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Vyas SK, Das A, Suryanarayana Murty U, Dixit VA. Sulfotransferase-mediated phase II drug metabolism prediction of substrates and sites using accessibility and reactivity-based algorithms. Mol Inform 2024; 43:e202400008. [PMID: 39110066 DOI: 10.1002/minf.202400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/18/2024] [Accepted: 06/24/2024] [Indexed: 10/16/2024]
Abstract
Sulphotransferases (SULTs) are a major phase II metabolic enzyme class contributing ~20 % to the Phase II metabolism of FDA-approved drugs. Ignoring the potential for SULT-mediated metabolism leaves a strong potential for drug-drug interactions, often causing late-stage drug discovery failures or black-boxed warnings on FDA labels. The existing models use only accessibility descriptors and machine learning (ML) methods for class and site of sulfonation (SOS) predictions for SULT. In this study, a variety of accessibility, reactivity, and hybrid models and algorithms have been developed to make accurate substrate and SOS predictions. Unlike the literature models, reactivity parameters for the aliphatic or aromatic hydroxyl groups (R/Ar-O-H), the Bond Dissociation Energy (BDE) gave accurate models with a True Positive Rate (TPR)=0.84 for SOS predictions. We offer mechanistic insights to explain these novel findings that are not recognized in the literature. The accessibility parameters like the ratio of Chemgauss4 Score (CGS) and Molecular Weight (MW) CGS/MW and distance from cofactor (Dis) were essential for class predictions and showed TPR=0.72. Substrates consistently had lower BDE, Dis, and CGS/MW than non-substrates. Hybrid models also performed acceptablely for SOS predictions. Using the best models, Algorithms gave an acceptable performance in class prediction: TPR=0.62, False Positive Rate (FPR)=0.24, Balanced accuracy (BA)=0.69, and SOS prediction: TPR=0.98, FPR=0.60, and BA=0.69. A rule-based method was added to improve the predictive performance, which improved the algorithm TPR, FPR, and BA. Validation using an external dataset of drug-like compounds gave class prediction: TPR=0.67, FPR=0.00, and SOS prediction: TPR=0.80 and FPR=0.44 for the best Algorithm. Comparisons with standard ML models also show that our algorithm shows higher predictive performance for classification on external datasets. Overall, these models and algorithms (SOS predictor) give accurate substrate class and site (SOS) predictions for SULT-mediated Phase II metabolism and will be valuable to the drug discovery community in academia and industry. The SOS predictor is freely available for academic/non-profit research via the GitHub link.
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Affiliation(s)
- Shivam Kumar Vyas
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati), Guwahati, Assam, 781101, India
| | - Avik Das
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS-Pilani), Vidya Vihar Campus 41, Pilani, Rajasthan, 333031, India
- Current address: Department of Primary Intelligence, IQVIA, Sarjapur-Marathahalli Outer Ring Road Embassy Tech Square, Bangalore, 560103 Karnataka, India
| | - Upadhyayula Suryanarayana Murty
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati), Guwahati, Assam, 781101, India
| | - Vaibhav A Dixit
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati), Guwahati, Assam, 781101, India
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Dixit VA, Murty US, Bajaj P, Blumberger J, de Visser SP. Mechanisms of Electron Transfer Rate Modulations in Cytochrome P450 BM3. J Phys Chem B 2022; 126:9737-9747. [PMID: 36384294 DOI: 10.1021/acs.jpcb.2c03967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cytochromes P450 BM3 (CYP450 BM3) catalyze reactions of industrial importance. Despite many successful biotransformations, robust (re)design for novel applications remains challenging. Rational design and evolutionary approaches are not always successful, highlighting a lack of complete understanding of the mechanisms of electron transfer (ET) modulations. Thus, the full potential of CYP450 reactions remains under-exploited. In this work, we report the first molecular dynamics (MD)-based explicit prediction of BM3 ET parameters (reorganization energies; λ and ET free energies; ΔG°), and log ET rates (log kET) using the Marcus theory. Overall, the calculated ET rates for the BM3 wild-type (WT), mutants (F393 and L86), ligand-bound state, and ion concentrations agree well with experimental data. In ligand-free (LF) BM3, mutations modulate kET via ET ΔG°. Simulations show that the experimental ET rate enhancement is due to increased driving force (more negative ΔG°) upon ligation. This increase is related to the protein reorganization required to accommodate the ligand in the binding pocket rather than binding interactions with the ligand. Our methodology (CYPWare 1.0) automates all the stages of the MD simulation step-up, energy calculations, and estimation of ET parameters. CYPWare 1.0 and this work thus represent an important advancement in the CYP450 ET rate predictions, which has the potential to guide the redesign of ET enzymes. This program and a Web tool are available on GitHub for academic research.
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Affiliation(s)
- Vaibhav A Dixit
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers,, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati) Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, 781101Guwahati, Assam, India
| | - Upadhyayula Suryanarayana Murty
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals & Fertilizers,, National Institute of Pharmaceutical Education and Research, Guwahati, (NIPER Guwahati) Govt. of India, Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, 781101Guwahati, Assam, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research, Hyderabad (NIPER Hyderabad), NH-9, Balanagar Main Road, Kukatpally Industrial Estate, Balanagar, Hyderabad500037, Telangana, India
| | - Jochen Blumberger
- Department of Physics and Astronomy, and Thomas Young Centre, University College London, Gower Street, LondonWC1E 6BT, U.K
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, ManchesterM17DN, U.K
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Cao M, Wang G, He H, Yue R, Zhao Y, Pan L, Huang W, Guo Y, Yin T, Ma L, Zhang D, Huang X. Hemoglobin-Based Oxygen Carriers: Potential Applications in Solid Organ Preservation. Front Pharmacol 2021; 12:760215. [PMID: 34916938 PMCID: PMC8670084 DOI: 10.3389/fphar.2021.760215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/10/2021] [Indexed: 12/30/2022] Open
Abstract
Ameliorating graft injury induced by ischemia and hypoxia, expanding the donor pool, and improving graft quality and recipient prognosis are still goals pursued by the transplant community. The preservation of organs during this process from donor to recipient is critical to the prognosis of both the graft and the recipient. At present, static cold storage, which is most widely used in clinical practice, not only reduces cell metabolism and oxygen demand through low temperature but also prevents cell edema and resists apoptosis through the application of traditional preservation solutions, but these do not improve hypoxia and increase oxygenation of the donor organ. In recent years, improving the ischemia and hypoxia of grafts during preservation and repairing the quality of marginal donor organs have been of great concern. Hemoglobin-based oxygen carriers (HBOCs) are “made of” natural hemoglobins that were originally developed as blood substitutes but have been extended to a variety of hypoxic clinical situations due to their ability to release oxygen. Compared with traditional preservation protocols, the addition of HBOCs to traditional preservation protocols provides more oxygen to organs to meet their energy metabolic needs, prolong preservation time, reduce ischemia–reperfusion injury to grafts, improve graft quality, and even increase the number of transplantable donors. The focus of the present study was to review the potential applications of HBOCs in solid organ preservation and provide new approaches to understanding the mechanism of the promising strategies for organ preservation.
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Affiliation(s)
- Min Cao
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Guoqing Wang
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongli He
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Zhao
- Anesthesiology, Southwest Medicine University, Luzhou, China
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Weiwei Huang
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Guo
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Yin
- Surgical Department, Chengdu Second People's Hospital, Chengdu, China
| | - Lina Ma
- Health Inspection and Quarantine, Chengdu Medical College, Chengdu, China
| | - Dingding Zhang
- Sichuan Provincial Key Laboratory for Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaobo Huang
- Department of Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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