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Ellaway JIJ, Anyango S, Nair S, Zaki HA, Nadzirin N, Powell HR, Gutmanas A, Varadi M, Velankar S. Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:034701. [PMID: 38774441 PMCID: PMC11106648 DOI: 10.1063/4.0000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]
Abstract
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe - Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.
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Affiliation(s)
- Joseph I. J. Ellaway
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Stephen Anyango
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Sreenath Nair
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Hossam A. Zaki
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island 02903, USA
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Harold R. Powell
- Imperial College London, Department of Life Sciences, London, United Kingdom
| | - Aleksandras Gutmanas
- WaveBreak Therapeutics Ltd., Clarendon House, Clarendon Road, Cambridge, United Kingdom
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Sameer Velankar
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
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2
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Kirby A, Graf D, Suchý M, Calvert ND, Charlton TA, Ben RN, Addison CL, Shuhendler A. It's a Trap! Aldolase-Prescribed C 4 Deoxyradiofluorination Affords Intracellular Trapping and the Tracing of Fructose Metabolism by PET. J Nucl Med 2024; 65:475-480. [PMID: 38272705 DOI: 10.2967/jnumed.123.266905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024] Open
Abstract
Fructose metabolism has been implicated in various diseases, including metabolic disorders, neurodegenerative disorders, cardiac disorders, and cancer. However, the limited availability of a quantitative imaging radiotracer has hindered its exploration in pathology and diagnostic imaging. Methods: We adopted a molecular design strategy based on the catalytic mechanism of aldolase, a key enzyme in fructolysis. We successfully synthesized a radiodeoxyfluorinated fructose analog, [18F]4-fluoro-4-deoxyfructose ([18F]4-FDF), in high molar activity. Results: Through heavy isotope tracing by mass spectrometry, we demonstrated that C4-deoxyfluorination of fructose led to effective trapping as fluorodeoxysorbitol and fluorodeoxyfructose-1-phosphate in vitro, unlike C1- and C6-fluorinated analogs that resulted in fluorolactate accumulation. This observation was consistent in vivo, where [18F]6-fluoro-6-deoxyfructose displayed substantial bone uptake due to metabolic processing whereas [18F]4-FDF did not. Importantly, [18F]4-FDF exhibited low uptake in healthy brain and heart tissues, known for their high glycolytic activity and background levels of [18F]FDG uptake. [18F]4-FDF PET/CT allowed for sensitive mapping of neuro- and cardioinflammatory responses to systemic lipopolysaccharide administration. Conclusion: Our study highlights the significance of aldolase-guided C4 radiodeoxyfluorination of fructose in enabling effective radiotracer trapping, overcoming limitations of C1 and C6 radioanalogs toward a clinically viable tool for imaging fructolysis in highly glycolytic tissues.
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Affiliation(s)
- Alexia Kirby
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada;
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Dominic Graf
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Mojmír Suchý
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Nicholas D Calvert
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Robert N Ben
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Christina L Addison
- Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada; and
| | - Adam Shuhendler
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada;
- Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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Zhang Y, Gao S, Xia S, Yang H, Bao X, Zhang Q, Xu Y. Linarin ameliorates ischemia-reperfusion injury by the inhibition of endoplasmic reticulum stress targeting AKR1B1. Brain Res Bull 2024; 207:110868. [PMID: 38181967 DOI: 10.1016/j.brainresbull.2024.110868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/18/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Due to various factors, there is still a lack of effective neuroprotective agents for ischemic stroke in clinical practice. Neuroinflammation and neuronal apoptosis mediated by endoplasmic reticulum stress are some of the important pathological mechanisms in ischemic stroke. Linarin has been reported to have anti-inflammation, antioxidant, and anti-apoptotic effects in myocardial ischemia, osteoarthritis, and kidney disease. Whether it exerts neuroprotective functions in ischemic stroke has not been investigated. The results showed that linarin could reduce the infarct volume in cerebral ischemia animal models, improve the neurological function scores and suppress the expression of inflammatory factors mediating the NF-κB. Meanwhile, it could protect the neurons from OGD/R-induced-apoptosis, which was related to the PERK-eIF2α pathway. Our results suggested linarin could inhibit neuronal inflammation and apoptosis induced by endoplasmic reticulum stress. Furthermore, the neuroprotective effect of linarin may be related to the inhibition of AKR1B1. Our study offers new insight into protecting against ischemia-reperfusion injury by linarin treatment in stroke.
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Affiliation(s)
- Yuqian Zhang
- Department of Neurology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, China
| | - Shenghan Gao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Department of Neurology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing 210008, China
| | - Shengnan Xia
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Haiyan Yang
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Xinyu Bao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Qingxiu Zhang
- Department of Neurology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, China; Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Department of Neurology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing 210008, China.
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210008, China; Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Department of Neurology, Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology and Institute of Translational Medicine for Brain Critical Diseases, Nanjing University, Nanjing 210008, China; Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing 210008, China; Jiangsu Provincial Key Discipline of Neurology, Nanjing 210008, China; Nanjing Neurology Medical Center, Nanjing 210008, China.
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Insights into the Substrate Uptake Mechanism of Mycobacterium Tuberculosis Ribose 5-Phosphate Isomerase and Perspectives on Drug Development. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
The active site of the dimeric ribose 5-phosphate isomerase B (RpiB) contains a solvent-exposed barrier formed by residues H12, R113, R137, and R141, which is closed upon the complexation of phosphate. The substrate ribose 5-phosphate (R5P) has to overcome the surface barrier to reach an internal cavity and then bind in the linear configuration of ribose to the interface between the two subunits. NMR and molecular dynamics simulation are suitable methods to describe the transient nature of the RpiB active site and help our understanding of the mechanism of substrate entrance. In this study, we show that the entrance of the nucleotides AMP/ADP into the internal cavity of mycobacterium tuberculosis RpiB (MtRpiB) does not involve a canonical open/close-lid conformational transition usually observed in many enzymes. Instead, a flipping mechanism in which the nucleotide phosphate interacts with the surface barrier followed by the flip of the nitrogenous base and ribose is responsible for changing the substrate/ligand orientation from a solvent-exposed to a buried state. Based on these results, we propose a substrate/inhibitor uptake mechanism that could provide a basis for rational drug design using MtRpiB, which is an essential enzyme and a good target for drug development.
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Balestri F, Poli G, Piazza L, Cappiello M, Moschini R, Signore G, Tuccinardi T, Mura U, Del Corso A. Dissecting the Activity of Catechins as Incomplete Aldose Reductase Differential Inhibitors through Kinetic and Computational Approaches. BIOLOGY 2022; 11:biology11091324. [PMID: 36138801 PMCID: PMC9495972 DOI: 10.3390/biology11091324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022]
Abstract
Simple Summary The increased glucose levels occurring in diabetes lead to several metabolic alterations responsible for the onset of the so-called diabetic complications, which include nephropathies, neuropathies, retinopathies, and cataract. An increased flux of glucose through the polyol pathway is considered the most relevant among these alterations. For this reason, the block of the polyol pathway, through the inhibition of the enzyme aldose reductase, is considered a valuable strategy to impair the onset of diabetic complications. However, aldose reductase also exerts a beneficial effect inside cells, since it can remove toxic aldehydes. Thus, to ameliorate the outcome of the use of aldose reductase inhibitors, the use of “differential inhibitors” has been proposed. These inhibitors should block the catalytic activity depending on the substrate the enzyme is working on, thus preserving the detoxifying action of the enzyme. In this work, derivatives of catechins are analyzed to evaluate their inhibitory action on aldose reductase. The study was conducted both in vitro on the isolated enzyme and in silico through a computational approach. Results demonstrated that gallocatechin gallate and catechin gallate act as differential inhibitors and that this action may be linked to an incomplete inhibitory effect. Abstract The inhibition of aldose reductase is considered as a strategy to counteract the onset of both diabetic complications, upon the block of glucose conversion in the polyol pathway, and inflammation, upon the block of 3-glutathionyl-4-hydroxynonenal reduction. To ameliorate the outcome of aldose reductase inhibition, minimizing the interference with the detoxifying role of the enzyme when acting on toxic aldehydes, “differential inhibitors”, i.e., molecules able to inhibit the enzyme depending on the substrate the enzyme is working on, has been proposed. Here we report the characterization of different catechin derivatives as aldose reductase differential inhibitors. The study, conducted through both a kinetic and a computational approach, highlights structural constraints of catechin derivatives relevant in order to affect aldose reductase activity. Gallocatechin gallate and catechin gallate emerged as differential inhibitors of aldose reductase able to preferentially affect aldoses and 3-glutathionyl-4-hydroxynonenal reduction with respect to 4-hydroxynonenal reduction. Moreover, the results highlight how, in the case of aldose reductase, a substrate may affect not only the model of action of an inhibitor, but also the degree of incompleteness of the inhibitory action, thus contributing to differential inhibitory phenomena.
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Affiliation(s)
- Francesco Balestri
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 12, 56126 Pisa, Italy
| | - Lucia Piazza
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
| | - Mario Cappiello
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Roberta Moschini
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Giovanni Signore
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 12, 56126 Pisa, Italy
| | - Umberto Mura
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
| | - Antonella Del Corso
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno, 51, 56123 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
- Correspondence: ; Tel.: +39-050-2211450
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Balestri F, Moschini R, Mura U, Cappiello M, Del Corso A. In Search of Differential Inhibitors of Aldose Reductase. Biomolecules 2022; 12:biom12040485. [PMID: 35454074 PMCID: PMC9024650 DOI: 10.3390/biom12040485] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Aldose reductase, classified within the aldo-keto reductase family as AKR1B1, is an NADPH dependent enzyme that catalyzes the reduction of hydrophilic as well as hydrophobic aldehydes. AKR1B1 is the first enzyme of the so-called polyol pathway that allows the conversion of glucose into sorbitol, which in turn is oxidized to fructose by sorbitol dehydrogenase. The activation of the polyol pathway in hyperglycemic conditions is generally accepted as the event that is responsible for a series of long-term complications of diabetes such as retinopathy, cataract, nephropathy and neuropathy. The role of AKR1B1 in the onset of diabetic complications has made this enzyme the target for the development of molecules capable of inhibiting its activity. Virtually all synthesized compounds have so far failed as drugs for the treatment of diabetic complications. This failure may be partly due to the ability of AKR1B1 to reduce alkenals and alkanals, produced in oxidative stress conditions, thus acting as a detoxifying agent. In recent years we have proposed an alternative approach to the inhibition of AKR1B1, suggesting the possibility of a differential inhibition of the enzyme through molecules able to preferentially inhibit the reduction of either hydrophilic or hydrophobic substrates. The rationale and examples of this new generation of aldose reductase differential inhibitors (ARDIs) are presented.
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Affiliation(s)
- Francesco Balestri
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
| | - Roberta Moschini
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
| | - Umberto Mura
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
| | - Mario Cappiello
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
- Correspondence:
| | - Antonella Del Corso
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
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