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Drogalin A, Monteiro LS, Alves MJ, Castro TG. Golgi α-mannosidase: opposing structures of Drosophila melanogaster and novel human model using molecular dynamics simulations and docking at different pHs. J Biomol Struct Dyn 2024; 42:2714-2725. [PMID: 37158092 DOI: 10.1080/07391102.2023.2209184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
The search for Golgi α-mannosidase II (GMII) potent and specific inhibitors has been a focus of many studies for the past three decades since this enzyme is a key target for cancer treatment. α-Mannosidases, such as those from Drosophila melanogaster or Jack bean, have been used as functional models of the human Golgi α-mannosidase II (hGMII) because mammalian mannosidases are difficult to purify and characterize experimentally. Meanwhile, computational studies have been seen as privileged tools able to explore assertive solutions to specific enzymes, providing molecular details of these macromolecules, their protonation states and their interactions. Thus, modelling techniques can successfully predict hGMII 3D structure with high confidence, speeding up the development of new hits. In this study, Drosophila melanogaster Golgi mannosidase II (dGMII) and a novel human model, developed in silico and equilibrated via molecular dynamics simulations, were both opposed for docking. Our findings highlight that the design of novel inhibitors should be carried out considering the human model's characteristics and the enzyme operating pH. A reliable model is evidenced, showing a good correlation between Ki/IC50 experimental data and theoretical ΔGbinding estimations in GMII, opening the possibility of optimizing the rational drug design of new derivatives.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Artem Drogalin
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Luís S Monteiro
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Maria José Alves
- Chemistry Centre, School of Sciences, University of Minho, Braga, Portugal
| | - Tarsila G Castro
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
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2
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Marino C, Bordoni AV. Deoxy sugars. General methods for carbohydrate deoxygenation and glycosidation. Org Biomol Chem 2022; 20:934-962. [PMID: 35014646 DOI: 10.1039/d1ob02001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Deoxy sugars represent an important class of carbohydrates, present in a large number of biomolecules involved in multiple biological processes. In various antibiotics, antimicrobials, and therapeutic agents the presence of deoxygenated units has been recognized as responsible for biological roles, such as adhesion or great affinity to receptors, or improved efficacy. The characterization of glycosidases and glycosyltranferases requires substrates, inhibitors and analogous compounds. Deoxygenated sugars are useful for carrying out specific studies for these enzymes. Deoxy sugars, analogs of natural substrates, may behave as substrates or inhibitors, or may not interact with the enzyme. They are also important for glycodiversification studies of bioactive natural products and glycobiological processes, which could contribute to discovering new therapeutic agents with greater efficacy by modification or replacement of sugar units. Deoxygenation of carbohydrates is, thus, of great interest and numerous efforts have been dedicated to the development of methods for the reduction of sugar hydroxyl groups. Given that carbohydrates are the most important renewable chemicals and are more oxidized than fossil raw materials, it is also important to have methods to selectively remove oxygen from certain atoms of these renewable raw materials. The different methods for removal of OH groups of carbohydrates and representative or recent applications of them are presented in this chapter. Glycosidic bonds in general, and 2-deoxy glycosidic linkages, are included. It is not the scope of this survey to cover all reports for each specific technique.
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Affiliation(s)
- Carla Marino
- CIHIDECAR, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
| | - Andrea V Bordoni
- Gerencia Química & Instituto de Nanociencia y Nanotecnología - Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, CONICET, Av. Gral. Paz 1499, B1650KNA San Martín, Buenos Aires, Argentina
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Lee ZY, Loo JSE, Wibowo A, Mohammat MF, Foo JB. Targeting cancer via Golgi α-mannosidase II inhibition: How far have we come in developing effective inhibitors? Carbohydr Res 2021; 508:108395. [PMID: 34280804 DOI: 10.1016/j.carres.2021.108395] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 11/22/2022]
Abstract
Dysregulation of glycosylation pathways has been well documented in several types of cancer, where it often participates in cancer development and progression, especially cancer metastasis. Hence, inhibition of glycosidases such as mannosidases can disrupt the biosynthesis of glycans on cell surface glycoproteins and modify their role in carcinogenesis and metastasis. Several reviews have delineated the role of N-glycosylation in cancer, but the data regarding effective inhibitors remains sparse. Golgi α-mannosidase has been an attractive therapeutic target for preventing the formation of ß1,6-branched complex type N-glycans. However, due to its high structural similarity to the broadly specific lysosomal α-mannosidase, undesired co-inhibition occurs and this leads to serious side effects that complicates its potential role as a therapeutic agent. Even though extensive efforts have been geared towards the discovery of effective inhibitors, no breakthrough has been achieved thus far which could allow for their use in clinical settings. Improving the specificity of current inhibitors towards Golgi α-mannosidase is requisite in progressing this class of compounds in cancer chemotherapy. In this review, we highlight a few potent and selective inhibitors discovered up to the present to guide researchers for rational design of further effective inhibitors to overcome the issue of specificity.
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Affiliation(s)
- Zheng Yang Lee
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia
| | - Jason Siau Ee Loo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia; Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia
| | - Agustono Wibowo
- Faculty of Applied Science, Universiti Teknologi MARA (UiTM) Pahang, Jengka Campus, 26400, Bandar Tun Abdul Razak Jengka, Pahang, Malaysia
| | - Mohd Fazli Mohammat
- Organic Synthesis Laboratory, Institute of Science, Universiti Teknologi MARA (UiTM), 40450, Shah Alam, Selangor, Malaysia
| | - Jhi Biau Foo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia; Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia.
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Klunda T, Hricovíni M, Šesták S, Kóňa J, Poláková M. Selective Golgi α-mannosidase II inhibitors: N-alkyl substituted pyrrolidines with a basic functional group. NEW J CHEM 2021. [DOI: 10.1039/d1nj01176f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic assays, molecular modeling and NMR studies of novel 1,4-dideoxy-1,4-imino-l-lyxitols provided new information on the GH38 family enzyme inhibitors and their selectivity.
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Affiliation(s)
- Tomáš Klunda
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Michal Hricovíni
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Sergej Šesták
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Juraj Kóňa
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Monika Poláková
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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A novel Golgi mannosidase inhibitor: Molecular design, synthesis, enzyme inhibition, and inhibition of spheroid formation. Bioorg Med Chem 2020; 28:115492. [PMID: 32291147 DOI: 10.1016/j.bmc.2020.115492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 11/23/2022]
Abstract
Effective chemotherapy for solid cancers is challenging due to a limitation in permeation that prevents anticancer drugs from reaching the center of the tumor, therefore unable to limit cancer cell growth. To circumvent this issue, we planned to apply the drugs directly at the center by first collapsing the outer structure. For this, we focused on cell-cell communication (CCC) between N-glycans and proteins at the tumor cell surface. Mature N-glycans establish CCC; however, CCC is hindered when numerous immature N-glycans are present at the cell surface. Inhibition of Golgi mannosidases (GMs) results in the transport of immature N-glycans to the cell surface. This can be employed to disrupt CCC. Here, we describe the molecular design and synthesis of an improved GM inhibitor with a non-sugar mimic scaffold that was screened from a compound library. The synthesized compounds were tested for enzyme inhibition ability and inhibition of spheroid formation using cell-based methods. Most of the compounds designed and synthesized exhibited GM inhibition at the cellular level. Of those, AR524 had higher inhibitory activity than a known GM inhibitor, kifunensine. Moreover, AR524 inhibited spheroid formation of human malignant cells at low concentration (10 µM), based on the disruption of CCC by GM inhibition.
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Liao J, Pan B, Liao G, Zhao Q, Gao Y, Chai X, Zhuo X, Wu Q, Jiao B, Pan W, Guo Z. Synthesis and immunological studies of β-1,2-mannan-peptide conjugates as antifungal vaccines. Eur J Med Chem 2019; 173:250-260. [DOI: 10.1016/j.ejmech.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/20/2019] [Accepted: 04/01/2019] [Indexed: 01/06/2023]
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Synthesis of N-benzyl substituted 1,4-imino-l-lyxitols with a basic functional group as selective inhibitors of Golgi α-mannosidase IIb. Bioorg Chem 2019; 83:424-431. [DOI: 10.1016/j.bioorg.2018.10.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
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Šamšulová V, Poláková M, Horák R, Šedivá M, Kvapil L, Hradil P. Synthetic approach to novel glycosyltriazole-3-hydroxyquinolone conjugates and their antimicrobial properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Bella M, Šesták S, Moncoľ J, Koóš M, Poláková M. Synthesis of 1,4-imino-L-lyxitols modified at C-5 and their evaluation as inhibitors of GH38 α-mannosidases. Beilstein J Org Chem 2018; 14:2156-2162. [PMID: 30202468 PMCID: PMC6122390 DOI: 10.3762/bjoc.14.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/24/2018] [Indexed: 01/01/2023] Open
Abstract
A synthetic approach to 1,4-imino-L-lyxitols with various modifications at the C-5 position is reported. These imino-L-lyxitol cores were used for the preparation of a series of N-(4-halobenzyl)polyhydroxypyrrolidines. An impact of the C-5 modification on the inhibition and selectivity against GH38 α-mannosidases from Drosophila melanogaster, the Golgi (GMIIb) and lysosomal (LManII) mannosidases and commercial jack bean α-mannosidase from Canavalia ensiformis was evaluated. The modification at C-5 affected their inhibitory activity against the target GMIIb enzyme. In contrast, no inhibition effect of the pyrrolidines against LManII was observed. The modification of the imino-L-lyxitol core is therefore a suitable motif for the design of inhibitors with desired selectivity against the target GMIIb enzyme.
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Affiliation(s)
- Maroš Bella
- Department of Glycochemistry, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38, Bratislava, Slovakia
| | - Sergej Šesták
- Department of Glycochemistry, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38, Bratislava, Slovakia
| | - Ján Moncoľ
- Department of Inorganic Chemistry, Faculty of Chemical and Food Technology, Radlinského 9, SK-812 37 Bratislava, Slovakia
| | - Miroslav Koóš
- Department of Glycochemistry, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38, Bratislava, Slovakia
| | - Monika Poláková
- Department of Glycochemistry, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38, Bratislava, Slovakia
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Šesták S, Bella M, Klunda T, Gurská S, Džubák P, Wöls F, Wilson IBH, Sladek V, Hajdúch M, Poláková M, Kóňa J. N-Benzyl Substitution of Polyhydroxypyrrolidines: The Way to Selective Inhibitors of Golgi α-Mannosidase II. ChemMedChem 2018; 13:373-383. [PMID: 29323461 DOI: 10.1002/cmdc.201700607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/04/2018] [Indexed: 12/24/2022]
Abstract
Inhibition of the biosynthesis of complex N-glycans in the Golgi apparatus influences progress of tumor growth and metastasis. Golgi α-mannosidase II (GMII) has become a therapeutic target for drugs with anticancer activities. One critical task for successful application of GMII drugs in medical treatments is to decrease their unwanted co-inhibition of lysosomal α-mannosidase (LMan), a weakness of all known potent GMII inhibitors. A series of novel N-substituted polyhydroxypyrrolidines was synthesized and tested with modeled GH38 α-mannosidases from Drosophila melanogaster (GMIIb and LManII). The most potent structures inhibited GMIIb (Ki =50-76 μm, as determined by enzyme assays) with a significant selectivity index of IC50 (LManII)/IC50 (GMIIb) >100. These compounds also showed inhibitory activities in in vitro assays with cancer cell lines (leukemia, IC50 =92-200 μm) and low cytotoxic activities in normal fibroblast cell lines (IC50 >200 μm). In addition, they did not show any significant inhibitory activity toward GH47 Aspergillus saitoiα1,2-mannosidase. An appropriate stereo configuration of hydroxymethyl and benzyl functional groups on the pyrrolidine ring of the inhibitor may lead to an inhibitor with the required selectivity for the active site of a target α-mannosidase.
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Affiliation(s)
- Sergej Šesták
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Maroš Bella
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Tomáš Klunda
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Soňa Gurská
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Petr Džubák
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Florian Wöls
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Iain B H Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Vladimir Sladek
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Marián Hajdúch
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Monika Poláková
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
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Bobovská A, Tvaroška I, Kóňa J. Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II. J Mol Graph Model 2016; 66:47-57. [PMID: 27035259 DOI: 10.1016/j.jmgm.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/28/2022]
Abstract
Human Golgi α-mannosidase II (GMII), a zinc ion co-factor dependent glycoside hydrolase (E.C.3.2.1.114), is a pharmaceutical target for the design of inhibitors with anti-cancer activity. The discovery of an effective inhibitor is complicated by the fact that all known potent inhibitors of GMII are involved in unwanted co-inhibition with lysosomal α-mannosidase (LMan, E.C.3.2.1.24), a relative to GMII. Routine empirical QSAR models for both GMII and LMan did not work with a required accuracy. Therefore, we have developed a fast computational protocol to build predictive models combining interaction energy descriptors from an empirical docking scoring function (Glide-Schrödinger), Linear Interaction Energy (LIE) method, and quantum mechanical density functional theory (QM-DFT) calculations. The QSAR models were built and validated with a library of structurally diverse GMII and LMan inhibitors and non-active compounds. A critical role of QM-DFT descriptors for the more accurate prediction abilities of the models is demonstrated. The predictive ability of the models was significantly improved when going from the empirical docking scoring function to mixed empirical-QM-DFT QSAR models (Q(2)=0.78-0.86 when cross-validation procedures were carried out; and R(2)=0.81-0.83 for a testing set). The average error for the predicted ΔGbind decreased to 0.8-1.1kcalmol(-1). Also, 76-80% of non-active compounds were successfully filtered out from GMII and LMan inhibitors. The QSAR models with the fragmented QM-DFT descriptors may find a useful application in structure-based drug design where pure empirical and force field methods reached their limits and where quantum mechanics effects are critical for ligand-receptor interactions. The optimized models will apply in lead optimization processes for GMII drug developments.
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Affiliation(s)
- Adela Bobovská
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic; Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovak Republic.
| | - Igor Tvaroška
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
| | - Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
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