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Mehmood A, Hakami MA, Ogaly HA, Subramaniyan V, Khalid A, Wadood A. Evolution of computational techniques against various KRAS mutants in search for therapeutic drugs: a review article. Cancer Chemother Pharmacol 2025; 95:52. [PMID: 40195161 DOI: 10.1007/s00280-025-04767-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 02/23/2025] [Indexed: 04/09/2025]
Abstract
KRAS was (Kirsten rat sarcoma viral oncogene homolog) revealed as an important target in current therapeutic cancer research because alteration of RAS (rat sarcoma viral oncogene homolog) protein has a critical role in malignant modification, tumor angiogenesis, and metastasis. For cancer treatment, designing competitive inhibitors for this attractive target was difficult. Nevertheless, computational investigations of the protein's dynamic behavior displayed the existence of temporary pockets that could be used to design allosteric inhibitors. The last decade witnessed intensive efforts to discover KRAS inhibitors. In 2021, the first KRAS G12C covalent inhibitor, AMG 510, received FDA (Food and drug administration) approval as an anticancer medication that paved the path for future treatment strategies against this target. Computer-aided drug designing discovery has long been used in drug development research targeting different KRAS mutants. In this review, the major breakthroughs in computational methods adapted to discover novel compounds for different mutations have been discussed. Undoubtedly, virtual screening and molecular dynamic (MD) simulation and molecular docking are the most considered approach, producing hits that can be employed in subsequent refinements. After comprehensive analysis, Afatinib and Quercetin were computationally identified as hits in different publications. Several authors conducted covalent docking studies with acryl amide warheads groups containing inhibitors. Future studies are needed to demonstrate their true potential. In-depth studies focusing on various allosteric pockets demonstrate that the switch I/II pocket is a suitable site for drug designing. In addition, machine learning and deep learning based approaches provide new insights for developing anti-KRAS drugs. We believe that this review provides extensive information to researchers globally and encourages further development in this particular area of research.
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Affiliation(s)
- Ayesha Mehmood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al- Quwayiyah, Riyadh, Saudi Arabia
| | - Hanan A Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Vetriselvan Subramaniyan
- Division of Pharmacology, School of Medical and Life Sciences, Sunway University No. 5, Jalan Universiti, Bandar Sunway, Selangor Darul Ehsan, 47500, Malaysia
| | - Asaad Khalid
- Health Research Center, Jazan University, 114, Jazan, 45142, Saudi Arabia
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan.
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Prasad SR, Kumar P, Mandal S, Mohan A, Chaurasia R, Shrivastava A, Nikhil P, Aishwarya D, Ramalingam P, Gajbhiye R, Singh S, Dasgupta A, Chourasia M, Ravichandiran V, Das P, Mandal D. Mechanistic insight into the role of mevalonate kinase by a natural fatty acid-mediated killing of Leishmania donovani. Sci Rep 2022; 12:16453. [PMID: 36180490 PMCID: PMC9525708 DOI: 10.1038/s41598-022-20509-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
We evaluated the anti-leishmanial efficacy of different saturated medium-chain fatty acids (FAs, C8–C18) where FA containing C8 chain, caprylic acid (CA), was found to be most potent against Leishmania donovani, the causative agent for visceral leishmaniasis (VL). Different analogs of CA with C8 linear chain, but not higher, along with a carboxyl/ester group showed a similar anti-leishmanial effect. Ergosterol depletion was the major cause of CA-mediated cell death. Molecular docking and molecular dynamic simulation studies indicated the enzyme mevalonate kinase (MevK) of the ergosterol biosynthesis pathway as a possible target of CA. Enzyme assays with purified recombinant MevK and CA/CA analogs confirmed the target with a competitive inhibition pattern. Using biochemical and biophysical studies; strong binding interaction between MevK and CA/CA analogs was established. Further, using parasites with overexpressed MevK and proteomics studies of CA-treated parasites the direct role of MevK as the target was validated. We established the mechanism of the antileishmanial effect of CA, a natural product, against VL where toxicity and drug resistance with current chemotherapeutics demand an alternative. This is the first report on the identification of an enzymatic target with kinetic parameters and mechanistic insights against any organism for a natural medium-chain FA.
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Affiliation(s)
- Surendra Rajit Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India
| | - Saptarshi Mandal
- Department of Chemistry, Indian Institute of Technology, Patna Bihta, Bihar, 801106, India
| | - Anu Mohan
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India
| | - Radhika Chaurasia
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India
| | - Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar University, G.B. Nagar, Uttar Pradesh, 201314, India
| | - Pallaprolu Nikhil
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
| | - Dande Aishwarya
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
| | - P Ramalingam
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
| | - Rahul Gajbhiye
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
| | - Shriya Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sitapur Rd, Sector-10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
| | - Arunava Dasgupta
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Sitapur Rd, Sector-10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mukesh Chourasia
- Amity Institute of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh, 201301, India
| | - V Ravichandiran
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India.,National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology, Patna Bihta, Bihar, 801106, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Export Promotions Industrial Park (EPIP), Vaishali District, Hajipur, Bihar, 844102, India.
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Hu X, Zhang J, Zhang Y, Jiao F, Wang J, Chen H, Ouyang L, Wang Y. Dual-target inhibitors of poly (ADP-ribose) polymerase-1 for cancer therapy: Advances, challenges, and opportunities. Eur J Med Chem 2022; 230:114094. [PMID: 34998039 DOI: 10.1016/j.ejmech.2021.114094] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 02/08/2023]
Abstract
PARP1 plays a crucial role in DNA damage repair, making it an essential target for cancer therapy. PARP1 inhibitors are widely used to treat BRCA-deficient malignancies, and six PARP inhibitors have been approved for clinical use. However, excluding the great clinical success of PARP inhibitors, the concomitant toxicity, drug resistance, and limited scope of application restrict their clinical efficacy. To find solutions to these problems, dual-target inhibitors have shown great potential. In recent years, several studies have linked PAPR1 to other primary cancer targets. Many dual-target inhibitors have been developed using structural fusion, linkage, or library construction methods, overcoming the defects of many single-target inhibitors of PARP1 and achieving great success in clinical cancer therapy. This review summarizes the advance of dual-target PARP1 inhibitors in recent years, focusing on their structural optimization process, structure-activity relationships (SARs), and in vitro or in vivo analysis results.
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Affiliation(s)
- Xinyue Hu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ya Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Fulun Jiao
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Hao Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Liang Ouyang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Chang X, Sun D, Shi D, Wang G, Chen Y, Zhang K, Tan H, Liu J, Liu B, Ouyang L. Design, synthesis, and biological evaluation of quinazolin-4(3 H)-one derivatives co-targeting poly(ADP-ribose) polymerase-1 and bromodomain containing protein 4 for breast cancer therapy. Acta Pharm Sin B 2021; 11:156-180. [PMID: 33532187 PMCID: PMC7838034 DOI: 10.1016/j.apsb.2020.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/08/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
This study was aimed to design the first dual-target small-molecule inhibitor co-targeting poly (ADP-ribose) polymerase-1 (PARP1) and bromodomain containing protein 4 (BRD4), which had important cross relation in the global network of breast cancer, reflecting the synthetic lethal effect. A series of new BRD4 and PARP1 dual-target inhibitors were discovered and synthesized by fragment-based combinatorial screening and activity assays that together led to the chemical optimization. Among these compounds, 19d was selected and exhibited micromole enzymatic potencies against BRD4 and PARP1, respectively. Compound 19d was further shown to efficiently modulate the expression of BRD4 and PARP1. Subsequently, compound 19d was found to induce breast cancer cell apoptosis and stimulate cell cycle arrest at G1 phase. Following pharmacokinetic studies, compound 19d showed its antitumor activity in breast cancer susceptibility gene 1/2 (BRCA1/2) wild-type MDA-MB-468 and MCF-7 xenograft models without apparent toxicity and loss of body weight. These results together demonstrated that a highly potent dual-targeted inhibitor was successfully synthesized and indicated that co-targeting of BRD4 and PARP1 based on the concept of synthetic lethality would be a promising therapeutic strategy for breast cancer.
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Key Words
- BC, breast cancer
- BET, bromodomain and extra-terminal domain
- BRCA1/2, breast cancer susceptibility gene 1/2
- BRD4
- BRD4, bromodomain 4
- CDK4/6, cyclin-dependent kinase 4/6
- DSB, DNA double-strand break
- Dual-target inhibitor
- EGFR, epidermal growth factor receptor
- ELISA, enzyme linked immunosorbent assay
- ER, estrogen receptor
- ESI-HR-MS, high-resolution mass spectra
- FDA, U.S. Food and Drug Administration
- FITC, fluorescein isothiocyanate isomer I
- HE, hematoxylin-eosin
- HPLC, high-performance liquid chromatography
- HR, homologous recombination
- HRD, homologous recombination deficiency
- IHC, immunohistochemistry
- NHEJ, nonhomologous end-joining
- PARP1
- PARP1, poly(ADP-ribose) polymerase-1
- PI, propidium iodide
- PK, pharmacokinetics
- PPI, protein−protein interaction
- Quinazolin-4(3H)-one derivatives
- SAR, structure–activity relationship
- SOP, standard operation process
- Synthetic lethality
- TCGA, the cancer genome atlas
- TGI, tumor growth inhibition
- TLC, thin-layer chromatography
- TNBC, triple-negative breast cancer
- TR-FRET, time-resolved fluorescence resonance energy transfer.
- shRNA, short hairpin RNA
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Affiliation(s)
| | | | | | | | | | | | | | - Jie Liu
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
| | - Bo Liu
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
| | - Liang Ouyang
- Corresponding authors. Tel./fax: +86 28 85503817 (Jie Liu), +86 28 85164063 (Bo Liu), +86 28 85503817 (Liang Ouyang).
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Wu HZ, Xiao JQ, Xiao SS, Cheng Y. KRAS: A Promising Therapeutic Target for Cancer Treatment. Curr Top Med Chem 2019; 19:2081-2097. [PMID: 31486755 DOI: 10.2174/1568026619666190905164144] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most commonly mutated oncogene in human cancer. The developments of many cancers depend on sustained expression and signaling of KRAS, which makes KRAS a high-priority therapeutic target. Scientists have not successfully developed drugs that target KRAS, although efforts have been made last three decades. In this review, we highlight the emerging experimental strategies of impairing KRAS membrane localization and the direct targeting of KRAS. We also conclude the combinatorial therapies and RNA interference technology for the treatment of KRAS mutant cancers. Moreover, the virtual screening approach to discover novel KRAS inhibitors and synthetic lethality interactors of KRAS are discussed in detail.
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Affiliation(s)
- Hai-Zhou Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Jia-Qi Xiao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Song-Shu Xiao
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yan Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
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Nussinov R, Jang H, Tsai CJ, Liao TJ, Li S, Fushman D, Zhang J. Intrinsic protein disorder in oncogenic KRAS signaling. Cell Mol Life Sci 2017; 74:3245-3261. [PMID: 28597297 PMCID: PMC11107717 DOI: 10.1007/s00018-017-2564-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022]
Abstract
How Ras, and in particular its most abundant oncogenic isoform K-Ras4B, is activated and signals in proliferating cells, poses some of the most challenging questions in cancer cell biology. In this paper, we ask how intrinsically disordered regions in K-Ras4B and its effectors help promote proliferative signaling. Conformational disorder allows spanning long distances, supports hinge motions, promotes anchoring in membranes, permits segments to fulfil multiple roles, and broadly is crucial for activation mechanisms and intensified oncogenic signaling. Here, we provide an overview illustrating some of the key mechanisms through which conformational disorder can promote oncogenesis, with K-Ras4B signaling serving as an example. We discuss (1) GTP-bound KRas4B activation through membrane attachment; (2) how farnesylation and palmitoylation can promote isoform functional specificity; (3) calmodulin binding and PI3K activation; (4) how Ras activates its RASSF5 cofactor, thereby stimulating signaling of the Hippo pathway and repressing proliferation; and (5) how intrinsically disordered segments in Raf help its attachment to the membrane and activation. Collectively, we provide the first inclusive review of the roles of intrinsic protein disorder in oncogenic Ras-driven signaling. We believe that a broad picture helps to grasp and formulate key mechanisms in Ras cancer biology and assists in therapeutic intervention.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Shuai Li
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Jian Zhang
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
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