Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights
Tropheryma whipplei the causative agent of Whipple disease, presents a diagnostic challenge due to its diverse symptomatology, including weight loss, abdominal pain, diarrhea, joint pain, fever, and occasionally neurological manifestations. Its resistance to fluoroquinolones complicates treatment fu...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Pharmacology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fphar.2025.1630038/full |
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| author | Zarrin Basharat Calvin R. Wei Madiha Islam Ibrar Ahmed Ibrar Ahmed Hanan A. Ogaly Fatimah A. M. Al-Zahrani Yasir Waheed Yasir Waheed Yasir Waheed Yasir Waheed Seil Kim Seil Kim Seil Kim |
| author_facet | Zarrin Basharat Calvin R. Wei Madiha Islam Ibrar Ahmed Ibrar Ahmed Hanan A. Ogaly Fatimah A. M. Al-Zahrani Yasir Waheed Yasir Waheed Yasir Waheed Yasir Waheed Seil Kim Seil Kim Seil Kim |
| author_sort | Zarrin Basharat |
| collection | DOAJ |
| description | Tropheryma whipplei the causative agent of Whipple disease, presents a diagnostic challenge due to its diverse symptomatology, including weight loss, abdominal pain, diarrhea, joint pain, fever, and occasionally neurological manifestations. Its resistance to fluoroquinolones complicates treatment further. Traditional methods for antibiotic susceptibility testing are ineffective as Tropheryma whipplei cannot be cultured in axenic media. To address this, we explored potential drug targets within its core genome as no drug targets from this bacterium have been studied so far. murE, a macrolide-resistant enzyme, emerged as a promising candidate exhibiting both resistance and drug target characteristics. We screened over 1,000 lead-like Ayurvedic compounds against the target enzyme UDP-N-acetylmuramyl-tripeptide synthetase and identified three promising candidates: (1) Ergost-5-en-3-ol (3beta,24xi), (2) [6]-Gingerdiol 3-monoacetate, and (3) Valtrate. DiffDock and GNINA rescoring yielded consistent binding strength rankings. Molecular dynamics simulations over 100 nanoseconds confirmed stable interactions with these compounds. ADMET analysis indicated low water solubility, but coupling with cyclodextrin SBE-β-CD improved solubility. None of the compounds showed hepatotoxic effects, though Valtrate exhibited AMES toxicity. Based on the favorable properties, we propose scaffold hopping and further in vitro/in vivo studies on [6]-Gingerdiol 3-monoacetate. Our findings offer potential avenues for combating T. whipplei infections, addressing the limitations posed by antibiotic resistance. |
| format | Article |
| id | doaj-art-a502bbd543b04e40be528d4434fdfff0 |
| institution | DOAJ |
| issn | 1663-9812 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Pharmacology |
| spelling | doaj-art-a502bbd543b04e40be528d4434fdfff02025-08-20T03:02:51ZengFrontiers Media S.A.Frontiers in Pharmacology1663-98122025-08-011610.3389/fphar.2025.16300381630038Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insightsZarrin Basharat0Calvin R. Wei1Madiha Islam2Ibrar Ahmed3Ibrar Ahmed4Hanan A. Ogaly5Fatimah A. M. Al-Zahrani6Yasir Waheed7Yasir Waheed8Yasir Waheed9Yasir Waheed10Seil Kim11Seil Kim12Seil Kim13Alpha Genomics Private Limited, Islamabad, PakistanDepartment of Research and Development, Shing Huei Group, Taipei, TaiwanDepartment of Biotechnology and Genetic Engineering, Hazara University, Mansehra, PakistanAlpha Genomics Private Limited, Islamabad, PakistanMicrobiological Analysis Team, Group of Biometrology, The Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of KoreaChemistry Department, College of Science, King Khalid University, Abha, Saudi ArabiaChemistry Department, College of Science, King Khalid University, Abha, Saudi ArabiaNUST School of Health Sciences, National University of Sciences and Technology (NUST), Islamabad, PakistanOperational Research Center in Healthcare, Near East University, Nicosia, TürkiyeSzéchenyi István University, Győr, HungaryVIZJA University, Warsaw, PolandMicrobiological Analysis Team, Group of Biometrology, The Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea0Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea1Department of Bio-Analysis Science, University of Science and Technology, Daejeon, Republic of KoreaTropheryma whipplei the causative agent of Whipple disease, presents a diagnostic challenge due to its diverse symptomatology, including weight loss, abdominal pain, diarrhea, joint pain, fever, and occasionally neurological manifestations. Its resistance to fluoroquinolones complicates treatment further. Traditional methods for antibiotic susceptibility testing are ineffective as Tropheryma whipplei cannot be cultured in axenic media. To address this, we explored potential drug targets within its core genome as no drug targets from this bacterium have been studied so far. murE, a macrolide-resistant enzyme, emerged as a promising candidate exhibiting both resistance and drug target characteristics. We screened over 1,000 lead-like Ayurvedic compounds against the target enzyme UDP-N-acetylmuramyl-tripeptide synthetase and identified three promising candidates: (1) Ergost-5-en-3-ol (3beta,24xi), (2) [6]-Gingerdiol 3-monoacetate, and (3) Valtrate. DiffDock and GNINA rescoring yielded consistent binding strength rankings. Molecular dynamics simulations over 100 nanoseconds confirmed stable interactions with these compounds. ADMET analysis indicated low water solubility, but coupling with cyclodextrin SBE-β-CD improved solubility. None of the compounds showed hepatotoxic effects, though Valtrate exhibited AMES toxicity. Based on the favorable properties, we propose scaffold hopping and further in vitro/in vivo studies on [6]-Gingerdiol 3-monoacetate. Our findings offer potential avenues for combating T. whipplei infections, addressing the limitations posed by antibiotic resistance.https://www.frontiersin.org/articles/10.3389/fphar.2025.1630038/fullTropheryma whippleiWhipple’s diseaseAyurvedavirtual screeningMD simulation |
| spellingShingle | Zarrin Basharat Calvin R. Wei Madiha Islam Ibrar Ahmed Ibrar Ahmed Hanan A. Ogaly Fatimah A. M. Al-Zahrani Yasir Waheed Yasir Waheed Yasir Waheed Yasir Waheed Seil Kim Seil Kim Seil Kim Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights Frontiers in Pharmacology Tropheryma whipplei Whipple’s disease Ayurveda virtual screening MD simulation |
| title | Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights |
| title_full | Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights |
| title_fullStr | Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights |
| title_full_unstemmed | Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights |
| title_short | Exploring murE protein inhibitors of Tropheryma whipplei through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights |
| title_sort | exploring mure protein inhibitors of tropheryma whipplei through pharmacoinformatic approaches incorporating solubility enhancing formulation insights |
| topic | Tropheryma whipplei Whipple’s disease Ayurveda virtual screening MD simulation |
| url | https://www.frontiersin.org/articles/10.3389/fphar.2025.1630038/full |
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