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Luque FJ, Muñoz-Torrero D. Acetylcholinesterase: A Versatile Template to Coin Potent Modulators of Multiple Therapeutic Targets. Acc Chem Res 2024. [PMID: 38333993 PMCID: PMC10882973 DOI: 10.1021/acs.accounts.3c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
ConspectusThe enzyme acetylcholinesterase (AChE) hydrolyzes the neurotransmitter acetylcholine (ACh) at cholinergic synapses of the peripheral and central nervous system. Thus, it is a prime therapeutic target for diseases that occur with a cholinergic deficit, prominently Alzheimer's disease (AD). Working at a rate near the diffusion limit, it is considered one of nature's most efficient enzymes. This is particularly meritorious considering that its catalytic site is buried at the bottom of a 20-Å-deep cavity, which is preceded by a bottleneck with a diameter shorter than that of the trimethylammonium group of ACh, which has to transit through it. Not only the particular architecture and amino acid composition of its active site gorge enable AChE to largely overcome this potential drawback, but it also offers plenty of possibilities for the design of novel inhibitor drug candidates.In this Account, we summarize our different approaches to colonize the vast territory of the AChE gorge in the pursuit of increased occupancy and hence of inhibitors with increased affinity. We pioneered the use of molecular hybridization to design inhibitors with extended binding at the CAS, reaching affinities among the highest reported so far. Further application of molecular hybridization to grow CAS extended binders by attaching a PAS-binding moiety through suitable linkers led to multisite inhibitors that span the whole length of the gorge, reaching the PAS and even interacting with midgorge residues. We show that multisite AChE inhibitors can also be successfully designed the other way around, by starting with an optimized PAS binder and then colonizing the gorge and CAS. Molecular hybridization from a multicomponent reaction-derived PAS binder afforded a single-digit picomolar multisite AChE inhibitor with more than 1.5 million-fold increased potency relative to the initial hit. This illustrates the powerful alliance between molecular hybridization and gorge occupancy for designing potent AChE inhibitors.Beyond AChE, we show that the stereoelectronic requirements imposed by the AChE gorge for multisite binding have a templating effect that leads to compounds that are active in other key biological targets in AD and other neurological and non-neurological diseases, such as BACE-1 and the aggregation of amyloidogenic proteins (β-amyloid, tau, α-synuclein, prion protein, transthyretin, and human islet amyloid polypeptide). The use of known pharmacophores for other targets as the PAS-binding motif enables the rational design of multitarget agents with multisite binding within AChE and activity against a variety of targets or pathological events, such as oxidative stress and the neuroinflammation-modulating enzyme soluble epoxide hydrolase, among others.We hope that our results can contribute to the development of drug candidates that can modify the course of neurodegeneration and may inspire future works that exploit the power of molecular hybridization in other proteins featuring large cavities.
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Affiliation(s)
- F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, E-08921 Santa Coloma de Gramenet, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
- Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
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2
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Monteiro KLC, Dos Santos Alcântara MG, Freire NML, Brandão EM, do Nascimento VL, Dos Santos Viana LM, de Aquino TM, da Silva-Júnior EF. BACE-1 Inhibitors Targeting Alzheimer's Disease. Curr Alzheimer Res 2023; 20:131-148. [PMID: 37309767 DOI: 10.2174/1567205020666230612155953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023]
Abstract
The accumulation of amyloid-β (Aβ) is the main event related to Alzheimer's disease (AD) progression. Over the years, several disease-modulating approaches have been reported, but without clinical success. The amyloid cascade hypothesis evolved and proposed essential targets such as tau protein aggregation and modulation of β-secretase (β-site amyloid precursor protein cleaving enzyme 1 - BACE-1) and γ-secretase proteases. BACE-1 cuts the amyloid precursor protein (APP) to release the C99 fragment, giving rise to several Aβ peptide species during the subsequent γ-secretase cleavage. In this way, BACE-1 has emerged as a clinically validated and attractive target in medicinal chemistry, as it plays a crucial role in the rate of Aβ generation. In this review, we report the main results of candidates in clinical trials such as E2609, MK8931, and AZD-3293, in addition to highlighting the pharmacokinetic and pharmacodynamic-related effects of the inhibitors already reported. The current status of developing new peptidomimetic, non-peptidomimetic, naturally occurring, and other class inhibitors are demonstrated, considering their main limitations and lessons learned. The goal is to provide a broad and complete approach to the subject, exploring new chemical classes and perspectives.
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Affiliation(s)
- Kadja Luana Chagas Monteiro
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Marcone Gomes Dos Santos Alcântara
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Nathalia Monteiro Lins Freire
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Esaú Marques Brandão
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Vanessa Lima do Nascimento
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Líbni Maísa Dos Santos Viana
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970, Maceió, Alagoas, Brazil
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3
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Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer's Disease Therapy. Molecules 2022; 27:molecules27144372. [PMID: 35889246 PMCID: PMC9320338 DOI: 10.3390/molecules27144372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
In over a century since its discovery, Alzheimer’s disease (AD) has continued to be a global health concern due to its incurable nature and overwhelming increase among older people. In this paper, we give an overview of the efforts of researchers towards identifying potent BACE1 exosite-binding antibodies and allosteric inhibitors. Herein, we apply computer-aided drug design (CADD) methods to unravel the interactions of some proposed psychotic and meroterpenoid BACE1 allosteric site inhibitors. This study is aimed at validating the allosteric potentials of these selected compounds targeted at BACE1 inhibition. Molecular docking, molecular dynamic (MD) simulations, and post-MD analyses are carried out on these selected compounds, which have been experimentally proven to exhibit allosteric inhibition on BACE1. The SwissDock software enabled us to identify more than five druggable pockets on the BACE1 structural surface using docking. Besides the active site region, a melatonin derivative (compound 1) previously proposed as a BACE1 allostery inhibitor showed appreciable stability at eight different subsites on BACE1. Refinement with molecular dynamic (MD) simulations shows that the identified non-catalytic sites are potential allostery sites for compound 1. The allostery and binding mechanism of the selected potent inhibitors show that the smaller the molecule, the easier the attachment to several enzyme regions. This finding hereby establishes that most of these selected compounds failed to exhibit strong allosteric binding with BACE1 except for compound 1. We hereby suggest that further studies and additional identification/validation of other BACE1 allosteric compounds be done. Furthermore, this additional allosteric site investigation will help in reducing the associated challenges with designing BACE1 inhibitors while exploring the opportunities in the design of allosteric BACE1 inhibitors.
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4
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Selected Natural Products in Neuroprotective Strategies for Alzheimer's Disease-A Non-Systematic Review. Int J Mol Sci 2022; 23:ijms23031212. [PMID: 35163136 PMCID: PMC8835836 DOI: 10.3390/ijms23031212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Neurodegenerative disorders such as Alzheimer’s disease (AD) are distinguished by the irreversible degeneration of central nervous system function and structure. AD is characterized by several different neuropathologies—among others, it interferes with neuropsychiatrical controls and cognitive functions. This disease is the number one neurodegenerative disorder; however, its treatment options are few and, unfortunately, ineffective. In the new strategies devised for AD prevention and treatment, the application of plant-based natural products is especially popular due to lesser side effects associated with their taking. Moreover, their neuroprotective activities target different pathological mechanisms. The current review presents the anti-AD properties of several natural plant substances. The paper throws light on products under in vitro and in vivo trials and compiles information on their mechanism of actions. Knowledge of the properties of such plant compounds and their combinations will surely lead to discovering new potent medicines for the treatment of AD with lesser side effects than the currently available pharmacological proceedings.
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5
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Ugbaja SC, Lawal M, Kumalo H. An Overview of β-Amyloid Cleaving Enzyme 1 (Bace1) in Alzheimer's Disease Therapy Elucidating its Exosite-Binding Antibody and Allosteric Inhibitor. Curr Med Chem 2021; 29:114-135. [PMID: 34102967 DOI: 10.2174/0929867328666210608145357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
Over decades of its identification, numerous past and ongoing researches have focused on the therapeutic roles of β-amyloid cleaving enzyme 1 (BACE1) as a target in treating Alzheimer's disease (AD). Although the initial BACE1 inhibitors at phase-3 clinical trials tremendously reduced β-amyloid-associated plaques in patients with AD, the researchers eventually discontinued the tests due to the lack of potency. This discontinuation has resulted in limited drug development and discovery targeted at BACE1, despite the high demand for dementia and AD therapies. It is, therefore, imperative to describe the detailed underlying biological basis of the BACE1 therapeutic option in neurological diseases. Herein, we highlight BACE1 bioactivity, genetic properties, and role in neurodegenerative therapy. We review research contributions to BACE1 exosite-binding antibody and allosteric inhibitor development as AD therapies. The review also covers BACE1 biological function, the disease-associated mechanisms, and the enzyme conditions for amyloid precursor protein sites splitting. Based on the present review, we suggest further studies on anti-BACE1 exosite antibodies and BACE1 allosteric inhibitors. Non-active site inhibition might be the way forward to BACE1 therapy in Alzheimer's neurological disorder.
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Affiliation(s)
- Samuel C Ugbaja
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Monsurat Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Hezekiel Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4001, South Africa
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6
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Viayna E, Coquelle N, Cieslikiewicz-Bouet M, Cisternas P, Oliva CA, Sánchez-López E, Ettcheto M, Bartolini M, De Simone A, Ricchini M, Rendina M, Pons M, Firuzi O, Pérez B, Saso L, Andrisano V, Nachon F, Brazzolotto X, García ML, Camins A, Silman I, Jean L, Inestrosa NC, Colletier JP, Renard PY, Muñoz-Torrero D. Discovery of a Potent Dual Inhibitor of Acetylcholinesterase and Butyrylcholinesterase with Antioxidant Activity that Alleviates Alzheimer-like Pathology in Old APP/PS1 Mice. J Med Chem 2020; 64:812-839. [PMID: 33356266 DOI: 10.1021/acs.jmedchem.0c01775] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The combination of the scaffolds of the cholinesterase inhibitor huprine Y and the antioxidant capsaicin results in compounds with nanomolar potencies toward human acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) that retain or improve the antioxidant properties of capsaicin. Crystal structures of their complexes with AChE and BChE revealed the molecular basis for their high potency. Brain penetration was confirmed by biodistribution studies in C57BL6 mice, with one compound (5i) displaying better brain/plasma ratio than donepezil. Chronic treatment of 10 month-old APP/PS1 mice with 5i (2 mg/kg, i.p., 3 times per week, 4 weeks) rescued learning and memory impairments, as measured by three different behavioral tests, delayed the Alzheimer-like pathology progression, as suggested by a significantly reduced Aβ42/Aβ40 ratio in the hippocampus, improved basal synaptic efficacy, and significantly reduced hippocampal oxidative stress and neuroinflammation. Compound 5i emerges as an interesting anti-Alzheimer lead with beneficial effects on cognitive symptoms and on some underlying disease mechanisms.
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Affiliation(s)
- Elisabet Viayna
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Nicolas Coquelle
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS UMR 5075, F-38054 Grenoble, France.,Large Scale Structures Group, Institut Laue-Langevin, F-38042 Grenoble Cedex 9, France
| | | | - Pedro Cisternas
- Center of Aging and Regeneration UC (CARE-UC), Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O'Higgins 340, P.O. Box 114, 8331150 Santiago, Chile
| | - Carolina A Oliva
- Center of Aging and Regeneration UC (CARE-UC), Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O'Higgins 340, P.O. Box 114, 8331150 Santiago, Chile
| | - Elena Sánchez-López
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, E-28031 Madrid, Spain
| | - Miren Ettcheto
- Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, E-28031 Madrid, Spain.,Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Neuroscience, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.,Department of Biochemistry and Biotechnology, Faculty of Medicine and Health Sciences, University Rovira i Virgili, E-43201 Reus, Spain
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Angela De Simone
- Department of Drug Science and Technology, University of Turin, I-10125 Torino, Italy
| | - Mattia Ricchini
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Marisa Rendina
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Mégane Pons
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, PO Box 3288, 71345 Shiraz, Iran
| | - Belén Pérez
- Department of Pharmacology, Therapeutics and Toxicology, Autonomous University of Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Vincenza Andrisano
- Department for Life Quality Studies, University of Bologna, Corso d'Augusto 237, I-47921 Rimini, Italy
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées BP73, 91993 Brétigny sur Orge, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées BP73, 91993 Brétigny sur Orge, France
| | - Maria Luisa García
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, E-28031 Madrid, Spain
| | - Antoni Camins
- Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, E-28031 Madrid, Spain.,Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Neuroscience, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ludovic Jean
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Nibaldo C Inestrosa
- Center of Aging and Regeneration UC (CARE-UC), Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O'Higgins 340, P.O. Box 114, 8331150 Santiago, Chile.,Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, 6200000 Punta Arenas, Chile
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS UMR 5075, F-38054 Grenoble, France
| | - Pierre-Yves Renard
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
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7
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Spatiotemporal identification of druggable binding sites using deep learning. Commun Biol 2020; 3:618. [PMID: 33110179 PMCID: PMC7591901 DOI: 10.1038/s42003-020-01350-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Identification of novel protein binding sites expands druggable genome and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble the object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, that considers protein conformations as 3D-images, binding sites as objects on these images to detect, and conformational ensembles of proteins as 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding site in G protein-coupled receptor. BiteNet outperforms state-of-the-art methods both in terms of accuracy and speed, taking about 1.5 minutes to analyze 1000 conformations of a protein with ~2000 atoms. Kozlovskii and Popov present BiteNet, a new computational method utilizing deep learning principles for rapid detection of binding sites. BiteNet considers proteins as 3D images, enabling rapid detection of allosteric sites from either static protein structures or its dynamic ensembles.
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8
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Pérez-Areales FJ, Garrido M, Aso E, Bartolini M, De Simone A, Espargaró A, Ginex T, Sabate R, Pérez B, Andrisano V, Puigoriol-Illamola D, Pallàs M, Luque FJ, Loza MI, Brea J, Ferrer I, Ciruela F, Messeguer A, Muñoz-Torrero D. Centrally Active Multitarget Anti-Alzheimer Agents Derived from the Antioxidant Lead CR-6. J Med Chem 2020; 63:9360-9390. [PMID: 32706255 DOI: 10.1021/acs.jmedchem.0c00528] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oxidative stress is a major pathogenic factor in Alzheimer's disease, but it should not be tackled alone rather together with other key targets to derive effective treatments. The combination of the scaffold of the polar antioxidant lead 7-methoxy-2,2-dimethylchroman-6-ol (CR-6) with that of the lipophilic cholinesterase inhibitor 6-chlorotacrine results in compounds with favorable brain permeability and multiple activities in vitro (acetylcholinesterase, butyrylcholinesterase, β-site amyloid precursor protein (APP) cleaving enzyme-1 (BACE-1), and Aβ42 and tau aggregation inhibition). In in vivo studies on wild-type and APP/presenilin 1 (PS1) mice, two selected compounds were well tolerated and led to positive trends, albeit statistically nonsignificant in some cases, on memory performance, amyloid pathology (reduced amyloid burden and potentiated non-amyloidogenic APP processing), and oxidative stress (reduced cortical oxidized proteins and increased antioxidant enzymes superoxide dismutase 2 (SOD2), catalase, glutathione peroxidase 1 (GPX1), and heme oxygenase 1 (Hmox1) and transcription factor nuclear factor-erythroid 2-related factor 2 (Nrf2)). These compounds emerge as interesting brain-permeable multitarget compounds, with a potential as anti-Alzheimer agents beyond that of the original lead CR-6.
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Affiliation(s)
- F Javier Pérez-Areales
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), E-08028 Barcelona, Spain
| | - María Garrido
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Ester Aso
- Department of Pathology and Experimental Therapeutics, Neurosciences Institute, University of Barcelona (UB) and Bellvitge University Hospital-IDIBELL, E-08908 L'Hospitalet de Llobregat, Spain
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, University of Bologna, I-40126 Bologna, Italy
| | - Angela De Simone
- Department of Drug Science and Technology, University of Turin, I-10125 Torino, Italy
| | - Alba Espargaró
- Department of Pharmacy, Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), E-08028 Barcelona, Spain
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, IBUB, and Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona (UB), E-08921 Santa Coloma de Gramenet, Spain
| | - Raimon Sabate
- Department of Pharmacy, Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), E-08028 Barcelona, Spain
| | - Belén Pérez
- Department of Pharmacology, Therapeutics, and Toxicology, Autonomous University of Barcelona, E-08193 Bellaterra, Spain
| | - Vincenza Andrisano
- Department for Life Quality Studies, University of Bologna, I-47921 Rimini, Italy
| | - Dolors Puigoriol-Illamola
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Neuroscience (NeuroUB), University of Barcelona (UB), E-08028 Barcelona, Spain
| | - Mercè Pallàs
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Neuroscience (NeuroUB), University of Barcelona (UB), E-08028 Barcelona, Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, IBUB, and Institute of Theoretical and Computational Chemistry (IQTC), University of Barcelona (UB), E-08921 Santa Coloma de Gramenet, Spain
| | - María Isabel Loza
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Av. de Barcelona s/n, E-15782 Santiago de Compostela, Spain
| | - José Brea
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Av. de Barcelona s/n, E-15782 Santiago de Compostela, Spain
| | - Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, Neurosciences Institute, University of Barcelona (UB) and Bellvitge University Hospital-IDIBELL, E-08908 L'Hospitalet de Llobregat, Spain.,CIBERNED, E-28031 Madrid, Spain
| | - Francisco Ciruela
- Department of Pathology and Experimental Therapeutics, Neurosciences Institute, University of Barcelona (UB) and Bellvitge University Hospital-IDIBELL, E-08908 L'Hospitalet de Llobregat, Spain
| | - Angel Messeguer
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), E-08028 Barcelona, Spain
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9
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Bafna D, Ban F, Rennie PS, Singh K, Cherkasov A. Computer-Aided Ligand Discovery for Estrogen Receptor Alpha. Int J Mol Sci 2020; 21:E4193. [PMID: 32545494 PMCID: PMC7352601 DOI: 10.3390/ijms21124193] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Breast cancer (BCa) is one of the most predominantly diagnosed cancers in women. Notably, 70% of BCa diagnoses are Estrogen Receptor α positive (ERα+) making it a critical therapeutic target. With that, the two subtypes of ER, ERα and ERβ, have contrasting effects on BCa cells. While ERα promotes cancerous activities, ERβ isoform exhibits inhibitory effects on the same. ER-directed small molecule drug discovery for BCa has provided the FDA approved drugs tamoxifen, toremifene, raloxifene and fulvestrant that all bind to the estrogen binding site of the receptor. These ER-directed inhibitors are non-selective in nature and may eventually induce resistance in BCa cells as well as increase the risk of endometrial cancer development. Thus, there is an urgent need to develop novel drugs with alternative ERα targeting mechanisms that can overcome the limitations of conventional anti-ERα therapies. Several functional sites on ERα, such as Activation Function-2 (AF2), DNA binding domain (DBD), and F-domain, have been recently considered as potential targets in the context of drug research and discovery. In this review, we summarize methods of computer-aided drug design (CADD) that have been employed to analyze and explore potential targetable sites on ERα, discuss recent advancement of ERα inhibitor development, and highlight the potential opportunities and challenges of future ERα-directed drug discovery.
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Affiliation(s)
| | | | | | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.B.); (F.B.); (P.S.R.); (K.S.)
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10
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Mermelstein DJ, McCammon JA, Walker RC. pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study. J Mol Recognit 2018; 32:e2765. [PMID: 30264484 DOI: 10.1002/jmr.2765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/25/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023]
Abstract
Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states. We observed a difference in dynamics between double-protonated, mono-protonated, and double-deprotonated states over the known pH range of higher activity. These differences include Tyr 71-aspartyl dyad proximity and active water lifetime. This work indicates that Tyr 71 stabilizes catalytic water in the aspartyl dyad active site, enabling BACE-1 activity.
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Affiliation(s)
- Daniel J Mermelstein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.,Department of Scientific Research Computing and Analytics, GlaxoSmithKline PLC, Collegeville, Pennsylvania
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11
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Krivák R, Hoksza D. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J Cheminform 2018; 10:39. [PMID: 30109435 PMCID: PMC6091426 DOI: 10.1186/s13321-018-0285-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 06/29/2018] [Indexed: 01/29/2023] Open
Abstract
Background Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex computational drug design efforts. Although many methods have been published to date, only few of them are suitable for use in automated pipelines or for processing large datasets.
These use cases require stability and speed, which disqualifies many of the recently introduced tools that are either template based or available only as web servers. Results We present P2Rank, a stand-alone template-free tool for prediction of ligand binding sites based on machine learning. It is based on prediction of ligandability of local chemical neighbourhoods that are centered on points placed on the solvent accessible surface of a protein.
We show that P2Rank outperforms several existing tools, which include two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite). P2Rank belongs to the fastest available tools (requires under 1 s for prediction on one protein), with additional advantage of multi-threaded implementation. Conclusions P2Rank is a new open source software package for ligand binding site prediction from protein structure. It is available as a user-friendly stand-alone command line program and a Java library. P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases. Thanks to its speed and ability to make fully automated predictions, it is particularly well suited for processing large datasets or as a component of scalable structural bioinformatics pipelines. Electronic supplementary material The online version of this article (10.1186/s13321-018-0285-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radoslav Krivák
- Department of Software Engineering, Charles University, Prague, Czech Republic.
| | - David Hoksza
- Department of Software Engineering, Charles University, Prague, Czech Republic.
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12
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Kumar AP, Lukman S. Allosteric binding sites in Rab11 for potential drug candidates. PLoS One 2018; 13:e0198632. [PMID: 29874286 PMCID: PMC5991966 DOI: 10.1371/journal.pone.0198632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
Rab11 is an important protein subfamily in the RabGTPase family. These proteins physiologically function as key regulators of intracellular membrane trafficking processes. Pathologically, Rab11 proteins are implicated in many diseases including cancers, neurodegenerative diseases and type 2 diabetes. Although they are medically important, no previous study has found Rab11 allosteric binding sites where potential drug candidates can bind to. In this study, by employing multiple clustering approaches integrating principal component analysis, independent component analysis and locally linear embedding, we performed structural analyses of Rab11 and identified eight representative structures. Using these representatives to perform binding site mapping and virtual screening, we identified two novel binding sites in Rab11 and small molecules that can preferentially bind to different conformations of these sites with high affinities. After identifying the binding sites and the residue interaction networks in the representatives, we computationally showed that these binding sites may allosterically regulate Rab11, as these sites communicate with switch 2 region that binds to GTP/GDP. These two allosteric binding sites in Rab11 are also similar to two allosteric pockets in Ras that we discovered previously.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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13
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Cossins BP, Lawson ADG, Shi J. Computational Exploration of Conformational Transitions in Protein Drug Targets. Methods Mol Biol 2018; 1762:339-365. [PMID: 29594780 DOI: 10.1007/978-1-4939-7756-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Protein drug targets vary from highly structured to completely disordered; either way dynamics governs function. Hence, understanding the dynamical aspects of how protein targets function can enable improved interventions with drug molecules. Computational approaches offer highly detailed structural models of protein dynamics which are becoming more predictive as model quality and sampling power improve. However, the most advanced and popular models still have errors owing to imperfect parameter sets and often cannot access longer timescales of many crucial biological processes. Experimental approaches offer more certainty but can struggle to detect and measure lightly populated conformations of target proteins and subtle allostery. An emerging solution is to integrate available experimental data into advanced molecular simulations. In the future, molecular simulation in combination with experimental data may be able to offer detailed models of important drug targets such that improved functional mechanisms or selectivity can be accessed.
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Affiliation(s)
- Benjamin P Cossins
- Computer-Aided Drug Design and Structural Biology, UCB Pharma, Slough, UK.
| | | | - Jiye Shi
- Computer-Aided Drug Design and Structural Biology, UCB Pharma, Slough, UK
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14
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Correction: Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors. PLoS One 2017; 12:e0190327. [PMID: 29267385 PMCID: PMC5739478 DOI: 10.1371/journal.pone.0190327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Design, synthesis and multitarget biological profiling of second-generation anti-Alzheimer rhein-huprine hybrids. Future Med Chem 2017. [PMID: 28632395 DOI: 10.4155/fmc-2017-0049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIM Simultaneous modulation of several key targets of the pathological network of Alzheimer's disease (AD) is being increasingly pursued as a promising option to fill the critical gap of efficacious drugs against this condition. MATERIALS & METHODS A short series of compounds purported to hit multiple targets of relevance in AD has been designed, on the basis of their distinct basicities estimated from high-level quantum mechanical computations, synthesized, and subjected to assays of inhibition of cholinesterases, BACE-1, and Aβ42 and tau aggregation, of antioxidant activity, and of brain permeation. RESULTS Using, as a template, a lead rhein-huprine hybrid with an interesting multitarget profile, we have developed second-generation compounds, designed by the modification of the huprine aromatic ring. Replacement by [1,8]-naphthyridine or thieno[3,2-e]pyridine systems resulted in decreased, although still potent, acetylcholinesterase or BACE-1 inhibitory activities, which are more balanced relative to their Aβ42 and tau antiaggregating and antioxidant activities. CONCLUSION Second-generation naphthyridine- and thienopyridine-based rhein-huprine hybrids emerge as interesting brain permeable compounds that hit several crucial pathogenic factors of AD.
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