1
|
Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [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: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
Collapse
Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| |
Collapse
|
2
|
Abdel-Rahman SA, Świderek K, Gabr MT. First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators. RSC Med Chem 2023; 14:1767-1777. [PMID: 37731692 PMCID: PMC10507805 DOI: 10.1039/d3md00150d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
The interaction of the inducible co-stimulator (ICOS) with its ligand (ICOSL) plays key roles in T-cell differentiation and activation of T-cell to B-cell functions. The ICOS/ICOSL pathway is a validated target for T-cell lymphomas induced by the proliferation of T-follicular helper (Tfh) cells. Moreover, the inhibition of ICOS/ICOSL interaction can decrease the enhancement of immunosuppressive regulatory T cells (Tregs) in both hematologic malignancies and solid tumors. However, targeting ICOS/ICOSL interaction is currently restricted to monoclonal antibodies (mAbs) and there are no small molecules in existence that can block ICOS/ICOSL. To fill this gap, we report herein the first time-resolved fluorescence resonance energy transfer (TR-FRET) assay to evaluate the ability of small molecules to inhibit ICOS/ICOSL interaction. Implementation of the developed TR-FRET assay in high-throughput screening (HTS) of a focused chemical library resulted in the identification of AG-120 as a first-in-class inhibitor of ICOS/ICOSL interaction. We further employed docking studies and molecular dynamics (MD) simulations to identify the plausible mechanism of blocking ICOS/ICOSL complex formation by AG-120. Using the structure-activity relationship (SAR) by catalog approach, we identified AG-120-X with an IC50 value of 4.68 ± 0.47 μM in the ICOS/ICOSL TR-FRET assay. Remarkably, AG-120-X revealed a dose-dependent ability to block ICOS/ICOSL interaction in a bioluminescent cellular assay based on co-culturing Jurkat T cells expressing ICOS and CHO-K1 cells expressing ICOSL. This work will pave the way for future drug discovery efforts aiming at the development of small molecule inhibitors of ICOS/ICOSL interaction as potential therapeutics for cancer as well as other diseases.
Collapse
Affiliation(s)
- Somaya A Abdel-Rahman
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine New York NY 10065 USA
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellon Spain
| | - Moustafa T Gabr
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine New York NY 10065 USA
| |
Collapse
|
3
|
Müller P, Meta M, Meidner JL, Schwickert M, Meyr J, Schwickert K, Kersten C, Zimmer C, Hammerschmidt SJ, Frey A, Lahu A, de la Hoz-Rodríguez S, Agost-Beltrán L, Rodríguez S, Diemer K, Neumann W, Gonzàlez FV, Engels B, Schirmeister T. Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study. Int J Mol Sci 2023; 24:ijms24087226. [PMID: 37108388 PMCID: PMC10138721 DOI: 10.3390/ijms24087226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
Collapse
Affiliation(s)
- Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jan Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Albin Lahu
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | | | - Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Kira Diemer
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Wilhelm Neumann
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Florenci V Gonzàlez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| |
Collapse
|
4
|
Kar RK. Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems. Drug Discov Today 2023; 28:103374. [PMID: 36174967 DOI: 10.1016/j.drudis.2022.103374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
Collapse
Affiliation(s)
- Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
| |
Collapse
|
5
|
Serrano-Aparicio N, Ferrer S, Świderek K. Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies. Pharmaceuticals (Basel) 2022; 15:ph15050531. [PMID: 35631358 PMCID: PMC9143130 DOI: 10.3390/ph15050531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
20S proteasome is a main player in the protein degradation pathway in the cytosol, thus intervening in multiple pivotal cellular processes. Over the years the proteasome has emerged as a crucial target for the treatment of many diseases such as neurodegenerative diseases, cancer, autoimmune diseases, developmental disorders, cystic fibrosis, diabetes, cardiac diseases, atherosclerosis, and aging. In this work, the mechanism of proteasome covalent inhibition with bisbenzyl-protected homobelactosin C (hBelC) was explored using quantum mechanics/molecular mechanics (QM/MM) methods. Molecular dynamic simulations were used to describe key interactions established between the hBelC and its unique binding mode in the primed site of the β5 subunit. The free energy surfaces were computed to characterize the kinetics and thermodynamics of the inhibition process. This study revealed that although the final inhibition product for hBelC is formed according to the same molecular mechanism as one described for hSalA, the free energy profile of the reaction pathway differs significantly from the one previously reported for γ-lactam-β-lactone containing inhibitors in terms of the height of the activation barrier as well as the stabilization of the final product. Moreover, it was proved that high stabilization of the covalent adduct formed between β5-subunit and hBelC, together with the presence of aminocarbonyl side chain in the structure of the inhibitor which prevents the hydrolysis of the ester bond from taking place, determines its irreversible character.
Collapse
|
6
|
Serrano-Aparicio N, Moliner V, Świderek K. On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Natalia Serrano-Aparicio
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| |
Collapse
|
7
|
Mihalovits LM, Ferenczy GG, Keserű GM. Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors. Comput Struct Biotechnol J 2021; 19:4486-4496. [PMID: 34471494 PMCID: PMC8379283 DOI: 10.1016/j.csbj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The kinact value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant Ki of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated Ki and kinact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect Ki, the noncovalent affinity, and importantly alter kinact, the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties.
Collapse
Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| |
Collapse
|
8
|
Galmés MÀ, Nödling AR, Luk L, Świderek K, Moliner V. Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. ACS Catal 2021; 11:8635-8644. [PMID: 35875595 PMCID: PMC9299431 DOI: 10.1021/acscatal.1c02150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Convergent evolution has resulted in nonhomologous enzymes that
contain similar active sites that catalyze the same primary and secondary
reactions. Comparing how these enzymes achieve their reaction promiscuity
can yield valuable insights to develop functions from the optimization
of latent activities. In this work, we have focused on the promiscuous
amidase activity in the esterase from Bacillus subtilis (Bs2) and compared with the same activity in the promiscuous lipase
B from Candida antarctica (CALB). The
study, combining multiscale quantum mechanics/molecular mechanics
(QM/MM) simulations, deep machine learning approaches, and experimental
characterization of Bs2 kinetics, confirms the amidase activity of
Bs2 and CALB. The computational results indicate that both enzymes
offer a slightly different reaction environment reflected by electrostatic
effects within the active site, thus resulting in a different reaction
mechanism during the acylation step. A convolutional neural network
(CNN) has been used to understand the conserved amino acids among
the evolved protein family and suggest that Bs2 provides a more robust
protein scaffold to perform future mutagenesis studies. Results derived
from this work will help reveal the origin of enzyme promiscuity,
which will find applications in enzyme (re)design, particularly in
creating a highly active amidase.
Collapse
Affiliation(s)
- Miquel À. Galmés
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alexander R. Nödling
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Louis Luk
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Katarzyna Świderek
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| |
Collapse
|