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Jedwabny W, Cierpicki T, Grembecka J, Dyguda-Kazimierowicz E. Validation of approximate nonempirical scoring model for menin-mixed lineage leukemia inhibitors. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2350-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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2
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Jedwabny W, Lodola A, Dyguda-Kazimierowicz E. Theoretical Model of EphA2-Ephrin A1 Inhibition. Molecules 2018; 23:molecules23071688. [PMID: 29997324 PMCID: PMC6099714 DOI: 10.3390/molecules23071688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 02/03/2023] Open
Abstract
This work aims at the theoretical description of EphA2-ephrin A1 inhibition by small molecules. Recently proposed ab initio-based scoring models, comprising long-range components of interaction energy, is tested on lithocholic acid class inhibitors of this protein–protein interaction (PPI) against common empirical descriptors. We show that, although limited to compounds with similar solvation energy, the ab initio model is able to rank the set of selected inhibitors more effectively than empirical scoring functions, aiding the design of novel compounds.
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Affiliation(s)
- Wiktoria Jedwabny
- Department of Chemistry, Wrocław University of Science and Technology, 50370 Wrocław, Poland.
| | - Alessio Lodola
- Department of Food and Drug, University of Parma, 43100 Parma, Italy.
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3
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Jedwabny W, Kłossowski S, Purohit T, Cierpicki T, Grembecka J, Dyguda-Kazimierowicz E. Theoretical models of inhibitory activity for inhibitors of protein-protein interactions: targeting menin-mixed lineage leukemia with small molecules. MEDCHEMCOMM 2017; 8:2216-2227. [PMID: 29456828 PMCID: PMC5774433 DOI: 10.1039/c7md00170c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/06/2017] [Indexed: 12/28/2022]
Abstract
A computationally affordable, non-empirical model based on electrostatic multipole and dispersion terms successfully predicts the binding affinity of inhibitors of menin–MLL protein–protein interactions.
Development and binding affinity predictions of inhibitors targeting protein–protein interactions (PPI) still represent a major challenge in drug discovery efforts. This work reports application of a predictive non-empirical model of inhibitory activity for PPI inhibitors, exemplified here for small molecules targeting the menin–mixed lineage leukemia (MLL) interaction. Systematic ab initio analysis of menin–inhibitor complexes was performed, revealing the physical nature of these interactions. Notably, the non-empirical protein–ligand interaction energy comprising electrostatic multipole and approximate dispersion terms (E(10)El,MTP + EDas) produced a remarkable correlation with experimentally measured inhibitory activities and enabled accurate activity prediction for new menin–MLL inhibitors. Importantly, this relatively simple and computationally affordable non-empirical interaction energy model outperformed binding affinity predictions derived from commonly used empirical scoring functions. This study demonstrates high relevance of the non-empirical model we developed for binding affinity prediction of inhibitors targeting protein–protein interactions that are difficult to predict using empirical scoring functions.
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Affiliation(s)
- Wiktoria Jedwabny
- Department of Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland . ; Tel: +48 71 320 3200
| | - Szymon Kłossowski
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Trupta Purohit
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Tomasz Cierpicki
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Jolanta Grembecka
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Edyta Dyguda-Kazimierowicz
- Department of Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland . ; Tel: +48 71 320 3200
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4
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Jedwabny W, Panecka-Hofman J, Dyguda-Kazimierowicz E, Wade RC, Sokalski WA. Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. J Comput Aided Mol Des 2017; 31:715-728. [PMID: 28688090 PMCID: PMC5570812 DOI: 10.1007/s10822-017-0035-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/16/2017] [Indexed: 11/15/2022]
Abstract
There is a need for improved and generally applicable scoring functions for fragment-based approaches to ligand design. Here, we evaluate the performance of a computationally efficient model for inhibitory activity estimation, which is composed only of multipole electrostatic energy and dispersion energy terms that approximate long-range ab initio quantum mechanical interaction energies. We find that computed energies correlate well with inhibitory activity for a compound series with varying substituents targeting two subpockets of the binding site of Trypanosoma brucei pteridine reductase 1. For one subpocket, we find that the model is more predictive for inhibitory activity than the ab initio interaction energy calculated at the MP2 level. Furthermore, the model is found to outperform a commonly used empirical scoring method. Finally, we show that the results for the two subpockets can be combined, which suggests that this simple nonempirical scoring function could be applied in fragment–based drug design.
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Affiliation(s)
- Wiktoria Jedwabny
- Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Joanna Panecka-Hofman
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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Mechanisms for the synthesis of conjugated enynes from diphenylacetylene and trimethylsilylacetylene catalyzed by a nickel(0) complex: DFT study of ligand-controlled selectivity. J Mol Model 2015; 21:135. [DOI: 10.1007/s00894-015-2672-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
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6
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Giedroyć-Piasecka W, Dyguda-Kazimierowicz E, Beker W, Mor M, Lodola A, Sokalski WA. Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model. J Phys Chem B 2014; 118:14727-36. [PMID: 25420234 DOI: 10.1021/jp5059287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is an enzyme responsible for the deactivating hydrolysis of fatty acid ethanolamide neuromodulators. FAAH inhibitors have gained considerable interest due to their possible application in the treatment of anxiety, inflammation, and pain. In the context of inhibitor design, the availability of reliable computational tools for predicting binding affinity is still a challenging task, and it is now well understood that empirical scoring functions have several limitations that in principle could be overcome by quantum mechanics. Herein, systematic ab initio analyses of FAAH interactions with a series of inhibitors belonging to the class of the N-alkylcarbamic acid aryl esters have been performed. In contrast to our earlier studies of other classes of enzyme-inhibitor complexes, reasonable correlation with experimental results required us to consider correlation effects along with electrostatic term. Therefore, the simplest comprehensive nonempirical model allowing for qualitative predictions of binding affinities for FAAH ligands consists of electrostatic multipole and second-order dispersion terms. Such a model has been validated against the relative stabilities of the benchmark S66 set of biomolecular complexes. As it does not involve parameters fitted to experimentally derived data, this model offers a unique opportunity for generally applicable inhibitor design and virtual screening.
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Affiliation(s)
| | | | - Wiktor Beker
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
| | - Marco Mor
- Pharmacy Department, Università di Parma , Parma, Italy
| | | | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
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Szefczyk B, Sokalski WA. Physical Nature of Intermolecular Interactions in [BMIM][PF6] Ionic Liquid. J Phys Chem B 2014; 118:2147-56. [DOI: 10.1021/jp411363d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Borys Szefczyk
- Institute
of Physical and
Theoretical Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - W. Andrzej Sokalski
- Institute
of Physical and
Theoretical Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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8
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Beker W, Langner KM, Dyguda-Kazimierowicz E, Feliks M, Sokalski WA. Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances. J Comput Chem 2013; 34:1797-9. [DOI: 10.1002/jcc.23326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Wiktor Beker
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wrocław University of Technology; 50-370 Wrocław, Poland
| | - Karol M. Langner
- Leiden Institute of Chemistry, 2300 RA Leiden University; Leiden, The NetherlandsDpt. Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Edyta Dyguda-Kazimierowicz
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wrocław University of Technology; 50-370 Wrocław, Poland
| | - Mikołaj Feliks
- Institut de Biologie Structurale, F-38027; Grenoble France
| | - W. Andrzej Sokalski
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wrocław University of Technology; 50-370 Wrocław, Poland
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9
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Swiderek K, Paneth P. Importance of the lactate dehydrogenase quaternary structure in theoretical calculations. J Phys Chem B 2010; 114:3393-7. [PMID: 20155895 DOI: 10.1021/jp100026z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using the example of lactate dehydrogenase, we show that enzyme quaternary structure has an important influence on the structure of the active site and that models that comprise all amino acids in the vicinity of an active site, but are missing this structural information, can lead to incorrect results. We also show that binding isotope effects are very sensitive to the geometric parameters, and thus one should be very cautious when interpreting results obtained with models that are too coarse. In terms of the type of hydrogen bonds, our results indicate that binding isotope effects are pronounced only when a hydrogen bond exhibits some covalent character.
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Technical University of Lodz, ulica Zeromskiego 116, 90-924 Lodz, Poland
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Dea-Ayuela MA, Pérez-Castillo Y, Meneses-Marcel A, Ubeira FM, Bolas-Fernández F, Chou KC, González-Díaz H. HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. Bioorg Med Chem 2008; 16:7770-6. [PMID: 18662882 DOI: 10.1016/j.bmc.2008.07.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 06/23/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022]
Abstract
The toxicity and inefficacy of actual organic drugs against Leishmaniosis justify research projects to find new molecular targets in Leishmania species including Leishmania infantum (L. infantum) and Leishmaniamajor (L. major), both important pathogens. In this sense, quantitative structure-activity relationship (QSAR) methods, which are very useful in Bioorganic and Medicinal Chemistry to discover small-sized drugs, may help to identify not only new drugs but also new drug targets, if we apply them to proteins. Dyneins are important proteins of these parasites governing fundamental processes such as cilia and flagella motion, nuclear migration, organization of the mitotic splinde, and chromosome separation during mitosis. However, despite the interest for them as potential drug targets, so far there has been no report whatsoever on dyneins with QSAR techniques. To the best of our knowledge, we report here the first QSAR for dynein proteins. We used as input the Spectral Moments of a Markov matrix associated to the HP-Lattice Network of the protein sequence. The data contain 411 protein sequences of different species selected by ClustalX to develop a QSAR that correctly discriminates on average between 92.75% and 92.51% of dyneins and other proteins in four different train and cross-validation datasets. We also report a combined experimental and theoretic study of a new dynein sequence in order to illustrate the utility of the model to search for potential drug targets with a practical example. First, we carried out a 2D-electrophoresis analysis of L. infantum biological samples. Next, we excised from 2D-E gels one spot of interest belonging to an unknown protein or protein fragment in the region M<20,200 and pI<4. We used MASCOT search engine to find proteins in the L. major data base with the highest similarity score to the MS of the protein isolated from L. infantum. We used the QSAR model to predict the new sequence as dynein with probability of 99.99% without relying upon alignment. In order to confirm the previous function annotation we predicted the sequences as dynein with BLAST and the omniBLAST tools (96% alignment similarity to dyneins of other species). Using this combined strategy, we have successfully identified L. infantum protein containing dynein heavy chain, and illustrated the potential use of the QSAR model as a complement to alignment tools.
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11
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Langner KM, Kedzierski P, Sokalski WA, Leszczynski J. Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane. J Phys Chem B 2007; 110:9720-7. [PMID: 16686524 DOI: 10.1021/jp056836b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.
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Affiliation(s)
- Karol M Langner
- Wroclaw University of Technology, Wyb.Wyspianskiego 27, 50-370 Wroclaw, Poland
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12
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Dyguda-Kazimierowicz E, Sokalski WA, Leszczyński J. Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions. J Mol Model 2007; 13:839-49. [PMID: 17384969 DOI: 10.1007/s00894-007-0192-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate that an S(N)2-like mechanism of ThiK, with gamma-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198 are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic activity of ThiK upon mutation of Cys198 to aspartate.
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Affiliation(s)
- Edyta Dyguda-Kazimierowicz
- Department of Chemistry, Wrocław University of Technology, Wyb.Wyspiańskiego 27, 50-370, Wrocław, Poland.
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Grzywa R, Dyguda-Kazimierowicz E, Sieńczyk M, Feliks M, Sokalski WA, Oleksyszyn J. The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity. J Mol Model 2007; 13:677-83. [PMID: 17587094 DOI: 10.1007/s00894-007-0193-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 02/27/2007] [Indexed: 01/18/2023]
Abstract
Urokinase-type plasminogen activator (uPA) is a trypsin-like serine protease that plays a crucial role in angiogenesis process. In addition to its physiological role in healthy organisms, angiogenesis is extremely important in cancer growth and metastasis, resulting in numerous attempts to understand its control and to develop new approaches to anticancer therapy. The alpha-aminoalkylphosphonate diphenyl esters are well known as highly efficient serine protease inhibitors. However, their mode of binding has not been verified experimentally in details. For a group of average and potent phosphonic inhibitors of urokinase, flexible docking calculations were performed to gain an insight into the active site interactions responsible for observed enzyme inhibition. The docking results are consistent with the previously suggested mode of inhibitors binding. Subsequently, rigorous ab initio study of binding energy was carried out, followed by its decomposition according to the variation-perturbation procedure to reveal stabilization energy constituents with clear physical meaning. Availability of the experimental inhibitory activities and comparison with theoretical binding energy allows for the validation of theoretical models of inhibition, as well as estimation of the possible potential for binding affinity prediction. Since the docking results accompanied by molecular mechanics optimization suggested that several crucial active site contacts were too short, the optimal distances corresponding to the minimum ab initio interaction energy were also evaluated. Despite the deficiencies of force field-optimized enzyme-inhibitor structures, satisfactory agreement with experimental inhibitory activity was obtained for the electrostatic interaction energy, suggesting its possible application in the binding affinity prediction.
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Affiliation(s)
- Renata Grzywa
- Department of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370, Wrocław, Poland
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Białas A, Grembecka J, Krowarsch D, Otlewski J, Potempa J, Mucha A. Exploring the Sn binding pockets in gingipains by newly developed inhibitors: structure-based design, chemistry, and activity. J Med Chem 2006; 49:1744-53. [PMID: 16509589 DOI: 10.1021/jm0600141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Arg-gingipains (Rgps) and Lys-gingipain (Kgp) are cysteine proteinases secreted by Porphyromonas gingivalis, the major pathogen implicated in periodontal disease. Gingipains are essential to the bacterium for its virulence and survival, and development of inhibitors targeting these proteins provides an approach to treat periodontal diseases. Here, we present the first example of structure-based design of gingipains inhibitors, with the use of the crystal structure of RgpB and the homology model of Kgp. Chloromethyl ketones were selected as suitable compounds to explore the specificity of the Sn binding region of both enzymes. Three series of inhibitors bearing Arg or Lys at P1 and different substituents at P2 and P3 were designed, synthesized, and tested. High potency (k(obs)/[I] approximately 10(7) M(-1) s(-1)) was achieved for small ligands, such as the dipeptide analogues. The detailed analysis of Sn binding pockets revealed the molecular basis of inhibitory affinity and provided insight into the structure-activity relationship.
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Affiliation(s)
- Arkadiusz Białas
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspiańskiego 27, 50-370 Wrocław, Poland
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Pilbák S, Tomin A, Rétey J, Poppe L. The essential tyrosine-containing loop conformation and the role of the C-terminal multi-helix region in eukaryotic phenylalanine ammonia-lyases. FEBS J 2006; 273:1004-19. [PMID: 16478474 DOI: 10.1111/j.1742-4658.2006.05127.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Besides the post-translationally cyclizing catalytic Ala-Ser-Gly triad, Tyr110 and its equivalents are of the most conserved residues in the active site of phenylalanine ammonia-lyase (PAL, EC 4.3.1.5), histidine ammonia-lyase (HAL, EC 4.3.1.3) and other related enzymes. The Tyr110Phe mutation results in the most pronounced inactivation of PAL indicating the importance of this residue. The recently published X-ray structures of PAL revealed that the Tyr110-loop was either missing (for Rhodospridium toruloides) or far from the active site (for Petroselinum crispum). In bacterial HAL ( approximately 500 amino acids) and plant and fungal PALs ( approximately 710 amino acids), a core PAL/HAL domain ( approximately 480 amino acids) with >or= 30% sequence identity along the different species is common. In plant and fungal PAL a approximately 100-residue long C-terminal multi-helix domain is present. The ancestor bacterial HAL is thermostable and, in all of its known X-ray structures, a Tyr83-loop-in arrangement has been found. Based on the HAL structures, a Tyr110-loop-in conformation of the P. crispum PAL structure was constructed by partial homology modeling, and the static and dynamic behavior of the loop-in/loop-out structures were compared. To study the role of the C-terminal multi-helix domain, Tyr-loop-in/loop-out model structures of two bacterial PALs (Streptomyces maritimus, 523 amino acids and Photorhabdus luminescens, 532 amino acids) lacking this C-terminal domain were also built. Molecular dynamics studies indicated that the Tyr-loop-in conformation was more rigid without the C-terminal multi-helix domain. On this basis it is hypothesized that a role of this C-terminal extension is to decrease the lifetime of eukaryotic PAL by destabilization, which might be important for the rapid responses in the regulation of phenylpropanoid biosynthesis.
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Affiliation(s)
- Sarolta Pilbák
- Institute for Organic Chemistry and Research Group for Alkaloid Chemistry, Budapest University of Technology and Economics, Hungary
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16
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Grabowski SJ, Sokalski WA. Different types of hydrogen bonds: correlation analysis of interaction energy components. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.937] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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