1
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Roe DR, Brooks BR. MPI-parallelization of the grid inhomogeneous solvation theory calculation. J Comput Chem 2024; 45:633-637. [PMID: 38071482 PMCID: PMC10922152 DOI: 10.1002/jcc.27278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 03/02/2024]
Abstract
The grid inhomogeneous solvation theory (GIST) method requires the often time-consuming calculation of water-water and water-solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP, GPUs, and particle mesh Ewald. This article details how the speed of this calculation can be increased by parallelizing it with MPI, where trajectory frames are divided among multiple processors. This requires very little communication between individual processes during trajectory processing, meaning the calculation scales well to large processor counts. This article also details how the entropy calculation, which must happen after trajectory processing since it requires information from all trajectory frames, is parallelized via MPI. This parallelized GIST method has been implemented in the freely-available CPPTRAJ analysis software.
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Affiliation(s)
- Daniel R. Roe
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
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2
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Fischer AL, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibl F, Quoika PK, Gschwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics. J Chem Theory Comput 2024; 20:2321-2333. [PMID: 38373307 PMCID: PMC10938642 DOI: 10.1021/acs.jctc.3c01106] [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: 10/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
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Affiliation(s)
- Anna-Lena
M. Fischer
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Anna Tichy
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Robert F. Wild
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Patrick K. Quoika
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | | | - Stefano Forli
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Andrew B. Ward
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Klaus R. Liedl
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Martin Zacharias
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | - Monica L. Fernández-Quintero
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
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3
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Ji J, Carpentier B, Chakraborty A, Nangia S. An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale. J Chem Theory Comput 2024; 20:1656-1672. [PMID: 37018141 PMCID: PMC10902853 DOI: 10.1021/acs.jctc.3c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Indexed: 04/06/2023]
Abstract
The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Arindam Chakraborty
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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4
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Zhong H, Wang X, Chen S, Wang Z, Wang H, Xu L, Hou T, Yao X, Li D, Pan P. Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. J Med Chem 2024; 67:138-151. [PMID: 38153295 DOI: 10.1021/acs.jmedchem.3c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Androgen receptor (AR) is the primary target for treating prostate cancer (PCa), which inevitably progresses due to drug-resistant mutations. Bromodomain-containing protein 4 (BRD4) has been a new potential drug target for PCa treatment. Herein, we report the rational design and discovery of novel BRD4 inhibitors through computer-aided drug design (CADD), and a hit compound SQ-1 (IC50 = 676 nM) was identified by structure-based virtual screening (SBVS) with the conserved water network. To optimize the structure of SQ-1, the free energy landscape was constructed, and the binding mechanism was explored by characterizing the water profile and the dissociation mechanism. Finally, the compound SQ-17 with improved inhibitory activity (IC50 < 100 nM) was discovered, which showed potent antiproliferative activity against LNCaP. These data highlighted a successful attempt to identify and optimize a small molecule by comprehensive CADD application and provided essential clues for developing novel therapeutics for PCa treatment.
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Affiliation(s)
- Haiyang Zhong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinyue Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shicheng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huating Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaojun Yao
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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5
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Hoerschinger V, Waibl F, Pomarici ND, Loeffler JR, Deane CM, Georges G, Kettenberger H, Fernández-Quintero ML, Liedl KR. PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. J Chem Inf Model 2023; 63:6964-6971. [PMID: 37934909 PMCID: PMC10685443 DOI: 10.1021/acs.jcim.3c01490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023]
Abstract
The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface in terms of surface patches, denoting separated areas of the surface with a common physical property. We highlight its applicability to elucidate protease substrate specificity and antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.
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Affiliation(s)
- Valentin
J. Hoerschinger
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Nancy D. Pomarici
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Guy Georges
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg 82377, Germany
| | - Hubert Kettenberger
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg 82377, Germany
| | - Monica L. Fernández-Quintero
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, 6020 Innsbruck, Austria
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6
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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7
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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8
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Bulavko ES, Pak MA, Ivankov DN. In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein. Biomolecules 2023; 13:1269. [PMID: 37627334 PMCID: PMC10452222 DOI: 10.3390/biom13081269] [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: 07/10/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.
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Affiliation(s)
| | | | - Dmitry N. Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 121205, Russia
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9
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Wu R, Metternich JB, Kamenik AS, Tiwari P, Harrison JA, Kessen D, Akay H, Benzenberg LR, Chan TWD, Riniker S, Zenobi R. Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data. Nat Commun 2023; 14:2913. [PMID: 37217470 PMCID: PMC10203302 DOI: 10.1038/s41467-023-38463-z] [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: 10/26/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Mass spectrometry is a powerful technique for the structural and functional characterization of biomolecules. However, it remains challenging to accurately gauge the gas-phase structure of biomolecular ions and assess to what extent native-like structures are maintained. Here we propose a synergistic approach which utilizes Förster resonance energy transfer and two types of ion mobility spectrometry (i.e., traveling wave and differential) to provide multiple constraints (i.e., shape and intramolecular distance) for structure-refinement of gas-phase ions. We add microsolvation calculations to assess the interaction sites and energies between the biomolecular ions and gaseous additives. This combined strategy is employed to distinguish conformers and understand the gas-phase structures of two isomeric α-helical peptides that might differ in helicity. Our work allows more stringent structural characterization of biologically relevant molecules (e.g., peptide drugs) and large biomolecular ions than using only a single structural methodology in the gas phase.
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Affiliation(s)
- Ri Wu
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Jonas B Metternich
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Anna S Kamenik
- Laboratorium für Physikalische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Prince Tiwari
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
- Laboratory of Atmospheric Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Julian A Harrison
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Dennis Kessen
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
- University of Münster, MEET Battery Research Center, Corrensstrasse 46, 48149, Münster, Germany
| | - Hasan Akay
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Lukas R Benzenberg
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland.
| | - Renato Zenobi
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland.
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10
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Shi J, Cho JH, Hwang W. Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding. J Chem Theory Comput 2023; 19:1875-1887. [PMID: 36820489 PMCID: PMC10848206 DOI: 10.1021/acs.jctc.2c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 02/24/2023]
Abstract
Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.
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Affiliation(s)
- Jie Shi
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 777843, United States
| | - Jae-Hyun Cho
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
| | - Wonmuk Hwang
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843, United States
- Department
of Physics and Astronomy, Texas A&M
University, College Station, Texas 77843, United States
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11
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Sarkar S, Gupta VK, Sharma S, Shen T, Gupta V, Mirzaei M, Graham SL, Chitranshi N. Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene. J Biomol Struct Dyn 2023; 41:1458-1478. [PMID: 34971346 DOI: 10.1080/07391102.2021.2021991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alterations in the nuclear retinoid X receptor (RXRs) signalling have been implicated in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, stroke, multiple sclerosis and glaucoma. Single nucleotide polymorphisms (SNPs) are the main cause underlying single nucleic acid variations which in turn determine heterogeneity within various populations. These genetic polymorphisms have been suggested to associate with various degenerative disorders in population-wide analysis. This bioinformatics study was designed to investigate, search, retrieve and identify deleterious SNPs which may affect the structure and function of various RXR isoforms through a computational and molecular modelling approach. Amongst the 1,813 retrieved SNPs several were found to be deleterious with rs140464195_G139R, rs368400425_R358W and rs368586400_L383F RXRα mutant variants being the most detrimental ones causing changes in the interatomic interactions and decreasing the flexibility of the mutant proteins. Molecular genetics analysis identified seven missense mutations in RXRα/β/γ isoforms. Two novel mutations SNP IDs (rs1588299621 and rs1057519958) were identified in RXRα isoform. We used several in silico prediction tools such as SIFT, PolyPhen, I-Mutant, Protein Variation Effect Analyzer (PROVEAN), PANTHER, SNP&Go, PhD-SNP and SNPeffect to predict pathogenicity and protein stability associated with RXR mutations. The structural assessment by DynaMut tool revealed that hydrogen bonds were affected along with hydrophobic and carbonyl interactions resulting in reduced flexibility at the mutated residue positions but ultimately stabilizing the molecule as a whole. Summarizing, analysis of the missense mutations in RXR isoforms showed a mix of conclusive and inconclusive genotype-phenotype correlations suggesting the use of sophisticated computational analysis tools for studying RXR variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumalya Sarkar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Vivek K Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Samridhi Sharma
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Ting Shen
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Melbourne, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
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12
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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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13
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Ebrahim HY, Mady MS, Atya HB, Ali SA, Elsayed HE, Moharram FA. Melaleuca rugulosa (Link) Craven Tannins: Appraisal of anti-inflammatory, radical scavenging activities, and molecular modeling studies. JOURNAL OF ETHNOPHARMACOLOGY 2022; 298:115596. [PMID: 35987414 DOI: 10.1016/j.jep.2022.115596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Genus Melaleuca or tea tree species are well known to be an important source of biological active oils and extracts. The biological significance appears in their usage for treatment of several clinical disorder owing to their traditional uses as anti-inflammatory, antibacterial, antifungal, and cytotoxic activities. AIM OF THE STUDY Our study aimed to investigate the metabolic profile of the M. rugulosa polyphenol-rich fraction along with determination of its anti-inflammatory potential, free radical scavenging and antiaging activities supported with virtual understanding of the mode of action using molecular modeling strategy. MATERIALS AND METHODS The anti-inflammatory activity of the phenolic rich fraction was investigated through measuring its inhibitory activity against inflammatory mediators viz tumor necrosing factor receptor-2 (TNF-α) and cyclooxygenases 1/2 (COX-1/2) in a cell free and cell-based assays. Moreover, the radical scavenging activity was determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH), oxygen radical absorbance capacity (ORAC) and β-carotene assays, while the antiaging activity in anti-elastase, anti-collagenase, and anti-tyrosinase inhibitory assays. Finally, the biological findings were supported with molecular docking study using MOE software. RESULTS The chromatographic purification of the polyphenol-rich fraction of Melaleuca rugulosa (Link) Craven afforded fourteen phytoconstituents (1-14). The anti-inflammatory gauging experiments demonstrated inhibition of inflammatory-linked enzymes COX-1/2 and the TNF-α at low μg/mL levels in the enzyme-based assays. Further investigation of the underlying mechanism was inferred from the quantification of protein levels and gene expression in the lipopolysaccharide (LPS)-activated murine macrophages (RAW264.7) in vitro model. The results revealed the reduction of protein synthesis of COX-1/2 and TNF-α with the down regulation of gene expression. The cell free in vitro radical scavenging assessment of the polyphenol-rich fraction revealed a significant DPPH reduction, peroxyl radicals scavenging, and β-carotene peroxidation inhibition. Besides, the polyphenol-rich fraction showed a considerable inhibition of the skin aging-related enzymes as elastase, collagenase, and tyrosinase. Ultimately, the computational molecular modelling studies uncovered the potential binding poses and relevant molecular interactions of the identified polyphenols with their targeted enzymes. Particularly, terflavin C (8) which showed a favorable binding pose at the elastase binding pocket, while rosmarinic acid (14) demonstrated the best binding pose at the COX-2 catalytic domain. In short, natural polyphenols are potential candidates for the management of free radicals, inflammation, and skin aging related conditions. CONCLUSION Natural polyphenols are potential candidates for the management of free radicals, inflammation, and skin aging related conditions.
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Affiliation(s)
- Hassan Y Ebrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University. Ein Helwan, Cairo, 11795, Egypt.
| | - Mohamed S Mady
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University. Ein Helwan, Cairo, 11795, Egypt.
| | - Hanaa B Atya
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Ein-Helwan, Helwan, Cairo, 11795, Egypt.
| | - Sahar A Ali
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Ein-Helwan, Helwan, Cairo, 11795, Egypt.
| | - Heba E Elsayed
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University. Ein Helwan, Cairo, 11795, Egypt.
| | - Fatma A Moharram
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University. Ein Helwan, Cairo, 11795, Egypt.
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14
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Waibl F, Kraml J, Hoerschinger VJ, Hofer F, Kamenik AS, Fernández-Quintero ML, Liedl KR. Grid inhomogeneous solvation theory for cross-solvation in rigid solvents. J Chem Phys 2022; 156:204101. [PMID: 35649837 DOI: 10.1063/5.0087549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information to enhance structure-based binding predictions. We have recently extended GIST toward chloroform as a solvent to allow the prediction of passive membrane permeability. Here, we further generalize the GIST algorithm toward all solvents that can be modeled as rigid molecules. This restriction is inherent to the method and is already present in the inhomogeneous solvation theory. Here, we show that our approach can be applied to various solvent molecules by comparing the results of GIST simulations with thermodynamic integration (TI) calculations and experimental results. Additionally, we analyze and compare a matrix consisting of 100 entries of ten different solvent molecules solvated within each other. We find that the GIST results are highly correlated with TI calculations as well as experiments. For some solvents, we find Pearson correlations of up to 0.99 to the true entropy, while others are affected by the first-order approximation more strongly. The enthalpy-entropy splitting provided by GIST allows us to extend a recently published approach, which estimates higher order entropies by a linear scaling of the first-order entropy, to solvents other than water. Furthermore, we investigate the convergence of GIST in different solvents. We conclude that our extension to GIST reliably calculates localized thermodynamic properties for different solvents and thereby significantly extends the applicability of this widely used method.
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Affiliation(s)
- Franz Waibl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Johannes Kraml
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Valentin J Hoerschinger
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Florian Hofer
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Anna S Kamenik
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
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15
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Engineering surface amphiphilicity of polymer nanostructures. Prog Polym Sci 2022. [DOI: 10.1016/j.progpolymsci.2021.101489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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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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17
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Maksudov F, Daraei A, Sesha A, Marx KA, Guthold M, Barsegov V. Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves. Acta Biomater 2021; 136:327-342. [PMID: 34606991 PMCID: PMC8627496 DOI: 10.1016/j.actbio.2021.09.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/31/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
Structural mechanisms underlying the mechanical properties of fibrin fibers are elusive. We combined tensile testing of uncrosslinked fibrin polymers in vitro and in silico to explore their material properties. The experimental stress (σ) - strain (ε) curves for fibrin fibers are characterized by elastic deformations with a weaker elastic response for ε<160% due to unraveling of αC tethers and straightening of fibrin protofibrils, and a stronger response for ε>160% owing to unfolding of the coiled coils and γ nodules in fibrin monomers. Fiber rupture for strains ε>212% is due to dissociation of the knob-hole bonds and rupture of D:D interfaces. We developed the Fluctuating Bilinear Spring model to interpret the σ-ε profiles in terms of the free energy for protofibril alignment ΔG0 = 10.1-11.5 kBT, Young's moduli for protofibril alignment Yu = 1.9-3.2 MPa and stretching Ya = 5.7-9.7 MPa, strain scale ε˜≈ 12-40% for fiber rupture, and protofibril cooperativity m= 3.6-8. We applied the model to characterize the fiber strength σcr≈ 12-13 MPa, deformability εcr≈ 222%, and rupture toughness U≈ 9 MJ/m3, and to resolve thermodynamic state functions, 96.9 GJ/mol entropy change for protofibril alignment (at room temperature) and 113.6 GJ/mol enthalpy change for protofibril stretching, which add up to 210.5 GJ/mol free-energy change. Fiber elongation is associated with protofibril dehydration and sliding mechanism to create an ordered protofibril array. Fibrin fibers behave like a hydrogel; protofibril dehydration and water expulsion account for ∼94-98% of the total free-energy changes for fiber elongation and rupture. STATEMENT OF SIGNIFICANCE: Structural mechanisms underlying the mechanical properties of fibrin fibers, major components of blood clots and obstructive thrombi, are elusive. We performed tensile testing of uncrosslinked fibrin polymers in vitro and in silico to explore their material properties. Fluctuating Bilinear Spring theory was developed to interpret the stress-strain profiles in terms of the energy for protofibril alignment, elastic moduli for protofibril alignment and stretching, and strain scale for fiber rupture, and to probe the limits of fiber strength, extensibility and toughness. Fibrin fibers behave like a hydrogel. Fiber elongation is defined by the protofibril dehydration and sliding. Structural rearrangements in water matrix control fiber elasticity. These results contribute to fundamental understanding of blood clot breakage that underlies thrombotic embolization.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Ali Daraei
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States
| | - Anuj Sesha
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States.
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18
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de O Araújo J, Pinheiro S, Zamora WJ, Alves CN, Lameira J, Lima AH. Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9). Sci Rep 2021; 11:23003. [PMID: 34837010 PMCID: PMC8626507 DOI: 10.1038/s41598-021-02366-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. Besides, clustering results for the native dimer showed accessible cavities to drugs. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Jéssica de O Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Silvana Pinheiro
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - William J Zamora
- School of Chemistry & Faculty of Pharmacy, University of Costa Rica, San Pedro, San José, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT-CONARE), Pavas, San José, Costa Rica
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, 66075-110, Belém, Pará, Brasil.
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19
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Anisimov YA, Evitts RW, Cree DE, Wilson LD. Polyaniline/Biopolymer Composite Systems for Humidity Sensor Applications: A Review. Polymers (Basel) 2021; 13:2722. [PMID: 34451261 PMCID: PMC8400915 DOI: 10.3390/polym13162722] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/08/2021] [Indexed: 11/18/2022] Open
Abstract
The development of polyaniline (PANI)/biomaterial composites as humidity sensor materials represents an emerging area of advanced materials with promising applications. The increasing attention to biopolymer materials as desiccants for humidity sensor components can be explained by their sustainability and propensity to absorb water. This review represents a literature survey, covering the last decade, which is focused on the interrelationship between the core properties and moisture responsiveness of multicomponent polymer/biomaterial composites. This contribution provides an overview of humidity-sensing materials and the corresponding sensors that emphasize the resistive (impedance) type of PANI devices. The key physicochemical properties that affect moisture sensitivity include the following: swelling, water vapor adsorption capacity, porosity, electrical conductivity, and enthalpies of adsorption and vaporization. Some key features of humidity-sensing materials involve the response time, recovery time, and hysteresis error. This work presents a discussion on various types of humidity-responsive composite materials that contain PANI and biopolymers, such as cellulose, chitosan and structurally related systems, along with a brief overview of carbonaceous and ceramic materials. The effect of additive components, such as polyvinyl alcohol (PVA), for film fabrication and their adsorption properties are also discussed. The mechanisms of hydration and proton transfer, as well as the relationship with conductivity is discussed. The literature survey on hydration reveals that the textural properties (surface area and pore structure) of a material, along with the hydrophile-lipophile balance (HLB) play a crucial role. The role of HLB is important in PANI/biopolymer materials for understanding hydration phenomena and hydrophobic effects. Fundamental aspects of hydration studies that are relevant to humidity sensor materials are reviewed. The experimental design of humidity sensor materials is described, and their relevant physicochemical characterization methods are covered, along with some perspectives on future directions in research on PANI-based humidity sensors.
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Affiliation(s)
- Yuriy A. Anisimov
- Department of Chemistry, University of Saskatchewan, 110 Science Place (Room 156 Thorvaldson Building), Saskatoon, SK S7N 5C9, Canada;
| | - Richard W. Evitts
- Department of Chemical and Biological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada;
| | - Duncan E. Cree
- Department of Mechanical Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada
| | - Lee D. Wilson
- Department of Chemistry, University of Saskatchewan, 110 Science Place (Room 156 Thorvaldson Building), Saskatoon, SK S7N 5C9, Canada;
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20
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Sánchez-Morán H, Weltz JS, Schwartz DK, Kaar JL. Understanding Design Rules for Optimizing the Interface between Immobilized Enzymes and Random Copolymer Brushes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26694-26703. [PMID: 34081428 DOI: 10.1021/acsami.1c02443] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A long-standing goal in the field of biotechnology is to develop and understand design rules for the stabilization of enzymes upon immobilization to materials. While immobilization has sometimes been successful as a strategy to stabilize enzymes, the design of synthetic materials that stabilize enzymes remains largely empirical. We sought to overcome this challenge by investigating the mechanistic basis for the stabilization of immobilized lipases on random copolymer brush surfaces comprised of poly(ethylene glycol) methacrylate (PEGMA) and sulfobetaine methacrylate (SBMA), which represent novel heterogeneous supports for immobilized enzymes. Using several related but structurally diverse lipases, including Bacillus subtilis lipase A (LipA), Rhizomucor miehei lipase, Candida rugosa lipase, and Candida antarctica lipase B (CALB), we showed that the stability of each lipase at elevated temperatures was strongly dependent on the fraction of PEGMA in the brush layer. This dependence was explained by developing and applying a new algorithm to quantify protein surface hydrophobicity, which involved using unsupervised cluster analysis to identify clusters of hydrophobic atoms. Characterization of the lipases showed that the optimal brush composition correlated with the free energy of solvation per enzyme surface area, which ranged from -17.1 kJ/mol·nm2 for LipA to -11.8 kJ/mol·nm2 for CALB. Additionally, using this algorithm, we found that hydrophobic patches consisting of aliphatic residues had a higher free energy than patches consisting of aromatic residues. By providing the basis for rationally tuning the interface between enzymes and materials, this understanding will transform the use of materials to reliably ruggedize enzymes under extreme conditions.
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Affiliation(s)
- Héctor Sánchez-Morán
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - James S Weltz
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
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21
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Chen L, Cruz A, Roe DR, Simmonett AC, Wickstrom L, Deng N, Kurtzman T. Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory. J Chem Theory Comput 2021; 17:2714-2724. [PMID: 33830762 DOI: 10.1021/acs.jctc.0c01185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range nonbonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME)-based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields potential energy calculations that are precisely consistent with modern simulation engines and performs these calculations at a dramatically faster speed than prior implementations. Here, we apply PME-GIST end-state analyses to 32 small molecules whose solvation free energies are close to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy contribution from the second and higher order entropy terms that are truncated in GIST by the differences between entropies calculated in TI and GIST. With a simple correction for the high order entropy terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2 = 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood based on perturbations of the solvent in a region extending a few solvation shells from the solute. We have integrated PME-GIST into the open-source molecular dynamics analysis software CPPTRAJ.
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Affiliation(s)
- Lieyang Chen
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
| | - Anthony Cruz
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
| | - Daniel R Roe
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Lauren Wickstrom
- Department of Science, Borough of Manhattan Community College, The City University of New York, New York, New York 10007, United States
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, New York 10038, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
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22
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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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23
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Quantum Chemical Microsolvation by Automated Water Placement. Molecules 2021; 26:molecules26061793. [PMID: 33806731 PMCID: PMC8005176 DOI: 10.3390/molecules26061793] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). This protocol enabled us to rigorously define the number, position, and orientation of individual solvent molecules and to determine their interaction with the solute based on physical quantities. The generated solute-solvent clusters served as an input for subsequent quantum chemical investigations. We showcased the applicability, scope, and limitations of this computational approach for a number of small molecules, including urea, 2-aminobenzothiazole, (+)-syn-benzotriborneol, benzoic acid, and helicene. Our results show excellent agreement with the available ab initio molecular dynamics data and experimental results.
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24
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de Izarra A, Choi C, Jang YH, Lansac Y. Ionic Liquid for PEDOT:PSS Treatment. Ion Binding Free Energy in Water Revealing the Importance of Anion Hydrophobicity. J Phys Chem B 2021; 125:1916-1923. [DOI: 10.1021/acs.jpcb.0c10068] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ambroise de Izarra
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Changwon Choi
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Yves Lansac
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay, 91405 Orsay, France
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25
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Roldan-Cruz C, Garcia-Hernandez A, Alvarez-Ramirez J, Vernon-Carter E. Effect of the stirring speed in the in vitro activity of α-amylase. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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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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27
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Carretas-Valdez MI, Moreno-Cordova EN, Ibarra-Hernandez BG, Cinco-Moroyoqui FJ, Castillo-Yañez FJ, Casas-Flores S, Osuna-Amarillas PS, Islas-Osuna MA, Arvizu-Flores AA. Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant. Int J Biol Macromol 2020; 164:2701-2710. [PMID: 32827617 DOI: 10.1016/j.ijbiomac.2020.08.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.
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Affiliation(s)
- Manuel I Carretas-Valdez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Elena N Moreno-Cordova
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Brisa G Ibarra-Hernandez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Cinco-Moroyoqui
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Castillo-Yañez
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, Col. Lomas 4a sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Pablo S Osuna-Amarillas
- Universidad Estatal de Sonora, Carretera Navojoa-Huatabampo km 5, Navojoa, Sonora 85874, Mexico
| | - Maria A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, Laboratorio de Genética y Biología Molecular de Plantas, Carr. Gustavo Enrique Astiazarán Rosas, N0. 46. Col. La Victoria, Hermosillo, Sonora 83304, Mexico.
| | - Aldo A Arvizu-Flores
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico.
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28
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Biler M, Crean RM, Schweiger AK, Kourist R, Kamerlin SCL. Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. J Am Chem Soc 2020; 142:20216-20231. [PMID: 33180505 PMCID: PMC7735706 DOI: 10.1021/jacs.0c10701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity, and selectivity of this enzyme are only poorly understood to date, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the nonconverted or poorly converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering.
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Affiliation(s)
- Michal Biler
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Rory M. Crean
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Anna K. Schweiger
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
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29
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Waibl F, Fernández-Quintero ML, Kamenik AS, Kraml J, Hofer F, Kettenberger H, Georges G, Liedl KR. Conformational Ensembles of Antibodies Determine Their Hydrophobicity. Biophys J 2020; 120:143-157. [PMID: 33220303 PMCID: PMC7820740 DOI: 10.1016/j.bpj.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids. However, those scales cannot describe the nonadditive effects of a residue’s surrounding on its hydrophobicity. Therefore, they are inherently limited in their ability to describe the impact of subtle differences in molecular structure on the overall hydrophobicity. Here, we introduce a physics-based approach to describe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (GIST). We apply this method to assess the effects of starting structures, conformational sampling, and protonation states on the hydrophobicity of antibodies. Our results reveal that high-quality starting structures, i.e., crystal structures, are crucial for the prediction of hydrophobicity and that conformational sampling can compensate errors introduced by the starting structure. On the other hand, sampling of protonation states only leads to good results when combined with high-quality structures, whereas it can even be detrimental otherwise. We conclude by pointing out that a single static homology model may not be adequate for predicting hydrophobicity.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Anna S Kamenik
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Florian Hofer
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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30
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Kraml J, Hofer F, Kamenik AS, Waibl F, Kahler U, Schauperl M, Liedl KR. Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. J Chem Inf Model 2020; 60:3843-3853. [PMID: 32639731 PMCID: PMC7460078 DOI: 10.1021/acs.jcim.0c00289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 11/28/2022]
Abstract
Reliable information on partition coefficients plays a key role in drug development, as solubility decisively affects bioavailability. In a physicochemical context, the partition coefficient of a solute between two different solvents can be described as a function of solvation free energies. Hence, substantial scientific efforts have been made toward accurate predictions of solvation free energies in various solvents. The grid inhomogeneous solvation theory (GIST) facilitates the calculation of solvation free energies. In this study, we introduce an extended version of the GIST algorithm, which enables the calculation for chloroform in addition to water. Furthermore, GIST allows localization of enthalpic and entropic contributions. We test our approach by calculating partition coefficients between water and chloroform for a set of eight small molecules. We report a Pearson correlation coefficient of 0.96 between experimentally determined and calculated partition coefficients. The capability to reliably predict partition coefficients between water and chloroform and the possibility to localize their contributions allow the optimization of a compound's partition coefficient. Therefore, we presume that this methodology will be of great benefit for the efficient development of pharmaceuticals.
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Affiliation(s)
- Johannes Kraml
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Ursula Kahler
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and
Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80−82, A-6020 Innsbruck, Austria
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31
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Kahler U, Kamenik AS, Waibl F, Kraml J, Liedl KR. Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin. Biophys J 2020; 119:652-666. [PMID: 32697976 PMCID: PMC7399559 DOI: 10.1016/j.bpj.2020.06.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/16/2020] [Accepted: 06/29/2020] [Indexed: 11/04/2022] Open
Abstract
Biomolecular recognition between proteins follows complex mechanisms, the understanding of which can substantially advance drug discovery efforts. Here, we track each step of the binding process in atomistic detail with molecular dynamics simulations using trypsin and its inhibitor bovine pancreatic trypsin inhibitor (BPTI) as a model system. We use umbrella sampling to cover a range of unbinding pathways. Starting from these simulations, we subsequently seed classical simulations at different stages of the process and combine them to a Markov state model. We clearly identify three kinetically separated states (an unbound state, an encounter state, and the final complex) and describe the mechanisms that dominate the binding process. From our model, we propose the following sequence of events. The initial formation of the encounter complex is driven by long-range interactions because opposite charges in trypsin and BPTI draw them together. The encounter complex features the prealigned binding partners with binding sites still partially surrounded by solvation shells. Further approaching leads to desolvation and increases the importance of van der Waals interactions. The native binding pose is adopted by maximizing short-range interactions. Thereby side-chain rearrangements ensure optimal shape complementarity. In particular, BPTI’s P1 residue adapts to the S1 pocket and prime site residues reorient to optimize interactions. After the paradigm of conformation selection, binding-competent conformations of BPTI and trypsin are already present in the apo ensembles and their probabilities increase during this proposed two-step association process. This detailed characterization of the molecular forces driving the binding process includes numerous aspects that have been discussed as central to the binding of trypsin and BPTI and protein complex formation in general. In this study, we combine all these aspects into one comprehensive model of protein recognition. We thereby contribute to enhance our general understanding of this fundamental mechanism, which is particularly critical as the development of biopharmaceuticals continuously gains significance.
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Affiliation(s)
- Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria.
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32
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Kamenik AS, Kraml J, Hofer F, Waibl F, Quoika PK, Kahler U, Schauperl M, Liedl KR. Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. J Chem Inf Model 2020; 60:3508-3517. [PMID: 32551643 PMCID: PMC7388155 DOI: 10.1021/acs.jcim.0c00280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The relation of surface polarity and conformational preferences is decisive for cell permeability and thus bioavailability of macrocyclic drugs. Here, we employ grid inhomogeneous solvation theory (GIST) to calculate solvation free energies for a series of six macrocycles in water and chloroform as a measure of passive membrane permeability. We perform accelerated molecular dynamics simulations to capture a diverse structural ensemble in water and chloroform, allowing for a direct profiling of solvent-dependent conformational preferences. Subsequent GIST calculations facilitate a quantitative measure of solvent preference in the form of a transfer free energy, calculated from the ensemble-averaged solvation free energies in water and chloroform. Hence, the proposed method considers how the conformational diversity of macrocycles in polar and apolar solvents translates into transfer free energies. Following this strategy, we find a striking correlation of 0.92 between experimentally determined cell permeabilities and calculated transfer free energies. For the studied model systems, we find that the transfer free energy exceeds the purely water-based solvation free energies as a reliable estimate of cell permeability and that conformational sampling is imperative for a physically meaningful model. We thus recommend this purely physics-based approach as a computational tool to assess cell permeabilities of macrocyclic drug candidates.
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Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Florian Hofer
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Patrick K Quoika
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, Innsbruck A-6020 Austria
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33
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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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