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Agamennone M, Storchi L, Marrone A, Paciotti R. Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study. J Comput Aided Mol Des 2021; 35:751-770. [PMID: 34110550 PMCID: PMC8213589 DOI: 10.1007/s10822-021-00393-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
A multilayered computational workflow was designed to identify a druggable binding site on the surface of the E200K pathogenic mutant of the human prion protein, and to investigate the effect of the binding of small molecules in the inhibition of the early aggregation of this protein. At this purpose, we developed an efficient computational tool to scan the molecular interaction properties of a whole MD trajectory, thus leading to the characterization of plausible binding regions on the surface of PrP-E200K. These structural data were then employed to drive structure-based virtual screening and fragment-based approaches to the seeking of small molecular binders of the PrP-E200K. Six promising compounds were identified, and their binding stabilities were assessed by MD simulations. Therefore, analyses of the molecular electrostatic potential similarity between the bound complexes and unbound protein evidenced their potential activity as charged-based inhibitors of the PrP-E200K early aggregation.
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Affiliation(s)
| | - Loriano Storchi
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy
- Molecular Discovery Limited, Middlesex, London, UK
| | - Alessandro Marrone
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Roberto Paciotti
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy.
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Hyeon JW, Noh R, Choi J, Lee SM, Lee YS, An SSA, No KT, Lee J. BMD42-2910, a Novel Benzoxazole Derivative, Shows a Potent Anti-prion Activity and Prolongs the Mean Survival in an Animal Model of Prion Disease. Exp Neurobiol 2020; 29:93-105. [PMID: 32122111 PMCID: PMC7075655 DOI: 10.5607/en.2020.29.1.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/04/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Prion diseases are a group of neurodegenerative and fatal central nervous system disorders. The pathogenic mechanism involves the conversion of cellular prion protein (PrPC) to an altered scrapie isoform (PrPSc), which accumulates in amyloid deposits in the brain. However, no therapeutic drugs have demonstrated efficacy in clinical trials. We previously reported that BMD42-29, a synthetic compound discovered in silico, is a novel anti-prion compound that inhibits the conversion of PrPC to protease K (PK)-resistant PrPSc fragments (PrPres). In the present study, 14 derivatives of BMD42-29 were obtained from BMD42-29 by modifying in the side chain by in silico feedback, with the aim to determine whether they improve anti-prion activity. These derivatives were assessed in a PrPSc-infected cell model and some derivatives were further tested using real time-quaking induced conversion (RT-QuIC). Among them, BMD42-2910 showed high anti-prion activity at low concentrations in vitro and also no toxic effects in a mouse model. Interestingly, abundant PrPres was reduced in brains of mice infected with prion strain when treated with BMD42-2910, and the mice survived longer than control mice and even that treated with BMD42-29. Finally, high binding affinity was predicted in the virtual binding sites (Asn159, Gln 160, Lys194, and Glu196) when PrPC was combined with BMD-42-2910. Our findings showed that BMD42-2910 sufficiently reduces PrPres generation in vitro and in vivo and may be a promising novel anti-prion compound.
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Affiliation(s)
- Jae Wook Hyeon
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28160, Korea
| | - Ran Noh
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28160, Korea
| | - Jiwon Choi
- Bioinformatics and Molecular Design Research Center, Yonsei University, Seoul 03722, Korea
| | - Sol Moe Lee
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28160, Korea
| | - Yeong Seon Lee
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28160, Korea
| | - Seong Soo A An
- Gachon Bio Nano Research Institute, Gachon University, Seongnam 13120, Korea
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center, Yonsei University, Seoul 03722, Korea.,Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jeongmin Lee
- Division of Research Planning, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28160, Korea
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Abstract
Recent advances in understanding of the molecular biology of prion diseases and improved clinical diagnostic techniques might allow researchers to think about therapeutic trials in Creutzfeldt-Jakob disease (CJD) patients. Some attempts have been made in the past and various compounds have been tested in single case reports and patient series. Controlled trials are rare. However, in the past few years, it has been demonstrated that clinical trials are feasible. The clinicians might face several specific problems when evaluating the efficacy of the drug in CJD, such as rareness of the disease, lack of appropriate preclinical tests and heterogeneous clinical presentation in humans. These problems have to be carefully addressed in future.
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Affiliation(s)
- Saima Zafar
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany; Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Aneeqa Noor
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany.
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Abstract
Although an effective therapy for prion disease has not yet been established, many advances have been made toward understanding its pathogenesis, which has facilitated research into therapeutics for the disease. Several compounds, including flupirtine, quinacrine, pentosan polysulfate, and doxycycline, have recently been used on a trial basis for patients with prion disease. Concomitantly, several lead antiprion compounds, including compound B (compB), IND series, and anle138b, have been discovered. However, clinical trials are still far from yielding significantly beneficial results, and the findings of lead compound studies in animals have highlighted new challenges. These efforts have highlighted areas that need improvement or further exploration to achieve more effective therapies. In this work, we review recent advances in prion-related therapeutic research and discuss basic scientific issues to be resolved for meaningful medical intervention of prion disease.
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Therapeutic Approaches to Prion Diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:433-453. [DOI: 10.1016/bs.pmbts.2017.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Abstract
Since the term protein was first coined in 1838 and protein was discovered to be the essential component of fibrin and albumin, all cellular proteins were presumed to play beneficial roles in plants and mammals. However, in 1967, Griffith proposed that proteins could be infectious pathogens and postulated their involvement in scrapie, a universally fatal transmissible spongiform encephalopathy in goats and sheep. Nevertheless, this novel hypothesis had not been evidenced until 1982, when Prusiner and coworkers purified infectious particles from scrapie-infected hamster brains and demonstrated that they consisted of a specific protein that he called a "prion." Unprecedentedly, the infectious prion pathogen is actually derived from its endogenous cellular form in the central nervous system. Unlike other infectious agents, such as bacteria, viruses, and fungi, prions do not contain genetic materials such as DNA or RNA. The unique traits and genetic information of prions are believed to be encoded within the conformational structure and posttranslational modifications of the proteins. Remarkably, prion-like behavior has been recently observed in other cellular proteins-not only in pathogenic roles but also serving physiological functions. The significance of these fascinating developments in prion biology is far beyond the scope of a single cellular protein and its related disease.
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Vetrugno V, Puopolo M, Cardone F, Capozzoli F, Ladogana A, Pocchiari M. The future for treating Creutzfeldt–Jakob disease. Expert Opin Orphan Drugs 2014. [DOI: 10.1517/21678707.2015.994605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Ludewigs H, Zuber C, Vana K, Nikles D, Zerr I, Weiss S. Therapeutic approaches for prion disorders. Expert Rev Anti Infect Ther 2014; 5:613-30. [PMID: 17678425 DOI: 10.1586/14787210.5.4.613] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Prion diseases are lethal for both humans and animals, and affected individuals die after several months following a rapid disease progression. Although researchers have attempted for decades to develop effective therapeutics for the therapy of human prion disorders, until now no efficient drug has been available on the market for transmissible spongiform encephalopathy (TSE) treatment or cure. Approximately 200 patients worldwide have died or suffer from variant Creutzfeldt-Jakob disease (CJD). Incidences for sporadic and familial CJD are approximately 1.5-2 per million per year and one per 10 million per year, respectively, in Europe. This review summarizes classical and modern trials for the development of effective anti-TSE drugs, introduces potential effective delivery systems, such as lentiviral and adeno-associated virus systems for antiprion components, including antibodies and siRNAs, and presents vaccination trials. Most of the antiprion drugs target prion protein PrP(c) and/or PrP(Sc). Alternative targets are receptors and coreceptors for PrP, that is, the 37/67-kDa laminin receptor and heparan sulfate proteoglycanes. We review clinical trials for the treatment of TSEs and describe hindrances and chances for a breakthrough in therapy of prion disorders.
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Affiliation(s)
- Heike Ludewigs
- Laboratorium für Molekulare Biologie, Genzentrum, Institut für Biochemie der LMU München, München, Germany.
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Nguyen T, Sakasegawa Y, Doh-Ura K, Go ML. Anti-prion activities and drug-like potential of functionalized quinacrine analogs with basic phenyl residues at the 9-amino position. Eur J Med Chem 2011; 46:2917-29. [PMID: 21531054 DOI: 10.1016/j.ejmech.2011.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/02/2011] [Accepted: 04/04/2011] [Indexed: 11/16/2022]
Abstract
In this paper, we report the synthesis and cell-based anti-prion activity of quinacrine analogs derived by replacing the basic alkyl side chain of quinacrine with 4-(4-methylpiperazin-I-yl)phenyl, (1-benzylpiperidin-4-yl) and their structural variants. Several promising analogs were found that have a more favorable anti-prion profile than quinacrine in terms of potency and activity across different prion-infected murine cell models. They also exhibited greater binding affinities for a human prion protein fragment (hPrP(121-231)) than quinacrine, and had permeabilities on the PAMPA-BBB assay that fall within the range of CNS permeant candidates. When evaluated on bidirectional assays on a Pgp overexpressing cell line, one analog was less susceptible to Pgp efflux activity compared to quinacrine. Taken together, the results point to an important role for the substituted 9-amino side chain attached to the acridine, tetrahydroacridine and quinoline scaffolds. The nature of this side chain influenced cell-based potency, PAMPA permeability and binding affinity to hPrP(121-231).
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Affiliation(s)
- Thuy Nguyen
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
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Abstract
IMPORTANCE OF THE FIELD Rapidly progressive dementia (RPD) has many possible etiologies and definitive treatment is reliant upon an accurate diagnosis from an appropriate diagnostic work-up. A large portion of the neurodegenerative causes of RPD are due to prion diseases (e.g., Creutzfeldt-Jakob disease). The study of prion diseases, for which there is no currently available treatment, has public health implications and is becoming increasingly more relevant to our understanding of other protein misfolding disorders including Alzheimer's disease, frontotemporal degeneration, and Parkinson's disease. AREAS COVERED IN THIS REVIEW This article begins with an overview of the etiologies and diagnostic work-up of RPD followed by a detailed review of the literature concerning the treatment of human prion diseases (1971 to present). WHAT THE READER WILL GAIN The reader will understand the differential diagnosis and work-up of RPD as it pertains to its treatment, as well as an in-depth understanding of treatments of human prion diseases. TAKE HOME MESSAGE An accurate diagnosis of the cause of RPD is of paramount importance when determining appropriate treatment. Most studies of the treatment for human prion diseases are case reports or case series, and results from only one randomized, placebo-controlled study have been reported in the literature (flupirtine). Studies have been hindered by disease heterogeneity and lack of standardized outcome measures. Although no effective prion disease treatment has been revealed through these studies, they provide important considerations for future studies.
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Affiliation(s)
- Brian S Appleby
- Johns Hopkins University School of Medicine, Division of Geriatric Psychiatry and Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Meyer 279, 600 N. Wolfe St., Baltimore, MD 21287, USA.
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Collinge J, Gorham M, Hudson F, Kennedy A, Keogh G, Pal S, Rossor M, Rudge P, Siddique D, Spyer M, Thomas D, Walker S, Webb T, Wroe S, Darbyshire J. Safety and efficacy of quinacrine in human prion disease (PRION-1 study): a patient-preference trial. Lancet Neurol 2009; 8:334-44. [PMID: 19278902 PMCID: PMC2660392 DOI: 10.1016/s1474-4422(09)70049-3] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The propagation of prions, the causative agents of Creutzfeldt-Jakob disease and other human prion diseases, requires post-translational conversion of normal cellular prion protein to disease-associated forms. The antimalarial drug quinacrine (mepacrine) prevents this conversion in vitro, and was given to patients with various prion diseases to assess its safety and efficacy in changing the course of these invariably fatal and untreatable diseases. METHODS Patients with prion disease were recruited via the UK national referral system and were offered a choice between quinacrine (300 mg daily), no quinacrine, or randomisation to immediate quinacrine or deferred quinacrine in an open-label, patient-preference trial. The primary endpoints were death and serious adverse events possibly or probably related to the study drug. This study is registered, ISRCTN 06722585. FINDINGS 107 patients with prion disease (45 sporadic, two iatrogenic, 18 variant, and 42 inherited) were enrolled, 23 in a pilot study and 84 in the main study. Only two patients chose randomisation; 40 took quinacrine during follow-up (37 who chose it at enrollment). Choice of treatment was associated with disease severity, with those least and most severely affected more likely to choose not to receive quinacrine. 78 (73%) patients died: one randomly assigned to deferred treatment, 26 of 38 who chose immediate quinacrine, and 51 of 68 who chose no quinacrine. Although adjusted mortality was lower in those who chose to take quinacrine than in those who did not, this was due to confounding with disease severity, and there was no difference in mortality between groups after adjustment. Four of 40 patients who took quinacrine had a transient response on neurological rating scales. Only two of 14 reported serious adverse events were judged quinacrine-related. INTERPRETATION Quinacrine at a dose of 300 mg per day was reasonably tolerated but did not significantly affect the clinical course of prion diseases in this observational study.
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Affiliation(s)
- John Collinge
- National Prion Clinic, National Hospital for Neurology and Neurosurgery, University College London Hospital National Health Service Foundation Trust, Queen Square, London WC1N 3BG, UK.
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Abstract
The transmissible spongiform encephalopathies are rapidly progressive and invariably fatal neurodegenerative diseases for which there are no proven efficacious treatments. Many approaches have been undertaken to find ways to prevent, halt, or reverse these prion diseases, with limited success to date. However, as both our understanding of pathogenesis and our ability to detect early disease increases, so do our potential therapeutic targets and our chances of finding effective drugs. There is increasing pressure to find effective decontaminants for blood supplies, as variant Creutzfeldt Jakob Disease (vCJD) has been shown to be transmissible by blood, and to find non-toxic preventative therapies, with ongoing cases of Bovine Spongiform Encephalopathy (BSE) and the spread of Chronic Wasting Disease (CWD). Within the realm of chemotherapeutic approaches, much research has focussed on blocking the conversion of the normal form of prion protein (PrP(c)) to its abnormal counterpart (PrP(res)). Structurally, these chemotherapeutic agents are often polyanionic or polycyclic and may directly bind PrP(c) or PrP(res), or act by redistributing, sequestering, or down-regulating PrP(c), thus preventing its conversion. There are also some polycationic compounds which proport to enhance the clearance of PrP(res). Other targets include accessory molecules such as the laminin receptor precursor which influences conversion, or cell signalling molecules which may be required for pathogenesis. Of recent interest are the possible neuroprotective effects of some drugs. Importantly, there is evidence that combining compounds may provide synergistic responses. This review provides an update on current testing methods, therapeutic targets, and promising candidates for chemical-based therapy.
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Affiliation(s)
- Valerie L Sim
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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Shetty AK, Steele RW. Prion diseases. Clin Pediatr (Phila) 1997; 36:1-7. [PMID: 9007341 DOI: 10.1177/000992289703600101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- A K Shetty
- Department of Pediatrics, Louisiana State University School of Medicine, New Orleans 70112, USA
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Affiliation(s)
- M Pocchiari
- Section of Persistent and Slow Virus Infections, Istituto Superiore di Sanità, Rome, Italy
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Abstract
The clinical features of 44 Finnish patients with Creutzfeldt-Jakob disease (CJD) were analyzed with special emphasis on the differences between the sporadic and familial forms. The 32 sporadic patients comprised all neuropathologically verified cases of CJD in 1974-89 in Finland. The 12 familial patients were members of the same pedigree where CJD has been linked with a mutation at codon 178 of the PRNP gene. The median age at the onset of the disease was 62.5 years and median duration 4.5 months in sporadic patients, and 49 years and 20.5 months in familial CJD, respectively. 90 percent of both sporadic and familial patients had myoclonus. Typical periodic EEG change was seen in 72% of sporadic patients, whereas the familial patients showed only a progressive slowing of EEG.
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Affiliation(s)
- J Kovanen
- Department of Neurology, University of Helsinki, Finland
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Case records of the massachusetts general hospital. Weekly clinicopathological exercises. Case 49-1983. A 75-year-old man with progressive dementia. N Engl J Med 1983; 309:1440-9. [PMID: 6355852 DOI: 10.1056/nejm198312083092307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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