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Panecka-Hofman J, Poehner I, Wade R. Anti-trypanosomatid structure-based drug design - lessons learned from targeting the folate pathway. Expert Opin Drug Discov 2022; 17:1029-1045. [PMID: 36073204 DOI: 10.1080/17460441.2022.2113776] [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: 11/04/2022]
Abstract
INTRODUCTION Trypanosomatidic parasitic infections of humans and animals caused by Trypanosoma brucei, Trypanosoma cruzi, and Leishmania species pose a significant health and economic burden in developing countries. There are few effective and accessible treatments for these diseases, and the existing therapies suffer from problems such as parasite resistance and side effects. Structure-based drug design (SBDD) is one of the strategies that has been applied to discover new compounds targeting trypanosomatid-borne diseases. AREAS COVERED We review the current literature (mostly over the last 5 years, searched in PubMed database on Nov 11th 2021) on the application of structure-based drug design approaches to identify new anti-trypanosomatidic compounds that interfere with a validated target biochemical pathway, the trypanosomatid folate pathway. EXPERT OPINION The application of structure-based drug design approaches to perturb the trypanosomatid folate pathway has successfully provided many new inhibitors with good selectivity profiles, most of which are natural products or their derivatives or have scaffolds of known drugs. However, the inhibitory effect against the target protein(s) often does not translate to anti-parasitic activity. Further progress is hampered by our incomplete understanding of parasite biology and biochemistry, which is necessary to complement SBDD in a multiparameter optimization approach to discovering selective anti-parasitic drugs.
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Affiliation(s)
- Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5a, 02-097 Warsaw, Poland
| | - Ina Poehner
- School of Pharmacy, University of Eastern Finland, Kuopio, Yliopistonranta 1C, PO Box 1627, FI-70211 Kuopio, Finland
| | - Rebecca Wade
- Center for Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 282, Heidelberg 69120, Germany.,Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany.,DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
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2
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Jedwabny W, Dyguda-Kazimierowicz E, Pernal K, Szalewicz K, Patkowski K. Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts. J Phys Chem A 2021; 125:1787-1799. [PMID: 33620223 PMCID: PMC8028329 DOI: 10.1021/acs.jpca.0c11347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/10/2021] [Indexed: 12/17/2022]
Abstract
A dispersion function Das in the form of a damped atom-atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised Das function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original Das. A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.
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Affiliation(s)
- Wiktoria Jedwabny
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Edyta Dyguda-Kazimierowicz
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Pernal
- Institute
of Physics, Łódź University
of Technology, Wólczańska
219, 90-924 Łódź, Poland
| | - Krzysztof Szalewicz
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United
States
| | - Konrad Patkowski
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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3
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Jedwabny W, Dyguda-Kazimierowicz E. Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors. J Mol Model 2019; 25:29. [PMID: 30613843 PMCID: PMC6321839 DOI: 10.1007/s00894-018-3897-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/04/2018] [Indexed: 01/12/2023]
Abstract
Halogenated ligands are nowadays commonly designed in order to increase their potency against protein targets. Although novel computational methods of evaluating the affinity of such halogenated inhibitors have emerged, they still lack the sufficient accuracy, which is especially noticeable in the case of empirical scoring functions, being the method of choice in the drug design process. Here, we evaluated a series of halogenated inhibitors of phosphodiesterase type 5 with ab initio methods, revealing the physical nature of ligand binding and determining the components of interaction energy that are essential for proper inhibitor ranking. In particular, a nonempirical scoring model combining long-range contributions to the interaction energy provided a significant correlation with experimental binding potency, outperforming a number of commonly used empirical scoring functions. Considering the low computational cost associated with remarkable predictive abilities of the aforementioned model, it could be used for rapid assessment of the ligand affinity in the process of rational design of novel halogenated compounds.
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Affiliation(s)
- Wiktoria Jedwabny
- Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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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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5
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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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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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Beker W, van der Kamp MW, Mulholland AJ, Sokalski WA. Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants. J Chem Theory Comput 2017; 13:945-955. [PMID: 28103023 DOI: 10.1021/acs.jctc.6b01131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a simple atomic multipole electrostatic model to rapidly evaluate the effects of mutation on enzyme activity and test its performance on wild-type and mutant ketosteroid isomerase. The predictions of our atomic multipole model are similar to those obtained with symmetry-adapted perturbation theory at a fraction of the computational cost. We further show that this approach is relatively insensitive to the precise amino acid side chain conformation in mutants and may thus be useful in computational enzyme (re)design.
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Affiliation(s)
- Wiktor Beker
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marc W van der Kamp
- School of Biochemistry, Biomedical Sciences Building, University Walk , Bristol BS8 1TD, United Kingdom.,BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, Tyndall Avenue, University of Bristol , Bristol BS8 1TQ, United Kingdom.,Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, Tyndall Avenue, University of Bristol , Bristol BS8 1TQ, United Kingdom.,Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - W Andrzej Sokalski
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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Pollock J, Borkin D, Lund G, Purohit T, Dyguda-Kazimierowicz E, Grembecka J, Cierpicki T. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J Med Chem 2015; 58:7465-74. [PMID: 26288158 PMCID: PMC4584387 DOI: 10.1021/acs.jmedchem.5b00975] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions.
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Affiliation(s)
- Jonathan Pollock
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dmitry Borkin
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - George Lund
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Trupta Purohit
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Edyta Dyguda-Kazimierowicz
- Molecular Modeling and Quantum Chemistry Group, Department of Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
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