1
|
Gilson MK, Kurtzman T. Free Energy Density of a Fluid and Its Role in Solvation and Binding. J Chem Theory Comput 2024; 20:2871-2887. [PMID: 38536144 PMCID: PMC11197885 DOI: 10.1021/acs.jctc.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. First, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f(R), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, fbulk, near a solute but should asymptotically approach fbulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential. Second, we use statistical thermodynamics to formulate a definition of the free energy density that satisfies these desiderata. Third, we show how any free energy density satisfying the desiderata may be used to analyze molecular processes in solution. In particular, because the spatial integral of f(R) equals the free energy of the system, it can be used to compute free energy changes that result from the rearrangement of solutes as well as the forces exerted on the solutes by the solvent. This enables the use of a thermodynamic analysis of water in protein binding sites to inform ligand design. Finally, we discuss related literature and address published concerns regarding the thermodynamic plausibility of a position-dependent free energy density. The theory presented here has applications in theoretical and computational chemistry and may be further generalizable beyond fluids, such as to solids and macromolecules.
Collapse
Affiliation(s)
- Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, and Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA, 92093, USA
| | - Tom Kurtzman
- PhD Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, 10016, USA; Department of Chemistry, Lehman College, The City University of New York, Bronx, New York, 10468, USA
| |
Collapse
|
2
|
Zamanos A, Ioannakis G, Emiris IZ. HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures. J Chem Inf Model 2024; 64:2594-2611. [PMID: 38552195 PMCID: PMC11005053 DOI: 10.1021/acs.jcim.3c01559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 04/09/2024]
Abstract
Water molecules are integral to the structural stability of proteins and vital for facilitating molecular interactions. However, accurately predicting their precise position around protein structures remains a significant challenge, making it a vibrant research area. In this paper, we introduce HydraProt (deep Hydration of Proteins), a novel methodology for predicting precise positions of water molecule oxygen atoms around protein structures, leveraging two interconnected deep learning architectures: a 3D U-net and a Multi-Layer Perceptron (MLP). Our approach starts by introducing a coarse voxel-based representation of the protein, which allows for rapid sampling of candidate water positions via the 3D U-net. These water positions are then assessed by embedding the water-protein relationship in the Euclidean space by means of an MLP. Finally, a postprocessing step is applied to further refine the MLP predictions. HydraProt surpasses existing state-of-the-art approaches in terms of precision and recall and has been validated on large data sets of protein structures. Notably, our method offers rapid inference runtime and should constitute the method of choice for protein structure studies and drug discovery applications. Our pretrained models, data, and the source code required to reproduce these results are accessible at https://github.com/azamanos/HydraProt.
Collapse
Affiliation(s)
- Andreas Zamanos
- Archimedes, Athena Research Center, Marousi 15125, Greece
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
| | - George Ioannakis
- Institute
for Language and Speech Processing, Athena
Research Center, Xanthi 67100, Greece
| | - Ioannis Z. Emiris
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
- Athena
Research Center, Marousi 15125, Greece
| |
Collapse
|
3
|
Ihnatenko I, Müller MJ, Orban OCF, Lindhof JC, Benítez D, Ortíz C, Dibello E, Seidl LL, Comini MA, Kunick C. The indole motif is essential for the antitrypanosomal activity of N5-substituted paullones. PLoS One 2023; 18:e0292946. [PMID: 38032881 PMCID: PMC10688702 DOI: 10.1371/journal.pone.0292946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023] Open
Abstract
Severe infections with potentially fatal outcomes are caused by parasites from the genera Trypanosoma and Leishmania (class Kinetoplastea). The diseases affect people of remote areas in the tropics and subtropics with limited access to adequate health care. Besides insufficient diagnostics, treatment options are limited, with tenuous developments in recent years. Therefore, new antitrypanosomal antiinfectives are required to fight these maladies. In the presented approach, new compounds were developed and tested on the target trypanothione synthetase (TryS). This enzyme is crucial to the kinetoplastids' unique trypanothione-based thiol redox metabolism and thus for pathogen survival. Preceding studies have shown that N5-substituted paullones display antitrypanosomal activity as well as TryS inhibition. Herein, this compound class was further examined regarding the structure-activity relationships (SAR). Diverse benzazepinone derivatives were designed and tested in cell-based assays on bloodstream Trypanosoma brucei brucei (T. b. brucei) and intracellular amastigotes of Leishmania infantum (L. infantum) as well as in enzyme-based assays on L. infantum TryS (LiTryS) and T. b. brucei TryS (TbTryS). While an exchange of just the substituent in the 9-position of paullones led to potent inhibitors on LiTryS and T. b. brucei parasites, new compounds lacking the indole moiety showed a total loss of activity in both assays. Conclusively, the indole as part of the paullone structure is pivotal for keeping the TryS inhibitory and antitrypanosomal activity of this substance class.
Collapse
Affiliation(s)
- Irina Ihnatenko
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
- PVZ-Center of Pharmaceutical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Marco J Müller
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
- PVZ-Center of Pharmaceutical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Oliver C F Orban
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
- PVZ-Center of Pharmaceutical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Jens C Lindhof
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
- PVZ-Center of Pharmaceutical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Diego Benítez
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Cecilia Ortíz
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Estefanía Dibello
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Síntesis Orgánica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Leonardo L Seidl
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcelo A Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Conrad Kunick
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
- PVZ-Center of Pharmaceutical Engineering, TU Braunschweig, Braunschweig, Germany
| |
Collapse
|
4
|
Mahanti M, Pal KB, Kumar R, Schulze M, Leffler H, Logan DT, Nilsson UJ. Ligand Sulfur Oxidation State Progressively Alters Galectin-3-Ligand Complex Conformations To Induce Affinity-Influencing Hydrogen Bonds. J Med Chem 2023; 66:14716-14723. [PMID: 37878264 PMCID: PMC10641817 DOI: 10.1021/acs.jmedchem.3c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Indexed: 10/26/2023]
Abstract
Galectins play biological roles in immune regulation and tumor progression. Ligands with high affinity for the shallow, hydrophilic galectin-3 ligand binding site rely primarily on a galactose core with appended aryltriazole moieties, making hydrophobic interactions and π-stacking. We designed and synthesized phenyl sulfone, sulfoxide, and sulfide-triazolyl thiogalactoside derivatives to create affinity-enhancing hydrogen bonds, hydrophobic and π-interactions. Crystal structures and thermodynamic analyses revealed that the sulfoxide and sulfone ligands form hydrogen bonds while retaining π-interactions, resulting in improved affinities and unique binding poses. The sulfoxide, bearing one hydrogen bond acceptor, leads to an affinity decrease compared to the sulfide, whereas the corresponding sulfone forms three hydrogen bonds, two directly with Asn and Arg side chains and one water-mediated to an Asp side chain, respectively, which alters the complex structure and increases affinity. These findings highlight that the sulfur oxidation state influences both the interaction thermodynamics and structure.
Collapse
Affiliation(s)
- Mukul Mahanti
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Kumar Bhaskar Pal
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Rohit Kumar
- Division
of Biochemistry & Structural Biology, Centre for Molecular Protein
Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Markus Schulze
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Hakon Leffler
- Department
of Laboratory Medicine, Section MIG, Lund
University, BMC-C1228b Klinikgatan 28, 221 84 Lund, Sweden
| | - Derek T. Logan
- Division
of Biochemistry & Structural Biology, Centre for Molecular Protein
Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
5
|
Yoon HR, Park GJ, Balupuri A, Kang NS. TWN-FS method: A novel fragment screening method for drug discovery. Comput Struct Biotechnol J 2023; 21:4683-4696. [PMID: 37841326 PMCID: PMC10568351 DOI: 10.1016/j.csbj.2023.09.037] [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: 07/17/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established and effective method for generating diverse and novel hits in drug design. Kinases are suitable targets for FBDD due to their well-defined structure. Water molecules contribute to structure and function of proteins and also influence the environment within the binding pocket. Water molecules form a variety of hydrogen-bonded cyclic water-ring networks, collectively known as topological water networks (TWNs). Analyzing the TWNs in protein binding sites can provide valuable insights into potential locations and shapes for fragments within the binding site. Here, we introduce TWN-based fragment screening (TWN-FS) method, a novel screening method that suggests fragments through grouped TWN analysis within the protein binding site. We used this method to screen known CDK2, CHK1, IGF1R and ERBB4 inhibitors. Our findings suggest that TWN-FS method has the potential to effectively screen fragments. The TWN-FS method package is available on GitHub at https://github.com/pkj0421/TWN-FS.
Collapse
Affiliation(s)
- Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Gyoung Jin Park
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| |
Collapse
|
6
|
Tošović J, Fijan D, Jukič M, Bren U. Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data. J Chem Inf Model 2022; 62:6105-6117. [PMID: 36351288 DOI: 10.1021/acs.jcim.2c00801] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This work describes the development and testing of a method for the identification and classification of conserved water molecules and their networks from molecular dynamics (MD) simulations. The conserved waters in the active sites of proteins influence protein-ligand binding. Recently, several groups have argued that a water network formed from conserved waters can be used to interpret the thermodynamic signature of the binding site. We implemented a novel methodology in which we apply the complex approach to categorize water molecules extracted from the MD simulation trajectories using clustering approaches. The main advantage of our methodology as compared to current state of the art approaches is the inclusion of the information on the orientation of hydrogen atoms to further inform the clustering algorithm and to classify the conserved waters into different subtypes depending on how strongly certain orientations are preferred. This information is vital for assessing the stability of water networks. The newly developed approach is described in detail as well as validated against known results from the scientific literature including comparisons with the experimental data on thermolysin, thrombin, and Haemophilus influenzae virulence protein SiaP as well as with the previous computational results on thermolysin. We observed excellent agreement with the literature and were also able to provide additional insights into the orientations of the conserved water molecules, highlighting the key interactions which stabilize them. The source code of our approach, as well as the utility tools used for visualization, are freely available on GitHub.
Collapse
Affiliation(s)
- Jelena Tošović
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000Maribor, Slovenia
| | | | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000Maribor, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000Koper, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000Maribor, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000Koper, Slovenia.,Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000Maribor, Slovenia
| |
Collapse
|
7
|
Praseetha NG, Divya UK, Nair S. Identifying the potential role of curcumin analogues as anti-breast cancer agents; an in silico approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Breast cancer ranks top among newly reported cancer cases and most of the women suffers from breast cancer. Development of target therapy using phytochemicals with minimal side effects is trending in health care research. Phytochemicals targets complex multiple signalling events in cancer and are pleiotropic in nature. Thus, the present study was conducted to check the effectivity of curcumin analogues (Capsaicin, Chlorogenic acid, Ferulic acid, Zingerone, Gingerol) against the receptors that are expressed in breast cancer cells and prove its ethno-medicinal value by using bioinformatic tools and softwares like PDB, Patch Dock, PubChem, Chimera and My Presto.
Result
Out of the various curcumin analogues studied, Ferulic acid showed best binding affinity with all the breast cancer cell specific receptors (FGF, MMP9, RNRM1, TGF-beta, DHFR, VEGF and aromatase) which was confirmed through the docking studies.
Conclusion
The current work was a preliminary step towards screening suitable drug candidate against breast cancer using in silico methods. This information can be used further to carry out in vivo studies using selected natural analogues of curcumin as a suitable drug candidate against breast cancer saving time and cost.
Collapse
|
8
|
Warsi MS, Habib S, Talha M, Khan S, Singh P, Mir AR, Abidi M, Ali A, Moinuddin. 4-Chloro-1,2-phenylenediamine induced structural perturbation and genotoxic aggregation in human serum albumin. Front Chem 2022; 10:1016354. [PMID: 36199663 PMCID: PMC9527296 DOI: 10.3389/fchem.2022.1016354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
4-Chloro-1,2-phenylenediamine (4-Cl-OPD) is a halogenated aromatic diamine used as a precursor in permanent hair color production. Despite its well-documented mutagenic and carcinogenic effects in various in vitro and in vivo models, its role in fibrillar aggregate formation and their genotoxic effect in therapeutic proteins has received less attention. The significance of human serum albumin (HSA) arises from its involvement in bio-regulatory and transport processes. HSA misfolding and aggregation are responsible for some of the most frequent neurodegenerative disorders. We used various complementary approaches to track the formation of amyloid fibrils and their genotoxic effect. Molecular dynamics study demonstrated the complex stability. The impact of 4-Cl-OPD on the structural dynamics of HSA was confirmed by Raman spectroscopy, X-ray diffraction, HPLC and SDS-PAGE. Fibrilllar aggregates were investigated using Congo red assay, DLS, and SEM. The genotoxic nature of 4-Cl-OPD was confirmed using plasmid nicking assay and DAPI staining, which revealed DNA damage and cell apoptosis. 4-Cl-OPD provides a model system for studying fibrillar aggregation and their genotoxic potential in the current investigation. Future studies should investigate the inhibition of the aggregation/fibrillation process, which may yield valuable clinical insights.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Moinuddin
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| |
Collapse
|
9
|
Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
Collapse
Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
10
|
Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, Czodrowski P, Krewald V, Hausch F. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chem Sci 2021; 12:14758-14765. [PMID: 34820091 PMCID: PMC8597852 DOI: 10.1039/d1sc04638a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 01/30/2023] Open
Abstract
Methyl groups can have profound effects in drug discovery but the underlying mechanisms are diverse and incompletely understood. Here we report the stereospecific effect of a single, solvent-exposed methyl group in bicyclic [4.3.1] aza-amides, robustly leading to a 2 to 10-fold increase in binding affinity for FK506-binding proteins (FKBPs). This resulted in the most potent and efficient FKBP ligands known to date. By a combination of co-crystal structures, isothermal titration calorimetry (ITC), density-functional theory (DFT), and 3D reference interaction site model (3D-RISM) calculations we elucidated the origin of the observed affinity boost, which was purely entropically driven and relied on the displacement of a water molecule at the protein-ligand-bulk solvent interface. The best compounds potently occupied FKBPs in cells and enhanced bone morphogenic protein (BMP) signaling. Our results show how subtle manipulation of the solvent network can be used to design atom-efficient ligands for difficult, solvent-exposed binding pockets.
Collapse
Affiliation(s)
- Jürgen M Kolos
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany .,Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sebastian Pomplun
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sascha Jung
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Benedikt Rieß
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Patrick L Purder
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Andreas M Voll
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Stephanie Merz
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Monika Gnatzy
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Thomas M Geiger
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Ingrid Quist-Løkken
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Jerome Jatzlau
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Toril Holien
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Andreas Bracher
- Research Department Cellular Biochemistry, Max Planck Institute of Biochemistry Am Klopferspitz 18, 82152 Planegg Germany
| | - Christian Meyners
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Paul Czodrowski
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Vera Krewald
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Felix Hausch
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| |
Collapse
|
11
|
Rübbelke M, Hamilton J, Binder F, Bauer M, King J, Nar H, Zeeb M. Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain. J Med Chem 2021; 64:15629-15638. [PMID: 34672548 DOI: 10.1021/acs.jmedchem.1c00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Necroptosis is a form of programmed cell death that in case of misregulation can lead to inflammatory diseases. Mixed lineage kinase domain-like protein (MLKL), the effector protein in the canonical necroptosis signaling pathway, becomes activated by phosphorylation. Here, we report the identification of novel reversible binders of the MLKL executioner domain by a protein NMR-detected fragment-based screen. Determination of protein fragment costructures using NMR spectroscopy revealed a small molecule binding site that is distinct from the previously identified binding site of covalent MLKL inhibitors. Affinity optimization of the initially prioritized hit with millimolar affinity was achieved by NMR-guided structure-based design and yielded fragment-like molecules with a KD of 50 μM. Furthermore, we demonstrate that the improved fragment competes for the same binding site as nonyl-maltoside, a detergent that in conjunction with phytic acid activates the MLKL executioner domain.
Collapse
Affiliation(s)
- Martin Rübbelke
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| | - James Hamilton
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| | - Florian Binder
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| | - Margit Bauer
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| | - Jim King
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, Connecticut 06877, United States
| | - Herbert Nar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| | - Markus Zeeb
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
| |
Collapse
|
12
|
Rahman F, Nguyen TM, Adekoya OA, Campestre C, Tortorella P, Sylte I, Winberg JO. Inhibition of bacterial and human zinc-metalloproteases by bisphosphonate- and catechol-containing compounds. J Enzyme Inhib Med Chem 2021; 36:819-830. [PMID: 33757387 PMCID: PMC7993378 DOI: 10.1080/14756366.2021.1901088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Compounds containg catechol or bisphosphonate were tested as inhibitors of the zinc metalloproteases, thermolysin (TLN), pseudolysin (PLN) and aureolysin (ALN) which are bacterial virulence factors, and the human matrix metalloproteases MMP-9 and -14. Inhibition of virulence is a putative strategy in the development of antibacterial drugs, but the inhibitors should not interfere with human enzymes. Docking indicated that the inhibitors bound MMP-9 and MMP-14 with the phenyl, biphenyl, chlorophenyl, nitrophenyl or methoxyphenyl ringsystem in the S1'-subpocket, while these ringsystems entered the S2'- or S1 -subpockets or a region involving amino acids in the S1'- and S2'-subpockets of the bacterial enzymes. An arginine conserved among the bacterial enzymes seemed to hinder entrance deeply into the S1'-subpocket. Only the bisphosphonate containing compound RC2 bound stronger to PLN and TLN than to MMP-9 and MMP-14. Docking indicated that the reason was that the conserved arginine (R203 in TLN and R198 in PLN) interacts with phosphate groups of RC2.
Collapse
Affiliation(s)
- Fatema Rahman
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Tra-Mi Nguyen
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Cristina Campestre
- Department of Pharmacy, University of "G. d'Annunzio" Chieti, Chieti, Italy
| | - Paolo Tortorella
- Department of Pharmacy, Science of Pharmacy, University "A. Moro" Bari, Bari, Italy
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
13
|
Andreev S, Pantsar T, Tesch R, Kahlke N, El-Gokha A, Ansideri F, Grätz L, Romasco J, Sita G, Geibel C, Lämmerhofer M, Tarozzi A, Knapp S, Laufer SA, Koch P. Addressing a Trapped High-Energy Water: Design and Synthesis of Highly Potent Pyrimidoindole-Based Glycogen Synthase Kinase-3β Inhibitors. J Med Chem 2021; 65:1283-1301. [PMID: 34213342 DOI: 10.1021/acs.jmedchem.0c02146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In small molecule binding, water is not a passive bystander but rather takes an active role in the binding site, which may be decisive for the potency of the inhibitor. Here, by addressing a high-energy water, we improved the IC50 value of our co-crystallized glycogen synthase kinase-3β (GSK-3β) inhibitor by nearly two orders of magnitude. Surprisingly, our results demonstrate that this high-energy water was not displaced by our potent inhibitor (S)-3-(3-((7-ethynyl-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)piperidin-1-yl)propanenitrile ((S)-15, IC50 value of 6 nM). Instead, only a subtle shift in the location of this water molecule resulted in a dramatic decrease in the energy of this high-energy hydration site, as shown by the WaterMap analysis combined with microsecond timescale molecular dynamics simulations. (S)-15 demonstrated both a favorable kinome selectivity profile and target engagement in a cellular environment and reduced GSK-3 autophosphorylation in neuronal SH-SY5Y cells. Overall, our findings highlight that even a slight adjustment in the location of a high-energy water can be decisive for ligand binding.
Collapse
Affiliation(s)
- Stanislav Andreev
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Roberta Tesch
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Niclas Kahlke
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Ahmed El-Gokha
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Chemistry Department, Faculty of Science, Menoufia University, Gamal Abdel-Nasser Street, 32511 Shebin El-Kom, Egypt
| | - Francesco Ansideri
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lukas Grätz
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jenny Romasco
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Giulia Sita
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Christian Geibel
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Stefan A Laufer
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery (TüCAD2), Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Pierre Koch
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| |
Collapse
|
14
|
Kwon OS, Ahn S, Jeon JE, Park IG, Won TH, Sim CJ, Park HG, Oh DC, Oh KB, Noh M, Shin J. Psammocindoles A-C: Isolation, Synthesis, and Bioactivity of Indole-γ-lactams from the Sponge Psammocinia vermis. Org Lett 2021; 23:4667-4671. [PMID: 34060857 DOI: 10.1021/acs.orglett.1c01410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Psammocindoles A-C (1-3), a new class of indole alkaloids, were isolated from a Psammocinia vermis sponge. By combined spectroscopic analyses, the structures of these compounds were determined to be the indole-γ-lactams derived from three amino acid residues. In addition, an enantiomer psammocindole D (4), and the N-lactam isomers isopsammocindoles A-D (5-8) were also synthesized. These natural products and synthetic analogues were found to significantly stimulate adiponectin secretion in human bone marrow mesenchymal stem cells.
Collapse
Affiliation(s)
- Oh-Seok Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungjin Ahn
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju-Eun Jeon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - In Guk Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae Hyung Won
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Chung J Sim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejeon 34430, Republic of Korea
| | - Hyeung-Geun Park
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Bong Oh
- College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Minsoo Noh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
15
|
Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
Collapse
Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | | |
Collapse
|
16
|
Spitaleri A, Zia SR, Di Micco P, Al-Lazikani B, Soler MA, Rocchia W. Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case. J Phys Chem Lett 2021; 12:49-58. [PMID: 33300337 PMCID: PMC7812613 DOI: 10.1021/acs.jpclett.0c03075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/03/2020] [Indexed: 05/13/2023]
Abstract
Water plays a key role in biomolecular recognition and binding. Despite the development of several computational and experimental approaches, it is still challenging to comprehensively characterize water-mediated effects on the binding process. Here, we investigate how water affects the binding of Src kinase to one of its inhibitors, PP1. Src kinase is a target for treating several diseases, including cancer. We use biased molecular dynamics simulations, where the hydration of predetermined regions is tuned at will. This computational technique efficiently accelerates the SRC-PP1 binding simulation and allows us to identify several key and yet unexplored aspects of the solvent's role. This study provides a further perspective on the binding phenomenon, which may advance the current drug design approaches for the development of new kinase inhibitors.
Collapse
Affiliation(s)
- Andrea Spitaleri
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
- Center
for Omics Sciences, Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Syeda R. Zia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Patrizio Di Micco
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Bissan Al-Lazikani
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Miguel A. Soler
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
| |
Collapse
|
17
|
Cramer DL, Cheng B, Tian J, Clements JH, Wypych RM, Martin SF. Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions. Eur J Med Chem 2020; 208:112771. [PMID: 32916312 PMCID: PMC7680455 DOI: 10.1016/j.ejmech.2020.112771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 12/18/2022]
Abstract
Understanding how making structural changes in small molecules affects their binding affinities for targeted proteins is central to improving strategies for rational drug design. To assess the effects of varying the nature of nonpolar groups upon binding entropies and enthalpies, we designed and prepared a set of Grb2-SH2 domain ligands, Ac-pTyr-Ac6c-Asn-(CH2)n-R, in which the size and electrostatic nature of R groups at the pTyr+3 site were varied. The complexes of these ligands with the Grb2-SH2 domain were evaluated in a series of studies in which the binding thermodynamics were determined using isothermal titration calorimetry, and binding interactions were examined in crystallographic studies of two different complexes. Notably, adding nonpolar groups to the pTyr+3 site leads to higher binding affinities, but the magnitude and energetic origins of these effects vary with the nature of the R substituent. For example, enhancements to binding affinities using aliphatic R groups are driven by more favorable changes in binding entropies, whereas aryl R groups improve binding free energies through a combination of more favorable changes in binding enthalpies and entropies. However, enthalpy/entropy compensation plays a significant role in these associations and mitigates against any significant variation in binding free energies, which vary by only 0.8 kcal•mol-1, with changes in the electrostatic nature and size of the R group. Crystallographic studies show that differences in ΔG° or ΔH° correlate with buried nonpolar surface area, but they do not correlate with the total number of polar or van der Waals contacts. The relative number of ordered water molecules and relative order in the side chains at pTyr+3 correlate with differences in -TΔS°. Overall, these studies show that burial of nonpolar surface can lead to enhanced binding affinities arising from dominating entropy- or enthalpy-driven hydrophobic effects, depending upon the electrostatic nature of the apolar R group.
Collapse
Affiliation(s)
- David L Cramer
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Bo Cheng
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Jianhua Tian
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Rachel M Wypych
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- Department of Chemistry and the Institute of Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA.
| |
Collapse
|
18
|
Abstract
Phosphonopeptides are phosphorus analogues of peptides and have been widely applied as enzyme inhibitors and antigens to induce catalytic antibodies. Phosphonopeptides generally contain one aminoalkylphosphonic acid residue and include phosphonopeptides with C-terminal aminoalkylphosphonic acids and phosphonopeptides with a phosphonamidate bond. The phosphonamidate bond in the phosphonopeptides is generally formed via phosphonylation with phosphonochloridates, condensation with coupling reagents and enzymes, and phosphinylation followed by oxidation. Pseudo four-component condensation reaction of amides, aldehydes, alkyl dichlorophosphites, and amino/peptide esters is an alternative, convergent, and efficient strategy for synthesis of phosphonopeptides through simultaneous construction of aminoalkylphosphonic acids and formation of the phosphonamidate bond. This review focuses on the synthetic methods of phosphonopeptides containing a phosphonamidate bond.
Collapse
Affiliation(s)
- Jiaxi Xu
- State Key Laboratory of Chemical Resource Engineering, Department of Organic Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
19
|
Hüfner-Wulsdorf T, Klebe G. Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms. J Chem Inf Model 2020; 60:6654-6665. [DOI: 10.1021/acs.jcim.0c01133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| |
Collapse
|
20
|
Zaucha J, Softley CA, Sattler M, Frishman D, Popowicz GM. Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data. Chem Commun (Camb) 2020; 56:15454-15457. [PMID: 33237041 DOI: 10.1039/d0cc04383d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We develop a residual deep learning model, hotWater (https://pypi.org/project/hotWater/), to identify key water interaction sites on proteins for binding models and drug discovery. This is tested on new crystal structures, as well as cryo-EM and NMR structures from the PDB and in crystallographic refinement with promising results.
Collapse
Affiliation(s)
- Jan Zaucha
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany.
| | | | | | | | | |
Collapse
|
21
|
Glöckner S, Klebe G. Simultaneous determination of thermodynamic and kinetic data by isothermal titration calorimetry. Biochim Biophys Acta Gen Subj 2020; 1865:129772. [PMID: 33191201 DOI: 10.1016/j.bbagen.2020.129772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Thermodynamic and binding kinetic data increasingly support and guide the drug optimization process. METHODS Because ITC thermograms contain binding thermodynamic and kinetic information, an efficient protocol for the simultaneous extraction of thermodynamic and kinetic data for 1:1 protein ligand reactions from AFFINImeter kinITC in one single experiment are presented. RESULTS The effort to apply this protocol requires the same time as for the standard protocol but increases the precision of both thermodynamic and kinetic data. CONCLUSIONS The protocol enables reliable extraction of both thermodynamic and kinetic data for 1:1 protein-ligand binding reactions with improved precision compared to the 'standard protocol'. GENERAL SIGNIFICANCE Thermodynamic and kinetic data are recorded under exactly the same conditions in solution without any labeling or immobilization from a protein sample that is not 100% active and would otherwise render the extraction of kinetic parameters impossible.
Collapse
Affiliation(s)
- Steffen Glöckner
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
| | - Gerhard Klebe
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
| |
Collapse
|
22
|
Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H 1. J Comput Aided Mol Des 2020; 34:1045-1062. [PMID: 32572668 DOI: 10.1007/s10822-020-00328-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/18/2020] [Indexed: 02/02/2023]
Abstract
Cetirizine, a major metabolite of hydroxyzine, became a marketed second-generation H1 antihistamine that is orally active and has a rapid onset of action, long duration of effects and a very good safety record at recommended doses. The approved drug is a racemic mixture of (S)-cetirizine and (R)-cetirizine, the latter being the levorotary enantiomer that also exists in the market as a third-generation, non-sedating and highly selective antihistamine. Both enantiomers bind tightly to the human histamine H1 receptor (hH1R) and behave as inverse agonists but the affinity and residence time of (R)-cetirizine are greater than those of (S)-cetirizine. In blood plasma, cetirizine exists in the zwitterionic form and more than 90% of the circulating drug is bound to human serum albumin (HSA), which acts as an inactive reservoir. Independent X-ray crystallographic work has solved the structure of the hH1R:doxepin complex and has identified two drug-binding sites for cetirizine on equine serum albumin (ESA). Given this background, we decided to model a membrane-embedded hH1R in complex with either (R)- or (S)-cetirizine and also the complexes of both ESA and HSA with these two enantiomeric drugs to analyze possible differences in binding modes between enantiomers and also among targets. The ensuing molecular dynamics simulations in explicit solvent and additional computational chemistry calculations provided structural and energetic information about all of these complexes that is normally beyond current experimental possibilities. Overall, we found very good agreement between our binding energy estimates and extant biochemical and pharmacological evidence. A much higher degree of solvent exposure in the cetirizine-binding site(s) of HSA and ESA relative to the more occluded orthosteric binding site in hH1R is translated into larger positional fluctuations and considerably lower affinities for these two nonspecific targets. Whereas it is demonstrated that the two known pockets in ESA provide enough stability for cetirizine binding, only one such site does so in HSA due to a number of amino acid replacements. At the histamine-binding site in hH1R, the distinct interactions established between the phenyl and chlorophenyl moieties of the two enantiomers with the amino acids lining up the pocket and between their free carboxylates and Lys179 in the second extracellular loop account for the improved pharmacological profile of (R)-cetirizine.
Collapse
|
23
|
Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors. ACS Chem Biol 2020; 15:675-685. [PMID: 32027480 DOI: 10.1021/acschembio.9b00895] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thermodynamics and kinetics of protein-ligand binding are both important aspects for the design of novel drug molecules. Presently, thermodynamic data are collected with isothermal titration calorimetry, while kinetic data are mostly derived from surface plasmon resonance. The new method of kinITC provides both thermodynamic and kinetic data from calorimetric titration measurements. The present study demonstrates the convenient collection of calorimetric data suitable for both thermodynamic and kinetic analysis for two series of congeneric ligands of human carbonic anhydrase II and correlates these findings with structural data obtained by macromolecular crystallography to shed light on the importance of shape complementarity for thermodynamics and kinetics governing a protein-ligand binding event. The study shows how minute chemical alterations change preferred ligand conformation and can be used to manipulate thermodynamic and kinetic signatures of binding. They give rise to the observation that analogous n-alkyl and n-alkyloxy derivatives of identical chain length swap their binding kinetic properties at unchanged binding affinity.
Collapse
Affiliation(s)
- Steffen Glöckner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph P Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| |
Collapse
|
24
|
Spaggiari G, Di Pizio A, Cozzini P. Sweet, umami and bitter taste receptors: State of the art of in silico molecular modeling approaches. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
25
|
Sandner A, Hüfner-Wulsdorf T, Heine A, Steinmetzer T, Klebe G. Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem 2019; 62:9753-9771. [PMID: 31633354 DOI: 10.1021/acs.jmedchem.9b01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.
Collapse
Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| |
Collapse
|
26
|
Heider F, Pantsar T, Kudolo M, Ansideri F, De Simone A, Pruccoli L, Schneider T, Goettert MI, Tarozzi A, Andrisano V, Laufer SA, Koch P. Pyridinylimidazoles as GSK3β Inhibitors: The Impact of Tautomerism on Compound Activity via Water Networks. ACS Med Chem Lett 2019; 10:1407-1414. [PMID: 31620226 DOI: 10.1021/acsmedchemlett.9b00177] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
Glycogen synthase kinase-3β (GSK3β) is involved in many pathological conditions and represents an attractive drug target. We previously reported dual GSK3β/p38α mitogen-activated protein kinase inhibitors and identified N-(4-(4-(4-fluorophenyl)-2-methyl-1H-imidazol-5-yl)pyridin-2-yl)cyclopropanecarboxamide (1) as a potent dual inhibitor of both target kinases. In this study, we aimed to design selective GSK3β inhibitors based on our pyridinylimidazole scaffold. Our efforts resulted in several novel and potent GSK3β inhibitors with IC50 values in the low nanomolar range. 5-(2-(Cyclopropanecarboxamido)pyridin-4-yl)-4-cyclopropyl-1H-imidazole-2-carboxamide (6g) displayed very good kinase selectivity as well as metabolical stability and inhibited GSK3β activity in neuronal SH-SY5Y cells. Interestingly, we observed the importance of the 2-methylimidazole's tautomeric state for the compound activity. Finally, we reveal how this crucial tautomerism effect is surmounted by imidazole-2-carboxamides, which are able to stabilize the binding via enhanced water network interactions, regardless of their tautomeric state.
Collapse
Affiliation(s)
- Fabian Heider
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 14, 72076 Tübingen, Germany
| | - Mark Kudolo
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Francesco Ansideri
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Angela De Simone
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D’Augusto, 237, 47921 Rimini, Italy
| | - Letizia Pruccoli
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D’Augusto, 237, 47921 Rimini, Italy
| | - Taiane Schneider
- Cell Culture Laboratory, Postgraduate Program in Biotechnology, University of Vale do Taquari (Univates), Lajeado, RS 95900-00, Brazil
| | - Marcia Inês Goettert
- Cell Culture Laboratory, Postgraduate Program in Biotechnology, University of Vale do Taquari (Univates), Lajeado, RS 95900-00, Brazil
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D’Augusto, 237, 47921 Rimini, Italy
| | - Vincenza Andrisano
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D’Augusto, 237, 47921 Rimini, Italy
| | - Stefan A. Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Pierre Koch
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| |
Collapse
|
27
|
Geschwindner S, Ulander J. The current impact of water thermodynamics for small-molecule drug discovery. Expert Opin Drug Discov 2019; 14:1221-1225. [DOI: 10.1080/17460441.2019.1664468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Ulander
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|
28
|
Heider F, Ansideri F, Tesch R, Pantsar T, Haun U, Döring E, Kudolo M, Poso A, Albrecht W, Laufer SA, Koch P. Pyridinylimidazoles as dual glycogen synthase kinase 3β/p38α mitogen-activated protein kinase inhibitors. Eur J Med Chem 2019; 175:309-329. [DOI: 10.1016/j.ejmech.2019.04.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/29/2019] [Accepted: 04/13/2019] [Indexed: 12/11/2022]
|
29
|
Choi KE, Chae E, Balupuri A, Yoon HR, Kang NS. Topological Water Network Analysis Around Amino Acids. Molecules 2019; 24:molecules24142653. [PMID: 31336667 PMCID: PMC6681432 DOI: 10.3390/molecules24142653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
Water molecules play a key role in protein stability, folding, function and ligand binding. Protein hydration has been studied using free energy perturbation algorithms. However, the study of protein hydration without free energy calculation is also an active field of research. Accordingly, topological water network (TWN) analysis has been carried out instead of free energy calculation in the present work to investigate hydration of proteins. Water networks around 20 amino acids in the aqueous solution were explored through molecular dynamics (MD) simulations. These simulation results were compared with experimental observations. Water molecules from the protein data bank structures showed TWN patterns similar to MD simulations. This work revealed that TWNs are effected by the surrounding environment. TWNs could provide valuable clues about the environment around amino acid residues in the proteins. The findings from this study could be exploited for TWN-based drug discovery and development.
Collapse
Affiliation(s)
- Kwang-Eun Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Eunkyoung Chae
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| |
Collapse
|
30
|
Wrobleski ST, Moslin R, Lin S, Zhang Y, Spergel S, Kempson J, Tokarski JS, Strnad J, Zupa-Fernandez A, Cheng L, Shuster D, Gillooly K, Yang X, Heimrich E, McIntyre KW, Chaudhry C, Khan J, Ruzanov M, Tredup J, Mulligan D, Xie D, Sun H, Huang C, D’Arienzo C, Aranibar N, Chiney M, Chimalakonda A, Pitts WJ, Lombardo L, Carter PH, Burke JR, Weinstein DS. Highly Selective Inhibition of Tyrosine Kinase 2 (TYK2) for the Treatment of Autoimmune Diseases: Discovery of the Allosteric Inhibitor BMS-986165. J Med Chem 2019; 62:8973-8995. [DOI: 10.1021/acs.jmedchem.9b00444] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
31
|
Labbé CM, Pencheva T, Jereva D, Desvillechabrol D, Becot J, Villoutreix BO, Pajeva I, Miteva MA. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics. Nucleic Acids Res 2019; 45:W350-W355. [PMID: 28486703 PMCID: PMC5570140 DOI: 10.1093/nar/gkx397] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/28/2017] [Indexed: 12/20/2022] Open
Abstract
AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php.
Collapse
Affiliation(s)
- Céline M Labbé
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.,INSERM, U973 Paris, France
| | - Tania Pencheva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria
| | - Dessislava Jereva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria
| | - Dimitri Desvillechabrol
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.,INSERM, U973 Paris, France
| | - Jérôme Becot
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.,INSERM, U973 Paris, France
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.,INSERM, U973 Paris, France
| | - Ilza Pajeva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.,INSERM, U973 Paris, France
| |
Collapse
|
32
|
Sánchez-Murcia PA, Mills A, Cortés-Cabrera Á, Gago F. Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. J Comput Aided Mol Des 2019; 33:627-644. [DOI: 10.1007/s10822-019-00208-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 01/27/2023]
|
33
|
Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
Collapse
Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| |
Collapse
|
34
|
|
35
|
Magarkar A, Schnapp G, Apel AK, Seeliger D, Tautermann CS. Enhancing Drug Residence Time by Shielding of Intra-Protein Hydrogen Bonds: A Case Study on CCR2 Antagonists. ACS Med Chem Lett 2019; 10:324-328. [PMID: 30891134 DOI: 10.1021/acsmedchemlett.8b00590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
The target residence time (RT) for a given ligand is one of the important parameters that have to be optimized during drug design. It is well established that shielding the receptor-ligand hydrogen bond (H-bond) interactions from water has been one of the factors in increasing ligand RT. Building on this foundation, here we report that shielding an intra-protein H-bond, which confers rigidity to the binding pocket and which is not directly involved in drug-receptor interactions, can strongly influence RT for CCR2 antagonists. Based on our recently solved CCR2 structure with MK-0812 and molecular dynamics (MD) simulations, we show that the RT for this and structurally related ligands is directly dependent on the shielding of the Tyr120-Glu291 H-bond from the water. If solvated this H-bond is often broken, making the binding pocket flexible and leading to shorter RT.
Collapse
Affiliation(s)
- Aniket Magarkar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Anna-Katharina Apel
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Christofer S. Tautermann
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| |
Collapse
|
36
|
Klebe G. Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option? Drug Discov Today 2019; 24:943-948. [PMID: 30708050 DOI: 10.1016/j.drudis.2019.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
Thermodynamic profiles of ligand binding, particularly enthalpically favored binding signatures, have been suggested as a criterion to support the decision-making process around which compounds to select for further optimization in drug development. The concept was enthusiastically taken up, but turned out to be too superficial, either because many aspects determining thermodynamic profiles are insufficiently appreciated or because it is difficult to compare such data on a global scale. The impact of water, changes in protonation states, along with buffer dependencies and incompatible measurement conditions that are far from standard conditions hamper such broad-scale comparisons. However, thermodynamic signatures can make us aware of the impact of these aspects and provide important hints for improving our understanding of the binding process and defining criteria for drug optimization.
Collapse
Affiliation(s)
- Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
| |
Collapse
|
37
|
Gropp C, Husch T, Trapp N, Reiher M, Diederich F. Wasserstoffbrücken-Netzwerke: molekulare Erkennung zyklischer Alkohole in enantiomerenreinen alleno-acetylenischen Käfigrezeptoren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Tamara Husch
- Laboratorium für Physikalische Chemie; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Markus Reiher
- Laboratorium für Physikalische Chemie; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| |
Collapse
|
38
|
Gropp C, Husch T, Trapp N, Reiher M, Diederich F. Hydrogen-Bonded Networks: Molecular Recognition of Cyclic Alcohols in Enantiopure Alleno-Acetylenic Cage Receptors. Angew Chem Int Ed Engl 2018; 57:16296-16301. [DOI: 10.1002/anie.201810562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Tamara Husch
- Laboratorium für Physikalische Chemie; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| |
Collapse
|
39
|
Su H, Xu Y. Application of ITC-Based Characterization of Thermodynamic and Kinetic Association of Ligands With Proteins in Drug Design. Front Pharmacol 2018; 9:1133. [PMID: 30364164 PMCID: PMC6193069 DOI: 10.3389/fphar.2018.01133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
A comprehensive characterization of the thermodynamic and kinetic profiling of ligands binding to a given target protein is crucial for the hit selection as well as the hit-to-lead-to-drug evolution. Isothermal titration calorimetry (ITC), widely known as an invaluable tool to measure the thermodynamic data, has recently found its way to determine the binding kinetics too. The extensive application of ITC in measurement of both thermodynamic and kinetic data manifests unique roles of ITC in drug discovery and development. This mini-review concentrates on elaborating how to gain the thermodynamic and kinetic data using ITC, highlighting the importance of these data in lead discovery and optimization, and intends to provide an overview of the technical and conceptual advances that offer unprecedented access to protein–ligand recognition by ITC measurement.
Collapse
Affiliation(s)
- Haixia Su
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
40
|
Matter H, Güssregen S. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands. Bioorg Med Chem Lett 2018; 28:2343-2352. [PMID: 29880400 DOI: 10.1016/j.bmcl.2018.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022]
Abstract
Water is an essential part of protein binding sites and mediates interactions to ligands. Its displacement by ligand parts affects the free binding energy of resulting protein-ligand complexes. Therefore the characterization of solvation properties is important for design. Of particular interest is the propensity of localized water to be favorably displaced by a ligand. This review discusses two popular computational approaches addressing these questions, namely WaterMap based on statistical mechanics analysis of MD simulations and 3D RISM based on integral equation theory of liquids. The theoretical background and recent applications in structure-based design will be presented.
Collapse
Affiliation(s)
- Hans Matter
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| |
Collapse
|
41
|
Pantsar T, Poso A. Binding Affinity via Docking: Fact and Fiction. Molecules 2018; 23:molecules23081899. [PMID: 30061498 PMCID: PMC6222344 DOI: 10.3390/molecules23081899] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/03/2023] Open
Abstract
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known structure”. Since then, small molecule docking has been employed as a fast way to estimate the binding pose of a given compound within a specific target protein and also to predict binding affinity. Remarkably, the first docking method suggested by Kuntz and colleagues aimed to predict binding poses but very little was specified about binding affinity. This raises the question as to whether docking is the right tool to estimate binding affinity. The short answer is no, and this has been concluded in several comprehensive analyses. However, in this opinion paper we discuss several critical aspects that need to be reconsidered before a reliable binding affinity prediction through docking is realistic. These are not the only issues that need to be considered, but they are perhaps the most critical ones. We also consider that in spite of the huge efforts to enhance scoring functions, the accuracy of binding affinity predictions is perhaps only as good as it was 10–20 years ago. There are several underlying reasons for this poor performance and these are analyzed. In particular, we focus on the role of the solvent (water), the poor description of H-bonding and the lack of the systems’ true dynamics. We hope to provide readers with potential insights and tools to overcome the challenging issues related to binding affinity prediction via docking.
Collapse
Affiliation(s)
- Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany.
| |
Collapse
|
42
|
Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
Collapse
Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| |
Collapse
|
43
|
|
44
|
Gao DD, Dou HX, Su HX, Zhang MM, Wang T, Liu QF, Cai HY, Ding HP, Yang Z, Zhu WL, Xu YC, Wang HY, Li YX. From hit to lead: Structure-based discovery of naphthalene-1-sulfonamide derivatives as potent and selective inhibitors of fatty acid binding protein 4. Eur J Med Chem 2018; 154:44-59. [DOI: 10.1016/j.ejmech.2018.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/05/2023]
|
45
|
Fox JM, Zhao M, Fink MJ, Kang K, Whitesides GM. The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition. Annu Rev Biophys 2018; 47:223-250. [DOI: 10.1146/annurev-biophys-070816-033743] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.
Collapse
Affiliation(s)
- Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, Republic of Korea
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
- The Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
46
|
Schwertz G, Witschel MC, Rottmann M, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Amornwatcharapong W, Ittarat W, Schäfer A, Aponte RA, Trapp N, Chaiyen P, Diederich F. Potent Inhibitors ofPlasmodialSerine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold. ChemMedChem 2018; 13:931-943. [DOI: 10.1002/cmdc.201800053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/25/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Geoffrey Schwertz
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Matthias Rottmann
- Swiss Tropical and Public Health Institute (SwissTPH); Socinstrasse 57 4051 Basel Switzerland
- Universität Basel; Petersplatz 1 4003 Basel Switzerland
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science; Mahidol University; 272 Rama VI Road Bangkok 10400 Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology; 113 Thailand Science Park, Phahonyothin Road Pathumthani 12120 Thailand
| | - Anja Schäfer
- Swiss Tropical and Public Health Institute (SwissTPH); Socinstrasse 57 4051 Basel Switzerland
- Universität Basel; Petersplatz 1 4003 Basel Switzerland
| | | | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science; Mahidol University; 272 Rama VI Road Bangkok 10400 Thailand
- Department of Biomolecular Science and Engineering, School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| |
Collapse
|
47
|
Bucher D, Stouten P, Triballeau N. Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods. J Chem Inf Model 2018; 58:692-699. [DOI: 10.1021/acs.jcim.7b00642] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Denis Bucher
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Pieter Stouten
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | |
Collapse
|
48
|
Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J. Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Chemphyschem 2018; 19:873-879. [PMID: 29316128 DOI: 10.1002/cphc.201701104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/11/2022]
Abstract
Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (Ki ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.
Collapse
Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Magdalena Hořejší
- Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| |
Collapse
|
49
|
Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. J Chem Theory Comput 2018; 14:418-425. [PMID: 29161510 PMCID: PMC5760325 DOI: 10.1021/acs.jctc.7b00592] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.
Collapse
Affiliation(s)
- Kamran Haider
- Department of Physics, City College of New York, The City University of New York, 160 Convent Ave, New York, NY 10031
| | - Anthony Cruz
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
| | - Steven Ramsey
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, CA, 92093-0736
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York, NY 10468
- Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
- Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, 365 Fifth Avenue, New York, New York, 10016, United States
| |
Collapse
|
50
|
Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B. J Comput Aided Mol Des 2017; 31:915-928. [DOI: 10.1007/s10822-017-0066-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 01/24/2023]
|