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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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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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3
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Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. J Cheminform 2024; 16:7. [PMID: 38218937 PMCID: PMC10788035 DOI: 10.1186/s13321-024-00801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024] Open
Abstract
Within the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/ . Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists' selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.
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Affiliation(s)
- Tinghao Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Shaohua Sun
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Runzhou Wang
- School of Management, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Ting Li
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Bicheng Gan
- College of Petroleum Engineering, Northeast Petroleum University, Daqing, 163318, Heilongjiang, China
| | - Yuezhou Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China.
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Key Laboratory of Flexible Electronics of Zhejiang Province, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
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4
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Takebe K, Suzuki M, Kuwada-Kusunose T, Shirai S, Fukuzawa K, Takamiya T, Uzawa N, Iijima H. Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses. J Chem Inf Model 2023. [PMID: 37436881 DOI: 10.1021/acs.jcim.3c00331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
A third-generation inhibitor of catechol O-methyltransferase (COMT), opicapone (1), has the 3-nitrocatechol scaffold as do the second-generation inhibitors such as entacapone (2) and tolcapone (3), but only 1 can sustainably inhibit COMT activity making it suitable for a once-daily regimen. These improvements should be attributed to the optimized sidechain moiety (oxidopyridyloxadiazolyl group) of 1 substituted at the 5-position of the 3-nitrocatechol ring. We analyzed the role of the sidechain moiety by solving the crystal structures of COMT/S-adenosylmethionine (SAM)/Mg/1 and COMT/S-adenosylhomocysteine (SAH)/Mg/1 complexes. Fragment molecular orbital (FMO) calculations elucidated that the dispersion interaction between the sidechains of Leu 198 and Met 201 on the β6β7-loop and the oxidopyridine ring of 1 were unique and important in both complexes. In contrast, the catechol binding site made a remarkable difference in the sidechain conformation of Lys 144. The ε-amino group of Lys 144 was outside of the catalytic pocket and was replaced by a water molecule in the COMT/SAH/Mg/1 complex. No nitrocatechol inhibitor has ever been reported to make a complex with COMT and SAH. Thus, the conformational change of Lys 144 found in the COMT/SAH/Mg/1 complex is the first crystallographic evidence that supports the role of Lys 144 as a catalytic base to take out a proton ion from the reaction site to the outside of the enzyme. The fact that 1 generated a complex with SAH and COMT also suggests that 1 could inhibit COMT twofold, as a typical substrate mimic competitive inhibitor and as a product-inhibition enhancer.
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Affiliation(s)
- Katsuki Takebe
- Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Kuwada-Kusunose
- School of Dentistry at Matsudo, Nihon University, 2-870-1 Sakaecho-nishi, Matsudo, Chiba 271-8587, Japan
| | - Satoko Shirai
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo 142-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo 142-8501, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Takamiya
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Narikazu Uzawa
- Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Hiroshi Iijima
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
- CBI Research Institute, 3-11-1 Shibaura, Minato-ku, Tokyo 108-0023, Japan
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5
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Park R, Ongpipattanakul C, Nair SK, Bowers AA, Kuhlman B. Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nat Chem Biol 2023; 19:460-467. [PMID: 36509904 PMCID: PMC10065947 DOI: 10.1038/s41589-022-01206-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
Promiscuous enzymes that modify peptides and proteins are powerful tools for labeling biomolecules; however, directing these modifications to desired substrates can be challenging. Here, we use computational interface design to install a substrate recognition domain adjacent to the active site of a promiscuous enzyme, catechol O-methyltransferase. This design approach effectively decouples substrate recognition from the site of catalysis and promotes modification of peptides recognized by the recruitment domain. We determined the crystal structure of this novel multidomain enzyme, SH3-588, which shows that it closely matches our design. SH3-588 methylates directed peptides with catalytic efficiencies exceeding the wild-type enzyme by over 1,000-fold, whereas peptides lacking the directing recognition sequence do not display enhanced efficiencies. In competition experiments, the designer enzyme preferentially modifies directed substrates over undirected substrates, suggesting that we can use designed recruitment domains to direct post-translational modifications to specific sequence motifs on target proteins in complex multisubstrate environments.
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Affiliation(s)
- Rodney Park
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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6
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Chavarria D, Benfeito S, Soares P, Lima C, Garrido J, Serrão P, Soares-da-Silva P, Remião F, Oliveira PJ, Borges F. Boosting caffeic acid performance as antioxidant and monoamine oxidase B/catechol-O-methyltransferase inhibitor. Eur J Med Chem 2022; 243:114740. [PMID: 36116233 DOI: 10.1016/j.ejmech.2022.114740] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022]
Abstract
Increased oxidative stress (OS) and depletion of nigrostriatal dopamine (DA) are closely linked to the neurodegeneration observed in Parkinson's Disease (PD). Caffeic acid (CA)-based antioxidants were developed, and their inhibitory activities towards monoamine oxidases (MAOs) and catechol O-methyltransferases (COMT) were screened. The results showed that the incorporation of an extra double bond maintained or even boosted the antioxidant properties of CA. α-CN derivatives displayed redox potentials (Ep) similar to CA (1) and inhibited hMAO-B with low μM IC50 values. Moreover, catechol amides acted as MB-COMT inhibitors, showing IC50 values within the low μM range. In general, CA derivatives presented safe cytotoxicity profiles at concentrations up to 10 μM. The formation of reactive oxygen species (ROS) induced by CA derivatives may be underlying the cytotoxic effects observed at higher concentrations. Catechol amides 3-6, 8-11 at 10 μM protected cells against oxidative damage. Compounds 3 and 8 were predicted to cross the blood-brain barrier (BBB) by passive diffusion. In summary, we report for the first time BBB-permeant CA-based multitarget lead compounds that may restore DAergic neurotransmission (dual hMAO-B/MB-COMT inhibition) and prevent oxidative damage. The data represents a groundbreaking advancement towards the discovery of the next generation of new drugs for PD.
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Affiliation(s)
- Daniel Chavarria
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Sofia Benfeito
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro Soares
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Carla Lima
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Jorge Garrido
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; Department of Chemical Engineering, School of Engineering (ISEP), Polytechnic of Porto, 4200-072, Porto, Portugal
| | - Paula Serrão
- Department of Biomedicine - Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal; MedInUP - Center for Drug Discovery and Innovative Medicines, University of Porto, 4200-319, Porto, Portugal
| | - Patrício Soares-da-Silva
- Department of Biomedicine - Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal; MedInUP - Center for Drug Discovery and Innovative Medicines, University of Porto, 4200-319, Porto, Portugal
| | - Fernando Remião
- UCIBIO-REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Paulo J Oliveira
- CNC - Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology. University of Coimbra, UC Biotech Building, Cantanhede, Portugal
| | - Fernanda Borges
- CIQUP-IMS/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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7
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
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8
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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9
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Wang FY, Wei GL, Fan YF, Zhao DF, Wang P, Zou LW, Yang L. Inhibition of catechol- O-methyltransferase by natural pentacyclic triterpenes: structure-activity relationships and kinetic mechanism. J Enzyme Inhib Med Chem 2021; 36:1079-1087. [PMID: 34030574 PMCID: PMC8158265 DOI: 10.1080/14756366.2021.1928112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Inhibitors of COMT are clinically used for the treatment of Parkinson's disease. Here, we report the first natural pentacyclic triterpenoid-type COMT inhibitors and their structure-activity relationships and inhibition mechanism. The most potent compounds were found to be oleanic acid, betulinic acid and celastrol with IC50 values of 3.89-5.07 μM, that acted as mixed (uncompetitive plus non-competitive) inhibitors of COMT, representing a new skeleton of COMT inhibitor. Molecular docking suggested that they can specifically recognise and bind with the unique hydrophobic residues surrounding the catechol pocket. Furthermore, oleanic acid and betulinic acid proved to be less disruptive of mitochondrial membrane potential (MMP) compared to tolcapone, thus reducing the risk of liver toxicity. These findings could be used to produce an ideal lead compound and to guide synthetic efforts in generating related derivatives for further preclinical testing.
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Affiliation(s)
- Fang-Yuan Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gui-Lin Wei
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu-Fan Fan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dong-Fang Zhao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ping Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li-Wei Zou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling Yang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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10
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Cruz-Vicente P, Passarinha LA, Silvestre S, Gallardo E. Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches. Molecules 2021; 26:2193. [PMID: 33920326 PMCID: PMC8069930 DOI: 10.3390/molecules26082193] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative diseases (ND), including Alzheimer's (AD) and Parkinson's Disease (PD), are becoming increasingly more common and are recognized as a social problem in modern societies. These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide. Currently, there is no existing cure for AD nor PD and the clinically used drugs aim only at symptomatic relief, and are not capable of stopping neurodegeneration. Over the last years, several drug candidates reached clinical trials phases, but they were suspended, mainly because of the unsatisfactory pharmacological benefits. Recently, the number of compounds developed using in silico approaches has been increasing at a promising rate, mainly evaluating the affinity for several macromolecular targets and applying filters to exclude compounds with potentially unfavorable pharmacokinetics. Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico approaches to design novel drug candidates for AD and PD treatment will be presented. In addition, future perspectives for the treatment of these ND will also be briefly discussed.
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Affiliation(s)
- Pedro Cruz-Vicente
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Luís A. Passarinha
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
| | - Samuel Silvestre
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Eugenia Gallardo
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
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Wang FY, Wang P, Zhao DF, Gonzalez FJ, Fan YF, Xia YL, Ge GB, Yang L. Analytical methodologies for sensing catechol- O-methyltransferase activity and their applications. J Pharm Anal 2021; 11:15-27. [PMID: 33717608 PMCID: PMC7930641 DOI: 10.1016/j.jpha.2020.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 01/02/2023] Open
Abstract
Mammalian catechol-O-methyltransferases (COMT) are an important class of conjugative enzymes, which play a key role in the metabolism and inactivation of catechol neurotransmitters, catechol estrogens and a wide range of endobiotics and xenobiotics that bear the catechol group. Currently, COMT inhibitors are used in combination with levodopa for the treatment of Parkinson's disease in clinical practice. The crucial role of COMT in human health has raised great interest in the development of more practical assays for highly selective and sensitive detection of COMT activity in real samples, as well as for rapid screening and characterization of COMT inhibitors as drug candidates. This review summarizes recent advances in analytical methodologies for sensing COMT activity and their applications. Several lists of biochemical assays for measuring COMT activity, including the probe substrates, along with their analytical conditions and kinetic parameters, are presented. Finally, the challenges and future perspectives in the field, such as visualization of COMT activity in vivo and in situ, are highlighted. Collectively, this review article overviews the practical assays for measuring COMT activities in complex biological samples, which will strongly facilitate the investigations on the relevance of COMT to human diseases and promote the discovery of COMT inhibitors via high-throughput screening.
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Affiliation(s)
- Fang-Yuan Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ping Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dong-Fang Zhao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yu-Fan Fan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yang-Liu Xia
- School of Life Science and Medicine, Dalian University of Technology, Panjin, 124221, China
| | - Guang-Bo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ling Yang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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Liver says no: the ongoing search for safe catechol O-methyltransferase inhibitors to replace tolcapone. Drug Discov Today 2020; 25:1846-1854. [DOI: 10.1016/j.drudis.2020.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
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da Silva IR, Parise MR, Pereira M, da Silva RA. Prospecting for new catechol- O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson's disease: a study by molecular dynamics and structure-based virtual screening. J Biomol Struct Dyn 2020; 39:5872-5891. [PMID: 32691671 DOI: 10.1080/07391102.2020.1794963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative, chronic, and progressive disease, common in the elderly. The catechol-O-methyltransferase (COMT) is a monomeric enzyme involved in dopamine (DA) degradation, the neurotransmitter in deficit in patients with PD. The reference treatment of PD consists of levodopa (L-dopa) administration, which is the precursor of DA. The inhibition of COMT is an adjuvant treatment in PD since it keeps DA levels constant. The goal of this study was to identify drug candidates capable of inhibiting COMT for the treatment of PD and identify important fragments of these molecules. Initially, we analyzed the flexibility of COMT and defined its main conformations in solution regarding the absence (system I) and presence of the S-adenosyl-L-methionine (SAM) cofactor (system II) through molecular dynamics (MD) simulations. Two regions in these structures were selected for molecular docking, firstly the entire cavity where the cofactor and substrates are bound and secondly the specific biding region of the enzyme substrates. Based on the conformations of the MD, the virtual screening (VS) was performed against FDA Approved and Zinc Natural Products databases aiming at the selection of the best compounds. Subsequently, the absorption, distribution, metabolization, excretion, and toxicity (ADMET) properties, as well as drug-score and drug-likeness indexes of the most promising compounds were analyzed. After a detailed analysis of the compounds selected by structure-based VS, it was possible to highlight the fragments most frequently involved in their stability: 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole, 9H-Benz(c)indole(3,2,1-ij)(1,5)naphthyridin-9-one and (10R,13S)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17dodecahydrocyclopenta[a]phenanthren-3-one. The identification of these potential fragments is essential for the prospection of more specific inhibitors against COMT using the technique of Fragment-based lead discovery (FBLD). Besides, this study allowed us to identify the potential COMT inhibitors through a complete understanding of molecular-level interactions based on the flexibility of this protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Michelle Rocha Parise
- Laboratório de Farmacologia e Fisiologia, Universidade Federal de Jataí, Jataí, Brasil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brasil
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Akhtar MJ, Yar MS, Grover G, Nath R. Neurological and psychiatric management using COMT inhibitors: A review. Bioorg Chem 2020; 94:103418. [DOI: 10.1016/j.bioorg.2019.103418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022]
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Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ, Palsson BO. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. PLoS Biol 2019; 17:e2007050. [PMID: 30856169 PMCID: PMC6411097 DOI: 10.1371/journal.pbio.2007050] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/15/2019] [Indexed: 11/29/2022] Open
Abstract
We present a selection design that couples S-adenosylmethionine–dependent methylation to growth. We demonstrate its use in improving the enzyme activities of not only N-type and O-type methyltransferases by 2-fold but also an acetyltransferase of another enzyme category when linked to a methylation pathway in Escherichia coli using adaptive laboratory evolution. We also demonstrate its application for drug discovery using a catechol O-methyltransferase and its inhibitors entacapone and tolcapone. Implementation of this design in Saccharomyces cerevisiae is also demonstrated. Many important biological processes require methylation, e.g., DNA methylation and synthesis of flavoring compounds, neurotransmitters, and antibiotics. Most methylation reactions in cells are catalyzed by S-adenosylmethionine (SAM)–dependent methyltransferases (Mtases) using SAM as a methyl donor. Thus, SAM-dependent Mtases have become an important enzyme category of biotechnological interests and as healthcare targets. However, functional implementation and engineering of SAM-dependent Mtases remains difficult and is neither cost effective nor high throughput. Here, we are able to address these challenges by establishing a synthetic biology approach, which links Mtase activity to cell growth such that higher Mtase activity ultimately leads to faster cell growth. We show that better-performing variants of the examined Mtases can be readily obtained by growth selection after repetitive cell passages. We also demonstrate the usefulness of our approach for discovery of Mtase-specific drug candidates. We further show our approach is not only applicable in bacteria, exemplified by Escherichia coli, but also in eurkaryotic organisms such as budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Hao Luo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Anne Sofie L. Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lei Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Konstantin Schneider
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulla Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hanne B. Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bin Du
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Emre Özdemir
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus J. Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
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Baumann AN, Schüppel F, Eisold M, Kreppel A, de Vivie-Riedle R, Didier D. Oxidative Ring Contraction of Cyclobutenes: General Approach to Cyclopropylketones including Mechanistic Insights. J Org Chem 2018; 83:4905-4921. [DOI: 10.1021/acs.joc.8b00297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas N. Baumann
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Franziska Schüppel
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Michael Eisold
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Andrea Kreppel
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Dorian Didier
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377 Munich, Germany
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Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2016. J Med Chem 2017; 61:1774-1784. [PMID: 29087197 DOI: 10.1021/acs.jmedchem.7b01298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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O'Tuathaigh CMP, Moran PM, Zhen XC, Waddington JL. Translating advances in the molecular basis of schizophrenia into novel cognitive treatment strategies. Br J Pharmacol 2017; 174:3173-3190. [PMID: 28667666 DOI: 10.1111/bph.13938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/07/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023] Open
Abstract
The presence and severity of cognitive symptoms, including working memory, executive dysfunction and attentional impairment, contributes materially to functional impairment in schizophrenia. Cognitive symptoms have proved to be resistant to both first- and second-generation antipsychotic drugs. Efforts to develop a consensus set of cognitive domains that are both disrupted in schizophrenia and are amenable to cross-species validation (e.g. the National Institute of Mental Health Cognitive Neuroscience Treatment Research to Improve Cognition in Schizophrenia and Research Domain Criteria initiatives) are an important step towards standardization of outcome measures that can be used in preclinical testing of new drugs. While causative genetic mutations have not been identified, new technologies have identified novel genes as well as hitherto candidate genes previously implicated in the pathophysiology of schizophrenia and/or mechanisms of antipsychotic efficacy. This review comprises a selective summary of these developments, particularly phenotypic data arising from preclinical genetic models for cognitive dysfunction in schizophrenia, with the aim of indicating potential new directions for pro-cognitive therapeutics. Linked Articles This article is part of a themed section on Pharmacology of Cognition: a Panacea for Neuropsychiatric Disease? To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.19/issuetoc.
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Affiliation(s)
- Colm M P O'Tuathaigh
- School of Medicine, University College Cork, Brookfield Health Sciences Complex, Cork, Ireland
| | - Paula M Moran
- School of Psychology, University of Nottingham, Nottingham, UK
| | - Xuechu C Zhen
- Jiangsu Key Laboratory of Translational Research & Therapy for Neuropsychiatric Disorders and Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - John L Waddington
- Jiangsu Key Laboratory of Translational Research & Therapy for Neuropsychiatric Disorders and Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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19
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