Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase
Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded en...
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| Format: | Article |
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MDPI AG
2022-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/9/4502 |
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| author | María Conde-Giménez Juan José Galano-Frutos María Galiana-Cameo Alejandro Mahía Bruno L. Victor Sandra Salillas Adrián Velázquez-Campoy Rui M. M. Brito José Antonio Gálvez María D. Díaz-de-Villegas Javier Sancho |
| author_facet | María Conde-Giménez Juan José Galano-Frutos María Galiana-Cameo Alejandro Mahía Bruno L. Victor Sandra Salillas Adrián Velázquez-Campoy Rui M. M. Brito José Antonio Gálvez María D. Díaz-de-Villegas Javier Sancho |
| author_sort | María Conde-Giménez |
| collection | DOAJ |
| description | Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔ<i>G</i><sub>b</sub> values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme. |
| first_indexed | 2024-03-10T04:08:44Z |
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| id | doaj.art-f65482fe91274f0b8ab328ec6b5c92e3 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T04:08:44Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f65482fe91274f0b8ab328ec6b5c92e32023-11-23T08:18:06ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-04-01239450210.3390/ijms23094502Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine HydroxylaseMaría Conde-Giménez0Juan José Galano-Frutos1María Galiana-Cameo2Alejandro Mahía3Bruno L. Victor4Sandra Salillas5Adrián Velázquez-Campoy6Rui M. M. Brito7José Antonio Gálvez8María D. Díaz-de-Villegas9Javier Sancho10Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainCoimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, PortugalDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainCoimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, PortugalInstituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainInstituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainDepartamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, SpainPhenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔ<i>G</i><sub>b</sub> values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.https://www.mdpi.com/1422-0067/23/9/4502phenylketonuriapharmacological chaperoneslead optimizationalchemical free energy calculationsbinding energetics |
| spellingShingle | María Conde-Giménez Juan José Galano-Frutos María Galiana-Cameo Alejandro Mahía Bruno L. Victor Sandra Salillas Adrián Velázquez-Campoy Rui M. M. Brito José Antonio Gálvez María D. Díaz-de-Villegas Javier Sancho Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase International Journal of Molecular Sciences phenylketonuria pharmacological chaperones lead optimization alchemical free energy calculations binding energetics |
| title | Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase |
| title_full | Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase |
| title_fullStr | Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase |
| title_full_unstemmed | Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase |
| title_short | Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase |
| title_sort | alchemical design of pharmacological chaperones with higher affinity for phenylalanine hydroxylase |
| topic | phenylketonuria pharmacological chaperones lead optimization alchemical free energy calculations binding energetics |
| url | https://www.mdpi.com/1422-0067/23/9/4502 |
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