1
|
Li Q, Zhu Y, Meng X, Tong HHY, Liu H. Experiment and molecular dynamics simulations reveal proanthocyanidin B2 and B3 can inhibit prion aggregation by different mechanisms. J Biomol Struct Dyn 2024; 42:2424-2436. [PMID: 37144732 DOI: 10.1080/07391102.2023.2209663] [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: 12/28/2022] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Prion diseases are a group of fatal neurodegenerative diseases caused by the misfolding and aggregation of prion protein (PrP), and the inhibition of PrP aggregation is one of the most effective therapeutic strategies. Proanthocyanidin B2 (PB2) and B3 (PB3), the effective natural antioxidants have been evaluated for the inhibition of amyloid-related protein aggregation. Since PrP has similar aggregation mechanism with other amyloid-related proteins, will PB2 and PB3 affect the aggregation of PrP? In this paper, experimental and molecular dynamics (MD) simulation methods were combined to investigate the influence of PB2 and PB3 on PrP aggregation. Thioflavin T assays showed PB2 and PB3 could inhibit PrP aggregation in a concentrate-dependent manner in vitro. To understand the underlying mechanism, we performed 400 ns all-atom MD simulations. The results suggested PB2 could stabilize the α2 C-terminus and the hydrophobic core of protein by stabilizing two important salt bridges R156-E196 and R156-D202, and consequently made global structure of protein more stable. Surprisingly, PB3 could not stabilize PrP, which may inhibit PrP aggregation through a different mechanism. Since dimerization is the first step of aggregation, will PB3 inhibit PrP aggregation by inhibiting the dimerization? To verify our assumption, we then explored the effect of PB3 on protein dimerization by performing 800 ns MD simulations. The results suggested PB3 could reduce the residue contacts and hydrogen bonds between two monomers, preventing dimerization process of PrP. The possible inhibition mechanism of PB2 and PB3 on PrP aggregation could provide useful information for drug development against prion diseases.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Yongchang Zhu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
| |
Collapse
|
2
|
Neupane S, Khadka J, Rayamajhi S, Pandey AS. Binding modes of potential anti-prion phytochemicals to PrP C structures in silico. J Ayurveda Integr Med 2023; 14:100750. [PMID: 37453159 PMCID: PMC10368899 DOI: 10.1016/j.jaim.2023.100750] [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: 08/24/2020] [Revised: 03/13/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrPC) into a misfolded pathogenic form (PrPSc). One possible strategy to inhibit PrPSc formation is to stabilize the native conformation of PrPC and interfere with the conversion of PrPC to PrPSc. Many compounds have been shown to inhibit the conversion process, however, no promising drugs have been identified to cure prion diseases. OBJECTIVE This study aims to identify potential anti-prion compounds from plant phytochemicals by integrating traditional ethnobotanical knowledge with modern in silico drug design approaches. MATERIALS AND METHODS In the current study medicinal phytochemicals were docked with swapped and non-swapped crystal structures of PrPCin silico to identify potential anti-prions to determine their binding modes and interactions. RESULTS Eleven new phytochemicals were identified based on their binding energies and pharmacokinetic properties. The binding sites and interactions of the known and new anti-prion compounds are similar, and differences in binding modes occur in structures with very subtle differences in side chain conformations. Binding of these compounds poses steric hindrance to neighbouring molecules. Residues shown to be associated with the inhibition of PrPC to PrPSc conversion form interactions with most of the compounds. CONCLUSION Identified compounds might act as potent inhibitors of PrPC to PrPSc conversion. These might be attractive candidates for the development of novel anti-prion therapy although further tests in vitro cell cultures and in vivo mouse models are needed to confirm these findings.
Collapse
Affiliation(s)
- Sandesh Neupane
- Purbanchal University, Department of Biotechnology, SANN International College, Kathmandu, 44616, Nepal.
| | - Jenisha Khadka
- Purbanchal University, Department of Biotechnology, SANN International College, Kathmandu, 44616, Nepal.
| | - Sandesh Rayamajhi
- Purbanchal University, Department of Biotechnology, SANN International College, Kathmandu, 44616, Nepal.
| | - Arti S Pandey
- Department of Biochemistry, Kathmandu Medical College (Basic Sciences), Bhaktapur, 44800, Nepal.
| |
Collapse
|
3
|
Xu Z, Liu H, Wang S, Zhang Q, Yao X, Zhou S, Liu H. Unraveling the Molecular Mechanism of Prion H2 C-Terminus Misfolding by Metadynamics Simulations. ACS Chem Neurosci 2020; 11:772-782. [PMID: 32023408 DOI: 10.1021/acschemneuro.9b00679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Conformational transition from the normal cellular form of prion protein (PrPC) to the pathogenic "scrapie" form (PrPSc) is considered to be a key event in the occurrence of prion disease. Additionally, the H2 C-terminus is widely considered to be a vital site for PrP conformational transition, which can be used as an important region to explore the potential mechanism of PrP misfolding. Therefore, to study the misfolding mechanism of PrP, 500 ns well-tempered metadynamics simulations were performed by focusing on the H2 C-terminus of PrP. For comparison, three systems were designed in total, including PrP in neutral and acidic conditions, as well as H187R mutant. The resulting free energy surfaces (FESs) obtained from metadynamics simulations reveal that acidic conditions and H187R mutation can facilitate PrP misfolding by decreasing free energy barriers for conformational transition and forming energy stable conformational states. Further analyses aimed at H2 C-terminus show that due to the increase of positive charge on residue 187 in both acidic and H187R systems, the electrostatic repulsion of residue 187 and R136/R156 increases greatly, which disrupts the electrostatic interaction network around H2 C-terminus and exposes the hydrophobic core to the solvent. Taken together, acidic conditions and H187R mutation can accelerate PrP misfolding mainly by forming more energetically stable metastable conformations with lower free energy barriers, and electrostatic network disruption involving residue 187 drives the initial misfolding of H2 C-terminus. This study provides quantitative insight into the related function of the H2 C-terminus in the PrP misfolding process, which may guide H2 C-terminus mediated drug design in the future.
Collapse
Affiliation(s)
- Zerong Xu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Shuo Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Shuangyan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
4
|
Structural insight into conformational change in prion protein by breakage of electrostatic network around H187 due to its protonation. Sci Rep 2019; 9:19305. [PMID: 31848406 PMCID: PMC6917724 DOI: 10.1038/s41598-019-55808-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/04/2019] [Indexed: 11/10/2022] Open
Abstract
A conformational change from normal prion protein(PrPC) to abnormal prion protein(PrPSC) induces fatal neurodegenerative diseases. Acidic pH is well-known factors involved in the conformational change. Because the protonation of H187 is strongly linked to the change in PrP stability, we examined the charged residues R156, E196, and D202 around H187. Interestingly, there have been reports on pathological mutants, such as H187R, E196A, and D202N. In this study, we focused on how an acidic pH and pathological mutants disrupt this electrostatic network and how this broken network destabilizes PrP structure. To do so, we performed a temperature-based replica-exchange molecular dynamics (T-REMD) simulation using a cumulative 252 μs simulation time. We measured the distance between amino acids comprising four salt bridges (R156–E196/D202 and H187–E196/D202). Our results showed that the spatial configuration of the electrostatic network was significantly altered by an acidic pH and mutations. The structural alteration in the electrostatic network increased the RMSF value around the first helix (H1). Thus, the structural stability of H1, which is anchored to the H2–H3 bundle, was decreased. It induces separation of R156 from the electrostatic network. Analysis of the anchoring energy also shows that two salt-bridges (R156-E196/D202) are critical for PrP stability.
Collapse
|
5
|
Alaraidh IA, Okla MK, Alamri SA, AL‐ghamdi AA, Soufan WH, Allam AA, Fouda MMG, Gaffer HE. Synthesis of Bis‐(2‐thiazolyl)amine Analogues and Evaluation of Their Antibacterial, Antioxidant and Cytotoxic Activities. ChemistrySelect 2019. [DOI: 10.1002/slct.201902272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ibrahim A. Alaraidh
- Department of Botany and MicrobiologyCollege of ScienceKing Saud University, P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Mohammad K. Okla
- Department of Botany and MicrobiologyCollege of ScienceKing Saud University, P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Saudi A. Alamri
- Department of Botany and MicrobiologyCollege of ScienceKing Saud University, P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Abdullah A. AL‐ghamdi
- Department of Botany and MicrobiologyCollege of ScienceKing Saud University, P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Walid H. Soufan
- College of AgricultureKing Saud University P.O. Box 2455 Riyadh 11451 Saudia Arabia
| | - Ahmed A. Allam
- Department of ZoologyFaculty of ScienceBeni-Suef University Beni-Suef 65211 Egypt
| | - Moustafa M. G. Fouda
- Pretreatment and Finishing of Cellulosic-based Fibers DepartmentTextile Industries Research DivisionNational Research Centre 33 El-Buhouth Street, Dokki Cairo 12622 Egypt
| | - Hatem E. Gaffer
- DyeingPrinting and Auxiliaries DepartmentTextile Industries Research DivisionNational Research Centre 33 El-Buhouth Street, Dokki Cairo 12622 Egypt
| |
Collapse
|
6
|
Du Z, Valtierra S, Cardona LR, Dunne SF, Luan CH, Li L. Identifying Anti-prion Chemical Compounds Using a Newly Established Yeast High-Throughput Screening System. Cell Chem Biol 2019; 26:1664-1680.e4. [PMID: 31668517 DOI: 10.1016/j.chembiol.2019.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/31/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022]
Abstract
Prion-like protein aggregation underlies the pathology of a group of fatal neurodegenerative diseases in humans, including Alzheimer's disease (AD), Parkinson's disease, amyotrophic lateral sclerosis, and transmissible spongiform encephalopathy. At present, few high-throughput screening (HTS) systems are available for anti-prion small-molecule identification. Here we describe an innovative phenotypic HTS system in yeast that allows for efficient identification of chemical compounds that eliminate the yeast prion [SWI+]. We show that some identified anti-[SWI+] compounds can destabilize other non-[SWI+] prions, and their antagonizing effects can be prion- and/or variant specific. Intriguingly, among the identified hits are several previously identified anti-PrPSc compounds and a couple of US Food and Drug Administration-approved drugs for AD treatment, validating the efficacy of this HTS system. Moreover, a few hits can reduce proteotoxicity induced by expression of several pathogenic mammalian proteins. Thus, we have established a useful HTS system for identifying compounds that can potentially antagonize prionization and human proteinopathies.
Collapse
Affiliation(s)
- Zhiqiang Du
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Stephanie Valtierra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Luzivette Robles Cardona
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sara Fernandez Dunne
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Chicago, IL 60628, USA
| | - Chi-Hao Luan
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Chicago, IL 60628, USA
| | - Liming Li
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|