanidium hydrochloride (GdnHCl) causes unfolding of the antigen, its antibody and their complex, and a consequent increase in size is observed from FCS data. smFRET between EGFP (donor, D) and Alexa 594 (acceptor, A) bound to anti-EGFP VHH-His6 reveals a time dependent fluctuation in donor-acceptor distances. This suggests that the structure of the antigen-antibody complex is dynamic in nature and is not rigid.
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Affiliation(s)
- Debmalya Bhunia
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-700032, India.
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Ghosh C, Bhunia D, Ghosh S, Jana B, Ghosh S, Bhattacharyya K. Fluorescence Probing of Fluctuating Microtubule using a Covalent Fluorescent Probe: Effect of Taxol. ChemistrySelect 2016. [DOI: 10.1002/slct.201600353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Catherine Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Debmalya Bhunia
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
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Ghosh S, Bhattacharyya K. Single-molecule Spectroscopy: Exploring Heterogeneity in Chemical and Biological Systems. CHEM REC 2016; 16:601-13. [DOI: 10.1002/tcr.201500214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; 2A and 2B, Raja Subodh Chandra Mullick Rd Jadavpur, Kolkata West Bengal 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; 2A and 2B, Raja Subodh Chandra Mullick Rd Jadavpur, Kolkata West Bengal 700032 India
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