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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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Fındık V, Varınca Gerçik BT, Sinek Ö, Erdem SS, Ruiz-López MF. Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM:QM Computations. J Chem Inf Model 2022; 62:6775-6787. [PMID: 35980989 DOI: 10.1021/acs.jcim.2c00569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) enzymes are important drug targets, especially in oncology, and several inhibitors are currently under investigation in clinical trials for the treatment of lymphocytic leukemia, follicular lymphoma, breast, thyroid, colorectal, and lung cancer. Targeted covalent inhibitors hold significant promise for drug discovery research especially for kinases. Targeting the lysine residues attracts attention as a new strategy in designing targeted covalent inhibitors, since the lysine residue provides several advantages over the traditional cysteine residue. Recently, new highly selective covalent inhibitors of PI3Kδ with activated ester warheads, targeting the conserved Lys779 residue, were reported. Based on the observed kinetics, a covalent inhibition mechanism was proposed, but the atomistic details of the reaction are still not understood. Therefore, in the present work, we have conducted quantum chemical ONIOM M06-2X/6-31+G(d,p):PM6 calculations on the active site cluster structure of PI3Kδ to elucidate the microscopic details of the mechanism of the aminolysis reaction between Lys779 and the ester inhibitors. Our calculations clearly discriminate the noncovalent methyl ester inhibitor and the covalent inhibitors with activated phenolic esters. For the representative p-NO2, p-F, p-H, and p-OCH3 phenolic esters, the Gibbs free energy profiles of alternative mechanistic paths through either Asp782 or Asp911 demonstrate the modulatory role of active site aspartate residues. The most plausible path alters depending on the electron-withdrawing/donating nature of the p-substituted phenolate leaving group. Inhibitors with sufficiently strong electron-withdrawing group prefer direct dissociation of the leaving group from the tetrahedral zwitterion intermediate, while the ones with electron-donating group favor the formation of a neutral tetrahedral intermediate prior to the dissociation. The relative Gibbs free energy barriers of p-NO2 < p-F < p-H < p-OCH3 substituted phenyl esters display the same qualitative trend as the experimentally measured kinact/KI values. Our results provide in depth insight into the mechanism, which can pave the way for optimizing the inhibitor efficiency.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, 54000, Nancy, France.,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | | - Öykü Sinek
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
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3
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Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Top Catal 2021; 65:165-186. [DOI: 10.1007/s11244-021-01521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Jaikhan P, Buranrat B, Itoh Y, Chotitumnavee J, Kurohara T, Suzuki T. Identification of ortho-hydroxy anilide as a novel scaffold for lysine demethylase 5 inhibitors. Bioorg Med Chem Lett 2019; 29:1173-1176. [DOI: 10.1016/j.bmcl.2019.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 01/06/2023]
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Cortopassi WA, Celmar Costa Franca T, Krettli AU. A systems biology approach to antimalarial drug discovery. Expert Opin Drug Discov 2018; 13:617-626. [DOI: 10.1080/17460441.2018.1471056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Wilian Augusto Cortopassi
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
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Kumar K, Woo SM, Siu T, Cortopassi WA, Duarte F, Paton RS. Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine. Chem Sci 2018; 9:2655-2665. [PMID: 29719674 PMCID: PMC5903419 DOI: 10.1039/c7sc04905f] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/20/2018] [Indexed: 12/22/2022] Open
Abstract
The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of X-ray structures.
We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pKa. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.
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Affiliation(s)
- Kiran Kumar
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Shin M Woo
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Thomas Siu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Wilian A Cortopassi
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Fernanda Duarte
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Robert S Paton
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
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Qian P, Guo H, Wang L, Guo H. QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate? J Chem Theory Comput 2017; 13:2977-2986. [PMID: 28489369 DOI: 10.1021/acs.jctc.7b00069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein lysine methyltransferases (PKMTs) catalyze the methylation of lysine residues on histone proteins in the regulation of chromatin structure and gene expression. In contrast to many other PKMTs for which unmodified lysine is the methylation target, the enzymes in the Suv4-20 family are able to generate dimethylated product (H4K20me2) based exclusively on the monomethylated H4K20 substrate (H4K20me1). The origin of such substrate/product specificity is still not clear. Here, molecular dynamics (MD) and free energy (potential of mean force) simulations are undertaken using quantum mechanical/molecular mechanical (QM/MM) potentials to understand the substrate/product specificities of Suv4-20h2, a member of the Suv4-20 family. The free energy barriers for mono-, di-, and trimethylation in Suv4-20h2 obtained from the simulations are found to be well correlated with the specificities observed experimentally with the allowed dimethylation based on the H4K20me1 substrate and prohibited monomethylation and trimethylation based on H4K20 and H4K20me2, respectively. It is demonstrated that the reason for the relatively efficient dimethylation is an effective transition state (TS) stabilization through strengthening the CH···O interactions as well as the presence of a cation-π interaction at the transition state. The simulations also show that the failures of Suv4-20h2 to catalyze monomethylation and trimethylation are due, respectively, to a less effective TS stabilization and inability of the reactant complex containing H4K20me2 to adopt a reactive (near attack) configuration for methyl transfer. The results suggest that care must be exercised in the prediction of the substrate specificity based only on the existence of near attack configurations in substrate complexes.
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Affiliation(s)
- Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University , Tai'an 271018, Shandong, Peoples Republic of China
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Liang Wang
- Chemistry and Material Science Faculty, Shandong Agricultural University , Tai'an 271018, Shandong, Peoples Republic of China
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. J Phys Chem B 2017; 121:4023-4039. [PMID: 28306259 PMCID: PMC9724927 DOI: 10.1021/acs.jpcb.7b02320] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Keri A McKiernan
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Joseph Gomes
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle A Beauchamp
- Counsyl, Inc. , South San Francisco, California 94080, United States
| | - Teresa Head-Gordon
- Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
- Chemical Sciences Division, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Julia E Rice
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Departments of Computer Science, Structural Biology, and Program in Biophysics, Stanford University , Stanford, California 94305, United States
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Alberro N, Torrent-Sucarrat M, Arrastia I, Arrieta A, Cossío FP. Two-State Reactivity of Histone Demethylases Containing Jumonji-C Active Sites: Different Mechanisms for Different Methylation Degrees. Chemistry 2016; 23:137-148. [DOI: 10.1002/chem.201604219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
- Ikerbasque; Basque Foundation for Science; María Díaz de Haro 3, 6 floor 48013 Bilbao Spain
| | - Iosune Arrastia
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
| | - Ana Arrieta
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
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Cortopassi WA, Kumar K, Paton RS. Cation–π interactions in CREBBP bromodomain inhibition: an electrostatic model for small-molecule binding affinity and selectivity. Org Biomol Chem 2016; 14:10926-10938. [DOI: 10.1039/c6ob02234k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new model is presented to explain and predict binding affinity of aromatic and heteroaromatic ligands for the CREBBP bromodomain based on cation–π interaction strength.
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Affiliation(s)
| | - Kiran Kumar
- Chemistry Research Laboratory
- University of Oxford
- Oxford OX1 3TA
- UK
| | - Robert S. Paton
- Chemistry Research Laboratory
- University of Oxford
- Oxford OX1 3TA
- UK
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