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Ajmal A, Alkhatabi HA, Alreemi RM, Alamri MA, Khalid A, Abdalla AN, Alotaibi BS, Wadood A. Prospective virtual screening combined with bio-molecular simulation enabled identification of new inhibitors for the KRAS drug target. BMC Chem 2024; 18:57. [PMID: 38528576 DOI: 10.1186/s13065-024-01152-z] [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: 10/26/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Lung cancer is a disease with a high mortality rate and it is the number one cause of cancer death globally. Approximately 12-14% of non-small cell lung cancers are caused by mutations in KRASG12C. The KRASG12C is one of the most prevalent mutants in lung cancer patients. KRAS was first considered undruggable. The sotorasib and adagrasib are the recently approved drugs that selectively target KRASG12C, and offer new treatment approaches to enhance patient outcomes however drug resistance frequently arises. Drug development is a challenging, expensive, and time-consuming process. Recently, machine-learning-based virtual screening are used for the development of new drugs. In this study, we performed machine-learning-based virtual screening followed by molecular docking, all atoms molecular dynamics simulation, and binding energy calculations for the identifications of new inhibitors against the KRASG12C mutant. In this study, four machine learning models including, random forest, k-nearest neighbors, Gaussian naïve Bayes, and support vector machine were used. By using an external dataset and 5-fold cross-validation, the developed models were validated. Among all the models the performance of the random forest (RF) model was best on the train/test dataset and external dataset. The random forest model was further used for the virtual screening of the ZINC15 database, in-house database, Pakistani phytochemicals, and South African Natural Products database. A total of 100 ns MD simulation was performed for the four best docking score complexes as well as the standard compound in complex with KRASG12C. Furthermore, the top four hits revealed greater stability and greater binding affinities for KRASG12C compared to the standard drug. These new hits have the potential to inhibit KRASG12C and may help to prevent KRAS-associated lung cancer. All the datasets used in this study can be freely available at ( https://github.com/Amar-Ajmal/Datasets-for-KRAS ).
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Hind A Alkhatabi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21959, Saudi Arabia
| | - Roaa M Alreemi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21959, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, 45142, Saudi Arabia.
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra Univesity, Al- Quwayiyah, Riyadh, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
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Choe M, Titov DV. Genetically encoded tool for manipulation of ΔΨm identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573435. [PMID: 38234735 PMCID: PMC10793441 DOI: 10.1101/2023.12.27.573435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Mitochondrial membrane potential (ΔΨm) is one of the key parameters controlling cellular bioenergetics. Investigation of the role of ΔΨm in live cells is complicated by a lack of tools for its direct manipulation without off-target effects. Here, we adopted the uncoupling protein UCP1 from brown adipocytes as a genetically encoded tool for direct manipulation of ΔΨm. We validated the ability of exogenously expressed UCP1 to induce uncoupled respiration and lower ΔΨm in mammalian cells. UCP1 expression lowered ΔΨm to the same extent as chemical uncouplers but did not inhibit cell proliferation, suggesting that it manipulates ΔΨm without the off-target effects of chemical uncouplers. Using UCP1, we revealed that elevated ΔΨm is the driver of the Integrated Stress Response induced by ATP synthase inhibition in mammalian cells.
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Affiliation(s)
- Mangyu Choe
- Department of Nutritional Sciences and Toxicology, University of California; Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, CA 94720, USA
| | - Denis V Titov
- Department of Nutritional Sciences and Toxicology, University of California; Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, CA 94720, USA
- Center for Computational Biology, University of California; Berkeley, CA 94720, USA
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Qiu F, Wang Y, Du Y, Zeng C, Liu Y, Pan H, Ke C. Current evidence for J147 as a potential therapeutic agent in nervous system disease: a narrative review. BMC Neurol 2023; 23:317. [PMID: 37674139 PMCID: PMC10481599 DOI: 10.1186/s12883-023-03358-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Curcumin has anti-inflammatory, antioxidant, and anticancer effects and is used to treat diseases such as dermatological diseases, infection, stress, depression, and anxiety. J147, an analogue of curcumin, is designed and synthesized with better stability and bioavailability. Accumulating evidence demonstrates the potential role of J147 in the prevention and treatment of Alzheimer's disease, diabetic neuropathy, ischemic stroke, depression, anxiety, and fatty liver disease. In this narrative review, we summarized the background and biochemical properties of J147 and discussed the role and mechanism of J147 in different diseases. Overall, the mechanical attributes of J147 connote it as a potential target for the prevention and treatment of neurological diseases.
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Affiliation(s)
- Fang Qiu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, China
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Yanmei Wang
- Department of critical care medicine, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yunbo Du
- Department of critical care medicine, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, Guangdong, China
| | - Yuqiang Liu
- Department of Anesthesiology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518025, Guangdong, China.
| | - Haobo Pan
- Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
| | - Changneng Ke
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, China.
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