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Hagar FF, Abbas SH, Atef E, Abdelhamid D, Abdel-Aziz M. Benzimidazole scaffold as a potent anticancer agent with different mechanisms of action (2016-2023). Mol Divers 2024:10.1007/s11030-024-10907-8. [PMID: 39031290 DOI: 10.1007/s11030-024-10907-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/30/2024] [Indexed: 07/22/2024]
Abstract
Benzimidazole scaffolds have potent anticancer activity due to their structure similarity to nucleoside. In addition, benzimidazoles could function as hydrogen donors or acceptors and bind to different drug targets that participate in cancer progression. The literature had many anticancer agents containing benzimidazole cores that gained much interest. Provoked by our endless interest in benzimidazoles as anticancer agents, we summarized the successful trials of the benzimidazole scaffolds in this concern. Moreover, we discuss the substantial opportunities in cancer treatment using benzimidazole-based drugs that may direct medicinal chemists for a compelling future design of more active chemotherapeutic agents with potential clinical applications. The uniqueness of this work lies in the highlighted benzimidazole scaffold hybridization with different molecules and benzimidazole-metal complexes, detailed mechanisms of action, and the IC50 of the developed compounds determined by different laboratories after 2015.
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Affiliation(s)
- Fatma Fouad Hagar
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Samar H Abbas
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt.
| | - Eman Atef
- College of Pharmacy, West Coast University, Los Angeles, CA, USA
| | - Dalia Abdelhamid
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt.
- Raabe College of Pharmacy, Ohio Northern University, Ohio, USA.
| | - Mohamed Abdel-Aziz
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt
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2
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Boutalaka M, El Bahi S, Alaqarbeh M, El Alaouy MA, Koubi Y, Khatabi KE, Maghat H, Bouachrine M, Lakhlifi T. Computational investigation of imidazo[2,1-b]oxazole derivatives as potential mutant BRAF kinase inhibitors: 3D-QSAR, molecular docking, molecular dynamics simulation, and ADMETox studies. J Biomol Struct Dyn 2024; 42:5268-5287. [PMID: 37424193 DOI: 10.1080/07391102.2023.2233629] [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: 03/01/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
BRAF inhibitors are known to be an effective therapeutic target for treating melanoma and other types of cancer. Using 3D-QSAR, molecular docking, and MD simulations, this study evaluated various imidazo[2,1-b]oxazole derivatives that function as mutant BRAF kinase inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were used to create the 3D-QSAR models. CoMSIA/SEHA model has solid predictive power across several models (Q2 = 0.578; R2 = 0.828; R2pred = 0.74) and is the best model according to the numerous field models generated. The created model's predictive power was evaluated through external validation using a test set. CoMSIA/SEHA contour maps collect information that can be used to identify critical regions with solid anticancer activity. We developed four inhibitors with high predicted activity due to these observations. ADMET prediction was used to assess the toxicity of the proposed imidazo[2,1-b]oxazole compounds. The predictive molecules (T1-T4) demonstrated good ADMET properties, excluding the toxic active compounds 11r from the database. Molecular docking was also used to determine the patterns and modes of interactions between imidazo[2,1-b]oxazole ligands and receptors, which revealed that the proposed imidazo[2,1-b]oxazole scaffold was stable in the receptor's active site (PDB code: 4G9C). The suggested compounds (T1-T4) were subjected to molecular dynamics simulations lasting 100 ns to determine their binding free energies. The results showed that T2 had a more favorable binding free energy (-149.552 kJ/mol) than T1 (-112.556 kJ/mol), T3 (-115.503 kJ/mol), and T4 (-102.553 kJ/mol). The results suggest that the imidazo[2,1-b]oxazole compounds investigated in this study have potential as inhibitors of BRAF kinase and could be further developed as anticancer drugs. Highlights22 imidazo[2,1-b]oxazole compounds were subjected to research on three-dimensional quantitative conformational relationships.Using contour maps from 3D-QSAR models as a guide was used to figure out the areas and strategies for structural optimization.Combined molecular docking, molecular dynamics simulations, and binding free energy calculations to verify the inhibitor activity of the proposed 22 imidazo[2,1-b]oxazole compounds.Four potential B-RAF Kinase inhibitors were discovered, providing theoretical clues for developing a highly anticancer agent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meryem Boutalaka
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Salma El Bahi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | | | - Moulay Ahfid El Alaouy
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Yassine Koubi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Khalil El Khatabi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Hamid Maghat
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
- EST Khenifra, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Tahar Lakhlifi
- Department of Chemistry, Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University of Moulay Ismail, Meknes, Morocco
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3
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Allam RM, El Kerdawy AM, Gouda AE, Ahmed KA, Abdel-Mohsen HT. Benzimidazole-oxindole hybrids as multi-kinase inhibitors targeting melanoma. Bioorg Chem 2024; 146:107243. [PMID: 38457953 DOI: 10.1016/j.bioorg.2024.107243] [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: 12/28/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/10/2024]
Abstract
In the current study, a series of benzimidazole-oxindole conjugates 8a-t were designed and synthesized as type II multi-kinase inhibitors. They exhibited moderate to potent inhibitory activity against BRAFWT up to 99.61 % at 10 µM. Notably, compounds 8e, 8k, 8n and 8s demonstrated the most promising activity, with 99.44 to 99.61 % inhibition. Further evaluation revealed that 8e, 8k, 8n and 8s exhibit moderate to potent inhibitory effects on the kinases BRAFV600E, VEGFR-2, and FGFR-1. Additionally, compounds 8a-t were screened for their cytotoxicity by the NCI, and several compounds showed significant growth inhibition in diverse cancer cell lines. Compound 8e stood out with a GI50 range of 1.23 - 3.38 µM on melanoma cell lines. Encouraged by its efficacy, it was further investigated for its antitumor activity and mechanism of action, using sorafenib as a reference standard. The hybrid compound 8e exhibited potent cellular-level suppression of BRAFWT, VEGFR-2, and FGFR-1 in A375 cell line, surpassing the effects of sorafenib. In vivo studies demonstrate that 8e significantly inhibits the growth of B16F10 tumors in mice, leading to increased survival rates and histopathological tumor regression. Furthermore, 8e reduces angiogenesis markers, mRNA expression levels of VEGFR-2 and FGFR-1, and production of growth factors. It also downregulated Notch1 protein expression and decreased TGF-β1 production. Molecular docking simulations suggest that 8e binds as a promising type II kinase inhibitor in the target kinases interacting with the key regions in their kinase domain.
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Affiliation(s)
- Rasha M Allam
- Department of Pharmacology, Medical and Clinical Research Institute, National Research Centre, El-Buhouth St., Dokki, P.O. Box 12622, Cairo, Egypt
| | - Ahmed M El Kerdawy
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, United Kingdom; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, P.O. Box 11562, Cairo, Egypt
| | - Ahmed E Gouda
- Pharmaceutical Research Department, Nawah Scientific, Cairo, Egypt
| | - Kawkab A Ahmed
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Heba T Abdel-Mohsen
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, El-Buhouth St., Dokki, P.O. Box 12622, Cairo, Egypt.
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4
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Abdel-Mohsen HT, Ibrahim MA, Nageeb AM, El Kerdawy AM. Receptor-based pharmacophore modeling, molecular docking, synthesis and biological evaluation of novel VEGFR-2, FGFR-1, and BRAF multi-kinase inhibitors. BMC Chem 2024; 18:42. [PMID: 38395926 PMCID: PMC10893631 DOI: 10.1186/s13065-024-01135-0] [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: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
A receptor-based pharmacophore model describing the binding features required for the multi-kinase inhibition of the target kinases (VEGFR-2, FGFR-1, and BRAF) were constructed and validated. It showed a good overall quality in discriminating between the active and the inactive in a compiled test set compounds with F1 score of 0.502 and Mathew's correlation coefficient of 0.513. It described the ligand binding to the hinge region Cys or Ala, the glutamate residue of the Glu-Lys αC helix conserved pair, the DFG motif Asp at the activation loop, and the allosteric back pocket next to the ATP binding site. Moreover, excluded volumes were used to define the steric extent of the binding sites. The application of the developed pharmacophore model in virtual screening of an in-house scaffold dataset resulted in the identification of a benzimidazole-based scaffold as a promising hit within the dataset. Compounds 8a-u were designed through structural optimization of the hit benzimidazole-based scaffold through (un)substituted aryl substitution on 2 and 5 positions of the benzimidazole ring. Molecular docking simulations and ADME properties predictions confirmed the promising characteristics of the designed compounds in terms of binding affinity and pharmacokinetic properties, respectively. The designed compounds 8a-u were synthesized, and they demonstrated moderate to potent VEGFR-2 inhibitory activity at 10 µM. Compound 8u exhibited a potent inhibitory activity against the target kinases (VEGFR-2, FGFR-1, and BRAF) with IC50 values of 0.93, 3.74, 0.25 µM, respectively. The benzimidazole derivatives 8a-u were all selected by the NCI (USA) to conduct their anti-proliferation screening. Compounds 8a and 8d resulted in a potent mean growth inhibition % (GI%) of 97.73% and 92.51%, respectively. Whereas compounds 8h, 8j, 8k, 8o, 8q, 8r, and 8u showed a mean GI% > 100% (lethal effect). The most potent compounds on the NCI panel of 60 different cancer cell lines were progressed further to NCI five-dose testing. The benzimidazole derivatives 8a, 8d, 8h, 8j, 8k, 8o, 8q, 8r and 8u exhibited potent anticancer activity on the tested cell lines reaching sub-micromolar range. Moreover, 8u was found to induce cell cycle arrest of MCF-7 cell line at the G2/M phase and accumulating cells at the sub-G1 phase as a result of cell apoptosis.
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Affiliation(s)
- Heba T Abdel-Mohsen
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, P.O. 12622, Cairo, Egypt.
| | - Marwa A Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, P.O. 11562, Cairo, Egypt
| | - Amira M Nageeb
- High Throughput Molecular and Genetic Technology Lab, Center of Excellence for Advanced Sciences, Biochemistry Department, Biotechnology Research Institute, National Research Centre, Dokki, P.O. 12622, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, P.O. 11562, Cairo, Egypt
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
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5
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Sabt A, Khedr MA, Eldehna WM, Elshamy AI, Abdelhameed MF, Allam RM, Batran RZ. New pyrazolylindolin-2-one based coumarin derivatives as anti-melanoma agents: design, synthesis, dual BRAF V600E/VEGFR-2 inhibition, and computational studies. RSC Adv 2024; 14:5907-5925. [PMID: 38370458 PMCID: PMC10870110 DOI: 10.1039/d4ra00157e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Malignant melanoma is the most invasive skin cancer with the highest risk of death. The inhibition of BRAFV600E appears relevant for overcoming secondary resistance developed during melanoma treatment. BRAFV600E triggers angiogenesis via modification of the expression of angiogenic inducers, which play a crucial role in the metastasis of melanoma. Accordingly, the dual inhibition of the BRAFV600E/VEGFR-2 signaling pathway is considered a rational approach in the design of anti-melanoma candidates. In this study, a new class of pyrazolylindolin-2-one linked coumarin derivatives as dual BRAFV600E/VEGFR-2 inhibitors targeting A375 melanoma cells was designed. Target compounds were tailored to occupy the pockets of BRAFV600E and VEGFR-2. Most of the synthesized compounds demonstrated potent mean growth inhibitory activity against A375 cells. Compound 4j was the most active cytotoxic derivative, displaying an IC50 value at a low micromolar concentration of 0.96 μM with a significant safety profile. Moreover, 4j showed dual potent inhibitory activity against BRAFV600E and VEGFR-2 (IC50 = 1.033 and 0.64 μM, respectively) and was more active than the reference drug sorafenib. Furthermore, derivative 4j caused significant G0/G1 cell cycle arrest, induced apoptosis, and inhibited the migration of melanoma cells. Molecular docking showed that compound 4j achieved the highest ΔG value of -9.5 kcal mol-1 against BRAFV600E and significant ΔG of -8.47 kcal mol-1 against VEGFR-2. Furthermore, the structure-activity relationship study revealed that TPSA directly contributed to the anticancer activity of the tested compounds.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Mohammed A Khedr
- Department of Pharmaceutical Chemistry, College of Pharmacy, Kuwait University Safat 13110 Kuwait
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University 11795 Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh 33516 Egypt
| | - Abdelsamed I Elshamy
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Mohamed F Abdelhameed
- Pharmacology Department, Medical and Clinical Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Rasha M Allam
- Pharmacology Department, Medical and Clinical Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
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6
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Tian Y, Zhang M, Heng P, Hou H, Wang B. Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation for identification of potential ERK inhibitors. J Biomol Struct Dyn 2024; 42:2153-2161. [PMID: 37129289 DOI: 10.1080/07391102.2023.2204495] [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: 01/31/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
As the downstream component of the mitogen-activated protein kinases (MAPK) pathway, the extracellular signal-regulated kinase (ERK) is responsible for phosphorylating a broad range of substrates in cell proliferation, differentiation, and survival. Direct targeting the ERK proteins by the piperidinopyrimidine urea-based inhibitors has been demonstrated to be an effective way to block the MAPK signaling pathway in inhibiting tumor growth. In order to discover better inhibitors, a computer-aided drug design (CADD) approach was employed to reveal the pharmacological characteristics and mechanisms of action. The pharmacophore model was generated on the basis of the compounds with eight features, i.e., four hydrogen bond acceptor atoms, one hydrogen bond donor atom, and three hydrophobic centers. A total of 14 hit compounds were obtained through virtual screening. Two potential inhibitors, namely VS01 and VS02, have been identified by molecular docking and molecular dynamics simulations. Both compounds are capable of attaching to the ERK pocket precisely. The binding free energies of VS01 and VS02 are about 15 kJ/mol and 4 kJ/mol stronger than that of the clinic Ulixertinib because of the characteristic hydrogen bonding, electrostatic, and hydrophilic interactions. The present theoretical investigations shed new light on the rational design of the potential ERK inhibitors to stimulate further experimental tests.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yafeng Tian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Mi Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Panpan Heng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Hua Hou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Baoshan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People's Republic of China
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7
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Hong S, Jeon M, Kwon J, Park H, Lee G, Kim K, Ahn S. Targeting RAF Isoforms and Tumor Microenvironments in RAS or BRAF Mutant Colorectal Cancers with SJ-C1044 for Anti-Tumor Activity. Curr Issues Mol Biol 2023; 45:5865-5878. [PMID: 37504287 PMCID: PMC10378394 DOI: 10.3390/cimb45070371] [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: 06/04/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Colorectal cancer (CRC) is a significant global health issue characterized by a high prevalence of KRAS gene mutations. The RAS/MAPK pathway, involving KRAS, plays a crucial role in CRC progression. Although some RAS inhibitors have been approved, their efficacy in CRC is limited. To overcome these limitations, pan-RAF inhibitors targeting A-Raf, B-Raf, and C-Raf have emerged as promising therapeutic strategies. However, resistance to RAF inhibition and the presence of an immunosuppressive tumor microenvironment (TME) pose additional obstacles to effective therapy. Here, we evaluated the potential of a novel pan-RAF inhibitor, SJ-C1044, for targeting mutant KRAS-mediated signaling and inhibiting CRC cell proliferation. Notably, SJ-C1044 also exhibited inhibitory effects on immunokinases, specifically, CSF1R, VEGFR2, and TIE2, which play crucial roles in immune suppression. SJ-C1044 demonstrated potent antitumor activity in xenograft models of CRC harboring KRAS or BRAF mutations. Importantly, treatment with SJ-C1044 resulted in increased infiltration of T cells and reduced presence of tumor-associated macrophages and regulatory T cells within the TME. Thus, SJ-C1044 shows immunomodulatory potential and the ability to enhance antitumor responses. The study underscores the therapeutic potential of SJ-C1044 as a novel pan-RAF inhibitor capable of targeting oncogenic signaling pathways and overcoming immune suppression in CRC.
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Affiliation(s)
- Sungpyo Hong
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Myeongjin Jeon
- Research Center, Samjin Pharm. Co., Ltd., Seoul 07794, Republic of Korea; (M.J.); (G.L.)
| | - Jeonghee Kwon
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Hanbyeol Park
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Goeun Lee
- Research Center, Samjin Pharm. Co., Ltd., Seoul 07794, Republic of Korea; (M.J.); (G.L.)
| | - Kilwon Kim
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Soonkil Ahn
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
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Liu XJ, Zhao HC, Hou SJ, Zhang HJ, Cheng L, Yuan S, Zhang LR, Song J, Zhang SY, Chen SW. Recent development of multi-target VEGFR-2 inhibitors for the cancer therapy. Bioorg Chem 2023; 133:106425. [PMID: 36801788 DOI: 10.1016/j.bioorg.2023.106425] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/05/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Vascular epidermal growth factor receptor-2 (VEGFR-2), as an important tyrosine transmembrane protein, plays an important role in regulating endothelial cell proliferation and migration, regulating angiogenesis and other biological functions. VEGFR-2 is aberrantly expressed in many malignant tumors, and it is also related to the occurrence, development, and growth of tumors and drug resistance. Currently, there are nine VEGFR-2 targeted inhibitors approved by US.FDA for clinical use as anticancer drugs. Due to the limited clinical efficacy and potential toxicity of VEGFR inhibitors, it is necessary to develop new strategies to improve the clinical efficacy of VEGFR inhibitors. The development of multitarget therapy, especially dual-target therapy, has become a hot research field of cancer therapy, which may provide an effective strategy with higher therapeutic efficacy, pharmacokinetic advantages and low toxicity. Many groups have reported that the therapeutic effects could be improved by simultaneously inhibiting VEGFR-2 and other targets, such as EGFR, c-Met, BRAF, HDAC, etc. Therefore, VEGFR-2 inhibitors with multi-targeting capabilities have been considered to be promising and effective anticancer agents for cancer therapy. In this work, we reviewed the structure and biological functions of VEGFR-2, and summarized the drug discovery strategies, and inhibitory activities of VEGFR-2 inhibitors with multi-targeting capabilities reported in recent years. This work might provide the reference for the development of VEGFR-2 inhibitors with multi-targeting capabilities as novel anticancer agents.
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Affiliation(s)
- Xiu-Juan Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hong-Cheng Zhao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Medical College of China Three Gorges University, Yichang 443003, China
| | - Su-Juan Hou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hao-Jie Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Lei Cheng
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jian Song
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Sai-Yang Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Shi-Wu Chen
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
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9
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Xiao Z, Liu F, Cheng J, Wang Y, Zhou W, Zhang Y. B-Raf inhibitor vemurafenib counteracts sulfur mustard-induced epidermal impairment through MAPK/ERK signaling. Drug Chem Toxicol 2023; 46:226-235. [PMID: 34986718 DOI: 10.1080/01480545.2021.2021927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The chemical warfare agent sulfur mustard (SM) causes severe cutaneous lesions characterized by epidermal cell death, apoptosis, and inflammation. At present, the molecular mechanisms underlying SM-induced injury are not well understood, and there is no standard treatment protocol for SM-exposed patients. Here, we conducted a high-content screening of the Food and Drug Administration (FDA)-approved drug library of 1018 compounds against SM injury on an immortal human keratinocyte HaCaT cell line, focusing on cell survival. We found that the B-Raf inhibitor vemurafenib had an apparent therapeutic effect on HaCaT cells and resisted SM toxicity. Other tested B-Raf inhibitors, both type-I (dabrafenib and encorafenib) and type-II (RAF265 and AZ628), also exhibited potent therapeutic effects on SM-exposed HaCaT cells. Both SM and vemurafenib triggered extracellular signal-related kinase (ERK) activation. The therapeutic effect of vemurafenib in HaCaT cells during SM injury was ERK-dependent, indicating a specific role of ERK in keratinocyte regulatory mechanisms. Furthermore, vemurafenib partially improved cutaneous damage in a mouse ear vesicant model. Collectively, our results provide evidence that the B-Raf inhibitor vemurafenib is a potential therapeutic agent against SM injury, and oncogenic B-Raf might be an exciting new therapeutic target following exposure to mustard vesicating agents.
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Affiliation(s)
- Zhiyong Xiao
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Feng Liu
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Junping Cheng
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Ying Wang
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Wenxia Zhou
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
| | - Yongxiang Zhang
- Beijing Institute of Pharmacology & Toxicology, Beijing, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing, China
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10
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Li CC, Chi XJ, Wang J, Potter AL, Wang XJ, Yang CFJ. Small molecule RAF265 as an antiviral therapy acts against HSV-1 by regulating cytoskeleton rearrangement and cellular translation machinery. J Med Virol 2023; 95:e28226. [PMID: 36251738 DOI: 10.1002/jmv.28226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/11/2023]
Abstract
Host-targeting antivirals (HTAs) have received increasing attention for their potential as broad-spectrum antivirals that pose relatively low risk of developing drug resistance. The repurposing of pharmaceutical drugs for use as antivirals is emerging as a cost- and time- efficient approach to developing HTAs for the treatment of a variety of viral infections. In this study, we used a virus titer method to screen 30 small molecules for antiviral activity against Herpes simplex virus-1 (HSV-1). We found that the small molecule RAF265, an anticancer drug that has been shown to be a potent inhibitor of B-RAF V600E, reduced viral loads of HSV-1 by 4 orders of magnitude in Vero cells and reduced virus proliferation in vivo. RAF265 mediated cytoskeleton rearrangement and targeted the host cell's translation machinery, which suggests that the antiviral activity of RAF265 may be attributed to a dual inhibition strategy. This study offers a starting point for further advances toward clinical development of antivirals against HSV-1.
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Affiliation(s)
- Cui-Cui Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Department of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiao-Jing Chi
- Department of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Department of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Alexandra L Potter
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Department of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chi-Fu Jeffrey Yang
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA.,Division of Thoracic Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
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11
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Ercoli MF, Ramos PZ, Jain R, Pilotte J, Dong OX, Thompson T, Wells CI, Elkins JM, Edwards AM, Couñago RM, Drewry DH, Ronald PC. An open source plant kinase chemogenomics set. PLANT DIRECT 2022; 6:e460. [PMID: 36447653 PMCID: PMC9694430 DOI: 10.1002/pld3.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.
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Affiliation(s)
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - Rashmi Jain
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Joseph Pilotte
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Ty Thompson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Carrow I. Wells
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Jonathan M. Elkins
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
- Centre for Medicines DiscoveryUniversity of OxfordOxfordUK
| | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - David H. Drewry
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
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12
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Wang J, Tian WJ, Li CC, Zhang XZ, Fan K, Li SL, Wang XJ. Small-Molecule RAF265 as an Antiviral Therapy Acts against PEDV Infection. Viruses 2022; 14:v14102261. [PMID: 36298816 PMCID: PMC9611448 DOI: 10.3390/v14102261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the family Coronaviridae, causes acute diarrhea, vomiting, dehydration, and high mortality in newborn piglets, and has caused significant economic losses in the pig industry. There are currently no specific drugs available to treat PEDV. Viruses depend exclusively on the cellular machinery to ensure an efficient replication cycle. In the present study, we found that small-molecule RAF265, an anticancer drug that has been shown to be a potent inhibitor of RAF, reduced viral loads of PEDV by 4 orders of magnitude in Vero cells, and protected piglets from virus challenge. RAF265 reduced PEDV production by mediating cytoskeleton arrangement and targeting the host cell’s translation machinery. Treatment with RAF265 inhibited viral entry of PEDV S-glycoprotein pseudotyped viral vector particle (PEDV-pp), at half maximal effective concentrations (EC50) of 79.1 nM. RAF265 also presented potent inhibitory activity against viral infection by SARS-CoV-2-pp and SARS-CoV-pp. The present work may provide a starting point for further progress toward the development of antiviral strategies effective against coronavirus PEDV.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wen-Jun Tian
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Cui-Cui Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiu-Zhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kai Fan
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: (K.F.); (S.-L.L.); (X.-J.W.)
| | - Song-Li Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (K.F.); (S.-L.L.); (X.-J.W.)
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: (K.F.); (S.-L.L.); (X.-J.W.)
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13
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Jackson JJ, Shibuya GM, Ravishankar B, Adusumilli L, Bradford D, Brockstedt DG, Bucher C, Bui M, Cho C, Colas C, Cutler G, Dukes A, Han X, Hu DX, Jacobson S, Kassner PD, Katibah GE, Ko MYM, Kolhatkar U, Leger PR, Ma A, Marshall L, Maung J, Ng AA, Okano A, Pookot D, Poon D, Ramana C, Reilly MK, Robles O, Schwarz JB, Shakhmin AA, Shunatona HP, Sreenivasan R, Tivitmahaisoon P, Xu M, Zaw T, Wustrow DJ, Zibinsky M. Potent GCN2 Inhibitor Capable of Reversing MDSC-Driven T Cell Suppression Demonstrates In Vivo Efficacy as a Single Agent and in Combination with Anti-Angiogenesis Therapy. J Med Chem 2022; 65:12895-12924. [PMID: 36127295 DOI: 10.1021/acs.jmedchem.2c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
General control nonderepressible 2 (GCN2) protein kinase is a cellular stress sensor within the tumor microenvironment (TME), whose signaling cascade has been proposed to contribute to immune escape in tumors. Herein, we report the discovery of cell-potent GCN2 inhibitors with excellent selectivity against its closely related Integrated Stress Response (ISR) family members heme-regulated inhibitor kinase (HRI), protein kinase R (PKR), and (PKR)-like endoplasmic reticulum kinase (PERK), as well as good kinome-wide selectivity and favorable PK. In mice, compound 39 engages GCN2 at levels ≥80% with an oral dose of 15 mg/kg BID. We also demonstrate the ability of compound 39 to alleviate MDSC-related T cell suppression and restore T cell proliferation, similar to the effect seen in MDSCs from GCN2 knockout mice. In the LL2 syngeneic mouse model, compound 39 demonstrates significant tumor growth inhibition (TGI) as a single agent. Furthermore, TGI mediated by anti-VEGFR was enhanced by treatment with compound 39 demonstrating the complementarity of these two mechanisms.
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Affiliation(s)
- Jeffrey J Jackson
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Grant M Shibuya
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Buvana Ravishankar
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Lavanya Adusumilli
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Delia Bradford
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Dirk G Brockstedt
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Cyril Bucher
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Minna Bui
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Cynthia Cho
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Christoph Colas
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Gene Cutler
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Adrian Dukes
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Xinping Han
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Dennis X Hu
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Scott Jacobson
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Paul D Kassner
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - George E Katibah
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Michelle Yoo Min Ko
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Urvi Kolhatkar
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Paul R Leger
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Anqi Ma
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Lisa Marshall
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Jack Maung
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Andrew A Ng
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Akinori Okano
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Deepa Pookot
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Daniel Poon
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Chandru Ramana
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Maureen K Reilly
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Omar Robles
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Jacob B Schwarz
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Anton A Shakhmin
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Hunter P Shunatona
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Raashi Sreenivasan
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | | | - Mengshu Xu
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Thant Zaw
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - David J Wustrow
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Mikhail Zibinsky
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
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14
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Ali IH, Abdel-Mohsen HT, Mounier MM, Abo-elfadl MT, El Kerdawy AM, Ghannam IA. Design, Synthesis and Anticancer Activity of Novel 2-Arylbenzimidazole/2-Thiopyrimidines and 2-Thioquinazolin-4(3H)-ones Conjugates as Targeted RAF and VEGFR-2 Kinases Inhibitors. Bioorg Chem 2022; 126:105883. [DOI: 10.1016/j.bioorg.2022.105883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 01/03/2023]
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15
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Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C, Pichlmair A. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat Commun 2021; 12:7009. [PMID: 34853303 PMCID: PMC8636641 DOI: 10.1038/s41467-021-27192-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
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Affiliation(s)
- Friederike L Pennemann
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Assel Mussabekova
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Vincent Grass
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Teresa Maria Lavacca
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Cathleen Holze
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Lila Oubraham
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Yasmine Benamrouche
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Enrico Girardi
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rasha E Boulos
- Computer Science and Mathematics Department, School of Arts and Science, Lebanese American University, Byblos, Lebanon
| | - Rune Hartmann
- Aarhus University, Department of Molecular Biology and Genetics - Structural Biology, Aarhus, Denmark
| | - Giulio Superti-Furga
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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16
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Bekele RT, Samant AS, Nassar AH, So J, Garcia EP, Curran CR, Hwang JH, Mayhew DL, Nag A, Thorner AR, Börcsök J, Sztupinszki Z, Pan CX, Bellmunt J, Kwiatkowski DJ, Sonpavde GP, Van Allen EM, Mouw KW. RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics. J Clin Invest 2021; 131:147849. [PMID: 34554931 DOI: 10.1172/jci147849] [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: 02/03/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Bladder cancer is a genetically heterogeneous disease, and novel therapeutic strategies are needed to expand treatment options and improve clinical outcomes. Here, we identified a unique subset of urothelial tumors with focal amplification of the RAF1 (CRAF) kinase gene. RAF1-amplified tumors had activation of the RAF/MEK/ERK signaling pathway and exhibited a luminal gene expression pattern. Genetic studies demonstrated that RAF1-amplified tumors were dependent upon RAF1 activity for survival, and RAF1-activated cell lines and patient-derived models were sensitive to available and emerging RAF inhibitors as well as combined RAF plus MEK inhibition. Furthermore, we found that bladder tumors with HRAS- or NRAS-activating mutations were dependent on RAF1-mediated signaling and were sensitive to RAF1-targeted therapy. Together, these data identified RAF1 activation as a dependency in a subset making up nearly 20% of urothelial tumors and suggested that targeting RAF1-mediated signaling represents a rational therapeutic strategy.
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Affiliation(s)
- Raie T Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Amruta S Samant
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Amin H Nassar
- Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medical Oncology and
| | | | | | | | - Justin H Hwang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology and
| | - David L Mayhew
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology and
| | - Anwesha Nag
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Chong-Xian Pan
- VA Boston Healthcare System, Harvard Medical School, West Roxbury, Massachusetts, USA
| | - Joaquim Bellmunt
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - David J Kwiatkowski
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Eliezer M Van Allen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology and
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
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17
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Monaco KA, Delach S, Yuan J, Mishina Y, Fordjour P, Labrot E, McKay D, Guo R, Higgins S, Wang HQ, Liang J, Bui K, Green J, Aspesi P, Ambrose J, Mapa F, Griner L, Jaskelioff M, Fuller J, Crawford K, Pardee G, Widger S, Hammerman PS, Engelman JA, Stuart DD, Cooke VG, Caponigro G. LXH254, a Potent and Selective ARAF-Sparing Inhibitor of BRAF and CRAF for the Treatment of MAPK-Driven Tumors. Clin Cancer Res 2020; 27:2061-2073. [DOI: 10.1158/1078-0432.ccr-20-2563] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022]
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18
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In silico evaluation of some 4-(quinolin-2-yl)pyrimidin-2-amine derivatives as potent V600E-BRAF inhibitors with pharmacokinetics ADMET and drug-likeness predictions. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020. [DOI: 10.1186/s43094-020-00084-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
The resistance of V600E-BRAF to the vemurafenib and the side effects of the identified inhibitors trigger the research for a novel and more potent anti-melanoma agents. In this study, virtual docking screening along with pharmacokinetics ADMET and drug-likeness predictions were combined to evaluate some 4-(quinolin-2-yl)pyrimidin-2-amine derivatives as potent V600E-BRAF inhibitors.
Results
Some of the selected compounds exhibited better binding scores and favorable interaction with the V600E-BRAF enzyme. Out of the screened compounds, two most potent (5 and 9) having good Rerank scores (− 128.011 and − 126.258) emerged as effective and potent V600E-BRAF inhibitors that outperformed the FDA-approved V600E-BRAF inhibitor (vemurafenib, − 118.607). Thus, the molecular docking studies revealed that the studied compounds showed competing for inhibition of V600E-BRAF with vemurafenib at the binding site and possessed better pharmacological parameters based on the drug-likeness rules filters for the oral bioavailability, and ADMET risk parameters.
Conclusion
The docking analysis, drug-likeness rules filters, and ADMET study identified compounds (5 and 9) as the best hits against V600E-BRAF kinase with enhanced pharmacological properties. This recommends that these compounds may be developed as potent anti-melanoma agents.
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19
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Sullivan RJ, Hollebecque A, Flaherty KT, Shapiro GI, Rodon Ahnert J, Millward MJ, Zhang W, Gao L, Sykes A, Willard MD, Yu D, Schade AE, Crowe K, Flynn DL, Kaufman MD, Henry JR, Peng SB, Benhadji KA, Conti I, Gordon MS, Tiu RV, Hong DS. A Phase I Study of LY3009120, a Pan-RAF Inhibitor, in Patients with Advanced or Metastatic Cancer. Mol Cancer Ther 2020; 19:460-467. [PMID: 31645440 DOI: 10.1158/1535-7163.mct-19-0681] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/23/2019] [Accepted: 10/18/2019] [Indexed: 02/03/2023]
Abstract
Mutations in ERK signaling drive a significant percentage of malignancies. LY3009120, a pan-RAF and dimer inhibitor, has preclinical activity in RAS- and BRAF-mutated cell lines including BRAF-mutant melanoma resistant to BRAF inhibitors. This multicenter, open-label, phase I clinical trial (NCT02014116) consisted of part A (dose escalation) and part B (dose confirmation) in patients with advanced/metastatic cancer. In part A, oral LY3009120 was dose escalated from 50 to 700 mg twice a day on a 28-day cycle. In part B, 300 mg LY3009120 was given twice a day. The primary objective was to identify a recommended phase II dose (RP2D). Secondary objectives were to evaluate safety, pharmacokinetics, and preliminary efficacy. Identification of pharmacodynamic biomarkers was exploratory. In parts A and B, 35 and 16 patients were treated, respectively (N = 51). In part A, 6 patients experienced eight dose-limiting toxicities. The RP2D was 300 mg twice a day. Common (>10%) any-grade drug-related treatment-emergent adverse events were fatigue (n = 15), nausea (n = 12), dermatitis acneiform (n = 10), decreased appetite (n = 7), and maculopapular rash (n = 7). The median duration of treatment was 4 weeks; 84% of patients completed one or two cycles of treatment. Exposures observed at 300 mg twice a day were above the preclinical concentration associated with tumor regression. Eight patients had a best overall response of stable disease; there were no complete or partial clinical responses. Despite adequate plasma exposure levels, predicted pharmacodynamic effects were not observed.
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Affiliation(s)
- Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Antoine Hollebecque
- Drug Development Department (DITEP), Gustave Roussy Cancer Institute, Villejuif, France
| | - Keith T Flaherty
- Developmental Therapeutics, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | | | - Michael J Millward
- Linear Clinical Research, University of Western Australia, Perth, Australia
| | - Wei Zhang
- Eli Lilly and Company, Indianapolis, Indiana
| | - Ling Gao
- Eli Lilly and Company, Branchburg, New Jersey
| | | | | | - Danni Yu
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | | | | | | | | | | | | | - Ramon V Tiu
- Eli Lilly and Company, Indianapolis, Indiana
| | - David S Hong
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas.
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20
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Degirmenci U, Wang M, Hu J. Targeting Aberrant RAS/RAF/MEK/ERK Signaling for Cancer Therapy. Cells 2020; 9:E198. [PMID: 31941155 PMCID: PMC7017232 DOI: 10.3390/cells9010198] [Citation(s) in RCA: 296] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The RAS/RAF/MEK/ERK (MAPK) signaling cascade is essential for cell inter- and intra-cellular communication, which regulates fundamental cell functions such as growth, survival, and differentiation. The MAPK pathway also integrates signals from complex intracellular networks in performing cellular functions. Despite the initial discovery of the core elements of the MAPK pathways nearly four decades ago, additional findings continue to make a thorough understanding of the molecular mechanisms involved in the regulation of this pathway challenging. Considerable effort has been focused on the regulation of RAF, especially after the discovery of drug resistance and paradoxical activation upon inhibitor binding to the kinase. RAF activity is regulated by phosphorylation and conformation-dependent regulation, including auto-inhibition and dimerization. In this review, we summarize the recent major findings in the study of the RAS/RAF/MEK/ERK signaling cascade, particularly with respect to the impact on clinical cancer therapy.
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Affiliation(s)
- Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Mei Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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21
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Fujimoto J, Kurasawa O, Takagi T, Liu X, Banno H, Kojima T, Asano Y, Nakamura A, Nambu T, Hata A, Ishii T, Sameshima T, Debori Y, Miyamoto M, Klein MG, Tjhen R, Sang BC, Levin I, Lane SW, Snell GP, Li K, Kefala G, Hoffman ID, Ding SC, Cary DR, Mizojiri R. Identification of Novel, Potent, and Orally Available GCN2 Inhibitors with Type I Half Binding Mode. ACS Med Chem Lett 2019; 10:1498-1503. [PMID: 31620240 DOI: 10.1021/acsmedchemlett.9b00400] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022] Open
Abstract
General control nonderepressible 2 (GCN2) is a master regulator kinase of amino acid homeostasis and important for cancer survival in the tumor microenvironment under amino acid depletion. We initiated studies aiming at the discovery of novel GCN2 inhibitors as first-in-class antitumor agents and conducted modification of the substructure of sulfonamide derivatives with expected type I half binding on GCN2. Our synthetic strategy mainly corresponding to the αC-helix allosteric pocket of GCN2 led to significant enhancement in potency and a good pharmacokinetic profile in mice. In addition, compound 6d, which showed slow dissociation in binding on GCN2, demonstrated antiproliferative activity in combination with the asparagine-depleting agent asparaginase in an acute lymphoblastic leukemia (ALL) cell line, and it also displayed suppression of GCN2 pathway activation with asparaginase treatment in the ALL cell line and mouse xenograft model.
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Affiliation(s)
- Jun Fujimoto
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Osamu Kurasawa
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Terufumi Takagi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Xin Liu
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroshi Banno
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takuto Kojima
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasutomi Asano
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akito Nakamura
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tadahiro Nambu
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akito Hata
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tsuyoshi Ishii
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoya Sameshima
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasuyuki Debori
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Maki Miyamoto
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Michael G. Klein
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Richard Tjhen
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Bi-Ching Sang
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Irena Levin
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Scott Weston Lane
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Gyorgy P. Snell
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Ke Li
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Georgia Kefala
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Isaac D. Hoffman
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Steve C. Ding
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Douglas R. Cary
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ryo Mizojiri
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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22
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Abdel-Mohsen HT, Omar MA, El Kerdawy AM, Mahmoud AEE, Ali MM, El Diwani HI. Novel potent substituted 4-amino-2-thiopyrimidines as dual VEGFR-2 and BRAF kinase inhibitors. Eur J Med Chem 2019; 179:707-722. [PMID: 31284081 DOI: 10.1016/j.ejmech.2019.06.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 12/23/2022]
Abstract
In the present study, we report the discovery of a novel class of substituted 4-amino-2-thiopyrimidines as antiangiogenic and antiproliferative agents. Structural hybridization between 4-substituted aminopyrimidines (VEGFR-2 inhibitors) and 2-thioxopyrimidines (BRAF inhibitors) was carried out to afford substituted 4-amino-2-thiopyrimidines as type II dual VEGFR-2/BRAF inhibitors. Our design strategy was tailored such that the 4-amino-2-thiopyrimidine scaffold is to be accommodated in the central gate area of the inactive DFG-out conformation of both enzymes. On one side, the hydrophobic substituent on the 4-amino group would occupy the hydrophobic back pocket and on the other side the substituent on the sulfide moiety should extend to fit in the hinge region (front pocket). Molecular docking simulations confirmed the ability of the designed compounds to accomplish the key interactions in VEGFR-2 and BRAF active sites. Most of the synthesized substituted 4-amino-2-thiopyrimidines demonstrated potent VEGFR-2 inhibitory activity at submicromolar concentrations. Compounds 8a, 8d, 9c and 9e showed IC50 = 0.17, 0.12, 0.17 and 0.19 μM, respectively against VEGFR-2 in comparison to sorafenib (I) IC50 = 0.10 μM and regorafenib (II) IC50 = 0.005 μM. While compounds 9c, 9d and 10a showed IC50 = 0.15, 0.22 and 0.11 μM, respectively against BRAF-WT. At 10 μM concentration 9c revealed promising in vitro broad-spectrum antiproliferative activity against cancer cell lines with growth inhibition percent ranging from 10 to 90%. Moreover, compounds 7b, 8d, 9a, 9b, 9c and 9d showed potent activity against MCF7 cell line (IC50 = 17.18, 17.20, 19.98, 19.61, 13.02 and 16.54 μM, respectively). On the other hand, compounds 9c, 9d and 10d were found to be the most potent compounds against T-47D cell line (IC50 = 2.18, 8.09 and 4.36 μM, respectively). Studying the effect of the most potent compounds on VEGFR-2 level in MCF7 cell line revealed that 9c and 9d showed inhibition percent of 84 and 80%, respectively, in comparison to sorafenib (I) (% inhibition = 90%).
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Affiliation(s)
- Heba T Abdel-Mohsen
- Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries Research, National Research Centre, Dokki, Cairo, Egypt.
| | - Mohamed A Omar
- Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries Research, National Research Centre, Dokki, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt; Molecular Modeling Unit, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, New Giza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Abeer E E Mahmoud
- Department of Biochemistry, Division of Genetic Engineering and Biotechnology, National Research Centre, Cairo, Egypt
| | - Mamdouh M Ali
- Department of Biochemistry, Division of Genetic Engineering and Biotechnology, National Research Centre, Cairo, Egypt
| | - Hoda I El Diwani
- Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries Research, National Research Centre, Dokki, Cairo, Egypt
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23
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Savoia P, Fava P, Casoni F, Cremona O. Targeting the ERK Signaling Pathway in Melanoma. Int J Mol Sci 2019; 20:ijms20061483. [PMID: 30934534 PMCID: PMC6472057 DOI: 10.3390/ijms20061483] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/17/2019] [Accepted: 03/19/2019] [Indexed: 12/24/2022] Open
Abstract
The discovery of the role of the RAS/RAF/MEK/ERK pathway in melanomagenesis and its progression have opened a new era in the treatment of this tumor. Vemurafenib was the first specific kinase inhibitor approved for therapy of advanced melanomas harboring BRAF-activating mutations, followed by dabrafenib and encorafenib. However, despite the excellent results of first-generation kinase inhibitors in terms of response rate, the average duration of the response was short, due to the onset of genetic and epigenetic resistance mechanisms. The combination therapy with MEK inhibitors is an excellent strategy to circumvent drug resistance, with the additional advantage of reducing side effects due to the paradoxical reactivation of the MAPK pathway. The recent development of RAS and extracellular signal-related kinases (ERK) inhibitors promises to add new players for the ultimate suppression of this signaling pathway and the control of pathway-related drug resistance. In this review, we analyze the pharmacological, preclinical, and clinical trial data of the various MAPK pathway inhibitors, with a keen interest for their clinical applicability in the management of advanced melanoma.
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Affiliation(s)
- Paola Savoia
- Department of Health Science, University of Eastern Piedmont, via Solaroli 17, 28100 Novara, Italy.
| | - Paolo Fava
- Section of Dermatology, Department of Medical Science, University of Turin, 10124 Turin, Italy.
| | - Filippo Casoni
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 58, 20132 Milano, Italy.
- Università Vita Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy.
| | - Ottavio Cremona
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 58, 20132 Milano, Italy.
- Università Vita Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy.
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24
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Shaw J, Dale I, Hemsley P, Leach L, Dekki N, Orme JP, Talbot V, Narvaez AJ, Bista M, Martinez Molina D, Dabrowski M, Main MJ, Gianni D. Positioning High-Throughput CETSA in Early Drug Discovery through Screening against B-Raf and PARP1. SLAS DISCOVERY 2018; 24:121-132. [PMID: 30543471 PMCID: PMC6484527 DOI: 10.1177/2472555218813332] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Methods to measure cellular target engagement are increasingly being used in early drug discovery. The Cellular Thermal Shift Assay (CETSA) is one such method. CETSA can investigate target engagement by measuring changes in protein thermal stability upon compound binding within the intracellular environment. It can be performed in high-throughput, microplate-based formats to enable broader application to early drug discovery campaigns, though high-throughput forms of CETSA have only been reported for a limited number of targets. CETSA offers the advantage of investigating the target of interest in its physiological environment and native state, but it is not clear yet how well this technology correlates to more established and conventional cellular and biochemical approaches widely used in drug discovery. We report two novel high-throughput CETSA (CETSA HT) assays for B-Raf and PARP1, demonstrating the application of this technology to additional targets. By performing comparative analyses with other assays, we show that CETSA HT correlates well with other screening technologies and can be applied throughout various stages of hit identification and lead optimization. Our results support the use of CETSA HT as a broadly applicable and valuable methodology to help drive drug discovery campaigns to molecules that engage the intended target in cells.
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Affiliation(s)
- Joseph Shaw
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ian Dale
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Paul Hemsley
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Lindsey Leach
- 2 Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | | | - Jonathan P Orme
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Verity Talbot
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ana J Narvaez
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Michal Bista
- 5 Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | | | - Martin J Main
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK.,6 Medicines Discovery Catapult, Mereside, Alderley Park, UK
| | - Davide Gianni
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
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25
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Wang PF, Wang ZF, Qiu HY, Huang Y, Hu HM, Wang ZC, Zhu HL. Identification and Biological Evaluation of Novel Type II B-Raf V600E Inhibitors. ChemMedChem 2018; 13:2558-2566. [PMID: 30353975 DOI: 10.1002/cmdc.201800574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/14/2018] [Indexed: 12/15/2022]
Abstract
The mitogen-activated protein kinase (MAPK) pathway plays a vital role in signal transduction networks. Severe diseases may be triggered if it is disturbed by mutated components, especially the kinase B-RafV600E . New inhibitors of the kinase are needed as cases of relapse and resistance with the known drugs have been widely reported in the clinic. In the present work, a new class of B-RafV600E inhibitors was identified by fragment linking. In vitro and in vivo assays were used to demonstrate the pharmacological properties of the compounds. 3-{3-[4-Chloro-3-(trifluoromethyl)phenyl]ureido}-N-[1-(4-methoxyphenyl)-1H-pyrazol-4-yl]benzamide was the most potent agent with IC50 values of 0.035±0.004 μm (B-RafV600E kinase) and 0.39±0.04 μm (A375 cells). Furthermore, no obvious toxicity was observed. Collectively, the results favored justified the design rationale and hinted that this new chemotype might be worth studying further to develop novel B-Raf inhibitor candidates.
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Affiliation(s)
- Peng-Fei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
| | - Ze-Feng Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
| | - Han-Yue Qiu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
| | - Yue Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Hui-Min Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
| | - Zhong-Chang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P.R. China
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26
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New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors. Biochem J 2018; 475:2435-2455. [PMID: 29934490 PMCID: PMC6094398 DOI: 10.1042/bcj20180266] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/14/2018] [Accepted: 06/21/2018] [Indexed: 12/11/2022]
Abstract
Protein tyrosine sulfation is a post-translational modification best known for regulating extracellular protein–protein interactions. Tyrosine sulfation is catalysed by two Golgi-resident enzymes termed tyrosylprotein sulfotransferases (TPSTs) 1 and 2, which transfer sulfate from the cofactor PAPS (3′-phosphoadenosine 5′-phosphosulfate) to a context-dependent tyrosine in a protein substrate. A lack of quantitative tyrosine sulfation assays has hampered the development of chemical biology approaches for the identification of small-molecule inhibitors of tyrosine sulfation. In the present paper, we describe the development of a non-radioactive mobility-based enzymatic assay for TPST1 and TPST2, through which the tyrosine sulfation of synthetic fluorescent peptides can be rapidly quantified. We exploit ligand binding and inhibitor screens to uncover a susceptibility of TPST1 and TPST2 to different classes of small molecules, including the anti-angiogenic compound suramin and the kinase inhibitor rottlerin. By screening the Published Kinase Inhibitor Set, we identified oxindole-based inhibitors of the Ser/Thr kinase RAF (rapidly accelerated fibrosarcoma) as low-micromolar inhibitors of TPST1 and TPST2. Interestingly, unrelated RAF inhibitors, exemplified by the dual BRAF/VEGFR2 inhibitor RAF265, were also TPST inhibitors in vitro. We propose that target-validated protein kinase inhibitors could be repurposed, or redesigned, as more-specific TPST inhibitors to help evaluate the sulfotyrosyl proteome. Finally, we speculate that mechanistic inhibition of cellular tyrosine sulfation might be relevant to some of the phenotypes observed in cells exposed to anionic TPST ligands and RAF protein kinase inhibitors.
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27
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Kinoshita-Kikuta E, Kinoshita E, Ueda S, Ino Y, Kimura Y, Hirano H, Koike T. Increase in constitutively active MEK1 species by introduction of MEK1 mutations identified in cancers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:62-70. [PMID: 29753091 DOI: 10.1016/j.bbapap.2018.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/30/2022]
Abstract
The kinase MEK1 is an essential component of the mitogen-activated protein kinase cascades. Somatic mutations that have been identified in the MEK1-coding gene generally enhance kinase activity. Consequently, MEK1 has attracted much interest as a target for cancer therapy to block the aberrant activity. By using Phos-tag affinity electrophoresis, we found that the introduction of mutations detected in certain sporadic cancers or in MEK-inhibitor-resistant cancer cells produced constitutively active MEK1 species containing phosphorylated Ser-218 and Ser-222 residues; it also enhanced the constitutive activity of the kinase. Phosphorylation profiling of the mutants in the presence of inhibitors of RAF/MEK demonstrated that several mutations conferred resistance to multiple inhibitors as a result of an increase in the quantity of active MEK1 species containing the two phosphorylated Ser-218 and Ser-222 residues. Phos-tag-based phosphorylation profiling of MEK1 can therefore provide clinical insights into characteristics of individual mutations in the MEK1-coding gene.
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Affiliation(s)
- Emiko Kinoshita-Kikuta
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan.
| | - Sayaka Ueda
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
| | - Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Tohru Koike
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
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28
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Affiliation(s)
- Bogos Agianian
- Department of Biochemistry and Department of Medicine, Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Evripidis Gavathiotis
- Department of Biochemistry and Department of Medicine, Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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29
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Imidazo[1,2-a]pyridin-6-yl-benzamide analogs as potent RAF inhibitors. Bioorg Med Chem Lett 2017; 27:5221-5224. [PMID: 29107542 DOI: 10.1016/j.bmcl.2017.10.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022]
Abstract
A series of imidazo[1,2-a]pyridin-6-yl-benzamide analogs was designed as inhibitors of B-RAFV600E. Medicinal chemistry techniques were employed to explore the SAR for this series and improve selectivity versus P38 and VEGFR2.
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30
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Izar B, Sharfman W, Hodi FS, Lawrence D, Flaherty KT, Amaravadi R, Kim KB, Puzanov I, Sosman J, Dummer R, Goldinger SM, Lam L, Kakar S, Tang Z, Krieter O, McDermott DF, Atkins MB. A first-in-human phase I, multicenter, open-label, dose-escalation study of the oral RAF/VEGFR-2 inhibitor (RAF265) in locally advanced or metastatic melanoma independent from BRAF mutation status. Cancer Med 2017; 6:1904-1914. [PMID: 28719152 PMCID: PMC5548886 DOI: 10.1002/cam4.1140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
To establish the maximum tolerated dose (MTD), dose‐limiting toxicities (DLT), safety profile, and anti‐tumor efficacy of RAF265. We conducted a multicenter, open‐label, phase‐I, dose‐escalation trial of RAF265, an orally available RAF kinase/VEGFR‐2 inhibitor, in patients with advanced or metastatic melanoma. Pharmacokinetic (PK) analysis, pharmacodynamics (PD) and tumor response assessment were conducted. We evaluated metabolic tumor response by 18[F]‐fluorodeoxyglucose‐positron‐emission tomography (FDG‐PET), tissue biomarkers using immunohistochemistry (IHC), and modulators of angiogenesis. RAF265 has a serum half‐life of approximately 200 h. The MTD was 48 mg once daily given continuously. Among 77 patients, most common treatment‐related adverse effects were fatigue (52%), diarrhea (34%), weight loss (31%) and vitreous floaters (27%). Eight of 66 evaluable patients (12.1%) had an objective response, including seven partial and one complete response. Responses occurred in BRAF‐mutant and BRAF wild‐type (WT) patients. Twelve of 58 (20.7%) evaluable patients had a partial metabolic response. On‐treatment versus pretreatment IHC staining in 23 patients showed dose‐dependent p‐ERK inhibition. We observed a significant temporal increase in placental growth factor levels and decrease in soluble vascular endothelial growth factor receptor 2 (sVEGFR‐2) levels in all dose levels. RAF265 is an oral RAF/VEGFR‐2 inhibitor that produced antitumor responses, metabolic responses, and modulated angiogenic growth factor levels. Antitumor activity occurred in patients with BRAF‐mutant and BRAF‐WT disease. Despite low activity at tolerable doses, this study provides a framework for the development of pan‐RAF inhibitors and modulators of angiogenesis for the treatment of melanoma.
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Affiliation(s)
- Benjamin Izar
- Beth Israel Deaconess Medical Center, Boston, Massachusetts.,Center for Cancer Precision Medicine/Dana-Farber Cancer Institute and the Broad Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - William Sharfman
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | | | | | - Keith T Flaherty
- Massachusetts General Hospital, Boston, Massachusetts.,Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ravi Amaravadi
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Igor Puzanov
- Vanderbilt-Ingram Cancer Center, Vanderbilt, Tennessee
| | | | | | | | - Lyhping Lam
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts
| | - Shefali Kakar
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Zhongwen Tang
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | | | | | - Michael B Atkins
- Beth Israel Deaconess Medical Center, Boston, Massachusetts.,Georgetown-Lombardi Comprehensive Cancer Center, Washington, District of Columbia
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31
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Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PLoS One 2016; 11:e0166583. [PMID: 27861609 PMCID: PMC5115767 DOI: 10.1371/journal.pone.0166583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment.
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Affiliation(s)
- Timothy P. Heffron
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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