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Chakraborty I, Kar RK, Sarkar D, Kumar S, Maiti NC, Mandal AK, Bhunia A. Solvent Relaxation NMR: A Tool for Real-Time Monitoring Water Dynamics in Protein Aggregation Landscape. ACS Chem Neurosci 2021; 12:2903-2916. [PMID: 34292711 DOI: 10.1021/acschemneuro.1c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Solvent dynamics strongly induce the fibrillation of an amyloidogenic system. Probing the solvation mechanism is crucial as it enables us to predict different proteins' functionalities, such as the aggregation propensity, structural flexibility, and toxicity. This work shows that a straightforward NMR method in conjunction with phenomenological models gives a global and qualitative picture of water dynamics at different concentrations and temperatures. Here, we study amyloid system Aβ40 and its fragment AV20 (A21-V40) and G37L (mutation at Gly37 → Leu of AV20), having different aggregation and toxic properties. The independent validation of this method is elucidated using all-atom classical MD simulation. These two state-of-the-art techniques are pivotal in linking the effect of solvent environment in the near hydration-shell to their aggregation nature. The time-dependent modulation in solvent dynamics probed with the NMR solvent relaxation method can be further adopted to gain insight into amyloidogenesis and link with their toxicity profiles.
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Affiliation(s)
| | - Rajiv K. Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Dibakar Sarkar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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Dolai G, Giri RS, Roy S, Mandal B. Crystal structure and supramolecular arrangement of heterochiral tripeptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gobinda Dolai
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Rajat Subhra Giri
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Sayanta Roy
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Bhubaneswar Mandal
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
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Paul A, Viswanathan GK, Huber A, Arad E, Engel H, Jelinek R, Gazit E, Segal D. Inhibition of tau amyloid formation and disruption of its preformed fibrils by Naphthoquinone-Dopamine hybrid. FEBS J 2021; 288:4267-4290. [PMID: 33523571 DOI: 10.1111/febs.15741] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/02/2021] [Accepted: 01/28/2021] [Indexed: 01/10/2023]
Abstract
Misfolding and aggregation of tau protein, into pathological amyloids, are hallmarks of a group of neurodegenerative diseases collectively termed tauopathies and their modulation may be therapeutically valuable. Herein, we describe the synthesis and characterization of a dopamine-based hybrid molecule, naphthoquinone-dopamine (NQDA). Using thioflavin S assay, CD, transmission electron microscopy, dynamic light scattering, Congo Red birefringence, and large unilamellar vesicle leakage assays, we demonstrated its efficacy in inhibiting the in vitro aggregation of key tau-derived amyloidogenic fragments, PHF6 (VQIVYK) and PHF6* (VQIINK), prime drivers of aggregation of full-length tau in disease pathology. Isothermal titration calorimetry analysis revealed that the interaction between NQDA and PHF6 is spontaneous and has significant binding efficiency driven by both entropic and enthalpic processes. Furthermore, NQDA efficiently disassembled preformed fibrils of PHF6 and PHF6* into nontoxic species. Molecular dynamic simulations supported the in vitro results and provided a plausible mode of binding of NQDA with PHF6 fibril. NQDA was also capable of inhibiting the aggregation of full-length tau protein and disrupting its preformed fibrils in vitro in a dose-dependent manner. In a comparative study, the IC50 value (50% inhibition of fibril formation) of NQDA in inhibiting the aggregation of PHF6 (25 µm) was ~ 17 µm, which is lower than for other bona fide amyloid inhibitors, naphthoquinone-tryptophan, rosmarinic acid, epigallocatechin gallate, ~ 21, ~ 77, or ~ 19 µm, respectively. Comparable superiority of NQDA was observed for inhibition of PHF6*. These findings suggest that NQDA can be a useful scaffold for designing new therapeutics for Alzheimer's disease and other tauopathies.
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Affiliation(s)
- Ashim Paul
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Guru KrishnaKumar Viswanathan
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Adi Huber
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology & Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Hamutal Engel
- Blavatnik Center for Drug Discovery, Tel Aviv University, Israel
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology & Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel.,Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel.,Sagol Interdisciplinary School of Neuroscience, Tel Aviv University, Israel
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Kalita S, Kalita S, Paul A, Shah M, Kumar S, Mandal B. Site-specific single point mutation by anthranilic acid in hIAPP 8-37 enhances anti-amyloidogenic activity. RSC Chem Biol 2021; 2:266-273. [PMID: 34458787 PMCID: PMC8341151 DOI: 10.1039/d0cb00178c] [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: 10/03/2020] [Accepted: 12/24/2020] [Indexed: 12/01/2022] Open
Abstract
Amylin or hIAPP, together with insulin, plays a significant role in glucose metabolism. However, it undergoes β-sheet rich amyloid formation associated with pancreatic β-cell dysfunction leading to type-2 diabetes (T2D). Recent studies suggest that restricting β-sheet formation in it may halt amyloid formation, which may limit the risk for the disease. Several peptide-based inhibitors have been reported to prevent aggregation. However, most of them have limitations, including low binding efficiency, active only at higher doses, poor solubility, and proteolytic degradation. Insertion of non-coded amino acids renders proteolytically stable peptides. We incorporated a structurally rigid β-amino acid, Anthranilic acid (Ant), at different sites within the central hydrophobic region of hIAPP and developed two singly mutated hIAPP8–37 peptidomimetics. These peptidomimetics inhibited the amyloid formation of hIAPP substantially even at low concentration, as evident from in vitro ThT, CD, FT-IR, TEM, and Congo red staining birefringence results. These peptidomimetics also disrupted the preformed aggregates formed by hIAPP into non-toxic species. These β-amino acid-based peptidomimetics can be an attractive scaffold for therapeutic design towards T2D or other protein misfolding diseases. β-Amino acid based peptidomimetics are attractive scaffolds for therapeutics design towards T2D. They prevent amyloid formation of hIAPP by forming non-fibrillar non-toxic aggregates.![]()
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Affiliation(s)
- Sourav Kalita
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati Assam-781039 India
| | - Sujan Kalita
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati Assam-781039 India
| | - Ashim Paul
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati Assam-781039 India
| | - Manisha Shah
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati Assam-781039 India
| | - Sachin Kumar
- Department of Biosciences & Bioengineering, Indian Institute of Technology Guwahati Assam-781039 India
| | - Bhubaneswar Mandal
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati Assam-781039 India
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Samanta S, Rajasekhar K, Ramesh M, Murugan NA, Alam S, Shah D, Clement JP, Govindaraju T. Naphthalene Monoimide Derivative Ameliorates Amyloid Burden and Cognitive Decline in a Transgenic Mouse Model of Alzheimer's Disease. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202000225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sourav Samanta
- Bioorganic Chemistry Laboratory New Chemistry Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - Kolla Rajasekhar
- Bioorganic Chemistry Laboratory New Chemistry Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - Madhu Ramesh
- Bioorganic Chemistry Laboratory New Chemistry Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - Natarajan Arul Murugan
- Department of Theoretical Chemistry and Biology School of Chemistry Biotechnology and Health KTH Royal Institute of Technology S‐106 91 Stockholm Sweden
| | - Shadab Alam
- Bioorganic Chemistry Laboratory New Chemistry Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - Devanshi Shah
- Neuroscience Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - James Premdas Clement
- Neuroscience Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory New Chemistry Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P.O. Bengaluru 560064 India
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Paul A, Kumar S, Kalita S, Kalita S, Sarkar D, Bhunia A, Bandyopadhyay A, Mondal AC, Mandal B. An explicitly designed paratope of amyloid-β prevents neuronal apoptosis in vitro and hippocampal damage in rat brain. Chem Sci 2020; 12:2853-2862. [PMID: 34164050 PMCID: PMC8179358 DOI: 10.1039/d0sc04379f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Synthetic antibodies hold great promise in combating diseases, diagnosis, and a wide range of biomedical applications. However, designing a therapeutically amenable, synthetic antibody that can arrest the aggregation of amyloid-β (Aβ) remains challenging. Here, we report a flexible, hairpin-like synthetic paratope (SP1, ∼2 kDa), which prevents the aggregation of Aβ monomers and reverses the preformed amyloid fibril to a non-toxic species. Structural and biophysical studies further allowed dissecting the mode and affinity of molecular recognition events between SP1 and Aβ. Subsequently, SP1 reduces Aβ-induced neurotoxicity, neuronal apoptosis, and ROS-mediated oxidative damage in human neuroblastoma cells (SH-SY5Y). The non-toxic nature of SP1 and its ability to ameliorate hippocampal neurodegeneration in a rat model of AD demonstrate its therapeutic potential. This paratope engineering module could readily implement discoveries of cost-effective molecular probes to nurture the basic principles of protein misfolding, thus combating related diseases.
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Affiliation(s)
- Ashim Paul
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati (IITG) North Guwahati Assam-781039 India
| | - Sourav Kumar
- Neuroscience Research Unit, Department of Physiology, Raja Peary Mohan College Hooghly Uttarpara West Bengal-712258 India
| | - Sujan Kalita
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati (IITG) North Guwahati Assam-781039 India
| | - Sourav Kalita
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati (IITG) North Guwahati Assam-781039 India
| | - Dibakar Sarkar
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Anirban Bhunia
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Anupam Bandyopadhyay
- Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Punjab-140001 India
| | - Amal Chandra Mondal
- Neuroscience Research Unit, Department of Physiology, Raja Peary Mohan College Hooghly Uttarpara West Bengal-712258 India .,Laboratory of Cellular & Molecular Neurobiology, School of Life Sciences, Jawaharlal Nehru University New Delhi-110 067 India
| | - Bhubaneswar Mandal
- Laboratory of Peptide and Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati (IITG) North Guwahati Assam-781039 India
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Ding Y, Ting JP, Liu J, Al-Azzam S, Pandya P, Afshar S. Impact of non-proteinogenic amino acids in the discovery and development of peptide therapeutics. Amino Acids 2020; 52:1207-1226. [PMID: 32945974 PMCID: PMC7544725 DOI: 10.1007/s00726-020-02890-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
With the development of modern chemistry and biology, non-proteinogenic amino acids (NPAAs) have become a powerful tool for developing peptide-based drug candidates. Drug-like properties of peptidic medicines, due to the smaller size and simpler structure compared to large proteins, can be changed fundamentally by introducing NPAAs in its sequence. While peptides composed of natural amino acids can be used as drug candidates, the majority have shown to be less stable in biological conditions. The impact of NPAA incorporation can be extremely beneficial in improving the stability, potency, permeability, and bioavailability of peptide-based therapies. Conversely, undesired effects such as toxicity or immunogenicity should also be considered. The impact of NPAAs in the development of peptide-based therapeutics is reviewed in this article. Further, numerous examples of peptides containing NPAAs are presented to highlight the ongoing development in peptide-based therapeutics.
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Affiliation(s)
- Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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