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Singh A, Sonawane P, Kumar A, Singh H, Naumovich V, Pathak P, Grishina M, Khalilullah H, Jaremko M, Emwas AH, Verma A, Kumar P. Challenges and Opportunities in the Crusade of BRAF Inhibitors: From 2002 to 2022. ACS OMEGA 2023; 8:27819-27844. [PMID: 37576670 PMCID: PMC10413849 DOI: 10.1021/acsomega.3c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 08/15/2023]
Abstract
Serine/threonine-protein kinase B-Raf (BRAF; RAF = rapidly accelerated fibrosarcoma) plays an important role in the mitogen-activated protein kinase (MAPK) signaling cascade. Somatic mutations in the BRAF gene were first discovered in 2002 by Davies et al., which was a major breakthrough in cancer research. Subsequently, three different classes of BRAF mutants have been discovered. This class includes class I monomeric mutants (BRAFV600), class II BRAF homodimer mutants (non-V600), and class III BRAF heterodimers (non-V600). Cancers caused by these include melanoma, thyroid cancer, ovarian cancer, colorectal cancer, nonsmall cell lung cancer, and others. In this study, we have highlighted the major binding pockets in BRAF protein, their active and inactive conformations with inhibitors, and BRAF dimerization and its importance in paradoxical activation and BRAF mutation. We have discussed the first-, second-, and third-generation drugs approved by the Food and Drug Administration and drugs under clinical trials with all four different binding approaches with DFG-IN/OUT and αC-IN/OUT for BRAF protein. We have investigated particular aspects and difficulties with all three generations of inhibitors. Finally, this study has also covered recent developments in synthetic BRAF inhibitors (from their discovery in 2002 to 2022), their unique properties, and importance in inhibiting BRAF mutants.
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Affiliation(s)
- Ankit
Kumar Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Pankaj Sonawane
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Adarsh Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Harshwardhan Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Vladislav Naumovich
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Prateek Pathak
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Maria Grishina
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Habibullah Khalilullah
- Department
of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of
Pharmacy, Qassim University, Unayzah 51911, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health
Initiative and Red Sea Research Center, Division of Biological and
Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core
Laboratories, King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Amita Verma
- Bioorganic
and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical
Sciences, Sam Higginbottom University of
Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Pradeep Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
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2
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Maji L, Teli G, Raghavendra NM, Sengupta S, Pal R, Ghara A, Matada GSP. An updated literature on BRAF inhibitors (2018-2023). Mol Divers 2023:10.1007/s11030-023-10699-3. [PMID: 37470921 DOI: 10.1007/s11030-023-10699-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
BRAF is the most common serine-threonine protein kinase and regulates signal transduction from RAS to MEK inside the cell. The BRAF is a highly active isoform of RAF kinase. BRAF has two domains such as regulatory and kinase domains. The BRAF inhibitors bind in the c-terminus of the kinase domain and inhibit the downstream pathways. The mutation occurs mainly in the A-loop of the kinase domain. The mutation occurs due to a conversion of valine to glutamate/lysine/arginine/aspartic acid at 600th position. Among the diverse mutations, BRAFV600E is the most common and responsible for numerous cancer such as melanoma, colorectal, ovarian, and thyroid cancer. Due to mutations in RAC1, loss of PTEN, NF1, CCND1, USP28-FBW7 complex, COT overexpression, and CCND1 amplification, the BRAF kinase enzyme developed resistance over the commercially available BRAF inhibitors. There is still unmute urgence for the development of BRAF inhibitors to overcome the persistent limitation such as resistance, mutation, and adverse effects of drugs. In the current study, we described the structure, activation, downstream signaling pathway, and mutation of BRAF. Our group also provided a detailed review of BRAF inhibitors from the last five years (2018-2023) highlighting the structure-activity relationship, mechanistic study, and molecular docking studies. We hope that the current analysis will be a useful resource for researchers and provide chemists a glimpse into the future as design and development of more effective and secure BRAF kinase inhibitors. The development of BRAF inhibitors to overcome the persistent limitation such as resistance, mutation, and adverse effects of drugs. In depth description about different heterocyclic scaffolds (quinoline, imidazole, pyridine, triazole, pyrrole etc.) as BRAF inhibitors from the last five years (2018-2023) highlighting the structure-activity relationship, mechanistic study, and molecular docking studies.
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Affiliation(s)
- Lalmohan Maji
- Department of Pharmaceutical Chemistry, Integrated Drug Discovery Centre, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Ghanshyam Teli
- Department of Pharmaceutical Chemistry, Integrated Drug Discovery Centre, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | | | - Sindhuja Sengupta
- Department of Pharmaceutical Chemistry, Integrated Drug Discovery Centre, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Rohit Pal
- Department of Pharmaceutical Chemistry, Integrated Drug Discovery Centre, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Abhishek Ghara
- Department of Pharmaceutical Chemistry, Integrated Drug Discovery Centre, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
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Novel thiourea derivative compounds: thermal behavior, biological evaluation, Hirshfeld surfaces and frontier orbitals analyses, in silico ADMET profiling and molecular docking studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Yeşilkaynak T, Özkömeç FN, Çeşme M, Demirdöğen RE, Kutlu E, Kutlu HM, Emen FM. Synthesis of new thiourea derivatives and metal complexes: Thermal behavior, biological evaluation, in silico ADMET profiling and molecular docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Singh AK, Novak J, Kumar A, Singh H, Thareja S, Pathak P, Grishina M, Verma A, Yadav JP, Khalilullah H, Pathania V, Nandanwar H, Jaremko M, Emwas AH, Kumar P. Gaussian field-based 3D-QSAR and molecular simulation studies to design potent pyrimidine-sulfonamide hybrids as selective BRAF V600E inhibitors. RSC Adv 2022; 12:30181-30200. [PMID: 36329938 PMCID: PMC9585928 DOI: 10.1039/d2ra05751d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
The "RAS-RAF-MEK-ERK" pathway is an important signaling pathway in melanoma. BRAFV600E (70-90%) is the most common mutation in this pathway. BRAF inhibitors have four types of conformers: type I (αC-IN/DFG-IN), type II (αC-IN/DFG-OUT), type I1/2 (αC-OUT/DFG-IN), and type I/II (αC-OUT/DFG-OUT). First- and second-generation BRAF inhibitors show resistance to BRAFV600E and are ineffective against malignancies induced by dimer BRAF mutants causing 'paradoxical' activation. In the present study, we performed molecular modeling of pyrimidine-sulfonamide hybrids inhibitors using 3D-QSAR, molecular docking, and molecular dynamics simulations. Previous reports reveal the importance of pyrimidine and sulfonamide moieties in the development of BRAFV600E inhibitors. Analysis of 3D-QSAR models provided novel pyrimidine sulfonamide hybrid BRAFV600E inhibitors. The designed compounds share similarities with several structural moieties present in first- and second-generation BRAF inhibitors. A total library of 88 designed compounds was generated and molecular docking studies were performed with them. Four molecules (T109, T183, T160, and T126) were identified as hits and selected for detailed studies. Molecular dynamics simulations were performed at 900 ns and binding was calculated. Based on molecular docking and simulation studies, it was found that the designed compounds have better interactions with the core active site [the nucleotide (ADP or ATP) binding site, DFG motif, and the phospho-acceptor site (activation segment) of BRAFV600E protein than previous inhibitors. Similar to the FDA-approved BRAFV600E inhibitors the developed compounds have [αC-OUT/DFG-IN] conformation. Compounds T126, T160 and T183 interacted with DIF (Leu505), making them potentially useful against BRAFV600E resistance and malignancies induced by dimer BRAF mutants. The synthesis and biological evaluation of the designed molecules is in progress, which may lead to some potent BRAFV600E selective inhibitors.
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Affiliation(s)
- Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of PunjabGhuddaBathinda151401India
| | - Jurica Novak
- Department of Biotechnology, University of RijekaRijeka51000Croatia,Center for Artificial Intelligence and Cybersecurity, University of RijekaRijeka51000Croatia,Scientific and Educational Center ‘Biomedical Technologies’ School of Medical Biology, South Ural State UniversityChelyabinskRU-454080Russia
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of PunjabGhuddaBathinda151401India
| | - Harshwardhan Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of PunjabGhuddaBathinda151401India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of PunjabGhuddaBathinda151401India
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State UniversityChelyabinsk454008Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State UniversityChelyabinsk454008Russia
| | - Amita Verma
- Department of Pharmaceutical Sciences, Bioorganic and Medicinal Chemistry Research Laboratory, Sam Higginbottom University of Agriculture, Technology and SciencesPrayagraj211007India
| | - Jagat Pal Yadav
- Department of Pharmaceutical Sciences, Bioorganic and Medicinal Chemistry Research Laboratory, Sam Higginbottom University of Agriculture, Technology and SciencesPrayagraj211007India,Department of Pharmacology, Kamla Nehru Institute of Management and TechnologyFaridipurSultanpur228118India
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim UniversityUnayzah51911Saudi Arabia
| | - Vikas Pathania
- Clinical Microbiology & Bioactive Screening Laboratory, Council of Scientifc & Industrial Research -Institute of Microbial TechnologySector-39AChandigarh160036India
| | - Hemraj Nandanwar
- Clinical Microbiology & Bioactive Screening Laboratory, Council of Scientifc & Industrial Research -Institute of Microbial TechnologySector-39AChandigarh160036India
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST)Thuwal 23955-6900Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST)Thuwal 23955-6900Saudi Arabia
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of PunjabGhuddaBathinda151401India
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Zhao P, Wang X, Zhuang L, Huang S, Zhou Y, Yan Y, Shen R, Zhang F, Li J, Hu Q, Liu S, Zhang R, Dong P, Wan H, Bai C, He F, Tao W. Discovery of novel spiro compound as RAF kinase inhibitor with in vitro potency against KRAS mutant cancer. Bioorg Med Chem Lett 2022; 63:128666. [PMID: 35276360 DOI: 10.1016/j.bmcl.2022.128666] [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: 11/29/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 11/18/2022]
Abstract
The development of RAF inhibitors targeting cancers with wild type RAF kinase and/or RAS mutation has been challenging due to the paradoxical activation of the RAS-RAF-MEK-ERK cascade following RAF inhibitor treatment. Herein is the discovery and optimization of a series of RAF inhibitors with a novel spiro structure. The most potent spiro molecule 9 showed excellent in vitro potency against b/c RAF enzymes and RAS mutant H358 cancer cells with minimal paradoxical RAF signaling activation. Compound 9 also exhibited good drug-like properties as demonstrated by in vitro cytochrome P450 (CYP), liver microsome stability (LMS) data and moderate oral pharmacokinetics (PK) profiles in rat and mouse.
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Affiliation(s)
- Peng Zhao
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA.
| | - Xiangzhu Wang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Linghang Zhuang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Song Huang
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Yu Zhou
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Yuna Yan
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Ru Shen
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Fan Zhang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Jie Li
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Qiyue Hu
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Suxing Liu
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Rumin Zhang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Ping Dong
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Hong Wan
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Chang Bai
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Feng He
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Weikang Tao
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
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7
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Kirishnamaline G, Magdaline JD, Chithambarathanu T, Aruldhas D, Anuf AR. Theoretical investigation of structure, anticancer activity and molecular docking of thiourea derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Thabit MG, Mostafa AS, Selim KB, Elsayed MA, Nasr MN. Design, synthesis and molecular modeling of phenyl dihydropyridazinone derivatives as B-Raf inhibitors with anticancer activity. Bioorg Chem 2020; 103:104148. [DOI: 10.1016/j.bioorg.2020.104148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 06/25/2020] [Accepted: 07/26/2020] [Indexed: 12/29/2022]
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9
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Chavda J, Bhatt H. Systemic review on B-Raf V600E mutation as potential therapeutic target for the treatment of cancer. Eur J Med Chem 2020; 206:112675. [PMID: 32798788 DOI: 10.1016/j.ejmech.2020.112675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022]
Abstract
Cancer is one of the major public catastrophes worldwide and as per WHO, cancer is the leading cause of death universally after CVS disorders accounting for 9.6 million deaths in 2018. WHO statistics revealed five dangerous types of cancer viz. lung, breast, colorectal, prostate and skin. In male, lung cancer causes highest death, while in female, breast cancer causes the most. Alteration in MAPK signalling pathway plays a significant role in majority of cancer cases. Raf protein is activated by phosphorylation via downstream regulation of the MAPK pathway. Raf composed of 3 subtypes, viz. A-Raf, B-Raf, and C-Raf. B-Raf kinase plays a significant role in healthy cell growth in the MAPK pathway and the problem associated with B-Raf mutation leads to the development of cancer and other diseases. The progression of mutant B-Raf (B-RafV600E) protein is higher in cancer as compare to other diseases. In 2002, B-RafV600E mutation was identified for the first time in the development of cancer. The frequency of B-RafV600E mutation is higher in melanoma, thyroid, colorectal and ovarian cancer. We have covered small molecule B-RafV600E inhibitors reported in various literatures; from 2002 to 2020 and also covered clinical trial data. To widen the scope of readers, we compiled details of small molecules, specifically inhibiting B-RafV600E mutant and showing anti-proliferative activity against various cancer cell lines along with in-vivo data. We believe that the information covered here will be important in signifying the potentials of B-RafV600E mutation and its inhibitors as potent anticancer agents.
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Affiliation(s)
- Jaydeepsinh Chavda
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, India
| | - Hardik Bhatt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, India.
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