Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain
The PDZ family has drawn attention as possible drug targets because of the domains’ wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA r...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/11/15/2451 |
| _version_ | 1827618515127894016 |
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| author | Amy O. Stevens Samuel Luo Yi He |
| author_facet | Amy O. Stevens Samuel Luo Yi He |
| author_sort | Amy O. Stevens |
| collection | DOAJ |
| description | The PDZ family has drawn attention as possible drug targets because of the domains’ wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1–GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ–ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain. |
| first_indexed | 2024-03-09T10:09:44Z |
| format | Article |
| id | doaj.art-a817c33f3ee24961a30d9f7b8ed34db8 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-09T10:09:44Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-a817c33f3ee24961a30d9f7b8ed34db82023-12-01T22:53:21ZengMDPI AGCells2073-44092022-08-011115245110.3390/cells11152451Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ DomainAmy O. Stevens0Samuel Luo1Yi He2Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USAAlbuquerque Academy, Albuquerque, NM 87131, USADepartment of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USAThe PDZ family has drawn attention as possible drug targets because of the domains’ wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1–GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ–ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain.https://www.mdpi.com/2073-4409/11/15/2451PICK1PDZ domainBIO124dynamic allosterism |
| spellingShingle | Amy O. Stevens Samuel Luo Yi He Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain Cells PICK1 PDZ domain BIO124 dynamic allosterism |
| title | Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain |
| title_full | Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain |
| title_fullStr | Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain |
| title_full_unstemmed | Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain |
| title_short | Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain |
| title_sort | three binding conformations of bio124 in the pocket of the pick1 pdz domain |
| topic | PICK1 PDZ domain BIO124 dynamic allosterism |
| url | https://www.mdpi.com/2073-4409/11/15/2451 |
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