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Dickmann CGF, Milicevic Sephton S, Barker RA, Aigbirhio FI. PET Ligands for Imaging Mutant Huntingtin Aggregates: A Case Study in Non-For-Profit Scientific Management. Chembiochem 2024; 25:e202400152. [PMID: 38695673 DOI: 10.1002/cbic.202400152] [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: 02/19/2024] [Revised: 04/02/2024] [Indexed: 06/13/2024]
Abstract
Positron emission tomography imaging of misfolded proteins with high-affinity and selective radioligands has played a vital role in expanding our knowledge of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. The pathogenesis of Huntington's disease, a CAG trinucleotide repeat disorder, is similarly linked to the presence of protein fibrils formed from mutant huntingtin (mHTT) protein. Development of mHTT fibril-specific radioligands has been limited by the lack of structural knowledge around mHTT and a dearth of available hit compounds for medicinal chemistry refinement. Over the past decade, the CHDI Foundation, a non-for-profit scientific management organisation has orchestrated a large-scale screen of small molecules to identify high affinity ligands of mHTT, with lead compounds now reaching clinical maturity. Here we describe the mHTT radioligands developed to date and opportunities for further improvement of this radiotracer class.
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Affiliation(s)
- Catherine G F Dickmann
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Selena Milicevic Sephton
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Franklin I Aigbirhio
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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2
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Song RX, Nicklaus MC, Tarasova NI. Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries. J Comput Aided Mol Des 2024; 38:22. [PMID: 38753096 PMCID: PMC11098933 DOI: 10.1007/s10822-024-00562-4] [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: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 05/19/2024]
Abstract
Although the size of virtual libraries of synthesizable compounds is growing rapidly, we are still enumerating only tiny fractions of the drug-like chemical universe. Our capability to mine these newly generated libraries also lags their growth. That is why fragment-based approaches that utilize on-demand virtual combinatorial libraries are gaining popularity in drug discovery. These à la carte libraries utilize synthetic blocks found to be effective binders in parts of target protein pockets and a variety of reliable chemistries to connect them. There is, however, no data on the potential impact of the chemistries used for making on-demand libraries on the hit rates during virtual screening. There are also no rules to guide in the selection of these synthetic methods for production of custom libraries. We have used the SAVI (Synthetically Accessible Virtual Inventory) library, constructed using 53 reliable reaction types (transforms), to evaluate the impact of these chemistries on docking hit rates for 40 well-characterized protein pockets. The data shows that the virtual hit rates differ significantly for different chemistries with cross coupling reactions such as Sonogashira, Suzuki-Miyaura, Hiyama and Liebeskind-Srogl coupling producing the highest hit rates. Virtual hit rates appear to depend not only on the property of the formed chemical bond but also on the diversity of available building blocks and the scope of the reaction. The data identifies reactions that deserve wider use through increasing the number of corresponding building blocks and suggests the reactions that are more effective for pockets with certain physical and hydrogen bond-forming properties.
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Affiliation(s)
- Robert X Song
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Marc C Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Nadya I Tarasova
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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Chan BWGL, Lynch NB, Tran W, Joyce JM, Savage GP, Meutermans W, Montgomery AP, Kassiou M. Fragment-based drug discovery for disorders of the central nervous system: designing better drugs piece by piece. Front Chem 2024; 12:1379518. [PMID: 38698940 PMCID: PMC11063241 DOI: 10.3389/fchem.2024.1379518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Fragment-based drug discovery (FBDD) has emerged as a powerful strategy to confront the challenges faced by conventional drug development approaches, particularly in the context of central nervous system (CNS) disorders. FBDD involves the screening of libraries that comprise thousands of small molecular fragments, each no greater than 300 Da in size. Unlike the generally larger molecules from high-throughput screening that limit customisation, fragments offer a more strategic starting point. These fragments are inherently compact, providing a strong foundation with good binding affinity for the development of drug candidates. The minimal elaboration required to transition the hit into a drug-like molecule is not only accelerated, but also it allows for precise modifications to enhance both their activity and pharmacokinetic properties. This shift towards a fragment-centric approach has seen commercial success and holds considerable promise in the continued streamlining of the drug discovery and development process. In this review, we highlight how FBDD can be integrated into the CNS drug discovery process to enhance the exploration of a target. Furthermore, we provide recent examples where FBDD has been an integral component in CNS drug discovery programs, enabling the improvement of pharmacokinetic properties that have previously proven challenging. The FBDD optimisation process provides a systematic approach to explore this vast chemical space, facilitating the discovery and design of compounds piece by piece that are capable of modulating crucial CNS targets.
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Affiliation(s)
| | - Nicholas B. Lynch
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Jack M. Joyce
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
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Dichiara M, Cosentino G, Giordano G, Pasquinucci L, Marrazzo A, Costanzo G, Amata E. Designing drugs optimized for both blood-brain barrier permeation and intra-cerebral partition. Expert Opin Drug Discov 2024; 19:317-329. [PMID: 38145409 DOI: 10.1080/17460441.2023.2294118] [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: 10/08/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
INTRODUCTION With the increasing incidence and prevalence of neurological disorders globally, there is a paramount need for new pharmacotherapies. BBB effectively protects the brain but raises a profound challenge to drug permeation, with less than 2% of most drugs reaching the CNS. AREAS COVERED This article reviews aspects of the most recent design strategies, providing insights into ideas and concepts in CNS drug discovery. An overview of the products available on the market is given and why clinical trials are continuously failing is discussed. EXPERT OPINION Among the available CNS drugs, small molecules account for most successful CNS therapeutics due to their ability to penetrate the BBB through passive or carrier-mediated mechanisms. The development of new CNS drugs is very difficult. To date, there is a lack of effective drugs for alleviating or even reversing the progression of brain diseases. Particularly, the use of artificial intelligence strategies, together with more appropriate animal models, may enable the design of molecules with appropriate permeation, to elicit a biological response from the neurotherapeutic target.
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Affiliation(s)
- Maria Dichiara
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giuseppe Cosentino
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giorgia Giordano
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Lorella Pasquinucci
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Agostino Marrazzo
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Giuliana Costanzo
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
| | - Emanuele Amata
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Catania, Catania, Italy
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Shacham T, Offen D, Lederkremer GZ. Efficacy of therapy by MK-28 PERK activation in the Huntington's disease R6/2 mouse model. Neurotherapeutics 2024; 21:e00335. [PMID: 38368172 PMCID: PMC10937961 DOI: 10.1016/j.neurot.2024.e00335] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/19/2024] Open
Abstract
There is currently no disease-modifying therapy for Huntington's disease (HD). We recently described a small molecule, MK-28, which restored homeostasis in HD models by specifically activating PKR-like ER kinase (PERK). This activation boosts the unfolded protein response (UPR), thereby reducing endoplasmic reticulum (ER) stress, a central cytotoxic mechanism in HD and other neurodegenerative diseases. Here, we have tested the long-term effects of MK-28 in HD model mice. R6/2 CAG (160) mice were treated by lifetime intraperitoneal injections 3 times a week. CatWalk measurements of motor function showed strong improvement compared to untreated mice after only two weeks of MK-28 treatment and continued with time, most significantly at 1 mg/kg MK-28, approaching WT values. Seven weeks treatment significantly improved paw grip strength. Body weight recovered and glucose levels, which are elevated in HD mice, were significantly reduced. Treatment with another PERK activator, CCT020312 at 1 mg/kg, also caused amelioration, consistent with PERK activation. Lifespan, measured in more resilient R6/2 CAG (120) mice with daily IP injection, was much extended by 16 days (20%) with 0.3 mg/kg MK-28, and by 38 days (46%) with 1 mg/kg MK-28. No toxicity, measured by weight, blood glucose levels and blood liver function markers, was detectable in WT mice treated for 6 weeks with 6 mg/kg MK-28. Boosting of PERK activity by long-term treatment with MK-28 could be a safe and promising therapeutic approach for HD.
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Affiliation(s)
- Talya Shacham
- The Shmunis School of Biomedicine and Cancer Research, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Daniel Offen
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel; Department of Human Molecular Genetics and Biochemistry, Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z Lederkremer
- The Shmunis School of Biomedicine and Cancer Research, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel; Department of Human Molecular Genetics and Biochemistry, Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Stefan SM, Pahnke J, Namasivayam V. HD_BPMDS: a curated binary pattern multitarget dataset of Huntington's disease-targeting agents. J Cheminform 2023; 15:109. [PMID: 37978560 PMCID: PMC10655317 DOI: 10.1186/s13321-023-00775-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The discovery of both distinctive lead molecules and novel drug targets is a great challenge in drug discovery, which particularly accounts for orphan diseases. Huntington's disease (HD) is an orphan, neurodegenerative disease of which the pathology is well-described. However, its pathophysiological background and molecular mechanisms are poorly understood. To date, only 2 drugs have been approved on the US and European markets, both of which address symptomatic aspects of this disease only. Although several hundreds of agents were described with efficacy against the HD phenotype in in vitro and/or in vivo models, a successful translation into clinical use is rarely achieved. Two major impediments are, first, the lack of awareness and understanding of the interactome-the sum of key proteins, cascades, and mediators-that contributes to HD initiation and progression; and second, the translation of the little gained knowledge into useful model systems. To counteract this lack of data awareness, we manually compiled and curated the entire modulator landscape of successfully evaluated pre-clinical small-molecule HD-targeting agents which are annotated with substructural molecular patterns, physicochemical properties, as well as drug targets, and which were linked to benchmark databases such as PubChem, ChEMBL, or UniProt. Particularly, the annotation with substructural molecular patterns expressed as binary code allowed for the generation of target-specific and -unspecific fingerprints which could be used to determine the (poly)pharmacological profile of molecular-structurally distinct molecules.
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Affiliation(s)
- Sven Marcel Stefan
- Drug Development and Chemical Biology, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372, Oslo, Norway
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jens Pahnke
- Drug Development and Chemical Biology, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372, Oslo, Norway
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Jelgavas Iela 4, Rīga, 1004, Latvia
- Department of Neurobiology, The Georg S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Vigneshwaran Namasivayam
- Drug Development and Chemical Biology, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An Der Immenburg 4, 53121, Bonn, Germany.
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Van de Roovaart HJ, Nguyen N, Veenstra TD. Huntington's Disease Drug Development: A Phase 3 Pipeline Analysis. Pharmaceuticals (Basel) 2023; 16:1513. [PMID: 38004378 PMCID: PMC10674993 DOI: 10.3390/ph16111513] [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: 09/27/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Huntington's Disease (HD) is a severely debilitating neurodegenerative disorder in which sufferers exhibit different combinations of movement disorders, dementia, and behavioral or psychiatric abnormalities. The disorder is a result of a trinucleotide repeat expansion mutation that is inherited in an autosomal dominant manner. While there is currently no treatment to alter the course of HD, there are medications that lessen abnormal movement and psychiatric symptoms. ClinicalTrials.gov was searched to identify drugs that are currently in or have completed phase III drug trials for the treatment of HD. The described phase III trials were further limited to interventional studies that were recruiting, active not recruiting, or completed. In addition, all studies must have posted an update within the past year. PubMed was used to gather further information on these interventional studies. Of the nine clinical trials that met these criteria, eight involved the following drugs: metformin, dextromethorphan/quinidine, deutetrabenazine, valbenazine, Cellavita HD, pridopidine, SAGE-718, and RO7234292 (RG6042). Of these drug treatments, four are already FDA approved. This systematic review provides a resource that summarizes the present therapies for treating this devastating condition that are currently in phase III clinical trials in the United States.
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Affiliation(s)
| | | | - Timothy D. Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH 45314, USA; (H.J.V.d.R.); (N.N.)
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