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Durell SR, Ben-Naim A. Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions. J Phys Chem B 2021; 125:13137-13146. [PMID: 34850632 DOI: 10.1021/acs.jpcb.1c07802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the ΔG becoming more negative for the former and less negative for the latter with increasing temperature. Dissection of the free energy curves into enthalpy and entropy contributions, and further separation of the enthalpy term into solute-solute, solute-solvent, and solvent-solvent components provides insight into the physical molecular causes for the distinctive thermodynamic results. Finally, it is reasoned how the opposite temperature dependencies of the two types of hydrophilic interactions provide a rationale for the cold denaturation of proteins.
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Affiliation(s)
- Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute; National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Arieh Ben-Naim
- Department of Physical Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem 91904, Israel
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2
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Mahmud S, Elfiky AA, Amin A, Mohanto SC, Rahman E, Acharjee UK, Saleh A. Targeting SARS-CoV-2 nonstructural protein 15 endoribonuclease: an in silico perspective. Future Virol 2021. [PMID: 34290822 PMCID: PMC8285111 DOI: 10.2217/fvl-2020-0233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 06/22/2021] [Indexed: 12/20/2022]
Abstract
The newly emerged human coronavirus, SARS-CoV-2, had begun to spread last year and sparked worldwide. In this study, molecular docking is utilized to test some previously approved drugs against the SARS-CoV-2 nonstructural protein 15 (Nsp15). We screened 23 drugs, from which three (saquinavir, valrubicin and aprepitant) show a paramount predicted binding affinity (-9.1, -9.6 and -9.2 kcal/mol, respectively) against SARS-CoV-2 Nsp15. Moreover, saquinavir and aprepitant make nonbonded interactions with Leu201 in the active site cavity of Nsp15, while the drug valrubicin interacts with Arg199 and Leu201. This binding pattern may be effective against the targeted protein, leading to Nsp15 blockage and virus abolition. Additionally, the pharmacological properties of the screened drugs are known since they have been approved against different viruses.
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Affiliation(s)
- Shafi Mahmud
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Al Amin
- Institute of Biological Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Sumon Chandro Mohanto
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Ekhtiar Rahman
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Uzzal Kumar Acharjee
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Abu Saleh
- Genetic Engineering & Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
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3
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Bartling CRO, Jensen TMT, Henry SM, Colliander AL, Sereikaite V, Wenzler M, Jain P, Maric HM, Harpsøe K, Pedersen SW, Clemmensen LS, Haugaard-Kedström LM, Gloriam DE, Ho A, Strømgaard K. Targeting the APP-Mint2 Protein-Protein Interaction with a Peptide-Based Inhibitor Reduces Amyloid-β Formation. J Am Chem Soc 2021; 143:891-901. [PMID: 33398998 DOI: 10.1021/jacs.0c10696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There is an urgent need for novel therapeutic approaches to treat Alzheimer's disease (AD) with the ability to both alleviate the clinical symptoms and halt the progression of the disease. AD is characterized by the accumulation of amyloid-β (Aβ) peptides which are generated through the sequential proteolytic cleavage of the amyloid precursor protein (APP). Previous studies reported that Mint2, a neuronal adaptor protein binding both APP and the γ-secretase complex, affects APP processing and formation of pathogenic Aβ. However, there have been contradicting results concerning whether Mint2 has a facilitative or suppressive effect on Aβ generation. Herein, we deciphered the APP-Mint2 protein-protein interaction (PPI) via extensive probing of both backbone H-bond and side-chain interactions. We also developed a proteolytically stable, high-affinity peptide targeting the APP-Mint2 interaction. We found that both an APP binding-deficient Mint2 variant and a cell-permeable PPI inhibitor significantly reduced Aβ42 levels in a neuronal in vitro model of AD. Together, these findings demonstrate a facilitative role of Mint2 in Aβ formation, and the combination of genetic and pharmacological approaches suggests that targeting Mint2 is a promising therapeutic strategy to reduce pathogenic Aβ levels.
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Affiliation(s)
- Christian R O Bartling
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.,Department of Biology, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Thomas M T Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Shawna M Henry
- Department of Biology, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Anna L Colliander
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Vita Sereikaite
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Marcella Wenzler
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Palash Jain
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Hans M Maric
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Søren W Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Louise S Clemmensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Linda M Haugaard-Kedström
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
| | - Angela Ho
- Department of Biology, Boston University, 24 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark
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4
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The Conformational Plasticity Vista of PDZ Domains. Life (Basel) 2020; 10:life10080123. [PMID: 32726937 PMCID: PMC7460260 DOI: 10.3390/life10080123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/19/2020] [Accepted: 07/25/2020] [Indexed: 02/01/2023] Open
Abstract
The PDZ domain (PSD95-Discs large-ZO1) is a widespread modular domain present in the living organisms. A prevalent function in the PDZ family is to serve as scaffolding and adaptor proteins connecting multiple partners in signaling pathways. An explanation of the flexible functionality in this domain family, based just on a static perspective of the structure-activity relationship, might fall short. More dynamic and conformational aspects in the protein fold can be the reasons for such functionality. Folding studies indeed showed an ample and malleable folding landscape for PDZ domains where multiple intermediate states were experimentally detected. Allosteric phenomena that resemble energetic coupling between residues have also been found in PDZ domains. Additionally, several PDZ domains are modulated by post-translational modifications, which introduce conformational switches that affect binding. Altogether, the ability to connect diverse partners might arise from the intrinsic plasticity of the PDZ fold.
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Tavasoli B, Safa M, Dorgalaleh A, Ghasemi JB, Rezaei Makhouri F, Rezvani MR, Ahmadi A, Tabibian S, Jazebi M, Baghaipour MR, Zaker F. Molecular and clinical profile of congenital fibrinogen disorders in Iran, identification of two novel mutations. Int J Lab Hematol 2020; 42:619-627. [DOI: 10.1111/ijlh.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/25/2020] [Accepted: 05/01/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Behnaz Tavasoli
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Majid Safa
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
- Cellular & Molecular Research Center Iran University of Medical Sciences Tehran Iran
| | - Akbar Dorgalaleh
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Jahan B. Ghasemi
- Department of Chemistry Faculty of Sciences University of Tehran Tehran Iran
| | | | - Mohammad R. Rezvani
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Abbas Ahmadi
- Cellular & Molecular Research Center Kurdistan University of Medical Sciences Sanandaj Iran
| | - Shadi Tabibian
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
- Iranian Comprehensive Hemophilia Care Center Tehran Iran
| | | | | | - Farhad Zaker
- Department of Hematology and Blood Banking Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
- Cellular & Molecular Research Center Iran University of Medical Sciences Tehran Iran
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Rogers JM. Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis. Front Mol Biosci 2020; 7:100. [PMID: 32671094 PMCID: PMC7326784 DOI: 10.3389/fmolb.2020.00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022] Open
Abstract
Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.
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Affiliation(s)
- Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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7
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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Ahmed S, Islam N, Shahinozzaman M, Fakayode SO, Afrin N, Halim MA. Virtual screening, molecular dynamics, density functional theory and quantitative structure activity relationship studies to design peroxisome proliferator-activated receptor-γ agonists as anti-diabetic drugs. J Biomol Struct Dyn 2020; 39:728-742. [DOI: 10.1080/07391102.2020.1714482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sinthyia Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Nazrul Islam
- Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahinozzaman
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Sayo O. Fakayode
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, Arkansas, USA
| | - Nadia Afrin
- Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, Arkansas, USA
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9
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Sereikaitė V, Jensen TMT, Bartling CRO, Jemth P, Pless SA, Strømgaard K. Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations. Chembiochem 2018; 19:2136-2145. [PMID: 30073762 DOI: 10.1002/cbic.201800350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/09/2023]
Abstract
All proteins contain characteristic backbones formed of consecutive amide bonds, which can engage in hydrogen bonds. However, the importance of these is not easily addressed by conventional technologies that only allow for side-chain substitutions. By contrast, technologies such as nonsense suppression mutagenesis and protein ligation allow for manipulation of the protein backbone. In particular, replacing the backbone amide groups with ester groups, that is, amide-to-ester mutations, is a powerful tool to examine backbone-mediated hydrogen bonds. In this minireview, we showcase examples of how amide-to-ester mutations can be used to uncover pivotal roles of backbone-mediated hydrogen bonds in protein recognition, folding, function, and structure.
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Affiliation(s)
- Vita Sereikaitė
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Thomas M T Jensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Christian R O Bartling
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 75123, Uppsala, Sweden
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
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Di Silvio E, Bonetti D, Toto A, Morrone A, Gianni S. The mechanism of binding of the second PDZ domain from the Protein Tyrosine Phosphatase-BL to the Adenomatous Polyposis Coli tumor suppressor. Protein Eng Des Sel 2014; 27:249-53. [DOI: 10.1093/protein/gzu022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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