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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Farrell CC, Khanna S, Hoque MT, Plaga A, Basset N, Syed I, Biouss G, Aufreiter S, Marcon N, Bendayan R, Kim YI, O'Connor DL. Low-dose daily folic acid (400 μg) supplementation does not affect regulation of folate transporters found present throughout the terminal ileum and colon of humans: a randomized clinical trial. Am J Clin Nutr 2024; 119:809-820. [PMID: 38157986 DOI: 10.1016/j.ajcnut.2023.12.018] [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: 09/05/2023] [Revised: 11/23/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Folic acid supplementation during the periconceptional period reduces the risk of neural tube defects in infants, but concern over chronic folic acid exposure remains. An improved understanding of folate absorption may clarify potential risks. Folate transporters have been characterized in the small intestine, but less so in the colon of healthy, free-living humans. The impact of folic acid fortification or supplementation on regulation of these transporters along the intestinal tract is unknown. OBJECTIVE The objective was to characterize expression of folate transporters/receptor (FT/R) and folate hydrolase, glutamate carboxypeptidase II (GCPII), from the terminal ileum and throughout the colon of adults and assess the impact of supplemental folic acid. METHODS In this 16-wk open-labeled randomized clinical trial, adults consumed a low folic acid-containing diet, a folate-free multivitamin, and either a 400 μg folic acid supplement or no folic acid supplement. Dietary intakes and blood were assessed at baseline, 8 wk, and 16 wk (time of colonoscopy). Messenger RNA (mRNA) expression and protein expression of FT/R and GCPII were assessed in the terminal ileum, cecum, and ascending and descending colon. RESULTS Among 24 randomly assigned subjects, no differences in dietary folate intake or blood folate were observed at baseline. Mean ± SD red blood cell folate at 16 wk was 1765 ± 426 and 911 ± 242 nmol/L in the 400 and 0 μg folic acid group, respectively (P < 0.0001). Reduced folate carrier, proton-coupled folate transporter, and folate-receptor alpha expression were detected in the terminal ileum and colon, as were efflux transporters of breast cancer resistance protein and multidrug resistance protein-3. Other than a higher mRNA expression of FR-alpha and GCPII in the 400 μg supplement group in the ascending colon, no treatment differences were observed (P < 0.02). CONCLUSIONS Folate transporters are present throughout the terminal ileum and colon; there is little evidence that a low dose of folic acid supplementation affects colonic absorption. This trial was registered at clinicaltrials.gov as NCT03421483.
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Affiliation(s)
- Colleen C Farrell
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siya Khanna
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Md Tozammel Hoque
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Aneta Plaga
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nancy Basset
- Division of Gastroenterology, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ishba Syed
- Division of Gastroenterology, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - George Biouss
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada; Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susanne Aufreiter
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Norman Marcon
- Division of Gastroenterology, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Reina Bendayan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Young-In Kim
- Division of Gastroenterology, Department of Medicine, St. Michael's Hospital, Toronto, Ontario, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Deborah L O'Connor
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
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Fishchuk L, Skavinska O, Ievseienkova O, Rossokha Z, Sheiko L. GENETIC PREDICTORS OF TOXIC EFFECTS OF METHOTREXATE IN CANCER PATIENTS. Exp Oncol 2024; 45:399-408. [PMID: 38328850 DOI: 10.15407/exp-oncology.2023.04.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Today, methotrexate (MTX) is used in combination with other medicines to treat a wide range of malignancies. Despite its proven high efficacy, MTX often causes serious side effects, which may result in the need to reduce the dose of MTX or discontinue the drug altogether. This, in turn, can provoke the development of MTX resistance and cancer progression. Predicting the risk of MTX-induced toxicity is currently difficult due to the variability of pharmacokinetics and pharmacodynamics in different patients, so the scientific literature is intensively searching for potential biomarkers. Based on the data available in the current literature, we analyzed the relationship between variants in the genes encoding the key components of MTX intracellular metabolism and the MTX-induced side effects and drug response. According to the results of our work, the most studied variants are those of the SLC19A1 gene, which encodes the reduced folate carrier protein 1, and the MTHFR gene, which encodes the enzyme methylenetetrahydrofolate reductase. Studies of the effect of methylation of the promoter regions of genes on the therapeutic effect of MTX are also very promising. In conclusion, the study of molecular genetic markers of MTX toxicity is extremely relevant and necessary because it can help to avoid the effect of multidrug resistance and improve the quality of life and survival of patients.
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Affiliation(s)
- L Fishchuk
- State Institution "Reference-center for Molecular Diagnostic of Public Health Ministry of Ukraine", Kyiv, Ukraine
| | - O Skavinska
- State Institution "Reference-center for Molecular Diagnostic of Public Health Ministry of Ukraine", Kyiv, Ukraine
| | - O Ievseienkova
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Z Rossokha
- State Institution "Reference-center for Molecular Diagnostic of Public Health Ministry of Ukraine", Kyiv, Ukraine
| | - L Sheiko
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
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Wen A, Zhu Y, Yee SW, Park BI, Giacomini KM, Greenberg AS, Newman JW. The Impacts of Slc19a3 Deletion and Intestinal SLC19A3 Insertion on Thiamine Distribution and Brain Metabolism in the Mouse. Metabolites 2023; 13:885. [PMID: 37623829 PMCID: PMC10456376 DOI: 10.3390/metabo13080885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 08/26/2023] Open
Abstract
The Thiamine Transporter 2 (THTR2) encoded by SLC19A3 plays an ill-defined role in the maintenance of tissue thiamine, thiamine monophosphate, and thiamine diphosphate (TDP) levels. To evaluate the impact of THTR2 on tissue thiamine status and metabolism, we expressed the human SLC19A3 transgene in the intestine of total body Slc19a3 knockout (KO) mice. Male and female wildtype (WT) and transgenic (TG) mice were fed either 17 mg/kg (1×) or 85 mg/kg (5×) thiamine hydrochloride diet, while KOs were only fed the 5× diet. Thiamine vitamers in plasma, red blood cells, duodenum, brain, liver, kidney, heart, and adipose tissue were measured. Untargeted metabolomics were performed on the brain tissues of groups with equivalent plasma thiamine. KO mice had ~two- and ~three-fold lower plasma and brain thiamine levels than WT on the 5× diet. Circulating vitamers were sensitive to diet and equivalent in TG and WT mice. However, TG had 60% lower thiamine but normal brain TDP levels regardless of diet, with subtle differences in the heart and liver. The loss of THTR2 reduced levels of nucleic acid and amino acid derivatives in the brain. Therefore, mutation or inhibition of THTR2 may alter the brain metabolome and reduce the thiamine reservoir for TDP biosynthesis.
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Affiliation(s)
- Anita Wen
- Department of Nutrition, University of California, Davis, CA 95616, USA
- West Coast Metabolomics Center, Genome Center, University of California, Davis, CA 95616, USA
| | - Ying Zhu
- Gerald J. and Dorothy R. Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA 02111, USA
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 92521, USA
| | - Brian I. Park
- Gerald J. and Dorothy R. Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA 02111, USA
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 92521, USA
| | - Andrew S. Greenberg
- Gerald J. and Dorothy R. Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA 02111, USA
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - John W. Newman
- Department of Nutrition, University of California, Davis, CA 95616, USA
- West Coast Metabolomics Center, Genome Center, University of California, Davis, CA 95616, USA
- USDA Western Human Nutrition Research Center, Davis, CA 95616, USA
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