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Çınaroğlu S, Biggin PC. Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. J Chem Inf Model 2023; 63:6095-6108. [PMID: 37759363 PMCID: PMC10565830 DOI: 10.1021/acs.jcim.3c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Indexed: 09/29/2023]
Abstract
Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (R2 of 0.88 and an RMSE of 1.48 kcal/mol overall). Although one cannot know prospectively whether computed ITC values will be correct or not, this work shows that if experimental ITC data are available, then this in conjunction with computed ITC, can be used as a tool to know if the ensemble being simulated is representative of the true ensemble or not. That is important for allowing the correct interpretation of the detailed dynamics of the system with respect to the measured enthalpy. The results also suggest that computational calorimetry is becoming increasingly feasible. We provide the data set as a resource for the community, which could be used as a benchmark to help further progress in this area.
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Affiliation(s)
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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Ciccone L, Nencetti S, Rossello A, Orlandini E. Pomegranate: A Source of Multifunctional Bioactive Compounds Potentially Beneficial in Alzheimer's Disease. Pharmaceuticals (Basel) 2023; 16:1036. [PMID: 37513947 PMCID: PMC10385237 DOI: 10.3390/ph16071036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pomegranate fruit (PF) is a fruit rich in nutraceuticals. Nonedible parts of the fruit, especially peels, contain high amounts of bioactive components that have been largely used in traditional medicine, such as the Chinese, Unani, and Ayurvedic ones, for treating several diseases. Polyphenols such as anthocyanins, tannins, flavonoids, phenolic acids, and lignans are the major bioactive molecules present in PF. Therefore, PF is considered a source of natural multifunctional agents that exert simultaneously antioxidant, anti-inflammatory, antitumor, antidiabetic, cardiovascular, and neuroprotective activities. Recently, several studies have reported that the nutraceuticals contained in PF (seed, peel, and juice) have a potential beneficial role in Alzheimer's disease (AD). Research suggests that the neuroprotective effect of PF is mostly due to its potent antioxidant and anti-inflammatory activities which contribute to attenuate the neuroinflammation associated with AD. Despite the numerous works conducted on PF, to date the mechanism by which PF acts in combatting AD is not completely known. Here, we summarize all the recent findings (in vitro and in vivo studies) related to the positive effects that PF and its bioactive components can have in the neurodegeneration processes occurring during AD. Moreover, considering the high biotransformation characteristics of the nutraceuticals present in PF, we propose to consider the chemical structure of its active metabolites as a source of inspiration to design new molecules with the same beneficial effects but less prone to be affected by the metabolic degradation process.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Research Center "E. Piaggio", University of Pisa, 56122 Pisa, Italy
| | - Elisabetta Orlandini
- Research Center "E. Piaggio", University of Pisa, 56122 Pisa, Italy
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53, 56126 Pisa, Italy
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Tseng YL, Lu PC, Lee CC, He RY, Huang YA, Tseng YC, Cheng TJR, Huang JJT, Fang JM. Degradation of neurodegenerative disease-associated TDP-43 aggregates and oligomers via a proteolysis-targeting chimera. J Biomed Sci 2023; 30:27. [PMID: 37101169 PMCID: PMC10131537 DOI: 10.1186/s12929-023-00921-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) associated with TAR DNA-binding protein 43 (TDP-43) aggregation has been considered as a lethal and progressive motor neuron disease. Recent studies have shown that both C-terminal TDP-43 (C-TDP-43) aggregates and oligomers were neurotoxic and pathologic agents in ALS and frontotemporal lobar degeneration (FTLD). However, misfolding protein has long been considered as an undruggable target by applying conventional inhibitors, agonists, or antagonists. To provide this unmet medical need, we aim to degrade these misfolding proteins by designing a series of proteolysis targeting chimeras (PROTACs) against C-TDP-43. METHODS By applying filter trap assay, western blotting, and microscopy imaging, the degradation efficiency of C-TDP-43 aggregates was studied in Neuro-2a cells overexpressing eGFP-C-TDP-43 or mCherry-C-TDP-43. The cell viability was characterized by alarmarBlue assay. The beneficial and disaggregating effects of TDP-43 PROTAC were examined with the YFP-C-TDP-43 transgenic C. elegans by motility assay and confocal microscopy. The impact of TDP-43 PROTAC on C-TDP-43 oligomeric intermediates was monitored by fluorescence lifetime imaging microscopy and size exclusion chromatography in the Neuro-2a cells co-expressing eGFP-C-TDP-43 and mCherry-C-TDP-43. RESULTS Four PROTACs with different linker lengths were synthesized and characterized. Among these chimeras, PROTAC 2 decreased C-TDP-43 aggregates and relieved C-TDP-43-induced cytotoxicity in Neuro-2a cells without affecting endogenous TDP-43. We showed that PROTAC 2 bound to C-TDP-43 aggregates and E3 ligase to initiate ubiquitination and proteolytic degradation. By applying advanced microscopy, it was further shown that PROTAC 2 decreased the compactness and population of C-TDP-43 oligomers. In addition to cellular model, PROTAC 2 also improved the motility of transgenic C. elegans by reducing the C-TDP-43 aggregates in the nervous system. CONCLUSIONS Our study demonstrated the dual-targeting capacity of the newly-designed PROTAC 2 against both C-TDP-43 aggregates and oligomers to reduce their neurotoxicity, which shed light on the potential drug development for ALS as well as other neurodegenerative diseases.
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Affiliation(s)
- Yu-Ling Tseng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Po-Chao Lu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department and Graduate Institute of Pharmacology, National Taiwan University, Taipei, 100, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yin-Chen Tseng
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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Ciccone L, Nencetti S, Marino M, Battocchio C, Iucci G, Venditti I, Marsotto M, Montalesi E, Socci S, Bargagna B, Orlandini E. Pterostilbene fluorescent probes as potential tools for targeting neurodegeneration in biological applications. J Enzyme Inhib Med Chem 2022; 37:1812-1820. [PMID: 35758192 PMCID: PMC9246042 DOI: 10.1080/14756366.2022.2091556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several epidemiological studies suggest that a diet rich in fruit and vegetables reduces the incidence of neurodegenerative diseases. Resveratrol (Res) and its dimethylated metabolite, pterostibene (Ptb), have been largely studied for their neuroprotective action. The clinical use of Res is limited because of its rapid metabolism and its poor bioavailability. Ptb with two methoxy groups and one hydroxyl group has a good membrane permeability, metabolic stability and higher in vivo bioavailability in comparison with Res. The metabolism and pharmacokinetics of Ptb are still sparse, probably due to the lack of tools that allow following the Ptb destiny both in living cells and in vivo. In this contest, we propose two Ptb fluorescent derivatives where Ptb has been functionalised by benzofurazan and rhodamine-B-isothiocyanate, compounds 1 and 2, respectively. Here, we report the synthesis, the optical and structural characterisation of 1 and 2, and, their putative cytotoxicity in two different cell lines.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Pisa, Italy.,CISUP - Centre for Instrumentation Sharing, University of Pisa, Pisa, Italy
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Pisa, Italy.,CISUP - Centre for Instrumentation Sharing, University of Pisa, Pisa, Italy
| | - Maria Marino
- Department of Science, University Roma Tre, Rome, Italy
| | | | | | - Iole Venditti
- Department of Science, University Roma Tre, Rome, Italy
| | | | | | - Simone Socci
- Department of Earth Science, University of Pisa, Pisa, Italy
| | | | - Elisabetta Orlandini
- Department of Earth Science, University of Pisa, Pisa, Italy.,Research Centre E. Piaggio, University of Pisa, Pisa, Italy
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Wu T, Lin D, Cheng Y, Jiang S, Riaz MW, Fu N, Mou C, Ye M, Zheng Y. Amyloid Cascade Hypothesis for the Treatment of Alzheimer's Disease: Progress and Challenges. Aging Dis 2022; 13:1745-1758. [PMID: 36465173 PMCID: PMC9662281 DOI: 10.14336/ad.2022.0412] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/12/2022] [Indexed: 07/29/2023] Open
Abstract
The amyloid cascade hypothesis has always been a research focus in the therapeutic field of Alzheimer's disease (AD) since it was put forward. Numerous researchers attempted to find drugs for AD treatment based on this hypothesis. To promote the research of anti-AD drugs development, the current hypothesis and pathogenesis were reviewed with expounding of β-amyloid generation from its precursor protein and related transformations. Meanwhile, the present drug development strategies aimed at each stage in this hypothesis were also summarized. Several strategies especially immunotherapy showed the optimistic results in clinical trials, but only a small percentage of them eventually succeeded. In this review, we also tried to point out some common problems of drug development in preclinical and clinical studies which might be settled through multidisciplinary cooperation as well as the understanding that reinforces the amyloid cascade hypothesis.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Ding Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Yaqian Cheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Senze Jiang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Nina Fu
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Chenhao Mou
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Menglu Ye
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
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Targeted protein degraders march towards the clinic for neurodegenerative diseases. Ageing Res Rev 2022; 78:101616. [PMID: 35378298 DOI: 10.1016/j.arr.2022.101616] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 12/28/2022]
Abstract
Protein degraders are emerging as potent therapeutic tools to address neurological disorders and many complex diseases. It offered several key advantages, including the doses, drug resistance, and side effects over traditional occupancy-based inhibitors. Translation of chemical degraders into a clinical therapy for neurodegenerative disorders has a well-documented knowledge and resource gap. Researchers strive to develop clinical candidates employing chemical degraders' technologies, including hydrophobic tagging, molecular glues, proteolysis targeting chimeras (PROTACs), specific and nongenetic Inhibitor of Apoptosis Protein (IAP)-dependent protein erasers (SNIPERs), autophagy targeted chimeras, and autophagosome-tethered compounds for targeted degradation of pathological markers in neurodegenerative disease. Herein, we examined the present state of chemical-mediated targeted protein degradation in the quest for medications to treat neurodegenerative diseases. We further identified targeted degraders under clinical development for neurodegenerative diseases summarizing pertinent discoveries guiding the future of degradation therapeutics. We also addressed the necessary pharmacological interventions needed to achieve unprecedented therapeutic efficacy and its associated challenges.
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Bargagna B, Ciccone L, Nencetti S, Santos MA, Chaves S, Camodeca C, Orlandini E. Multifunctional Small Molecules as Potential Anti-Alzheimer's Disease Agents. Molecules 2021; 26:6015. [PMID: 34641559 PMCID: PMC8512147 DOI: 10.3390/molecules26196015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/14/2021] [Accepted: 09/29/2021] [Indexed: 01/17/2023] Open
Abstract
Alzheimer's disease (AD) is a severe multifactorial neurodegenerative disorder characterized by a progressive loss of neurons in the brain. Despite research efforts, the pathogenesis and mechanism of AD progression are not yet completely understood. There are only a few symptomatic drugs approved for the treatment of AD. The multifactorial character of AD suggests that it is important to develop molecules able to target the numerous pathological mechanisms associated with the disease. Thus, in the context of the worldwide recognized interest of multifunctional ligand therapy, we report herein the synthesis, characterization, physicochemical and biological evaluation of a set of five (1a-e) new ferulic acid-based hybrid compounds, namely feroyl-benzyloxyamidic derivatives enclosing different substituent groups, as potential anti-Alzheimer's disease agents. These hybrids can keep both the radical scavenging activity and metal chelation capacity of the naturally occurring ferulic acid scaffold, presenting also good/mild capacity for inhibition of self-Aβ aggregation and fairly good inhibition of Cu-induced Aβ aggregation. The predicted pharmacokinetic properties point towards good absorption, comparable to known oral drugs.
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Affiliation(s)
- Beatrice Bargagna
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53-55, 56100 Pisa, Italy;
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (S.N.); (C.C.)
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (S.N.); (C.C.)
| | - M. Amélia Santos
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Sílvia Chaves
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Caterina Camodeca
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (L.C.); (S.N.); (C.C.)
| | - Elisabetta Orlandini
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53-55, 56100 Pisa, Italy;
- Research Center “E. Piaggio”, University of Pisa, 56122 Pisa, Italy
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Physiological Metals Can Induce Conformational Changes in Transthyretin Structure: Neuroprotection or Misfolding Induction? CRYSTALS 2021. [DOI: 10.3390/cryst11040354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transthyretin (TTR) is a plasma homotetrameric protein that transports thyroxine and retinol. TTR itself, under pathological conditions, dissociates into partially unfolded monomers that aggregate and form fibrils. Metal ions such as Zn2+, Cu2+, Fe2+, Mn2+ and Ca2+ play a controversial role in the TTR amyloidogenic pathway. TTR is also present in cerebrospinal fluid (CSF), where it behaves as one of the major Aβ-binding-proteins. The interaction between TTR and Aβ is stronger in the presence of high concentrations of Cu2+. Crystals of TTR, soaked in solutions of physiological metals such as Cu2+ and Fe2+, but not Mn2+, Zn2+, Fe3+, Al3+, Ni2+, revealed an unusual conformational change. Here, we investigate the effects that physiological metals have on TTR, in order to understand if metals can induce a specific and active conformation of TTR that guides its Aβ-scavenging role. The capability of certain metals to induce and accelerate its amyloidogenic process is also discussed.
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