1
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Hou J, Lu Y, Chen Q, Liao X, Wu X, Sang K, White JC, Gardea-Torresdey JL, Xu J, Zhang J, Yang K, Zhu L, Lin D. Multifunctional biomolecular corona-inspired nanoremediation of antibiotic residues. Proc Natl Acad Sci U S A 2024; 121:e2409955121. [PMID: 39190351 PMCID: PMC11388419 DOI: 10.1073/pnas.2409955121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Facing complex and variable emerging antibiotic pollutants, the traditional development of functional materials is a "trial-and-error" process based on physicochemical principles, where laborious steps and long timescales make it difficult to accelerate technical breakthroughs. Notably, natural biomolecular coronas derived from highly tolerant organisms under significant contamination scenarios can be used in conjunction with nanotechnology to tackling emerging contaminants of concern. Here, super worms (Tubifex tubifex) with high pollutant tolerance were integrated with nano-zero valent iron (nZVI) to effectively reduce the content of 17 antibiotics in wastewater within 7 d. Inspired by the synergistic remediation, nZVI-augmented worms were constructed as biological nanocomposites. Neither nZVI (0.3 to 3 g/L) nor worms (104 to 105 per liter) alone efficiently degraded florfenicol (FF, as a representative antibiotic), while their composite removed 87% of FF (3 μmol/L). Under antibiotic exposure, biomolecules secreted by worms formed a corona on and modified the nZVI particle surface, enabling the nano-bio interface greater functionality, including responsiveness, enrichment, and reduction. Mechanistically, FF exposure activated glucose-alanine cycle pathways that synthesize organic acids and amines as major metabolites, which were assembled into vesicles and secreted, thereby interacting with nZVI in a biologically response design strategy. Lactic acid and urea formed hydrogen bonds with FF, enriched analyte presence at the heterogeneous interface. Succinic and lactic acids corroded the nZVI passivation layer and promoted electron transfer through surface conjugation. This unique strategy highlights biomolecular coronas as a complex resource to augment nano-enabled technologies and will provide shortcuts for rational manipulation of nanomaterial surfaces with coordinated multifunctionalities.
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Affiliation(s)
- Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Yuqi Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Qiqi Chen
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Liao
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kaijian Sang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT 06511
| | | | - Jiang Xu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jianying Zhang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- National Demonstration Center for Experimental Environment and Resources Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Lizhong Zhu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
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2
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Fasola E, Alboreggia G, Pieraccini S, Oliva F, Agharbaoui FE, Bollati M, Bertoni G, Recchia S, Marelli M, Piarulli U, Pellegrino S, Gazzola S. Conformational switch and multiple supramolecular structures of a newly identified self-assembling protein-mimetic peptide from Pseudomonas aeruginosa YeaZ protein. Front Chem 2022; 10:1038796. [PMID: 36583150 PMCID: PMC9792601 DOI: 10.3389/fchem.2022.1038796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein-mimetic peptides (PMPs) are shorter sequences of self-assembling proteins, that represent remarkable building blocks for the generation of bioinspired functional supramolecular structures with multiple applications. The identification of novel aminoacidic sequences that permit the access to valuable biocompatible materials is an attractive area of research. In this work, in silico analysis of the Pseudomonas aeruginosa YeaZ protein (PaYeaZ) led to the identification of a tetradecapeptide that represents the shortest sequence responsible for the YeaZ-YeaZ dimer formation. Based on its sequence, an innovative 20-meric peptide, called PMP-2, was designed, synthesized, and characterized in terms of secondary structure and self-assembly properties. PMP-2 conserves a helical character and self-assembles into helical nanofibers in non-polar solvents (DMSO and trifluoroethanol), as well as in dilute (0.5 mM) aqueous solutions. In contrast, at higher concentrations (>2 mM) in water, a conformational transition from α-helix to β-sheet occurs, which is accompanied by the Protein-mimetic peptide aggregation into 2D-sheets and formation supramolecular gel in aqueous environment. Our findings reveal a newly identified Protein-mimetic peptide that could turn as a promising candidate for future material applications.
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Affiliation(s)
- Elettra Fasola
- Science and High Technology Department, University of Insubria, Como, Italy
| | - Giulia Alboreggia
- Science and High Technology Department, University of Insubria, Como, Italy
| | | | | | | | - Michela Bollati
- CNR and Department of Biosciences, Institute of Biophysics, University of Milan, Milan, Italy
| | | | - Sandro Recchia
- Science and High Technology Department, University of Insubria, Como, Italy
| | - Marcello Marelli
- CNR-SCITEC—Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Milan, Italy
| | - Umberto Piarulli
- Science and High Technology Department, University of Insubria, Como, Italy,*Correspondence: Umberto Piarulli, ; Silvia Gazzola,
| | - Sara Pellegrino
- Pharmaceutical Science Department, University of Milan, Milan, Italy
| | - Silvia Gazzola
- Science and High Technology Department, University of Insubria, Como, Italy,*Correspondence: Umberto Piarulli, ; Silvia Gazzola,
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3
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Tang M, Liu YH, Liu H, Mao Q, Yu Q, Kitagishi H, Zhang YM, Xiao L, Liu Y. Supramolecular Dual Polypeptides Induced Tubulin Aggregation for Synergistic Cancer Theranostics. J Med Chem 2022; 65:13473-13481. [DOI: 10.1021/acs.jmedchem.2c01398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mian Tang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yao-Hua Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Hua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Qiyue Mao
- Department of Molecular Chemistry and Biochemistry, Doshisha University, Kyoto 610-0321, Japan
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Doshisha University, Kyoto 610-0321, Japan
| | - Ying-Ming Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, P. R. China
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4
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Mukherjee N, Roy R, Ghosh S, Ghosh S. Self‐Assembled Antimitotic Peptide Vesicle Designed from
α
,
β
‐Tubulin Heterodimer Interface for Anticancer Drug Delivery. Isr J Chem 2022. [DOI: 10.1002/ijch.202200019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nabanita Mukherjee
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India
| | - Satyajit Ghosh
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India
| | - Surajit Ghosh
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India
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5
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Abstract
Preserving the integrity of neuronal microtubules (MTs) has emerged as a promising strategy to inhibit the progression of neurodegenerative disorders such as Alzheimer's disease. Such a goal could be achieved by peptides that mimic the functional role of Tau, an MT-associated protein that stabilizes MTs by dynamically binding to their outer surface. This work examines the binding properties and MT-stabilizing potential of a 27-amino acid Tau oligopeptide from 300 ns Gaussian-accelerated molecular dynamics simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations on octameric MT models bound to two equivalent and independent Tau peptides. Bound peptides adopted extended conformations that are highly consistent with cryo-electron microscopy reports for full-length Tau bound to MTs. Anchoring points in three consecutive tubulin subunits were identified, with a relevant contribution of the Ser419-Val435 region to α-tubulin. Tau peptides strengthen the longitudinal protein-protein contacts within the MT lattice and exert a cooperative MT-stabilizing effect in MT complexes simultaneously bonded to taxol or peloruside A. Ser phosphorylation results in a larger peptide mobility, altered interaction profiles, and MT destabilization, which are in line with the loss of MT integrity resulting from the post-translational hyperphosphorylation of Tau. Our results shed light on the MT-stabilizing potential of Tau-mimetic peptides to act as novel neuroprotective agents targeting MTs.
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Affiliation(s)
- Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, Talcahuano 7100, Chile
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6
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Jana B, Barman S, Roy R, Das G, Mukherjee N, Adak A, Ghosh S. Fluorine Substituted Proline Enhances the Tubulin Binding Potential of a Tetrapeptide at the GTP Binding Pocket Causing the Inhibition of Microtubule Motility and an Antimitotic Effect. J Phys Chem B 2021; 125:8768-8780. [PMID: 34328335 DOI: 10.1021/acs.jpcb.1c04323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microtubule is regarded as the key target for designing anticancer and neurotherapeutic drugs due to its functional importance in eukaryotic cells including neurons. The microtubule is a dynamic hollow polymer tube consisting of α,β-tubulin heterodimer. Polymerization of α,β-tubulin heterodimer resulted in microtubule formation. GTP plays a crucial role in microtubule polymerization. It binds at the exchangeable binding site of the β-tubulin heterodimer, and it is one of the most crucial therapeutic hot spots for designing anticancer therapeutics. In this manuscript, we have shown using an in silico strategy and various in vitro and cellular experiments that the binding affinity to the tubulin and cancer therapeutic potential of an exchangeable GTP/GDP binding antimitotic tetrapeptide (SP: Ser-Leu-Arg-Pro) is increased through changing proline with the multifluorine substituted proline. This study showcases the importance of the proline amino acid and its pyrrolidine ring in the regulation of binding with tubulin at the GTP binding pocket.
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Affiliation(s)
- Batakrishna Jana
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Barman
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Nabanita Mukherjee
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Anindyasundar Adak
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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7
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Navarrete KR, Jiménez VA. Interdimeric Curvature in Tubulin-Tubulin Complexes Delineates the Microtubule-Destabilizing Properties of Plocabulin. J Chem Inf Model 2020; 60:4076-4084. [PMID: 32687349 DOI: 10.1021/acs.jcim.0c00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plocabulin is a novel microtubule (MT) destabilizer agent with potent antineoplastic activity. This compound binds to the maytansine site at the longitudinal interface between tubulin dimers and exerts a hinge-like effect that disrupts normal microtubule assembly. Plocabulin has emerged as a valuable model for the rational design of novel MT destabilizers because of its unique structural and mechanistic features. To make progress on this matter, detailed molecular-level understanding of the ligand-protein interactions responsible for plocabulin association and the conformation and energetic effects arising from plocabulin binding on the longitudinal interaction between tubulin dimers must be provided. In this work, fully atomistic MD simulations and MM/GBSA binding free-energy calculations were used to examine the association of plocabulin to one or two tubulin dimers in longitudinal arrangement. Our results revealed that plocabulin binding is favored by the addition of a second tubulin dimer and that this ligand promotes the assembly of curved tetrameric arrangements with strengthened longitudinal interdimeric interactions compared to ligand-free systems. The applicability of these findings to the rational discovery of novel MT destabilizers was tested using MD and MM/GBSA calculations as filtering tools to narrow the results of virtual screening among an FDA-approved drug database. Our results confirmed that tight-binding ligands do not necessarily exert the expected conformational and energetic effects on longitudinal tubulin-tubulin interactions, which is a matter to consider in future design strategies.
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Affiliation(s)
- Karen R Navarrete
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
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8
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Inaba H, Yamamoto T, Iwasaki T, Kabir AMR, Kakugo A, Sada K, Matsuura K. Fluorescent Tau-derived Peptide for Monitoring Microtubules in Living Cells. ACS OMEGA 2019; 4:11245-11250. [PMID: 31460226 PMCID: PMC6648849 DOI: 10.1021/acsomega.9b01089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/18/2019] [Indexed: 06/04/2023]
Abstract
Microtubules (MTs) are key cytoskeletal components that modulate various cellular activities with their dynamic structural changes, including polymerization and depolymerization. To monitor the dynamics of MTs in living cells, many drug-based fluorescent probes have been developed; however, these also potentially disturb the polymerization/depolymerization of MTs. Here, we report nondrug, peptide-based fluorescent probes to monitor MTs in living cells. We employed a Tau-derived peptide (TP) that has been shown to bind MTs without inhibiting polymerization/depolymerization in vitro. We show that a tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs as clear, fibrous structures. The binding of TP-TMR shows no apparent effects on polymerization/depolymerization of MTs induced by MT-targeted drugs and temperature change. The main uptake mechanism of TP-TMR was elucidated as endocytosis, and partial endosomal escape resulted in the binding of TP-TMR to MTs. TP-TMR exhibited no cytotoxicity compared with MT-targeted drug scaffolds. These results indicate that TP scaffolds can be exploited as useful MT-targeted tools in living cells, such as in long-term imaging of MTs.
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Affiliation(s)
- Hiroshi Inaba
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takahisa Yamamoto
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Takashi Iwasaki
- Department
of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Koyama-Minami 4-101, Tottori 680-8553, Japan
| | - Arif Md. Rashedul Kabir
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science and Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazunori Matsuura
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and Centre for Research
on Green Sustainable Chemistry, Tottori
University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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9
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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10
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019; 58:10553-10557. [DOI: 10.1002/anie.201903243] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/04/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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11
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Gandini E, Dapiaggi F, Oliva F, Pieraccini S, Sironi M. Well-Tempered MetaDynamics based method to evaluate universal peptidomimetics. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Jana B, Mondal P, Saha A, Adak A, Das G, Mohapatra S, Kurkute P, Ghosh S. Designed Tetrapeptide Interacts with Tubulin and Microtubule. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1123-1132. [PMID: 28558224 DOI: 10.1021/acs.langmuir.7b01326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microtubules regulate eukaryotic cell functions, which have tremendous implication in tumor progression. Thus, the design of novel approaches for controlling microtubule function is extremely important. In this manuscript, a novel tetrapeptide Ser-Leu-Arg-Pro (SLRP) has been designed and synthesized from a small peptide library consisting of 14 tetrapeptides, which perturbs microtubule function through interaction in the "anchor region". We have studied the role of peptides on microtubule function on a chemically functionalized 2D platform. Interestingly, we have found that SLRP binds with tubulin and inhibits the kinesin-driven microtubule motility on a kinesin-immobilized chemically functionalized 2D platform. Further, this peptide modulator interacts with intracellular tubulin/microtubule and depolymerizes the microtubule networks. These interesting findings of perturbation of microtubule function both on engineered platforms and inside the cell by this small peptide modulator inspired us to study the effect of this tetrapeptide on cancer cell proliferation. We found that the novel tetrapeptide modulator causes moderate cytotoxicity to the human breast cancer cell (MCF-7 cell), induces the apoptotic death of MCF-7 cell, and activates the tumor suppressor proteins p53 and cyclin-dependent kinase inhibitor 1 (p21). To the best of our knowledge, this is the shortest peptide discovered, which perturbs microtubule function both on an engineered 2D platform and inside the cell.
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Affiliation(s)
- Batakrishna Jana
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Prasenjit Mondal
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Abhijit Saha
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Anindyasundar Adak
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Gaurav Das
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saswat Mohapatra
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Prashant Kurkute
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
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13
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Chan JV, Ping Koh DX, Liu Y, Joseph TL, Lane DP, Verma CS, Tan YS. Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53. Oncotarget 2017; 8:112825-112840. [PMID: 29348869 PMCID: PMC5762554 DOI: 10.18632/oncotarget.22829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023] Open
Abstract
Murine double minute 4 protein (MDMX) is crucial for the regulation of the tumor suppressor protein p53. Phosphorylation of the N-terminal domain of MDMX is thought to affect its binding with the transactivation domain of p53, thus playing a role in p53 regulation. In this study, the effects of MDMX phosphorylation on the binding of p53 were investigated using molecular dynamics simulations. It is shown that in addition to the previously proposed mechanism in which phosphorylated Y99 of MDMX inhibits p53 binding through steric clash with P27 of p53, the N-terminal lid of MDMX also appears to play an important role in regulating the phosphorylation-dependent interactions between MDMX and p53. In the proposed mechanism, phosphorylated Y99 aids in pulling the lid into the p53-binding pocket, thus inhibiting the binding between MDMX and p53. Rebinding of p53 appears to be facilitated by the subsequent phosphorylation of Y55, which draws the lid away from the binding pocket by electrostatic attraction of the lid's positively charged N-terminus. The ability to target these mechanisms for the proper regulation of p53 could have important implications for understanding cancer biology and for drug development.
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Affiliation(s)
- Jane Vin Chan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Dawn Xin Ping Koh
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Yun Liu
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Thomas L Joseph
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
| | - David P Lane
- p53 Laboratory, Agency for Science, Technology and Research (ASTAR), Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore
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14
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Mohapatra S, Saha A, Mondal P, Jana B, Ghosh S, Biswas A, Ghosh S. Synergistic Anticancer Effect of Peptide-Docetaxel Nanoassembly Targeted to Tubulin: Toward Development of Dual Warhead Containing Nanomedicine. Adv Healthc Mater 2017; 6. [PMID: 27782376 DOI: 10.1002/adhm.201600718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/12/2016] [Indexed: 01/09/2023]
Abstract
Microtubule dynamics play a crucial role in cancer cell division. Various drugs are developed to target microtubule. Although a few of them show potential in treatment of cancer, but success rate is limited due to their poor bioavailability and lack of specificity. Thus, development of highly bioavailable and target specific anticancer drug is extremely necessary. To address these key issues, here, a combination of approaches such as development of a dodecapeptide-docetaxel nanoassembly targeted to tubulin and MUC1 (mucin 1, cell surface associated glycoprotein) targeting oligonucleotide aptamer conjugated liposome for delivering peptide-docetaxel nanoassembly into the breast cancer cell have been demonstrated. These studies reveal that the peptide forms nanoassembly and entraps docetaxel drug. Further, the liposomal formulation of peptide-docetaxel exerts synergistic anticancer effect, activates key mitotic check point proteins, and inhibits bipolar spindle formation, metastatic cancer cell migration, and growth of tumor mimicking 3D multicellular spheroid.
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Affiliation(s)
- Saswat Mohapatra
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 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 700 032 West Bengal India
| | - Abhijit Saha
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 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 700 032 West Bengal India
| | - Batakrishna Jana
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Subhajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Atanu Biswas
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 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 700 032 West Bengal India
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15
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Dapiaggi F, Pieraccini S, Potenza D, Vasile F, Macut H, Pellegrino S, Aliverti A, Sironi M. Computer aided design and NMR characterization of an oligopeptide targeting the Ebola virus VP24 protein. NEW J CHEM 2017. [DOI: 10.1039/c6nj04014d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nona-peptide RS, designed on the basis of computational studies, is able to interact with Ebola VP24 and potentially inhibit its interaction with KPNA.
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Affiliation(s)
| | - Stefano Pieraccini
- Dipartimento di Chimica
- Università degli Studi di Milano
- Milano
- Italy
- Istituto di Scienze e Tecnologie Molecolari (INSTM)
| | | | - Francesca Vasile
- Dipartimento di Chimica
- Università degli Studi di Milano
- Milano
- Italy
| | - Helena Macut
- DISFARM-Dipartimento di Scienze Farmaceutiche
- Sezione Chimica Generale e Organica “A. Marchesini”
- Milano
- Italy
| | - Sara Pellegrino
- DISFARM-Dipartimento di Scienze Farmaceutiche
- Sezione Chimica Generale e Organica “A. Marchesini”
- Milano
- Italy
| | | | - Maurizio Sironi
- Dipartimento di Chimica
- Università degli Studi di Milano
- Milano
- Italy
- Istituto di Scienze e Tecnologie Molecolari (INSTM)
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16
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Microtubule Destabilization Paves the Way to Parkinson's Disease. Mol Neurobiol 2016; 54:6762-6774. [PMID: 27757833 DOI: 10.1007/s12035-016-0188-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/30/2016] [Indexed: 01/20/2023]
Abstract
Microtubules are dynamic structures normally associated to the cell division, during which they form the mitotic spindle, as well as to the initial phases of specification and polarization of various cell types, including neurons. Although microtubules could have a role in the death of many cells and tissues, the microtubule-based degenerative mechanisms have been poorly investigated; nevertheless, during the last two decades, many clues have been accumulated suggesting the importance of the microtubule system during neurodegeneration. Thus, the aim of this review is to analyse how the changes of the microtubule cytoskeleton, in terms of organization and dynamics, as well as the failure of the microtubule-dependent neuronal processes, as axonal transport, may play a pivotal role in the chain of events leading to Parkinson's disease. Last but not least, since disease-modifying or neuroprotective strategies are a clinical priority in Parkinson's disease, we will also present the hints about the concrete possibility of a microtubule-targeted therapy, which would have the potentiality to block the running degenerative events and to prompt the regeneration of the lost tissues.
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17
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Jana B, Mohapatra S, Mondal P, Barman S, Pradhan K, Saha A, Ghosh S. α-Cyclodextrin Interacts Close to Vinblastine Site of Tubulin and Delivers Curcumin Preferentially to the Tubulin Surface of Cancer Cell. ACS APPLIED MATERIALS & INTERFACES 2016; 8:13793-13803. [PMID: 27228201 DOI: 10.1021/acsami.6b03474] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tubulin is the key cytoskeleton component, which plays a crucial role in eukaryotic cell division. Many anticancer drugs have been developed targeting the tubulin surface. Recently, it has been shown that few polyhydroxy carbohydrates perturb tubulin polymerization. Cyclodextrin (CD), a polyhydroxy carbohydrate, has been extensively used as the delivery vehicle for delivery of hydrophobic drugs to the cancer cell. However, interaction of CD with intracellular components has not been addressed before. In this Article, we have shown for the first time that α-CD interacts with tubulin close to the vinblastine site using molecular docking and Förster resonance energy transfer (FRET) experiment. In addition, we have shown that α-CD binds with intracellular tubulin/microtubule. It delivers a high amount of curcumin onto the cancer cell, which causes severe disruption of intracellular microtubules. Finally, we have shown that the inclusion complex of α-CD and curcumin (CCC) preferentially enters into the human lung cancer cell (A549) as compared to the normal lung fibroblast cell (WI38), causes apoptotic death, activates tumor suppressor protein (p53) and cyclin-dependent kinase inhibitor 1 (p21), and inhibits 3D spheroid growth of cancer cell.
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Affiliation(s)
- Batakrishna Jana
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saswat Mohapatra
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Prasenjit Mondal
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Surajit Barman
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Krishnangsu Pradhan
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Abhijit Saha
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division, and ‡Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology , 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
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18
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Natarajan K, Mohan J, Senapati S. Relating nucleotide-dependent conformational changes in free tubulin dimers to tubulin assembly. Biopolymers 2016; 99:282-91. [PMID: 23426572 DOI: 10.1002/bip.22153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/29/2012] [Indexed: 11/07/2022]
Abstract
The complex dynamic behavior of microtubules (MTs) is believed to be primarily due to the αβ-tubulin dimer architecture and its intrinsic GTPase activity. Hence, a detailed knowledge of the conformational variations of isolated α-GTP-β-GTP- and α-GTP-β-GDP-tubulin dimers in solution and their implications to interdimer interactions and stability is directly relevant to understand the MT dynamics. An attempt has been made here by combining molecular dynamics (MD) simulations and protein-protein docking studies that unravels key structural features of tubulin dimer in different nucleotide states and correlates their association to tubulin assembly. Results from simulations suggest that tubulin dimers and oligomers attain curved conformations in both GTP and GDP states. Results also indicate that the tubulin C-terminal domain and the nucleotide state are closely linked. Protein-protein docking in combination with MD simulations suggest that the GTP-tubulin dimers engage in relatively stronger interdimer interactions even though the interdimer interfaces are bent in both GTP and GDP tubulin complexes, providing valuable insights on in vitro finding that GTP-tubulin is a better assembly candidate than GDP-tubulin during the MT nucleation and elongation processes.
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Affiliation(s)
- Kathiresan Natarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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19
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Maffucci I, Contini A. An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides. J Chem Theory Comput 2016; 12:714-27. [DOI: 10.1021/acs.jctc.5b01211] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
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20
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Adak A, Mohapatra S, Mondal P, Jana B, Ghosh S. Design of a novel microtubule targeted peptide vesicle for delivering different anticancer drugs. Chem Commun (Camb) 2016; 52:7549-52. [DOI: 10.1039/c6cc01769j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel microtubule targeted peptide vesicle has been designed and developed for delivering both hydrophilic and hydrophobic drugs. It delivers both the drugs close to their intracellular targets, shows significant anticancer effect in both 2D monolayer and 3D spheroid cells.
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Affiliation(s)
- Anindyasundar Adak
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Saswat Mohapatra
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Prasenjit Mondal
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
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21
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Bhunia D, Mohapatra S, Kurkute P, Ghosh S, Jana B, Mondal P, Saha A, Das G, Ghosh S. Novel tubulin-targeted cell penetrating antimitotic octapeptide. Chem Commun (Camb) 2016; 52:12657-12660. [DOI: 10.1039/c6cc05110c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here, we have discovered an antimitotic cell penetrating octapeptide containing single Arg amino acid.
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Affiliation(s)
- Debmalya Bhunia
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Saswat Mohapatra
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Prashant Kurkute
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Subhajit Ghosh
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Batakrishna Jana
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Abhijit Saha
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Gaurav Das
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
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22
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Maffucci I, Clayden J, Contini A. Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides. J Phys Chem B 2015; 119:14003-13. [PMID: 26457452 DOI: 10.1021/acs.jpcb.5b07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Jonathan Clayden
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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23
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Maffucci I, Pellegrino S, Clayden J, Contini A. Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids. J Phys Chem B 2015; 119:1350-61. [PMID: 25528885 DOI: 10.1021/jp510775e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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24
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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25
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Pellegrino S, Ronda L, Annoni C, Contini A, Erba E, Gelmi ML, Piano R, Paredi G, Mozzarelli A, Bettati S. Molecular insights into dimerization inhibition of c-Maf transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2108-15. [PMID: 25220806 DOI: 10.1016/j.bbapap.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/01/2014] [Accepted: 09/02/2014] [Indexed: 01/01/2023]
Abstract
The Maf protein family belongs to the activator protein 1 (AP-1) superfamily of transcription factors that bind specific DNA target sequences through a basic region and exploit a leucine zipper (LZ) motif for protein-protein interactions leading to homo- or hetero-dimerization. Mafs unique DNA-binding domain contains a highly conserved extended homology region (EHR) that allows to recognize longer DNA sequences than other basic leucine zipper (bZIP) transcription factors. Inspired by the fact that overexpression of Mafs is observed in about 50% of cases of multiple myeloma, a hematological malignant disorder, we undertook a peptide inhibitor approach. The LZ domain of c-Maf, one of large Mafs, was produced by solid phase peptide synthesis. We characterized its secondary structure and dimerization properties, and found that dimerization and folding events are strictly coupled. Moreover, potential peptidic c-Maf dimerization inhibitors were computationally designed and synthesized. These compounds were demonstrated by circular dichroism (CD) spectroscopy and MALDI-TOF mass spectrometry to bind to c-Maf LZ monomers, to drive folding of their partially disordered structure and to efficiently compete with dimerization, suggesting a way for interfering with the function of c-Maf and, more generally, of intrinsically disordered proteins, till now considered undruggable targets.
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Affiliation(s)
- Sara Pellegrino
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Luca Ronda
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Chiara Annoni
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Alessandro Contini
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Emanuela Erba
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Maria Luisa Gelmi
- DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy
| | - Riccardo Piano
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gianluca Paredi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; SITEIA.PARMA Interdepartmental Center, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy.
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26
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Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis. J Mol Model 2014; 20:2178. [DOI: 10.1007/s00894-014-2178-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/11/2014] [Indexed: 12/14/2022]
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27
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Hatzakis NS. Single molecule insights on conformational selection and induced fit mechanism. Biophys Chem 2014; 186:46-54. [DOI: 10.1016/j.bpc.2013.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 01/24/2023]
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28
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Jana B, Biswas A, Mohapatra S, Saha A, Ghosh S. Single functionalized graphene oxide reconstitutes kinesin mediated intracellular cargo transport and delivers multiple cytoskeleton proteins and therapeutic molecules into the cell. Chem Commun (Camb) 2014; 50:11595-8. [DOI: 10.1039/c4cc04924a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinesin-1 mediated intracellular cargo transport is reconstituted using EGFP–Tris-NTA-GO (EGFP–TGO) as cargo. This functionalized nanoparticle can deliver multiple cytoskeleton proteins and antimitotic peptides into the cancer cell.
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Affiliation(s)
- Batakrishna Jana
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Atanu Biswas
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Saswat Mohapatra
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Abhijit Saha
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Surajit Ghosh
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Indian Institute of Chemical Biology Campus
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Chaurasia S, Pieraccini S, De Gonda R, Conti S, Sironi M. Molecular insights into the stabilization of protein–protein interactions with small molecule: The FKBP12–rapamycin–FRB case study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Calogero F, Borrelli S, Speciale G, Christodoulou MS, Cartelli D, Ballinari D, Sola F, Albanese C, Ciavolella A, Passarella D, Cappelletti G, Pieraccini S, Sironi M. 9-Fluorenone-2-Carboxylic Acid as a Scaffold for Tubulin Interacting Compounds. Chempluschem 2013; 78:663-669. [DOI: 10.1002/cplu.201300036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/08/2013] [Indexed: 12/26/2022]
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Pieraccini S, Rendine S, Jobichen C, Domadia P, Sivaraman J, Francescato P, Speranza G, Sironi M. Computer aided design of FtsZ targeting oligopeptides †. RSC Adv 2012; 3:1739-1743. [PMID: 30405903 DOI: 10.1039/c2ra21886k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
FtsZ is a protein involved in the bacterial division process and is thus an emerging target for antibacterial drugs. The network of interactions between FtsZ monomers necessary for exploitation of its biological function are studied here with molecular dynamics and free energy calculations. The results obtained led to the design of FtsZ targeting peptides which exhibited activity against the function of FtsZ in vitro.
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Affiliation(s)
- Stefano Pieraccini
- Dipartimento di Chimica and INSTM - UdR, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy.,Istituto di Scienze e tecnologie molecolari del CNR (CNR-ISTM), Via Golgi 19, 20133, Milano, Italy. ;
| | - Stefano Rendine
- Dipartimento di Chimica and INSTM - UdR, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy
| | - Chacko Jobichen
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Prerna Domadia
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - J Sivaraman
- Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Pierangelo Francescato
- Dipartimento di Chimica and INSTM - UdR, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy
| | - Giovanna Speranza
- Dipartimento di Chimica and INSTM - UdR, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy.,Istituto di Scienze e tecnologie molecolari del CNR (CNR-ISTM), Via Golgi 19, 20133, Milano, Italy. ;
| | - Maurizio Sironi
- Dipartimento di Chimica and INSTM - UdR, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy.,Istituto di Scienze e tecnologie molecolari del CNR (CNR-ISTM), Via Golgi 19, 20133, Milano, Italy. ;
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Molecular simulations of drug–receptor complexes in anticancer research. Future Med Chem 2012; 4:1961-70. [DOI: 10.4155/fmc.12.149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Molecular modeling and computer simulation techniques have matured significantly in recent years and proved their value in the study of drug–DNA, drug–DNA–protein, drug–protein and protein–protein interactions. Evolution in this area has gone hand-in-hand with an increased availability of structural data on biological macromolecules, major advances in molecular mechanics force fields and considerable improvements in computer technologies, most significantly processing speeds, multiprocessor programming and data-storage capacity. The information derived from molecular simulations of drug–receptor complexes can be used to extract structural and energetic information that is usually beyond current experimental possibilities, provide independent accounts of experimentally observed behavior, help in the interpretation of biochemical or pharmacological results, and open new avenues for research by posing novel relevant questions that can guide the design of new experiments. As drug-screening tools, ligand- and fragment-docking platforms stand out as powerful techniques that can provide candidate molecules for hit and lead development. This review provides an overall perspective of the main methods and focuses on some selected applications to both classical and novel anticancer targets.
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Contini A, Cappelletti G, Cartelli D, Fontana G, Gelmi ML. Molecular dynamics and tubulin polymerization kinetics study on 1,14-heterofused taxanes: evidence of stabilization of the tubulin head-to-tail dimer–dimer interaction. MOLECULAR BIOSYSTEMS 2012; 8:3254-61. [DOI: 10.1039/c2mb25326g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pieraccini S, De Gonda R, Sironi M. Molecular modeling of the inhibition of protein–protein interactions with small molecules: The IL2–IL2Rα case. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Rendine S, Pieraccini S, Sironi M. Vinblastine perturbation of tubulin protofilament structure: a computational insight. Phys Chem Chem Phys 2010; 12:15530-6. [PMID: 20978652 DOI: 10.1039/c0cp00594k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tubulin is a heterodimeric protein whose self assembly leads to the formation of protofilaments and of more complex structures called microtubules, key components of the cytoskeleton which have a fundamental role in the cell division process. Due to its biological function, tubulin is the target of many antitumoral molecules that exert their action on proliferating tumoral cells. Among these drugs, vinblastine has been widely used in therapy for a long time, albeit its mechanism of interaction with tubulin has remained elusive until recently. Vinblastine acts as a microtubule destabilizing agent and induces the formation of curved or ring-shaped tubulin polymers instead of linear protofilaments in vitro. In this paper we compare, using molecular dynamics simulations and free energy calculations, the network of interactions that allow the assembly of model linear protofilaments with those present in curved tubulin polymers complexed with vinblastine. It is shown that vinblastine, wedging between tubulin heterodimers, actually mediates part of the interactions between them and acts by crosslinking the two proteins, leading to the observed curved polymers rather than to their disassembly.
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Affiliation(s)
- Stefano Rendine
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy
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Nicolaus N, Zapke J, Riesterer P, Neudörfl JM, Prokop A, Oschkinat H, Schmalz HG. Azides Derived from Colchicine and their Use in Library Synthesis: a Practical Entry to New Bioactive Derivatives of an Old Natural Drug. ChemMedChem 2010; 5:661-5. [DOI: 10.1002/cmdc.201000063] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhang Y, Raudah S, Teo H, Teo GWS, Fan R, Sun X, Orner BP. Alanine-shaving mutagenesis to determine key interfacial residues governing the assembly of a nano-cage maxi-ferritin. J Biol Chem 2010; 285:12078-86. [PMID: 20139406 DOI: 10.1074/jbc.m109.092445] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fundamental process of protein self-assembly is governed by protein-protein interactions between subunits, which combine to form structures that are often on the nano-scale. The nano-cage protein, bacterioferritin from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for an alanine-shaving mutagenesis study to discover key amino acid residues at symmetry-related protein-protein interfaces that control protein stability and self-assembly. By inspection of these interfaces and "virtual alanine scanning," nine mutants were designed, expressed, purified, and characterized using transmission electron microscopy, size exclusion chromatography, dynamic light scattering, native PAGE, and temperature-dependent CD. Many of the selected amino acids act as hot spot residues. Four of these (Arg-30, which is located at the two-fold axis, and Arg-61, Tyr-114, and Glu-128, which are located at the three-fold axis), when individually mutated to alanine, completely shut down detectable solution formation of 24-mer, favoring a cooperatively folded dimer, suggesting that they may be oligomerization "switch residues." Furthermore, two residues, Arg-30 and Arg-61, when changed to alanine form mutants that are more thermodynamically stable than the native protein. This investigation into the structure and energetics of this self-assembling nano-cage protein not only can act as a jumping off point for the eventual design of novel protein nano-structures but can also help to understand the role that structure plays on the function of this important class of proteins.
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Affiliation(s)
- Yu Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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