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Bisaria I, Chauhan C, Muthu SA, Parvez S, Ahmad B. The effect of chrysin binding on the conformational dynamics and unfolding pathway of human serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124332. [PMID: 38676982 DOI: 10.1016/j.saa.2024.124332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Studies on the interactions between ligands and proteins provide insights into how a possible medication alters the structures and activities of the target or carrier proteins. The natural flavonoid aglycone Chrysin (CHR) has demonstrated anti-inflammatory, antioxidant, antiapoptotic, neuroprotective, and antineoplastic effects, both in vitro and in vivo. In this work, we investigated the impact of CHR binding on the as-yet-unexplored conformation, dynamics, and unfolding mechanism of human serum albumin (HSA). We determined CHR binding to HSA domain-II with the association constant (Ka) of 2.70 ± 0.21 × 105 M-1. The urea-induced sequential unfolding mechanism of HSA was used to elucidate the debatable binding location of CHR. CHR binding induced both secondary and tertiary structural alterations in the protein as studied by far-UV circular dichroism and intrinsic fluorescence spectroscopy. Red edge excitation shift (REES) indicated a decrease in conformational dynamics of the protein on the complex formation. This suggested an ordered compact and spatial arrangement of the CHR-boundmolecule. The binding of CHR was found to significantly modulate the urea-induced unfolding pathway of HSA. Urea-induced unfolding pathway of HSA became a two-state process (N-U) from a three-state process (N-I-U). The interaction of CHR is found to increase the thermal stability of the protein by ∼4 °C. This study focuses on the fundamental sciences and demonstrates how prospective medication compounds can alter the dynamics and stability of protein structure.
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Affiliation(s)
- Ishita Bisaria
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Chanchal Chauhan
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Shivani A Muthu
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Basir Ahmad
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
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Warrender AK, Pan J, Pudney C, Arcus VL, Kelton W. Red edge excitation shift spectroscopy is highly sensitive to tryptophan composition. J R Soc Interface 2023; 20:20230337. [PMID: 37935360 PMCID: PMC10645072 DOI: 10.1098/rsif.2023.0337] [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: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Red edge excitation shift (REES) spectroscopy relies on the unique emission profiles of fluorophore-solvent interactions to profile protein molecular dynamics. Recently, we reported the use of REES to compare the stability of 32 polymorphic IgG antibodies natively containing tryptophan reporter fluorophores. Here, we expand on this work to investigate the sensitivity of REES to variations in tryptophan content using a subset of IgG3 antibodies containing arginine to tryptophan polymorphisms. Structural analysis revealed that the additional tryptophan residues were situated in highly solvated environments. Subsequently, REES showed clear differences in fluorescence emission profiles when compared with the unmutated variants, thereby limiting direct comparison of their structural dynamics. These findings highlight the exquisite sensitivity of REES to minor variations in protein structure and tryptophan composition.
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Affiliation(s)
| | - Jolyn Pan
- Te Aka Mātuatua School of Science, University of Waikato, Hamilton, New Zealand
| | - Chris Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Vickery L. Arcus
- Te Aka Mātuatua School of Science, University of Waikato, Hamilton, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton, New Zealand
- Te Aka Mātuatua School of Science, University of Waikato, Hamilton, New Zealand
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Intrinsically Fluorescent Anti-Cancer Drugs. BIOLOGY 2022; 11:biology11081135. [PMID: 36009762 PMCID: PMC9405238 DOI: 10.3390/biology11081135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
At present, about one-third of the total protein targets in the pharmaceutical research sector are kinase-based. While kinases have been attractive targets to combat many diseases, including cancer, selective kinase inhibition has been challenging, because of the high degree of structural homology in the active site where many kinase inhibitors bind. Despite efficacy as cancer drugs, kinase inhibitors can exhibit limited target specificity and rationalizing their target profiles in the context of precise molecular mechanisms or rearrangements is a major challenge for the field. Spectroscopic approaches such as infrared, Raman, NMR and fluorescence have the potential to provide significant insights into drug-target and drug-non-target interactions because of sensitivity to molecular environment. This review places a spotlight on the significance of fluorescence for extracting information related to structural properties, discovery of hidden conformers in solution and in target-bound state, binding properties (e.g., location of binding sites, hydrogen-bonding, hydrophobicity), kinetics as well as dynamics of kinase inhibitors. It is concluded that the information gleaned from an understanding of the intrinsic fluorescence from these classes of drugs may aid in the development of future drugs with improved side-effects and less disease resistance.
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Wang F, Vasilyev V, Clayton AHA. Optical spectra and conformation pool of tyrosine kinase inhibitor PD153035 using a robust quantum mechanical conformation search. NEW J CHEM 2022. [DOI: 10.1039/d1nj04348j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most potent drug configuration is not necessarily the lowest energy conformer. The optical spectral profile of a flexible TKI depends on the distribution of the conformers and therefore the conditions such as environment (solvent).
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Affiliation(s)
- Feng Wang
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Vladislav Vasilyev
- National Computational Infrastructure, Australian National University, Canberra, ACT 0200, Australia
| | - Andrew H. A. Clayton
- Optical Sciences Centre, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia
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Kwok A, Camacho IS, Winter S, Knight M, Meade RM, Van der Kamp MW, Turner A, O'Hara J, Mason JM, Jones AR, Arcus VL, Pudney CR. A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability. Front Mol Biosci 2021; 8:778244. [PMID: 34926581 PMCID: PMC8681860 DOI: 10.3389/fmolb.2021.778244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
It is now over 30 years since Demchenko and Ladokhin first posited the potential of the tryptophan red edge excitation shift (REES) effect to capture information on protein molecular dynamics. While there have been many key efforts in the intervening years, a biophysical thermodynamic model to quantify the relationship between the REES effect and protein flexibility has been lacking. Without such a model the full potential of the REES effect cannot be realized. Here, we present a thermodynamic model of the tryptophan REES effect that captures information on protein conformational flexibility, even with proteins containing multiple tryptophan residues. Our study incorporates exemplars at every scale, from tryptophan in solution, single tryptophan peptides, to multitryptophan proteins, with examples including a structurally disordered peptide, de novo designed enzyme, human regulatory protein, therapeutic monoclonal antibodies in active commercial development, and a mesophilic and hyperthermophilic enzyme. Combined, our model and data suggest a route forward for the experimental measurement of the protein REES effect and point to the potential for integrating biomolecular simulation with experimental data to yield novel insights.
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Affiliation(s)
- A Kwok
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - I S Camacho
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - S Winter
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - R M Meade
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - M W Van der Kamp
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | | | - J M Mason
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - A R Jones
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - V L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - C R Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,BLOC Laboratories Limited, Bath, United Kingdom
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