Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling
Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schisto...
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Elsevier
2025-07-01
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| Series: | Results in Chemistry |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211715625002711 |
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| author | Mbalenhle Mfeka Olalekan Onisuru Ramesh Pandian Yasien Sayed Thandeka Khoza Ikechukwu Achilonu |
| author_facet | Mbalenhle Mfeka Olalekan Onisuru Ramesh Pandian Yasien Sayed Thandeka Khoza Ikechukwu Achilonu |
| author_sort | Mbalenhle Mfeka |
| collection | DOAJ |
| description | Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schistosome drug target, a careful selection of crystal structure space groups used for CADD is emphasized in this study. Sb28GST was successfully overexpressed and purified to grow protein crystals with a resolution of 2.4 Å in an orthorhombic space group system. High-throughput virtual screening (HTVS) of a flavonoid compound was performed on monoclinic 8ALS and orthorhombic 8BHZ Sb28GST to identify potential ligands. The results showed a diverse selection of hit compounds with apigenin 7-O-(2G-rhamnosyl)gentiobioside (apigenin) being the common ligand. However, quercetin-3-O-Beta-d-Glucose-7-O-Beta-D-Gentiobioside (quercetin) showed the highest affinity to 8ALS with a Glide gscore of −15.66 kcal/mol. Also, 500-ns molecular dynamics simulations (MDS) of the 8ALS-Sb28GST and 8BHZ-Sb28GST apo systems, as well as their corresponding apigenin and quercetin complexes, show two distinct trajectories which reveal significant differences in their dynamic behaviour and also showed varying interactions. This highlights the need for collective assessment of protein polymorphs to comprehensively understand protein dynamics. The inhibitory potency of apigenin and quercetin via a GSH-CDNB conjugation assay confirmed that they significantly reduced the specific enzyme activity of Sb28GST with both ligands having half-maximal inhibitory concentration (IC50) of 0.13 mM. Extrinsic fluorescence studies and thermal shift assay indicated that these compounds bind to the hydrophobic H-site and allosteric L-site at the dimer interface and have a minimal effect on the protein's thermal stability. |
| format | Article |
| id | doaj-art-38a5d8cd4c974ae39a99ef056e1deaa5 |
| institution | DOAJ |
| issn | 2211-7156 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
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| series | Results in Chemistry |
| spelling | doaj-art-38a5d8cd4c974ae39a99ef056e1deaa52025-08-20T03:02:26ZengElsevierResults in Chemistry2211-71562025-07-011610228810.1016/j.rechem.2025.102288Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modellingMbalenhle Mfeka0Olalekan Onisuru1Ramesh Pandian2Yasien Sayed3Thandeka Khoza4Ikechukwu Achilonu5Department of Biochemistry, School of Life Sciences, College of Agriculture, Engineering & Science, University of KwaZulu-Natal, Pietermaritzburg, 3209, South Africa; Protein Structure-Function and Research Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South AfricaProtein Structure-Function and Research Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South AfricaProtein Structure-Function and Research Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South AfricaProtein Structure-Function and Research Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South AfricaDepartment of Biochemistry, School of Life Sciences, College of Agriculture, Engineering & Science, University of KwaZulu-Natal, Pietermaritzburg, 3209, South AfricaProtein Structure-Function and Research Laboratory, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa; Corresponding author at: Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2000, South Africa.Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schistosome drug target, a careful selection of crystal structure space groups used for CADD is emphasized in this study. Sb28GST was successfully overexpressed and purified to grow protein crystals with a resolution of 2.4 Å in an orthorhombic space group system. High-throughput virtual screening (HTVS) of a flavonoid compound was performed on monoclinic 8ALS and orthorhombic 8BHZ Sb28GST to identify potential ligands. The results showed a diverse selection of hit compounds with apigenin 7-O-(2G-rhamnosyl)gentiobioside (apigenin) being the common ligand. However, quercetin-3-O-Beta-d-Glucose-7-O-Beta-D-Gentiobioside (quercetin) showed the highest affinity to 8ALS with a Glide gscore of −15.66 kcal/mol. Also, 500-ns molecular dynamics simulations (MDS) of the 8ALS-Sb28GST and 8BHZ-Sb28GST apo systems, as well as their corresponding apigenin and quercetin complexes, show two distinct trajectories which reveal significant differences in their dynamic behaviour and also showed varying interactions. This highlights the need for collective assessment of protein polymorphs to comprehensively understand protein dynamics. The inhibitory potency of apigenin and quercetin via a GSH-CDNB conjugation assay confirmed that they significantly reduced the specific enzyme activity of Sb28GST with both ligands having half-maximal inhibitory concentration (IC50) of 0.13 mM. Extrinsic fluorescence studies and thermal shift assay indicated that these compounds bind to the hydrophobic H-site and allosteric L-site at the dimer interface and have a minimal effect on the protein's thermal stability.http://www.sciencedirect.com/science/article/pii/S2211715625002711Schistosoma bovisPolymorphsHigh-throughput virtual screeningMolecular dynamics simulationsEmpirical, ligandBinding |
| spellingShingle | Mbalenhle Mfeka Olalekan Onisuru Ramesh Pandian Yasien Sayed Thandeka Khoza Ikechukwu Achilonu Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling Results in Chemistry Schistosoma bovis Polymorphs High-throughput virtual screening Molecular dynamics simulations Empirical, ligand Binding |
| title | Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling |
| title_full | Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling |
| title_fullStr | Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling |
| title_full_unstemmed | Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling |
| title_short | Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling |
| title_sort | crystal enigma understanding diverse protein conformational dynamics ligand selectivity and interaction in multi space group crystals using computational modelling |
| topic | Schistosoma bovis Polymorphs High-throughput virtual screening Molecular dynamics simulations Empirical, ligand Binding |
| url | http://www.sciencedirect.com/science/article/pii/S2211715625002711 |
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