1
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Ouabane M, Zaki K, Zaki H, Guendouzi A, Sbai A, Sekkate C, Lakhlifi T, Bouachrine M. Inhibition of the Janus kinase protein (JAK1) by the A. Pyrethrum Root Extract for the treatment of Vitiligo pathology. Design, Molecular Docking, ADME-Tox, MD Simulation, and in-silico investigation. Comput Biol Med 2024; 179:108816. [PMID: 38955123 DOI: 10.1016/j.compbiomed.2024.108816] [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: 02/13/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
This study delves into the therapeutic efficacy of A. pyrethrum in addressing vitiligo, a chronic inflammatory disorder known for inducing psychological distress and elevating susceptibility to autoimmune diseases. Notably, JAK inhibitors have emerged as promising candidates for treating immune dermatoses, including vitiligo. Our investigation primarily focuses on the anti-vitiligo potential of A. pyrethrum root extract, specifically targeting N-alkyl-amides, utilizing computational methodologies. Density Functional Theory (DFT) is deployed to meticulously scrutinize molecular properties, while comprehensive evaluations of ADME-Tox properties for each molecule contribute to a nuanced understanding of their therapeutic viability, showcasing remarkable drug-like characteristics. Molecular docking analysis probes ligand interactions with pivotal site JAK1, with all compounds demonstrating significant interactions; notably, molecule 6 exhibits the most interactions with crucial inhibition residues. Molecular dynamics simulations over 500ns further validate the importance and sustainability of these interactions observed in molecular docking, favoring energetically both molecules 6 and 1; however, in terms of stability, the complex with molecule 6 outperforms others. DFT analyses elucidate the distribution of electron-rich oxygen atoms and electron-poor regions within heteroatoms-linked hydrogens. Remarkably, N-alkyl-amides extracted from A. pyrethrum roots exhibit similar compositions, yielding comparable DFT and Electrostatic Potential (ESP) results with subtle distinctions. These findings underscore the considerable potential of A. pyrethrum root extracts as a natural remedy for vitiligo.
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Affiliation(s)
- Mohamed Ouabane
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco; Chemistry-Biology Applied to the Environment URL CNRT 13, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco
| | - Khadija Zaki
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco
| | - Hanane Zaki
- Biotechnology, Bioresources, And Bioinformatics Laboratory at the Higher School of Technology, 54000, Khenifra, Morocco
| | - Abdelkrim Guendouzi
- Laboratory of Chemistry, Synthesis, Properties and Applications, Department of Chemistry, Faculty of Science, University of Saida, Algeria
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco
| | - Chakib Sekkate
- Chemistry-Biology Applied to the Environment URL CNRT 13, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, My Ismail University, B.P. 11202, Meknes, 50000, Morocco.
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2
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Bairagya HR, Tasneem A, Sarmadhikari D. Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory. Proteins 2024; 92:735-749. [PMID: 38213131 DOI: 10.1002/prot.26665] [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: 11/12/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4-W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.
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Affiliation(s)
- Hridoy R Bairagya
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Alvea Tasneem
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Debapriyo Sarmadhikari
- Computational Drug Design and Bio-molecular Simulation Lab, Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
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3
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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.
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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
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4
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Ludwig J, Curado-Carballada C, Hammer SC, Schneider A, Diether S, Kress N, Ruiz-Barragán S, Osuna S, Hauer B. Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases. Angew Chem Int Ed Engl 2024; 63:e202318913. [PMID: 38270537 DOI: 10.1002/anie.202318913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-β-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.
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Affiliation(s)
- Julian Ludwig
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Christian Curado-Carballada
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Stephan C Hammer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andreas Schneider
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Svenja Diether
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Nico Kress
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Sergi Ruiz-Barragán
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- Departament de Fisica, Universitat Politecnica de Catalunya, Rambla Sant Nebridi 22, 08222, Terrassa, Barcelona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [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: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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6
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Zhao C, Kleiman DE, Shukla D. Resolving binding pathways and solvation thermodynamics of plant hormone receptors. J Biol Chem 2023; 299:105456. [PMID: 37949229 PMCID: PMC10704434 DOI: 10.1016/j.jbc.2023.105456] [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: 05/12/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Plant hormones are small molecules that regulate plant growth, development, and responses to biotic and abiotic stresses. They are specifically recognized by the binding site of their receptors. In this work, we resolved the binding pathways for eight classes of phytohormones (auxin, jasmonate, gibberellin, strigolactone, brassinosteroid, cytokinin, salicylic acid, and abscisic acid) to their canonical receptors using extensive molecular dynamics simulations. Furthermore, we investigated the role of water displacement and reorganization at the binding site of the plant receptors through inhomogeneous solvation theory. Our findings predict that displacement of water molecules by phytohormones contributes to free energy of binding via entropy gain and is associated with significant free energy barriers for most systems analyzed. Also, our results indicate that displacement of unfavorable water molecules in the binding site can be exploited in rational agrochemical design. Overall, this study uncovers the mechanism of ligand binding and the role of water molecules in plant hormone perception, which creates new avenues for agrochemical design to target plant growth and development.
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Affiliation(s)
- Chuankai Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diego E Kleiman
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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7
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Ghosh B, Layek S, Bhattacharyya D, Sengupta N. Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics. J Chem Phys 2023; 159:095101. [PMID: 37655772 DOI: 10.1063/5.0154977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes.
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Affiliation(s)
- Brataraj Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Sarbajit Layek
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, Bidhannagar, Kolkata, West Bengal 700064, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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8
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Klee LS, Gárdonyi M, Hüfner T, Heine A, Klebe G. Mutational Studies of Aldose Reductase to Trace a Transient Pocket Opening and to Explain Ligand Affinity Cliffs. ChemMedChem 2023; 18:e202300222. [PMID: 37278327 DOI: 10.1002/cmdc.202300222] [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: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Human aldose reductase, a target for the development of inhibitors for preventing diabetic complications, displays a transient specificity pocket which opens upon binding with specific, potent inhibitors. We investigated the opening mechanism of this pocket by mutating leucine residues involved in the gate keeping mechanism to alanine. Two isostructural inhibitors distinguished only by a single nitro to carboxy group replacement, have a 1000-fold difference in their binding affinity to the wild type. This difference is reduced to 10-fold in the mutated variants as the nitro derivative loses in affinity but conserves binding to the open transient pocket. The affinity of the carboxylate analog is minimally altered but the analog binding preference changes from the closed to open state of the transient pocket. Differences in the solvation properties of ligands and the transient pocket as well as changes from induced fit to conformational selections provide an explanation for the altered behavior of the ligands with respect to their binding to the different variants.
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Affiliation(s)
- Lea-Sophie Klee
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Marina Gárdonyi
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Hüfner
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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9
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Lazaric A, Pattni V, Fuegner K, Ben-Naim A, Heyden M. Solvation free energy arithmetic for small organic molecules. J Comput Chem 2023; 44:1263-1277. [PMID: 36866644 DOI: 10.1002/jcc.27081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/21/2022] [Accepted: 12/29/2022] [Indexed: 03/04/2023]
Abstract
Solvent-mediated interactions contribute to ligand binding affinities in computational drug design and provide a challenge for theoretical predictions. In this study, we analyze the solvation free energy of benzene derivatives in water to guide the development of predictive models for solvation free energies and solvent-mediated interactions. We use a spatially resolved analysis of local solvation free energy contributions and define solvation free energy arithmetic, which enable us to construct additive models to describe the solvation of complex compounds. The substituents analyzed in this study are carboxyl and nitro-groups due to their similar sterical requirements but distinct interactions with water. We find that nonadditive solvation free energy contributions are primarily attributed to electrostatics, which are qualitatively reproduced with computationally efficient continuum models. This suggests a promising route for the development of efficient and accurate models for the solvation of complex molecules with varying substitution patterns using solvation arithmetic.
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Affiliation(s)
- Aleksandar Lazaric
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Viren Pattni
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kaprao Fuegner
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| | - Arieh Ben-Naim
- Department of Physical Chemistry, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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10
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Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins 2023; 91:74-90. [PMID: 35964252 PMCID: PMC10087023 DOI: 10.1002/prot.26411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.
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Affiliation(s)
- Jas Kalayan
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arghya Chakravorty
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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11
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Wehrhan L, Leppkes J, Dimos N, Loll B, Koksch B, Keller BG. Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment. J Phys Chem B 2022; 126:9985-9999. [PMID: 36409613 DOI: 10.1021/acs.jpcb.2c05496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.
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Affiliation(s)
- Leon Wehrhan
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
| | - Jakob Leppkes
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Nicole Dimos
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
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12
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Waibl F, Kraml J, Fernández-Quintero ML, Loeffler JR, Liedl KR. Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. J Comput Aided Mol Des 2022; 36:101-116. [PMID: 35031880 PMCID: PMC8907097 DOI: 10.1007/s10822-021-00429-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 12/03/2022]
Abstract
Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent. One theory that has seen increased use is inhomogeneous solvation theory (IST). However, while many applications require accurate description of salt-water mixtures, no implementation of IST is currently able to estimate solvation properties involving more than one solvent species. Here, we present an extension to grid inhomogeneous solvation theory (GIST) that can take salt contributions into account. At the example of carbazole in 1 M NaCl solution, we compute the solvation energy as well as first and second order entropies. While the effect of the first order ion entropy is small, both the water-water and water-ion entropies contribute strongly. We show that the water-ion entropies are efficiently approximated using the Kirkwood superposition approximation. However, this approach cannot be applied to the water-water entropy. Furthermore, we test the quantitative validity of our method by computing salting-out coefficients and comparing them to experimental data. We find a good correlation to experimental salting-out constants, while the absolute values are overpredicted due to the approximate second order entropy. Since ions are frequently used in MD, either to neutralize the system or as a part of the investigated process, our method greatly extends the applicability of GIST. The use-cases range from biopharmaceuticals, where many assays require high salt concentrations, to environmental research, where solubility in sea water is important to model the fate of organic substances.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes Kraml
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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13
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Hajredini F, Ghose R. An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc. SCIENCE ADVANCES 2021; 7:eabj5836. [PMID: 34550748 PMCID: PMC8457666 DOI: 10.1126/sciadv.abj5836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BY-kinases constitute a protein tyrosine kinase family that encodes unique catalytic domains that deviate from those of eukaryotic kinases resembling P-loop nucleotide triphosphatases (NTPases) instead. We have used computational and supporting biochemical approaches using the catalytic domain of the Escherichia coli BY-kinase, Wzc, to illustrate mechanistic divergences between BY-kinases and NTPases despite their deployment of similar catalytic motifs. In NTPases, the “arginine finger” drives the reactive conformation of ATP while also displacing its solvation shell, thereby making favorable enthalpic and entropic contributions toward βγ-bond cleavage. In BY-kinases, the reactive state of ATP is enabled by ATP·Mg2+-induced global conformational transitions coupled to the conformation of the Walker-A lysine. While the BY-kinase arginine finger does promote the desolvation of ATP, it does so indirectly by generating an ordered active site in combination with other structural elements. Bacteria, using these mechanistic variations, have thus repurposed an ancient fold to phosphorylate on tyrosine.
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Affiliation(s)
- Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
- Corresponding author.
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14
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Samways ML, Taylor RD, Bruce Macdonald HE, Essex JW. Water molecules at protein-drug interfaces: computational prediction and analysis methods. Chem Soc Rev 2021; 50:9104-9120. [PMID: 34184009 DOI: 10.1039/d0cs00151a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The fundamental importance of water molecules at drug-protein interfaces is now widely recognised and a significant feature in structure-based drug design. Experimental methods for analysing the role of water in drug binding have many challenges, including the accurate location of bound water molecules in crystal structures, and problems in resolving specific water contributions to binding thermodynamics. Computational analyses of binding site water molecules provide an alternative, and in principle complete, structural and thermodynamic picture, and their use is now commonplace in the pharmaceutical industry. In this review, we describe the computational methodologies that are available and discuss their strengths and weaknesses. Additionally, we provide a critical analysis of the experimental data used to validate the methods, regarding the type and quality of experimental structural data. We also discuss some of the fundamental difficulties of each method and suggest directions for future study.
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Affiliation(s)
- Marley L Samways
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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15
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Fajardo TN, Heyden M. Dissecting the Conformational Free Energy of a Small Peptide in Solution. J Phys Chem B 2021; 125:4634-4644. [PMID: 33942611 DOI: 10.1021/acs.jpcb.1c00699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The free energy surface of a small peptide was analyzed based on an unbiased microsecond molecular dynamics simulation. The peptide sampled disordered conformational ensembles of distinct compactness, and its free energy was decomposed into separate contributions from the intramolecular potential energy, conformational entropy, and solvation free energy. The latter was further broken down into enthalpic and entropic contributions due to peptide-water and water-water interactions. This decomposition was enabled by a generalized linear response relation between the peptide-water interaction energy and the solvation free energy, which was empirically parametrized by explicit solvation free energy calculations for representative peptide conformations. This full dissection of the peptide free energy identifies individual contributions that stabilize and destabilize compact and extended peptide conformational ensembles and reveals the origin of a free energy barrier associated with transitions between them.
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Affiliation(s)
- Tawny N Fajardo
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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16
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Hüfner-Wulsdorf T, Klebe G. Mapping Water Thermodynamics on Drug Candidates via Molecular Building Blocks: a Strategy to Improve Ligand Design and Rationalize SAR. J Med Chem 2021; 64:4662-4676. [PMID: 33797902 DOI: 10.1021/acs.jmedchem.0c02115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The consideration of interactions involving water molecules in protein-ligand binding is widely appreciated in drug discovery nowadays. However, it is not ultimately clear how insights about these interactions translate into molecular design concepts. In this work, we introduce a computational strategy that, trained with high-precision experimental data, allows for the decomposition of water-related thermodynamic properties into chemically relevant building blocks (BBs) of a given ligand scaffold. For each of these BBs, a score based on solvation energy and entropy is computed, thus enabling the analysis of solvent-related affinity contributions for individual BBs. We find the nonvariable BB in a congeneric ligand pair to have a larger impact on the binding affinity than the variable part thus suggesting strong cooperative effects. Furthermore, we find enhanced solute-solvent interactions for a BB due to the presence of a C-F bond. Our investigation may be used to design drug molecules with tailored solvent thermodynamic properties.
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Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg 35037, Germany
| | - Gerhard Klebe
- Philipps Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg 35037, Germany
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17
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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18
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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 DOI: 10.1016/j.ejmech.2020.112771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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.
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19
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Olson B, Cruz A, Chen L, Ghattas M, Ji Y, Huang K, Ayoub S, Luchko T, McKay DJ, Kurtzman T. An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. J Comput Aided Mol Des 2020; 34:1219-1228. [PMID: 32918236 PMCID: PMC7486166 DOI: 10.1007/s10822-020-00341-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid inhomogeneous solvation theory maps were generated using AmberTools cpptraj-GIST, 3D reference interaction site model maps were created with AmberTools rism3d.snglpnt and hydration site analysis maps were created using SSTMap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
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Affiliation(s)
- Brian Olson
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
- Department of Biology and Chemistry, County College of Morris, 214 Center Grove Rd, Randolph, NJ, 07869, USA
| | - Anthony Cruz
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Lieyang Chen
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Mossa Ghattas
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Yeonji Ji
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Kunhui Huang
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Steven Ayoub
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, 91330, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, Center for Biological Physics, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, 91330, USA
| | - Daniel J McKay
- Ventus Therapeutics, Frederick-Banting, Montreal, QC, H9S 2A1, Canada
| | - Tom Kurtzman
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
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20
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Matricon P, Suresh RR, Gao ZG, Panel N, Jacobson KA, Carlsson J. Ligand design by targeting a binding site water. Chem Sci 2020; 12:960-968. [PMID: 34163862 PMCID: PMC8179138 DOI: 10.1039/d0sc04938g] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design. Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.![]()
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Affiliation(s)
- Pierre Matricon
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Nicolas Panel
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
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21
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Hassaan E, Hohn C, Ehrmann FR, Goetzke FW, Movsisyan L, Hüfner-Wulsdorf T, Sebastiani M, Härtsch A, Reuter K, Diederich F, Klebe G. Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT. J Med Chem 2020; 63:6802-6820. [PMID: 32515955 DOI: 10.1021/acs.jmedchem.0c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1-recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1-recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Frederik R Ehrmann
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - F Wieland Goetzke
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Levon Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tobias Hüfner-Wulsdorf
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Maurice Sebastiani
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Klaus Reuter
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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22
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Evans R, Hovan L, Tribello GA, Cossins BP, Estarellas C, Gervasio FL. Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies. J Chem Theory Comput 2020; 16:4641-4654. [PMID: 32427471 PMCID: PMC7467642 DOI: 10.1021/acs.jctc.0c00075] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on 18 chemically diverse ligands with a wide range of different binding affinities to a complex target; namely, human soluble epoxide hydrolase. The results suggest that metadynamics with a funnel-shaped restraint can be used to calculate, in a computationally affordable and relatively accurate way, the absolute binding free energy for small fragments. When used in combination with an optimal pathlike variable obtained using machine learning or with the Hamiltonian replica-exchange algorithm SWISH, this method can achieve reasonably accurate results for increasingly complex ligands, with a good balance of computational cost and speed. An additional benefit of using the combination of metadynamics and SWISH is that it also provides useful information about the role of water in the binding mechanism.
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Affiliation(s)
| | | | - Gareth A Tribello
- Atomistic Simulation Centre, Queen's University, Belfast BT7 1NN, United Kingdom
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23
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Olson B, Cruz A, Chen L, Ghattas M, Ji Y, Huang K, McKay DJ, Kurtzman T. An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.12275705.v1. [PMID: 32511289 PMCID: PMC7263766 DOI: 10.26434/chemrxiv.12275705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid Inhomogeneous Solvation Theory maps were generated using AmberTools cpptraj-GIST and Hydration Site Analysis maps were created using SSTmap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
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Affiliation(s)
- Brian Olson
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
- County College of Morris, Department of Biology and Chemistry, 214 Center Grove Rd, Randolph, NJ, United States of America, 07869
| | - Anthony Cruz
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Lieyang Chen
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Mossa Ghattas
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Yeonji Ji
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Kunhui Huang
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Daniel J McKay
- Ventus Therapeutics, 7150 Frederick-Banting Montreal, Quebec H9S 2A1
| | - Tom Kurtzman
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
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24
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Hüfner-Wulsdorf T, Klebe G. Role of Water Molecules in Protein–Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics. J Chem Inf Model 2020; 60:1818-1832. [DOI: 10.1021/acs.jcim.0c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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
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25
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Mitusińska K, Raczyńska A, Bzówka M, Bagrowska W, Góra A. Applications of water molecules for analysis of macromolecule properties. Comput Struct Biotechnol J 2020; 18:355-365. [PMID: 32123557 PMCID: PMC7036622 DOI: 10.1016/j.csbj.2020.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/26/2020] [Accepted: 02/01/2020] [Indexed: 01/12/2023] Open
Abstract
Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly via a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties. Here, we present a list of several software programs that use the information provided by water molecules to: i) analyse protein structures and provide the optimal positions of water molecules for protein hydration, ii) identify high-occupancy water sites in order to analyse ligand binding modes, and iii) detect and describe tunnels and cavities. The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on the functionality, transportation network and location of functionally relevant residues. Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.
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Affiliation(s)
| | | | | | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
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26
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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
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27
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Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. PLoS One 2019; 14:e0219473. [PMID: 31291328 PMCID: PMC6619770 DOI: 10.1371/journal.pone.0219473] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/25/2022] Open
Abstract
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site.
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Affiliation(s)
- Crystal Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | | | - Andriy Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - David A. Case
- Department of Chemistry, Lehman College, The City University of New York, Bronx, New York, United States of America
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tom Kurtzman
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Northridge, California, United States of America
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28
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Verteramo ML, Stenström O, Ignjatović MM, Caldararu O, Olsson MA, Manzoni F, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. J Am Chem Soc 2019; 141:2012-2026. [PMID: 30618244 DOI: 10.1021/jacs.8b11099] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Entropic contributions to the free energy of binding are particularly difficult to assess in this regard. Here we pinpoint the molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and molecular dynamics simulations followed by conformational entropy and grid inhomogeneous solvation theory (GIST) analyses. Using a pair of diastereomeric ligands that have essentially identical chemical potential in the unbound state, we reduced the problem of dissecting the thermodynamics to a comparison of the two protein-ligand complexes. While the free energies of binding are nearly equal for the R and S diastereomers, greater differences are observed for the enthalpy and entropy, which consequently exhibit compensatory behavior, ΔΔ H°(R - S) = -5 ± 1 kJ/mol and - TΔΔ S°(R - S) = 3 ± 1 kJ/mol. NMR relaxation experiments and molecular dynamics simulations indicate that the protein in complex with the S-stereoisomer has greater conformational entropy than in the R-complex. GIST calculations reveal additional, but smaller, contributions from solvation entropy, again in favor of the S-complex. Thus, conformational entropy apparently dominates over solvation entropy in dictating the difference in the overall entropy of binding. This case highlights an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.
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Affiliation(s)
- Maria Luisa Verteramo
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Olof Stenström
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | | | - Octav Caldararu
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Martin A Olsson
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Francesco Manzoni
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Laboratory Medicine , Lund University , 221 00 Lund , Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC , 225 92 Lund , Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf Ryde
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
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29
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Bruce Macdonald HE, Cave-Ayland C, Ross GA, Essex JW. Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations. J Chem Theory Comput 2018; 14:6586-6597. [PMID: 30451501 PMCID: PMC6293443 DOI: 10.1021/acs.jctc.8b00614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Computational methods
to calculate ligand binding affinities are
increasing in popularity, due to improvements in simulation algorithms,
computational resources, and easy-to-use software. However, issues
can arise in relative ligand binding free energy simulations if the
ligands considered have different active site water networks, as simulations
are typically performed with a predetermined number of water molecules
(fixed N ensembles) in preassigned locations. If an alchemical perturbation
is attempted where the change should result in a different active
site water network, the water molecules may not be able to adapt appropriately
within the time scales of the simulations—particularly if the
active site is occluded. By combining the grand canonical ensemble
(μVT) to sample active site water molecules, with conventional
alchemical free energy methods, the water network is able to dynamically
adapt to the changing ligand. We refer to this approach as grand canonical
alchemical perturbation (GCAP). In this work we demonstrate GCAP for
two systems; Scytalone Dehydratase (SD) and Adenosine A2A receptor. For both systems, GCAP is shown to perform
well at reproducing experimental binding affinities. Calculating the
relative binding affinities with a naïve, conventional
attempt to solvate the active site illustrates how poor results can
be if proper consideration of water molecules in occluded pockets
is neglected. GCAP results are shown to be consistent with time-consuming
double decoupling simulations. In addition, by obtaining the free
energy surface for ligand perturbations, as a function of both the
free energy coupling parameter and water chemical potential, it is
possible to directly deconvolute the binding energetics in terms of
protein–ligand direct interactions and protein binding site
hydration.
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Affiliation(s)
| | | | - Gregory A Ross
- Computational and Systems Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , New York, New York 10065 , United States
| | - Jonathan W Essex
- School of Chemistry , University of Southampton , Southampton , SO17 1BJ , U.K
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30
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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