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Chovatia P, Sanzone A, Hofman GJ, Dooley R, Pezzati B, Trist IML, Ouvry G. Harnessing conformational drivers in drug design. PROGRESS IN MEDICINAL CHEMISTRY 2024; 63:1-60. [PMID: 39370240 DOI: 10.1016/bs.pmch.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
This review article explores the pivotal role of conformational drivers in the discovery of drug-like molecules and illustrates their significance through real-life examples. Understanding molecular conformation is paramount to drug hunting as it can impact on- and off-target potency, metabolism, permeability, and solubility. Each conformational driver or effector is described and exemplified in a separate section. The final section is dedicated to NMR spectroscopy and illustrates its utility as an essential tool for conformational design.
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Affiliation(s)
| | | | | | - Ruth Dooley
- Evotec (UK) Ltd, Milton Park, Abingdon, United Kingdom
| | | | | | - Gilles Ouvry
- NRG Therapeutics, Stevenage Bioscience Catalyst, Stevenage, United Kingdom
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Mohamed AM, Abou-Ghadir OMF, Mostafa YA, Dahlous KA, Bräse S, Youssif BGM. Design and synthesis of new 1,2,4-oxadiazole/quinazoline-4-one hybrids with antiproliferative activity as multitargeted inhibitors. Front Chem 2024; 12:1447618. [PMID: 39281035 PMCID: PMC11393688 DOI: 10.3389/fchem.2024.1447618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/05/2024] [Indexed: 09/18/2024] Open
Abstract
Introduction The combination of BRAF and tyrosine kinase (TK) inhibitors has been demonstrated to be highly effective in inhibiting tumor development and is an approach for overcoming resistance in clinical trials. Accordingly, a novel series of 1,2,4-oxadiazole/quinazoline-4-one hybrids was developed as antiproliferative multitargeted inhibitors. Methods The structures of the newly synthesized compounds 9a-o were validated using IR, NMR, MS, and elemental techniques. 9a-o were tested as antiproliferative agents. Results and Discussion The results showed that the majority of the tested compounds showed significant antiproliferative action with 9b, 9c, 9h, 9k, and 9l being the most potent. Compounds 9b, 9c, 9h, 9k, and 9l were tested as EGFR and BRAFV600E inhibitors. These in vitro tests revealed that compounds 9b, 9c, and 9h are strong antiproliferative agents that may act as dual EGFR/BRAFV600E inhibitors. 9b, 9c, and 9h were further investigated for their inhibitory effect on mutant EGFR (EGFRT790M), and the results showed that the tested compounds had considerable inhibitory action. Cell cycle study and apoptosis detection demonstrated that compound 9b exhibits cell cycle arrest at the G2/M transition. Molecular docking simulations reveal the binding mechanism of the most active antiproliferative agents.
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Affiliation(s)
- Amira M Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Ola M F Abou-Ghadir
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Yaser A Mostafa
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Kholood A Dahlous
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Stefan Bräse
- Institute of Biological and Chemical Systems, IBCS-FMS, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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3
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Bialves TS, Bastos LL, Parra JAA, Moysés MN, Marques E, de Castro Pimenta AM, Quintela FM, Mariano DCB, Carvalho FC, de Melo-Minardi RC, Boyle RT. Interaction of DisBa01 peptide from Bothrops alternatus venom with BRAF melanoma receptors: Modeling and molecular docking. Int J Biol Macromol 2024; 274:133283. [PMID: 38909731 DOI: 10.1016/j.ijbiomac.2024.133283] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
Metastatic melanoma is highly aggressive and challenging, often leading to a grim prognosis. Its progression is swift, especially when mutations like BRAFV600E continuously activate pathways vital for cell growth and survival. Although several treatments target this mutation, resistance typically emerges over time. In recent decades, research has underscored the potential of snake venoms and peptides as bioactive substances for innovative drugs, including anti-coagulants, anti-microbial, and anti-cancer agents. Leveraging this knowledge, we propose employing a bioinformatics simulation approach to: a) Predict how well a peptide (DisBa01) from Bothrops alternatus snake venom binds to the melanoma receptor BRAFV600E via Molecular Docking. b) Identify the specific peptide binding sites on receptors and analyze their proximity to active receptor sites. c) Evaluate the behavior of resulting complexes through molecular dynamics simulations. d) Assess whether this peptide qualifies as a candidate for anti-melanoma therapy. Our findings reveal that DisBa01 enhances stability in the BRAFV600E melanoma receptor structure by binding to its RGD motif, an interaction absent in the BRAF WT model. Consequently, both docking and molecular dynamics simulations suggest that DisBa01 shows promise as a BRAFV600E inhibitor.
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Affiliation(s)
- Tatiane Senna Bialves
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
| | - Luana Luiza Bastos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Alexanders Amaya Parra
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maurício Nogueira Moysés
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edleusa Marques
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriano Monteiro de Castro Pimenta
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernando Marques Quintela
- Instituto Nacional de Pesquisas do Pantanal- Museu Paraense Emílio Goeldi, Av. Magalhães Barata, 376, Belém, Pará, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Frederico Chaves Carvalho
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raquel C de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robert Tew Boyle
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil
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4
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Lungu CN, Mangalagiu II, Gurau G, Mehedinti MC. Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides. Int J Mol Sci 2024; 25:7787. [PMID: 39063029 PMCID: PMC11276785 DOI: 10.3390/ijms25147787] [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: 06/06/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR type 2 angiogenesis and vascular morphogenesis as the tyrosine kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in both stimulating and inhibitory ways. This investigation aims to examine the molecular properties of VEGFR2, a molecule primarily involved in the processes of vasculogenesis and angiogenesis. These relationships were defined by the interactions between Vascular Endothelial Growth Factor receptor 2 (VEGFR2) and the structural features of the systems. The chemical space of the inhibitory peptides and stimulators was described using topological and energetic properties. Furthermore, chimeric models of stimulating and inhibitory proteins (for VEGFR2) were computed using the protein system structures. The interaction between the chimeric proteins and VEGFR was computed. The chemical space was further characterized using complex manifolds and high-dimensional data visualization. The results show that a slightly similar chemical area is shared by VEGFR2 and stimulating and inhibitory proteins. On the other hand, the stimulator peptides and the inhibitors have distinct chemical spaces.
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Affiliation(s)
- Claudiu N. Lungu
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Ionel I. Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Gabriela Gurau
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
| | - Mihaela Cezarina Mehedinti
- Department of Functional and Morphological Science, Faculty of Medicine and Pharmacy, Dunarea de Jos University, 800010 Galati, Romania; (G.G.); (M.C.M.)
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania
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5
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Fouad MA, Osman AA, Abdelhamid NM, Rashad MW, Nabawy AY, El Kerdawy AM. Discovery of dual kinase inhibitors targeting VEGFR2 and FAK: structure-based pharmacophore modeling, virtual screening, and molecular docking studies. BMC Chem 2024; 18:29. [PMID: 38347617 PMCID: PMC10863211 DOI: 10.1186/s13065-024-01130-5] [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: 11/03/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
VEGFR2 and FAK signaling pathways are interconnected and have synergistic effects on tumor angiogenesis, growth, and metastasis. Thus, instead of the conventional targeting of each of these proteins individually with a specific inhibitor, the present work aimed to discover novel dual inhibitors targeting both VEGFR2 and FAK exploiting their association. To this end, receptor-based pharmacophore modeling technique was opted to generate 3D pharmacophore models for VEGFR2 and FAK type II kinase inhibitors. The generated pharmacophore models were validated by assessing their ability to discriminate between active and decoy compounds in a pre-compiled test set of VEGFR2 and FAK active compounds and decoys. ZINCPharmer web tool was then used to screen the ZINC database purchasable subset using the validated pharmacophore models retrieving 42,616 hits for VEGFR2 and 28,475 hits for FAK. Subsequently, they were filtered using various filters leaving 13,023 and 6,832 survived compounds for VEGFR2 and FAK, respectively, with 124 common compounds. Based on molecular docking simulations, thirteen compounds were found to satisfy all necessary interactions with VEGFR2 and FAK kinase domains. Thus, they are predicted to have a possible dual VEGFR2/FAK inhibitory activity. Finally, SwissADME web tool showed that compound ZINC09875266 is not only promising in terms of binding pattern to our target kinases, but also in terms of pharmacokinetic properties.
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Affiliation(s)
- Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt.
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Alaa A Osman
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Noha M Abdelhamid
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Mai W Rashad
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ashrakat Y Nabawy
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, 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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Lemos LMS, Ọlọ Ba-Whẹ Nù OA, Olasupo IA, Balogun SO, Macho A, Pavan E, de Oliveira Martins DT. Brasiliensic acid: in vitro cytotoxic and genotoxic, in vivo acute toxicity and in silico pharmacological prediction of a new promising molecule. J Biomol Struct Dyn 2023:1-14. [PMID: 38054294 DOI: 10.1080/07391102.2023.2280713] [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: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
Brasiliensic acid (Bras) is a chromanone isolated from Calophyllum brasiliense Cambèss. bark extracts with confirmed potential activity on gastric ulcer and Helicobacter pylori infection. This study aimed to investigate the in vitro and in vivo toxicity of Bras and molecular docking studies on its interactions with the H. pylori virulence factors and selected gastric cancer-related proteins. Cytotoxicity was evaluated by alamarBlue© assay, genotoxicity by micronucleus and comet assays, and on cell cycle by flow cytometry, using Chinese hamster epithelial ovary cells. Bras was not cytotoxic to CHO-K1 cells, and caused no chromosomal aberrations, nor altered DNA integrity. Furthermore, Bras inhibited damages to DNA by H2O2 at 1.16 µM. No cell cycle arrest was observed, but apoptosis accounted for 31.2% of the cell death observed in the CHO-K1 at 24 h incubation of the IC50. Oral acute toxicity by Hippocratic screening test in mice showed no relevant behavioral change/mortality seen up to 1,000 mg/kg. The molecular docking approach indicated potential interactions between Bras and the various targets for peptic ulcer and gastric cancer, notably CagA virulence factor of H. pylori and VEGFR-2. In conclusion, Bras is apparently safe and an optimization for Bras can be considered for gastric ulcer and cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Larissa Maria Scalon Lemos
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
- Área de Farmacologia, Faculdade de Ciências da Saúde, Universidade do Estado de Mato Grosso (Unemat), Cáceres, MT, Brazil
| | | | | | - Sikiru Olaitan Balogun
- Programa de Pós-Graduação em Ciências da Saúde (PPGCS), Universidade Federal da Grande Dourados (UFGD), Dourados, MS, Brazil
| | - Antonio Macho
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada (NuPMIA). Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Eduarda Pavan
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
| | - Domingos Tabajara de Oliveira Martins
- Área de Farmacologia, Departamento de Ciências Básicas em Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), Cuiabá, MT, Brazil
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Chiodi D, Ishihara Y. "Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery. J Med Chem 2023; 66:5305-5331. [PMID: 37014977 DOI: 10.1021/acs.jmedchem.2c02015] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, California 92121, United States
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8
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Al-Wahaibi LH, El-Sheref EM, Hammouda MM, Youssif BGM. One-Pot Synthesis of 1-Thia-4-azaspiro[4.4/5]alkan-3-ones via Schiff Base: Design, Synthesis, and Apoptotic Antiproliferative Properties of Dual EGFR/BRAF V600E Inhibitors. Pharmaceuticals (Basel) 2023; 16:ph16030467. [PMID: 36986566 PMCID: PMC10056593 DOI: 10.3390/ph16030467] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
In this investigation, novel 4-((quinolin-4-yl)amino)-thia-azaspiro[4.4/5]alkan-3-ones were synthesized via interactions between 4-(2-cyclodenehydrazinyl)quinolin-2(1H)-one and thioglycolic acid catalyzed by thioglycolic acid. We prepared a new family of spiro-thiazolidinone derivatives in a one-step reaction with excellent yields (67-79%). The various NMR, mass spectra, and elemental analyses verified the structures of all the newly obtained compounds. The antiproliferative effects of 6a-e, 7a, and 7b against four cancer cells were investigated. The most effective antiproliferative compounds were 6b, 6e, and 7b. Compounds 6b and 7b inhibited EGFR with IC50 values of 84 and 78 nM, respectively. Additionally, 6b and 7b were the most effective inhibitors of BRAFV600E (IC50 = 108 and 96 nM, respectively) and cancer cell proliferation (GI50 = 35 and 32 nM against four cancer cell lines, respectively). Finally, the apoptosis assay results revealed that compounds 6b and 7b had dual EGFR/BRAFV600E inhibitory properties and showed promising antiproliferative and apoptotic activity.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Essmat M El-Sheref
- Chemistry Department, Faculty of Science, Minia University, El Minia 61519, Egypt
| | - Mohamed M Hammouda
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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Bialves TS, Bastos Junior CLQ, Cordeiro MF, Boyle RT. Snake venom, a potential treatment for melanoma. A systematic review. Int J Biol Macromol 2023; 231:123367. [PMID: 36690229 DOI: 10.1016/j.ijbiomac.2023.123367] [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: 10/11/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Despite advances in treating patients with melanoma, there are still many treatment challenges to overcome. Studies with snake venom-derived proteins/peptides describe their binding potential, and inhibition of some proliferative mechanisms in melanoma. The combined use of these compounds with current therapies could be the strategic gap that will help us discover more effective treatments for melanoma. The present study aimed to carry out a systematic review identifying snake venom proteins and peptides described in the literature with antitumor, antimetastatic, or antiangiogenic effects on melanoma and determine the mechanisms of action that lead to these anti-tumor effects. Snake venoms contain proteins and peptides which are antiaggregant, antimetastatic, and antiangiogenic. The in vivo results are encouraging, considering the reduction of metastases and tumor size after treatment. In addition to these results, it was reported that these venom compounds could act in combination with chemotherapeutics (Acurhagin-C; Macrovipecetin), sensitizing and preparing tumor cells for treatment. There is a consensus that snake venom is a promising strategy for the improvement of antimelanoma therapies, but it has been little explored in the current context, combined with inhibitors, immunotherapy or tumor microenvironment, for example. We suggest Lebein as a candidate for combination therapy with BRAF inhibitors.
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Affiliation(s)
- Tatiane Senna Bialves
- Programa de Pós-Graduação em Ciências Fisiológicas (PPGCF), Universidade Federal do Rio Grande - FURG, Av. Itália, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
| | - Claudio L Q Bastos Junior
- Programa de Pós-Graduação em Ciências Fisiológicas (PPGCF), Universidade Federal do Rio Grande - FURG, Av. Itália, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil
| | - Marcos Freitas Cordeiro
- Programa de Pós-Graduação em Biociências e Saúde (PPGBS), Universidade do Oeste de Santa Catarina - UNOESC, Rua Roberto Trompovski 224, Joaçaba, Santa Catarina, CEP 89600-000, Brazil.
| | - Robert Tew Boyle
- Programa de Pós-Graduação em Ciências Fisiológicas (PPGCF), Universidade Federal do Rio Grande - FURG, Av. Itália, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul 96203-900, Brazil
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10
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Nam Y, Kim C, Han J, Ryu S, Cho H, Song C, Kim ND, Kim N, Sim T. Identification of Thiazolo[5,4- b]pyridine Derivatives as c-KIT Inhibitors for Overcoming Imatinib Resistance. Cancers (Basel) 2022; 15:143. [PMID: 36612139 PMCID: PMC9817970 DOI: 10.3390/cancers15010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/18/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
c-KIT is a promising therapeutic target against gastrointestinal stromal tumor (GIST). In order to identify novel c-KIT inhibitors capable of overcoming imatinib resistance, we synthesized 31 novel thiazolo[5,4-b]pyridine derivatives and performed SAR studies. We observed that, among these substances, 6r is capable of inhibiting significantly c-KIT and suppressing substantially proliferation of GIST-T1 cancer cells. It is of note that 6r is potent against a c-KIT V560G/D816V double mutant resistant to imatinib. Compared with sunitinib, 6r possesses higher differential cytotoxicity on c-KIT D816V Ba/F3 cells relative to parental Ba/F3 cells. In addition, kinase panel profiling reveals that 6r has reasonable kinase selectivity. It was found that 6r remarkably attenuates proliferation of cancer cells via blockade of c-KIT downstream signaling, and induction of apoptosis and cell cycle arrest. Furthermore, 6r notably suppresses migration and invasion, as well as anchorage-independent growth of GIST-T1 cells. This study provides useful SAR information for the design of novel c-KIT inhibitors overcoming imatinib-resistance.
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Affiliation(s)
- Yunju Nam
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Chan Kim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Junghee Han
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - SeongShick Ryu
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hanna Cho
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Chiman Song
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Nam Doo Kim
- Voronoibio Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea
| | - Namkyoung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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Abudayah A, Daoud S, Al-Sha'er M, Taha M. Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study. Mol Inform 2022; 41:e2200049. [PMID: 35973966 DOI: 10.1002/minf.202200049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signaling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 µM.
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Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
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12
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Hassan RA, Hamed MI, Abdou AM, El-Dash Y. Novel antiproliferative agents bearing substituted thieno[2,3-d]pyrimidine scaffold as dual VEGFR-2 and BRAF kinases inhibitors and apoptosis inducers; design, synthesis and molecular docking. Bioorg Chem 2022; 125:105861. [DOI: 10.1016/j.bioorg.2022.105861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
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13
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Salem MG, El-Maaty DMA, El-Deen YIM, Elesawy BH, Askary AE, Saleh A, Saied EM, Behery ME. Novel 1,3-Thiazole Analogues with Potent Activity against Breast Cancer: A Design, Synthesis, In Vitro, and In Silico Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154898. [PMID: 35956848 PMCID: PMC9370021 DOI: 10.3390/molecules27154898] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 01/23/2023]
Abstract
Breast cancer is the most common cancer in women, responsible for over half a million deaths in 2020. Almost 75% of FDA-approved drugs are mainly nitrogen- and sulfur-containing heterocyclic compounds, implying the importance of such compounds in drug discovery. Among heterocycles, thiazole-based heterocyclic compounds have demonstrated a broad range of pharmacological activities. In the present study, a novel set of 1,3-thiazole derivatives was designed and synthesized based on the coupling of acetophenone derivatives, and phenacyl bromide was substituted as a key reaction step. The activity of synthesized compounds was screened against the proliferation of two breast cancer cell lines (MCF-7 and MDA-MB-231). Almost all compounds exhibited a considerable antiproliferative activity toward the breast cancer cells as compared to staurosporine, with no significant cytotoxicity toward the epithelial cells. Among the synthesized compounds, compound 4 exhibited the most potent antiproliferative activity, with an IC50 of 5.73 and 12.15 µM toward MCF-7 and MDA-MB-231 cells, respectively, compared to staurosporine (IC50 = 6.77 and 7.03 µM, respectively). Exploring the mechanistic insights responsible for the antiproliferative activity of compound 4 revealed that compound 4 possesses a significant inhibitory activity toward the vascular endothelial growth factor receptor-2 (VEGFR-2) with (IC50 = 0.093 µM) compared to Sorafenib (IC50 = 0.059 µM). Further, compound 4 showed the ability to induce programmed cell death by triggering apoptosis and necrosis in MCF-7 cells and to induce cell cycle arrest on MCF-7 cells at the G1 stage while decreasing the cellular population in the G2/M phase. Finally, detailed in silico molecular docking studies affirmed that this class of compounds possesses a considerable binding affinity toward VEGFR2 proteins. Overall, these results indicate that compound 4 could be a promising lead compound for developing potent anti-breast cancer compounds.
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Affiliation(s)
- Manar G. Salem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (M.G.S.); (Y.I.M.E.-D.)
| | - Dina M. Abu El-Maaty
- Biochemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 415222, Egypt;
| | - Yassmina I. Mohey El-Deen
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (M.G.S.); (Y.I.M.E.-D.)
| | - Basem H. Elesawy
- Department of Pathology, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ahmad El Askary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
- Correspondence: (E.M.S.); (M.E.B.)
| | - Mohammed El Behery
- The Division of Biochemistry, Chemistry Department, Faculty of Science, Port Said University, Port Said 42526, Egypt
- Correspondence: (E.M.S.); (M.E.B.)
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Abstract
B-Raf is a protein kinase participating to the regulation of many biological processes in cells. Several studies have demonstrated that this protein is frequently upregulated in human cancers, especially when it bears activating mutations. In the last years, few ATP-competitive inhibitors of B-Raf have been marketed for the treatment of melanoma and are currently under clinical evaluation on a variety of other types of cancer. Although the introduction of drugs targeting B-Raf has provided significant advances in cancer treatment, responses to ATP-competitive inhibitors remain limited, mainly due to selectivity issues, side effects, narrow therapeutic windows, and the insurgence of drug resistance. Impressive research efforts have been made so far towards the identification of novel ATP-competitive modulators with improved efficacy against cancers driven by mutant Raf monomers and dimers, some of them showing good promises. However, several limitations could still be envisioned for these compounds, according to literature data. Besides, increased attentions have arisen around approaches based on the design of allosteric modulators, polypharmacology, proteolysis targeting chimeras (PROTACs) and drug repurposing for the targeting of B-Raf proteins. The design of compounds acting through such innovative mechanisms is rather challenging. However, valuable therapeutic opportunities can be envisioned on these drugs, as they act through innovative mechanisms in which limitations typically observed for approved ATP-competitive B-Raf inhibitors are less prone to emerge. In this article, current approaches adopted for the design of non-ATP competitive inhibitors targeting B-Raf are described, discussing also on the possibilities, ligands acting through such innovative mechanisms could provide for the obtainment of more effective therapies.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
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15
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Imidazo[1,2-b]pyridazine as privileged scaffold in medicinal chemistry: An extensive review. Eur J Med Chem 2021; 226:113867. [PMID: 34607244 DOI: 10.1016/j.ejmech.2021.113867] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Imidazo[1,2-b]pyridazine scaffold represents an important class of heterocyclic nucleus which provides various bioactives molecules. Among them, the successful kinase inhibitor ponatinib led to a resurgence of interest in exploring new imidazo[1,2-b]pyridazine-containing derivatives for their putative therapeutic applications in medicine. This present review intends to provide a state-of-the-art of this framework in medicinal chemistry from 1966 to nowadays, unveiling different aspects of its structure-activity relationships (SAR). This extensive literature surveil may guide medicinal chemists for the quest of novel imidazo[1,2-b]pyridazine compounds with enhanced pharmacokinetics profile and efficiency.
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16
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Yang B, Zhou J, Wang F, Hu XW, Shi Y. Pyrazoline derivatives as tubulin polymerization inhibitors with one hit for Vascular Endothelial Growth Factor Receptor 2 inhibition. Bioorg Chem 2021; 114:105134. [PMID: 34246970 DOI: 10.1016/j.bioorg.2021.105134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/06/2021] [Accepted: 06/26/2021] [Indexed: 02/07/2023]
Abstract
In this work, to check the effect of the transposition of the rings in typical patterns, a series of pyrazoline derivatives 3a-3t bearing the characteristic 3,4,5-trimethoxy phenyl and thiophene moieties were synthesized and evaluated as tubulin polymerization inhibitors. Basically, as the concise output of our design, a majority of the synthesized compounds showed potency in inhibiting the tubulin polymerization. The top hit, 3q, exhibited potent anti-proliferation activity on cancer cell lines. It was comparable on tubulin-polymerization inhibition with the positive control Colchicine but lower toxic. The VEGFR2 inhibitory potency was introduced occasionally. The flow cytometry assay confirmed the apoptotic procedure and the confocal imaging revealed the tubulin-microtubule dynamics pattern. The anti-cancer mechanism of 3q was similar to Colchicine but not exactly the same on forming multi-polar spindles. The docking simulation visualized the possible binding patterns of 3q into tubulin and VEGFR2, respectively. The results inferred that further investigations on the transposition of the rings might lead to the improvement of tubulin polymerization inhibitory activity and the steadily introduction of the VEGFR2 inhibition.
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Affiliation(s)
- Bing Yang
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China.
| | - Jiahua Zhou
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China
| | - Fa Wang
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China
| | - Xiao-Wei Hu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Yujun Shi
- School of Chemistry and Chemical Engineering, Nantong University, Nantong, Jiangsu 226019, China.
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17
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Beeston HS, Klein T, Norman RA, Tucker JA, Anderson M, Ashcroft AE, Holdgate GA. Validation of ion mobility spectrometry - mass spectrometry as a screening tool to identify type II kinase inhibitors of FGFR1 kinase. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021:e9130. [PMID: 34038603 DOI: 10.1002/rcm.9130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 05/22/2023]
Abstract
RATIONALE The protein kinase FGFR1 regulates cellular processes in human development. As over-activity of FGFR1 is implicated with cancer, effective inhibitors are in demand. Type I inhibitors, which bind to the active form of FGFR1, are less effective than type II inhibitors, which bind to the inactive form. Screening to distinguish between type I and type II inhibitors is required. METHODS X-ray crystallography was used to indicate whether a range of potential inhibitors bind to the active or inactive FGFR1 kinase conformation. The binding affinity of each ligand to FGFR1 was measured using biochemical methods. Electrospray ionisation - ion mobility spectrometry - mass spectrometry (ESI-IMS-MS) in conjunction with collision-induced protein unfolding generated a conformational profile of each FGFR1-ligand complex. The results indicate that the protein's conformational profile depends on whether the inhibitor is type I or type II. RESULTS X-ray crystallography confirmed which of the kinase inhibitors bind to the active or inactive form of FGFR1 kinase. Collision-induced unfolding combined with ESI-IMS-MS showed distinct differences in the FGFR1 folding landscape for type I and type II inhibitors. Biochemical studies indicated a similar range of FGFR1 affinities for both types of inhibitors, thus providing confidence that the conformational variations detected using ESI-IMS-MS can be interpretated unequivocally and that this is an effective screening method. CONCLUSIONS A robust ESI-IMS-MS method has been implemented to distinguish between the binding mode of type I and type II inhibitors by monitoring the conformational unfolding profile of FGFR1. This rapid method requires low sample concentrations and could be used as a high-throughput screening technique for the characterisation of novel kinase inhibitors.
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Affiliation(s)
- Helen S Beeston
- Astbury Centre for Structural Molecular Biology & Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Tobias Klein
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Richard A Norman
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Julie A Tucker
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Malcolm Anderson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology & Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Geoffrey A Holdgate
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
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18
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Atta-Allah SR, AboulMagd AM, Farag PS. Design, microwave assisted synthesis, and molecular modeling study of some new 1,3,4-thiadiazole derivatives as potent anticancer agents and potential VEGFR-2 inhibitors. Bioorg Chem 2021; 112:104923. [PMID: 33932767 DOI: 10.1016/j.bioorg.2021.104923] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 04/14/2021] [Indexed: 11/19/2022]
Abstract
A green and efficient method was developed for the synthesis of 1,3,4-thiadiazole based compounds under microwave (MW) activation. The nucleophile N-(5-amino-1,3,4-thiadiazol-2-yl)thiophene-2-carboxamide (3) was synthesized and reacted with different carbon electrophilic reagents to afford thiadiazolo-pyrimidine or imidazolo-thiadiazoline derivatives (4-6 and 8), respectively. Furthermore, a one-pot reaction of 3 with p-chlorobenzaldehyde and different carbon electrophile/ or nucleophiles under microwave irradiation yields the cyclic thiadiazolo-pyrimidine derivatives 10-15. Additionally, nucleophilic substitution of aromatic amines and/or potassium salts of some heterocyclic compounds with chloroacetamido-thiadiazole 6 yields derivatives 16-20. All the new derivatives were synthesized by both conventional and MW irradiation methods. All the new 1,3,4-thiadiazole derivatives were evaluated against four cancer cell lines, HepG-2, MCF-7, HCT-116, and PC-3. The anti-proliferative activity of most of the synthesized compounds exhibited excellent broad-spectrum cytotoxic activity against the cancer cell lines with IC50 values ranging from 3.97 to 9.62 μM. Moreover, the enzymatic assessment of five derivatives (2,4b, 6, 8, 9a) against VEGFR-2 tyrosine kinase showed significant inhibitory activities with IC50 of 11.5, 8.2, 10.3, 10.5 and 9.4 nM respectively. Further studies revealed the ability of compound 9a to have a strong DNA-binding affinity of 36.06 μM via DNA/methyl green assay. Moreover, molecular docking study was carried out to reveal the binding interactions of compounds in the binding site of VEGFR-2 enzyme explaining the significant inhibitory activity of these derivatives. Finally, ADME/Tox studies was performed to predict the pharmacokinetics of the synthesized compounds.
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Affiliation(s)
- Saad R Atta-Allah
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, 11566 Cairo, Egypt.
| | - Asmaa M AboulMagd
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University (NUB), Beni-Suef, Egypt.
| | - Paula S Farag
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, 11566 Cairo, Egypt
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19
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Previtali V, Mihigo HB, Amet R, McElligott AM, Zisterer DM, Rozas I. Exploring the Anti-Cancer Mechanism of Novel 3,4'-Substituted Diaryl Guanidinium Derivatives. Pharmaceuticals (Basel) 2020; 13:ph13120485. [PMID: 33371382 PMCID: PMC7767381 DOI: 10.3390/ph13120485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
We previously identified a guanidinium-based lead compound that inhibited BRAF through a hypothetic type-III allosteric mechanism. Considering the pharmacophore identified in this lead compound (i.e., “lipophilic group”, “di-substituted guanidine”, “phenylguanidine polar end”), several modifications were investigated to improve its cytotoxicity in different cancer cell lines. Thus, several lipophilic groups were explored, the di-substituted guanidine was replaced by a secondary amine and the phenyl ring in the polar end was substituted by a pyridine. In a structure-based design approach, four representative derivatives were docked into an in-house model of an active triphosphate-containing BRAF protein, and the interactions established were analysed. Based on these computational studies, a variety of derivatives was synthesized, and their predicted drug-like properties calculated. Next, the effect on cell viability of these compounds was assessed in cell line models of promyelocytic leukaemia and breast, cervical and colorectal carcinomas. The potential of a selection of these compounds as apoptotic agents was assessed by screening in the promyelocytic leukaemia cell line HL-60. The toxicity against non-tumorigenic epithelial MCF10A cells was also investigated. These studies allowed for several structure-activity relationships to be derived. Investigations on the mechanism of action of representative compounds suggest a divergent effect on inhibition of the MAPK/ERK signalling pathway.
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Affiliation(s)
- Viola Previtali
- School of Chemistry, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin (TCD), 152-160 Pearse Street, D02R590 Dublin 2, Ireland; (V.P.); (H.B.M.)
| | - Helene B. Mihigo
- School of Chemistry, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin (TCD), 152-160 Pearse Street, D02R590 Dublin 2, Ireland; (V.P.); (H.B.M.)
| | - Rebecca Amet
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin (TCD), 152-160 Pearse Street, D02R590 Dublin 2, Ireland; (R.A.); (D.M.Z.)
| | - Anthony M. McElligott
- Trinity Translational Medicine Institute, Trinity College and St James’s Hospital, D02R590 Dublin 8, Ireland;
| | - Daniela M. Zisterer
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin (TCD), 152-160 Pearse Street, D02R590 Dublin 2, Ireland; (R.A.); (D.M.Z.)
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin (TCD), 152-160 Pearse Street, D02R590 Dublin 2, Ireland; (V.P.); (H.B.M.)
- Correspondence:
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20
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Al-Wahaibi LH, Gouda AM, Abou-Ghadir OF, Salem OIA, Ali AT, Farghaly HS, Abdelrahman MH, Trembleau L, Abdu-Allah HHM, Youssif BGM. Design and synthesis of novel 2,3-dihydropyrazino[1,2-a]indole-1,4-dione derivatives as antiproliferative EGFR and BRAF V600E dual inhibitors. Bioorg Chem 2020; 104:104260. [PMID: 32920363 DOI: 10.1016/j.bioorg.2020.104260] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/13/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022]
Abstract
Recent studies have shown additive and synergistic effects associated with the combination of kinase inhibitors. BRAFV600E and EGFR are attractive targets for many diseases treatments and have been studied extensively. In keeping with our interest in developing anticancer targeting EGFR and BRAFV600E, a novel series of 2,3-dihydropyrazino[1,2-a]indole-1,4-dione has been rationally designed, synthesized and evaluated for their antiproliferative activity against a panel of four human cancer cell lines. Compounds 20-23, 28-31, and 33 showed promising antiproliferative activities. These compounds were further tested for their inhibitory potencies against EGFR and BRAFV600E kinases with erlotinib as a reference drug. Compounds 23 and 33 exhibited equipotency to doxorubicin against the four cell lines and efficiently inhibited both EGFR (IC50 = 0.08 and 0.09 µM, respectively) and BRAFV600E (IC50 = 0.1 and 0.29 µM, respectively). In cell cycle study of MCF-7 cell line, compounds 23 and 33 induced apoptosis and exhibited cell cycle arrest in both Pre-G1 and G2/M phases. Molecular docking analyses revealed that the new compounds can fit snugly into the active sites of EGFR, and BRAFV600E kinases. Compound 23, 31 and 33 adopted similar binding orientations and interactions to those of erlotinib and vemurafenib.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman University
| | - Ahmed M Gouda
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Ola F Abou-Ghadir
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Ola I A Salem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Asmaa T Ali
- Biochemistry Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Hatem S Farghaly
- Biochemistry Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Mostafa H Abdelrahman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Laurent Trembleau
- School of Natural and Computing Sciences, University of Aberdeen, Meston Building, Aberdeen AB243UE, United Kingdom
| | - Hajjaj H M Abdu-Allah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
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21
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Selvam C, Mock CD, Mathew OP, Ranganna K, Thilagavathi R. Discovery of Vascular Endothelial Growth Factor Receptor‐2 (VEGFR‐2) Inhibitors by Ligand‐based Virtual High Throughput Screening. Mol Inform 2020; 39:e1900150. [DOI: 10.1002/minf.201900150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/25/2020] [Indexed: 01/22/2023]
Affiliation(s)
- Chelliah Selvam
- Department of Pharmaceutical Sciences, College of Pharmacy and Health SciencesTexas Southern University Houston TX 77004 USA
| | - Charlotta D. Mock
- Department of Pharmaceutical Sciences, College of Pharmacy and Health SciencesTexas Southern University Houston TX 77004 USA
| | - Omana P. Mathew
- Department of Pharmaceutical Sciences, College of Pharmacy and Health SciencesTexas Southern University Houston TX 77004 USA
| | - Kasturi Ranganna
- Department of Pharmaceutical Sciences, College of Pharmacy and Health SciencesTexas Southern University Houston TX 77004 USA
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of EngineeringKarpagam Academy of Higher Education Coimbatore India
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22
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Turwankar A, Ghaskadbi S. VEGF and FGF signaling during head regeneration in hydra. Gene 2019; 717:144047. [PMID: 31421190 DOI: 10.1016/j.gene.2019.144047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF) signaling pathways play important roles in the formation of the blood vascular system and nervous system across animal phyla. We have earlier reported VEGF and FGF from Hydra vulgaris Ind-Pune, a cnidarian with a defined body axis, an organized nervous system and a remarkable ability of regeneration. We have now identified three more components of VEGF and FGF signaling pathways from hydra. These include FGF-1, FGF receptor 1 (FGFR-1) and VEGF receptor 2 (VEGFR-2) with a view to deciphering their possible roles in regeneration. METHODS In silico analysis of proteins was performed using Clustal omega, Swiss model, MEGA 7.0, etc. Gene expression was studied by whole mount in situ hybridization. VEGF and FGF signaling was inhibited using specific pharmacological inhibitors and their effects on head regeneration were studied. RESULTS Expression patterns of the genes indicate a possible interaction between FGF-1 and FGFR-1 and also VEGF and VEGFR-2. Upon treatment of decapitated hydra with pharmacological inhibitor of FGFR-1 or VEGFR-2 for 48 h, head regeneration was delayed in treated as compared to untreated, control regenerates. When we studied the expression of head specific genes HyBra1 and HyKs1 and tentacle specific gene HyAlx in control and treated regenerates using whole mount in situ hybridization, expression of all the three genes was found to be adversely affected in treated regenerates. CONCLUSIONS The results suggest that VEGF and FGF signaling play important roles in regeneration of hypostome and tentacles in hydra.
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Affiliation(s)
- Anuprita Turwankar
- Developmental Biology Group, MACS-Agharkar Research Institute, Savitribai Phule Pune University, G.G. Agarkar Road, Pune 411004, India
| | - Surendra Ghaskadbi
- Developmental Biology Group, MACS-Agharkar Research Institute, Savitribai Phule Pune University, G.G. Agarkar Road, Pune 411004, India.
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23
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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: 39] [Impact Index Per Article: 7.8] [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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Yuan X, Yang Q, Liu T, Li K, Liu Y, Zhu C, Zhang Z, Li L, Zhang C, Xie M, Lin J, Zhang J, Jin Y. Design, synthesis and in vitro evaluation of 6-amide-2-aryl benzoxazole/benzimidazole derivatives against tumor cells by inhibiting VEGFR-2 kinase. Eur J Med Chem 2019; 179:147-165. [PMID: 31252306 DOI: 10.1016/j.ejmech.2019.06.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022]
Abstract
Herein, we have carried out a structural optimization campaign to discover the novel anti-tumor agents with our previously screened YQY-26 as the hit compound. A library of thirty-seven 6-amide-2-aryl benzoxazole/benzimidazole derivatives has been designed and synthesized based on the highly conserved active site of VEGFR-2. Several title compounds exhibited selective inhibitory activities against VEGFR-2 than EGFR kinases, which also displayed selective anti-proliferation potency against the HUVEC and HepG2 than the A549 and MDA-MB-231 cancer cell lines. The newly synthesized compounds were evaluated for anti-angiogenesis capability by chick chorioallantoic membrane (CAM) assay. Among them, compounds 9d showed the most potent anti-angiogenesis ability (79% inhibition at 10 nM/eggs), the efficient cytotoxic activities (in vitro against the HUVEC and HepG2 cell lines with IC50 values of 1.47 and 2.57 μM, respectively), and excellent VEGFR-2 kinase inhibition (IC50 = 0.051 μM). The molecular docking analysis revealed that compound 9d is a Type II inhibitor of VEGFR-2 kinase. These results indicated that the 6-amide-2-arylbenzoxazole and 6-amide-2-aryl benzimidazole derivatives are promising inhibitors of VEGFR-2 kinase for the potential treatment of anti-angiogenesis.
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Affiliation(s)
- Xu Yuan
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Qingyi Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China; School of Clinical Medicine, Dehong Vocational College, Mangshi, 678400, China
| | - Tongyan Liu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Ke Li
- Biomedical Department, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, PR China.
| | - Yuwen Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Changcheng Zhu
- Institute of Drug Research and Development, Kunming Pharmaceutical Corporation, Kunming, 650100, PR China
| | - Zhiyun Zhang
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650011, PR China
| | - Linghua Li
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650011, PR China
| | - Conghai Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Mingjin Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China
| | - Jun Lin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China.
| | - Jihong Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, 650500, PR China.
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, PR China.
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25
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Vascular Endothelial Growth Factor Receptor (VEGFR-2)/KDR Inhibitors: Medicinal Chemistry Perspective. MEDICINE IN DRUG DISCOVERY 2019. [DOI: 10.1016/j.medidd.2019.100009] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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26
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Wang Y, Peng C, Wang G, Xu Z, Luo Y, Wang J, Zhu W. Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation. Chem Biol Drug Des 2019; 93:934-948. [DOI: 10.1111/cbdd.13493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/31/2018] [Accepted: 01/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Yu Wang
- Hunan Province Key Laboratory of Materials Surface & Interface Science and TechnologyCollege of ScienceCentral South University of Forestry and Technology Changsha Hunan China
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Cheng Peng
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Guimin Wang
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Yongfeng Luo
- Hunan Province Key Laboratory of Materials Surface & Interface Science and TechnologyCollege of ScienceCentral South University of Forestry and Technology Changsha Hunan China
| | - Jinan Wang
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor ResearchDrug Discovery and Design CenterShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
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27
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Ghosh AK, Brindisi M, Sarkar A. The Curtius Rearrangement: Applications in Modern Drug Discovery and Medicinal Chemistry. ChemMedChem 2018; 13:2351-2373. [PMID: 30187672 DOI: 10.1002/cmdc.201800518] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 12/20/2022]
Abstract
The Curtius rearrangement is the thermal decomposition of an acyl azide derived from carboxylic acid to produce an isocyanate as the initial product. The isocyanate can undergo further reactions to provide amines and their derivatives. Due to its tolerance for a large variety of functional groups and complete retention of stereochemistry during rearrangement, the Curtius rearrangement has been used in the synthesis of a wide variety of medicinal agents with amines and amine-derived functional groups such as ureas and urethanes. The current review outlines various applications of the Curtius rearrangement in drug discovery and medicinal chemistry. In particular, the review highlights some widely used rearrangement methods, syntheses of some key agents for popular drug targets and FDA-approved drugs. In addition, the review highlights applications of the Curtius rearrangement in continuous-flow protocols for the scale-up of active pharmaceutical ingredients.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Anindya Sarkar
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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28
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Morris SM, Mhyre AJ, Carmack SS, Myers CH, Burns C, Ye W, Ferrer M, Olson JM, Klinghoffer RA. A modified gene trap approach for improved high-throughput cancer drug discovery. Oncogene 2018; 37:4226-4238. [PMID: 29717260 PMCID: PMC6076322 DOI: 10.1038/s41388-018-0274-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 03/01/2018] [Accepted: 03/23/2018] [Indexed: 01/22/2023]
Abstract
While advances in laboratory automation has dramatically increased throughout of compound screening efforts, development of robust cell-based assays in relevant disease models remain resource-intensive and time-consuming, presenting a bottleneck to drug discovery campaigns. To address this issue, we present a modified gene trap approach to efficiently generate pathway-specific reporters that result in a robust "on" signal when the pathway of interest is inhibited. In this proof-of-concept study, we used vemurafenib and trametinib to identify traps that specifically detect inhibition of the mitogen-activated protein kinase (MAPK) pathway in a model of BRAFV600E driven human malignant melanoma. We demonstrate that insertion of our trap into particular loci results in remarkably specific detection of MAPK pathway inhibitors over compounds targeting any other pathway or cellular function. The accuracy of our approach was highlighted in a pilot screen of ~6000 compounds where 40 actives were detected, including 18 MEK, 10 RAF, and 3 ERK inhibitors along with a few compounds representing previously under-characterized inhibitors of the MAPK pathway. One such compound, bafetinib, a second generation BCR/ABL inhibitor, reduced phosphorylation of ERK and when combined with trametinib, both in vitro and in vivo, reduced growth of vemurafenib resistant melanoma cells. While piloted in a model of BRAF-driven melanoma, our results set the stage for using this approach to rapidly generate reporters against any transcriptionally active pathway across a wide variety of disease-relevant cell-based models to expedite drug discovery efforts.
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Affiliation(s)
- Shelli M Morris
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J Mhyre
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Savanna S Carmack
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carrie H Myers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Pediatric Hematology/Oncology, University of Washington School of Medicine, Seattle, WA, USA.
- Seattle Children's Hospital, Seattle, WA, USA.
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29
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Sun W, Fang S, Yan H. Discovery of novel picolinamide-based derivatives as novel VEGFR-2 kinase inhibitors: synthesis, in vitro biological evaluation and molecular docking. MEDCHEMCOMM 2018; 9:1054-1058. [PMID: 30108994 DOI: 10.1039/c8md00057c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/18/2018] [Indexed: 01/07/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) plays a crucial role in tumor angiogenesis, and inhibition of the VEGFR-2 signaling pathway has emerged as an attractive target for cancer therapy. In our effort, a novel series of picolinamide-based derivatives were designed and synthesized as potent and effective VEGFR-2 inhibitors. All the newly prepared compounds were evaluated in vitro for their antiproliferative activity against A549 and HepG2 cell lines. Among the new compounds, 8j and 8l exhibited better activity against both A549 and HepG2 cell lines. Molecular docking was performed to investigate the binding capacity and binding mode with VEGFR-2 (PDB code: ; 4ASD).
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Affiliation(s)
- Wuji Sun
- Beijing Key Laboratory of Environmental and Viral Oncology , College of Life Science and Bioengineering , Beijing University of Technology , Pingleyuan Street No. 100, Chaoyang District , Beijing , 100124 , China .
| | - Shubiao Fang
- Tong Yi Tang Pharmaceutical Co., Ltd. , Sui'an Industrial Park of Zhangpu County , Fujian Province 363200 , China
| | - Hong Yan
- Beijing Key Laboratory of Environmental and Viral Oncology , College of Life Science and Bioengineering , Beijing University of Technology , Pingleyuan Street No. 100, Chaoyang District , Beijing , 100124 , China .
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30
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Design and synthesis of new potent anticancer benzothiazole amides and ureas featuring pyridylamide moiety and possessing dual B-Raf(V600E) and C-Raf kinase inhibitory activities. Eur J Med Chem 2016; 115:201-16. [PMID: 27017549 DOI: 10.1016/j.ejmech.2016.02.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
A new series of benzothiazole amide and urea derivatives tethered with the privileged pyridylamide moiety by ether linkage at the 6-position of benzothiazole (22 final compounds) has been designed and synthesized as potent anticancer sorafenib analogs. A selected group of twelve derivatives was appraised for its antiproliferative activity over a panel of 60 human cancer cell lines at a single dose concentration of 10 μM at National Cancer Institute (NCI, USA). Compounds 4b, 5a, 5b and 5d exhibited promising growth inhibitions and thus were further tested in advanced 5-dose testing assay to determine their GI50 values. The cellular based assay results revealed that 3,5-bis-trifluoromethylphenyl (5b) urea member is the best derivative with superior potency and efficacy compared to sorafenib as well as notable extended spectrum activity covering 57 human cancer cell lines. Kinase screening of compound 5b showed its kinase inhibitory effect against both B-Raf(V600E) and C-Raf. Moreover, the most potent derivatives in cells were investigated for their RAF inhibitory activities, and the results were rationalized with the molecular docking study. Profiling of CYP450 and hERG channel inhibitory effects for the active compounds revealed their low possibilities to exhibit undesirable drug-drug interactions and cardiac side effects.
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31
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Volkamer A, Eid S, Turk S, Rippmann F, Fulle S. Identification and Visualization of Kinase-Specific Subpockets. J Chem Inf Model 2016; 56:335-46. [PMID: 26735903 DOI: 10.1021/acs.jcim.5b00627] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The identification and design of selective compounds is important for the reduction of unwanted side effects as well as for the development of tool compounds for target validation studies. This is, in particular, true for therapeutically important protein families that possess conserved folds and have numerous members such as kinases. To support the design of selective kinase inhibitors, we developed a novel approach that allows identification of specificity determining subpockets between closely related kinases solely based on their three-dimensional structures. To account for the intrinsic flexibility of the proteins, multiple X-ray structures of the target protein of interest as well as of unwanted off-target(s) are taken into account. The binding pockets of these protein structures are calculated and fused to a combined target and off-target pocket, respectively. Subsequently, shape differences between these two combined pockets are identified via fusion rules. The approach provides a user-friendly visualization of target-specific areas in a binding pocket which should be explored when designing selective compounds. Furthermore, the approach can be easily combined with in silico alanine mutation studies to identify selectivity determining residues. The potential impact of the approach is demonstrated in four retrospective experiments on closely related kinases, i.e., p38α vs Erk2, PAK1 vs PAK4, ITK vs AurA, and BRAF vs VEGFR2. Overall, the presented approach does not require any profiling data for training purposes, provides an intuitive visualization of a large number of protein structures at once, and could also be applied to other target classes.
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Affiliation(s)
- Andrea Volkamer
- BioMed X Innovation Center , Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Sameh Eid
- BioMed X Innovation Center , Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Samo Turk
- BioMed X Innovation Center , Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Friedrich Rippmann
- Global Computational Chemistry, Merck KGaA , Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Simone Fulle
- BioMed X Innovation Center , Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
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32
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Development of anti-angiogenic tyrosine kinases inhibitors: molecular structures and binding modes. Cancer Chemother Pharmacol 2016; 77:905-26. [DOI: 10.1007/s00280-016-2961-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
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33
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Liu HC, Tang SZ, Lu S, Ran T, Wang J, Zhang YM, Xu AY, Lu T, Chen YD. Studies on [5,6]-Fused Bicyclic Scaffolds Derivatives as Potent Dual B-RafV600E/KDR Inhibitors Using Docking and 3D-QSAR Approaches. Int J Mol Sci 2015; 16:24451-74. [PMID: 26501259 PMCID: PMC4632759 DOI: 10.3390/ijms161024451] [Citation(s) in RCA: 9] [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: 09/06/2015] [Revised: 09/22/2015] [Accepted: 10/07/2015] [Indexed: 01/07/2023] Open
Abstract
Research and development of multi-target inhibitors has attracted increasing attention as anticancer therapeutics. B-RafV600E synergistically works with vascular endothelial growth factor receptor 2 (KDR) to promote the occurrence and progression of cancers, and the development of dual-target drugs simultaneously against these two kinds of kinase may offer a better treatment advantage. In this paper, docking and three-dimensional quantitative structure activity relationship (3D-QSAR) studies were performed on a series of dual B-Raf/KDR inhibitors with a novel hinge-binding group, [5,6]-fused bicyclic scaffold. Docking studies revealed optimal binding conformations of these compounds interacting with both B-Raf and KDR. Based on these conformations, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) 3D-QSAR models were constructed, and the best CoMFA (q²=0.542, r²=0.989 for B-Raf; q²=0.768, r²=0.991 for KDR) and CoMSIA models (q²=0.519, r²=0.992 for B-Raf; q²=0.849, r²=0.993 for KDR) were generated. Further external validations confirmed their predictability, yielding satisfactory correlation coefficients (r²pred=0.764 (CoMFA), r²pred=0.841 (CoMSIA) for B-Raf, r²pred=0.912 (CoMFA), r²pred=0.846 (CoMSIA) for KDR, respectively). Through graphical analysis and comparison on docking results and 3D-QSAR contour maps, key amino acids that affect the ligand-receptor interactions were identified and structural features influencing the activities were discussed. New potent derivatives were designed, and subjected to preliminary pharmacological evaluation. The study may offer useful references for the modification and development of novel dual B-Raf/KDR inhibitors.
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Affiliation(s)
- Hai-Chun Liu
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - San-Zhi Tang
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - Shuai Lu
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - Ting Ran
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - Jian Wang
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - Yan-Min Zhang
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - An-Yang Xu
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
| | - Tao Lu
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211169, China.
| | - Ya-Dong Chen
- School of Science, China Pharmaceutical University, Nanjing 211169, China.
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Investigation of new 2-aryl substituted Benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors targeting vascular endothelial growth factor receptor 2. Eur J Med Chem 2015; 103:29-43. [PMID: 26318056 DOI: 10.1016/j.ejmech.2015.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 02/06/2023]
Abstract
Vascular Endothelial Growth Factor (VEGF) pathway has emerged as one of the most important positive modulators of Angiogenesis, a central process implicated in tumour growth and metastatic dissemination. This led to the design and development of anti-VEGF monoclonal antibodies and small-molecule ATP-competitive VEGFR-inhibitors. In this study, we describe the synthesis and the biological evaluation of novel 2-aryl substituted benzothiopyrano-fused pyrimidines 1a-i, 2a-i and 3a-i. The ability of the compounds to target the VEGF pathway was determined in vitro exploiting the compounds' antiproliferative efficacy against HUVEC cells. The VEGFR-2 inhibition was confirmed by enzymatic assays on recombinant human kinase insert domain receptor (KDR), by cell-based phospho-VEGFR-2 inhibition assays, and by ex vivo rat aortic ring tests. The selectivity profile of the best performing derivatives belonging to series 2 was further explored combining modeling studies and additional assays in a panel of human cell lines and other kinases.
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35
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Su P, Wang J, Shi Y, Pan X, Shao R, Zhang J. Discovery of biphenyl-aryl ureas as novel VEGFR-2 inhibitors. Part 4: exploration of diverse hinge-binding fragments. Bioorg Med Chem 2015; 23:3228-36. [PMID: 25982075 DOI: 10.1016/j.bmc.2015.04.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 01/07/2023]
Abstract
VEGFR-2 plays an essential role in angiogenesis and is an important target for cancer therapy. A series of biphenyl-aryl ureas were synthesized and evaluated as novel VEGFR-2 inhibitors. The pyridine, methylamine carbonyl pyridine and pivaloyl amide pyridine were introduced as novel hinge binding fragment. The majority of title compounds displayed potent VEGFR-2 inhibition. In particular, L1, L9, W14 and W15 exhibited significant enzymatic inhibitory activity with IC50 values of 0.36nM, 0.22nM, 0.15nM and 0.14nM. Compounds L1, L9 and W15 displayed potent antiproliferative activity against A549 and SMMC-7721 cells. SAR study suggested that incorporation of 3-trifluoromethyl and methylamine carbonyl on terminal pyridine could improve VEGFR-2 inhibitory activity. Molecular docking illustrated that urea moiety formed two critical hydrogen bonds with the DFG residues of VEGFR-2. The results indicated that these biphenyl-aryl ureas could serve as promising lead compounds for further optimization.
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Affiliation(s)
- Ping Su
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Jinfeng Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Yaling Shi
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Ruili Shao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China.
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36
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Marino KA, Sutto L, Gervasio FL. The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase. J Am Chem Soc 2015; 137:5280-3. [PMID: 25868080 DOI: 10.1021/jacs.5b01421] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein kinases play a key role in regulating cellular processes. Kinase dysfunction can lead to disease, making them an attractive target for drug design. The B-Raf kinase is a key target for the treatment of melanoma since a single mutation (V600E) is found in more than 50% of all malignant melanomas. Despite the importance of B-Raf in melanoma treatment, the molecular mechanism by which the mutation increases kinase activity remains elusive. Since kinases are tightly regulated by a conformational transition between an active and inactive state, which is difficult to capture experimentally, large-scale enhanced-sampling simulations are performed to examine the mechanism by which the V600E mutation enhances the activity of the B-Raf monomer. The results reveal that the mutation has a twofold effect. First, the mutation increases the barrier of the active to inactive transition trapping B-Raf in the active state. The mutation also increases the flexibility of the activation loop which might speed-up the rate-limiting step of phosphorylation. Both effects can be explained by the formation of salt-bridges with the Glu600 residue.
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Affiliation(s)
| | - Ludovico Sutto
- Department of Chemistry, University College London, London, U.K
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37
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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38
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Goodwin NC, Cianchetta G, Burgoon HA, Healy J, Mabon R, Strobel ED, Allen J, Wang S, Hamman BD, Rawlins DB. Discovery of a Type III Inhibitor of LIM Kinase 2 That Binds in a DFG-Out Conformation. ACS Med Chem Lett 2015; 6:53-7. [PMID: 25589930 PMCID: PMC4291701 DOI: 10.1021/ml500242y] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/07/2014] [Indexed: 12/22/2022] Open
Abstract
The first allosteric, type III inhibitor of LIM-kinase 2 (LIMK2) is reported. A series of molecules that feature both an N-phenylsulfonamide and tertiary amide were not only very potent at LIMK2 but also were extremely selective against a panel of other kinases. Enzymatic kinetic studies showed these molecules to be noncompetitive with ATP, suggesting allosteric inhibition. X-ray crystallography confirmed that these sulfonamides are a rare example of a type III kinase inhibitor that binds away from the highly conserved hinge region and instead resides in the hydrophobic pocket formed in the DFG-out conformation of the kinase, thus accounting for the high level of selectivity observed.
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Affiliation(s)
- Nicole C. Goodwin
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Giovanni Cianchetta
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Hugh A. Burgoon
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Jason Healy
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Ross Mabon
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Eric D. Strobel
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
| | - Jason Allen
- Lexicon
Pharmaceuticals, 8800
Technology Forest Place, The Woodlands, Texas 77381, United States
| | - Shuli Wang
- Lexicon
Pharmaceuticals, 8800
Technology Forest Place, The Woodlands, Texas 77381, United States
| | - Brian D. Hamman
- Lexicon
Pharmaceuticals, 8800
Technology Forest Place, The Woodlands, Texas 77381, United States
| | - David B. Rawlins
- Lexicon
Pharmaceuticals, 350
Carter Road, Princeton, New
Jersey 08540, United
States
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Sapi J, Schmidt F, Van Hijfte L, George P. Interfacing chemical biology and drug discovery: report from the 50th International Conference on Medicinal Chemistry of the SCT (French Medicinal Chemistry Society), July 2-4, 2014, Rouen, France. ACS Chem Biol 2014; 9:2702-7. [PMID: 25476010 DOI: 10.1021/cb5009469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janos Sapi
- SCT Vice-President, UMR CNRS 7312, Université de Reims-Champagne-Ardenne, 51 rue Cognacq-Jay, F-51069 Reims Cedex, France
| | - Frédéric Schmidt
- SCT Communication Officer, Institut Curie, Research Center, CNRS UMR3666, INSERM U1143, 26 rue d’Ulm, F-75248 Paris, France
| | - Luc Van Hijfte
- NovAliX, BioParc, 850 Blvd Sébastien Brant, BP 30170, F-67405 Illkirch Cedex, France
| | - Pascal George
- SCT President,
Independent Scientific Expert and Adviser, F-78730 Longvilliers, France
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Keri RS, Patil MR, Patil SA, Budagumpi S. A comprehensive review in current developments of benzothiazole-based molecules in medicinal chemistry. Eur J Med Chem 2014; 89:207-51. [PMID: 25462241 DOI: 10.1016/j.ejmech.2014.10.059] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/19/2014] [Accepted: 10/20/2014] [Indexed: 02/08/2023]
Abstract
Benzothiazole (BTA) and its derivatives are the most important heterocyclic compounds, which are common and integral feature of a variety of natural products and pharmaceutical agents. BTA shows a variety of pharmacological properties, and its analogs offer a high degree of structural diversity that has proven useful for the search of new therapeutic agents. The broad spectrum of pharmacological activity in individual BTA derivative indicates that, this series of compounds is of an undoubted interest. The related research and developments in BTA-based medicinal chemistry have become a rapidly developing and increasingly active topic. Particularly, numerous BTA-based compounds as clinical drugs have been extensively used in practice to treat various types of diseases with high therapeutic potency. This work systematically gives a comprehensive review in current developments of BTA-based compounds in the whole range of medicinal chemistry as anticancer, antibacterial, antifungal, antiinflammatory, analgesic, anti-HIV, antioxidant, anticonvulsant, antitubercular, antidiabetic, antileishmanial, antihistaminic, antimalarial and other medicinal agents. It is believed that, this review article is helpful for new thoughts in the quest for rational designs of more active and less toxic BTA-based drugs, as well as more effective diagnostic agents and pathologic probes.
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Affiliation(s)
- Rangappa S Keri
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore 562112, Karnataka, India.
| | - Mahadeo R Patil
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore 562112, Karnataka, India
| | - Siddappa A Patil
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore 562112, Karnataka, India
| | - Srinivasa Budagumpi
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore 562112, Karnataka, India
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Vidavalur S, Gajula MB, Tadikonda R, Nakka M, Dega S, Yadav SK, Voosala C. PTSA catalyzed straightforward protocol for the synthesis of 2-(N-acyl)aminobenzimidazoles and 2-(N-acyl)aminobenzothiazoles in PEG. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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El-Nassan HB. Recent progress in the identification of BRAF inhibitors as anti-cancer agents. Eur J Med Chem 2014; 72:170-205. [DOI: 10.1016/j.ejmech.2013.11.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/05/2013] [Accepted: 11/18/2013] [Indexed: 12/26/2022]
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43
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Abstract
Activating BRAF mutations, leading to constitutive activation of the MAPK signaling pathway, are common in a variety of human cancers. Several small molecule BRAF inhibitors have been developed during the last years and shown promising results in clinical trials, especially for metastatic melanoma, while they have been less effective in colon cancer. Two inhibitors, vemurafenib and dabrafenib, have been approved for treatment of melanoma. Unfortunately, in most patients who initially respond the tumors eventually develop acquired resistance to the BRAF inhibitors. So far, a number of resistance mechanisms have been identified, including secondary NRAS mutations and BRAF alternative splicing, leading to reactivation of the MAPK pathway. Other alterations, both upstream and downstream of BRAF can have the same effect, and activation of alternative pathways can also play a role in resistance to BRAF inhibitors. In addition, intra-tumor heterogeneity with the presence of clones of tumor cells lacking BRAF mutations needs to be considered, since wildtype BRAF can be activated by inhibitors designed to target mutated BRAF. Combination of the BRAF inhibitor dabrafenib with the MEK inhibitor trametinib has significantly prolonged progression free survival compared to dabrafenib alone in metastatic melanoma. Combination treatments of BRAF inhibitors with other agents may not only circumvent or delay resistance, but may also lead to fewer side effects, such as development of secondary squamous tumors. Several clinical trials are underway for many different BRAF mutation positive cancers with BRAF inhibitors alone or in combination with other small molecule inhibitors, immunotherapies or conventional chemotherapy.
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44
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van Linden OPJ, Kooistra AJ, Leurs R, de Esch IJP, de Graaf C. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space. J Med Chem 2013; 57:249-77. [PMID: 23941661 DOI: 10.1021/jm400378w] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.
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Affiliation(s)
- Oscar P J van Linden
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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45
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Okaniwa M, Hirose M, Arita T, Yabuki M, Nakamura A, Takagi T, Kawamoto T, Uchiyama N, Sumita A, Tsutsumi S, Tottori T, Inui Y, Sang BC, Yano J, Aertgeerts K, Yoshida S, Ishikawa T. Discovery of a Selective Kinase Inhibitor (TAK-632) Targeting Pan-RAF Inhibition: Design, Synthesis, and Biological Evaluation of C-7-Substituted 1,3-Benzothiazole Derivatives. J Med Chem 2013; 56:6478-94. [DOI: 10.1021/jm400778d] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Masanori Okaniwa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaaki Hirose
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeo Arita
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masato Yabuki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akito Nakamura
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Terufumi Takagi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomohiro Kawamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Noriko Uchiyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akihiko Sumita
- CMC Center, Takeda Pharmaceutical Company Limited, 17-85 Jusohonmachi 2-chome,
Yodogawa-ku, Osaka 532-8686, Japan
| | - Shunichirou Tsutsumi
- CMC Center, Takeda Pharmaceutical Company Limited, 17-85 Jusohonmachi 2-chome,
Yodogawa-ku, Osaka 532-8686, Japan
| | - Tsuneaki Tottori
- CMC Center, Takeda Pharmaceutical Company Limited, 17-85 Jusohonmachi 2-chome,
Yodogawa-ku, Osaka 532-8686, Japan
| | - Yoshitaka Inui
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Bi-Ching Sang
- Structural Biology, Takeda California, Inc., 10410 Science Center Drive,
San Diego, California 92121, United States
| | - Jason Yano
- Structural Biology, Takeda California, Inc., 10410 Science Center Drive,
San Diego, California 92121, United States
| | - Kathleen Aertgeerts
- Structural Biology, Takeda California, Inc., 10410 Science Center Drive,
San Diego, California 92121, United States
| | - Sei Yoshida
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoyasu Ishikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-8555, Japan
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46
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Ji X, Zhou Y, Wang J, Zhao L, Jiang H, Liu H. Au(I)/Ag(I)-Catalyzed Cascade Approach for the Synthesis of Benzo[4,5]imidazo[1,2-c]pyrrolo[1,2-a]quinazolinones. J Org Chem 2013; 78:4312-8. [DOI: 10.1021/jo400228g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Xun Ji
- State Key Laboratory of Drug
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning
110016, China
| | - Yu Zhou
- State Key Laboratory of Drug
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinfang Wang
- State Key Laboratory of Drug
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Linxiang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning
110016, China
| | - Hualiang Jiang
- State Key Laboratory of Drug
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning
110016, China
| | - Hong Liu
- State Key Laboratory of Drug
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Abstract
VEGF is an important signaling protein involved in both vasculogenesis and angiogenesis. As an essential receptor protein tyrosine kinase propagating cellular signal transduction processes, VEGFR-2 is a central target for drug discovery against tumor-associated angiogenesis. Since the autophosphorylation of VEGFR-2 represents a key step in this signal pathway that contributes to angiogenesis, the discovery of small molecule inhibitors that block this reaction has attracted great interest for novel drugs research and development. Advances in the understanding of catalytic cleft and the conformational changes of DFG motif have resulted in the development of small molecule inhibitors known as type I and type II. High-resolution crystal structures of various inhibitors in complex with the receptor offer an insight into the relationship among binding modes, inhibition mechanisms, activity, selectivity and resistance. To control selectivity, improve activity and introduce intellectual property novelty, the strategies for the further development are discussed through structural and conformational analysis in this review.
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48
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Xie Y, Chen X, Qin J, Kong X, Ye F, Jiang Y, Liu H, Jiang H, Marmorstein R, Luo C. Identification and synthesis of N-(thiophen-2-yl) benzamide derivatives as BRAF(V600E) inhibitors. Bioorg Med Chem Lett 2013; 23:2306-12. [PMID: 23489628 DOI: 10.1016/j.bmcl.2013.02.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/04/2013] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
Abstract
The V600E BRAF kinase mutation, which activates the downstream MAPK signaling pathway, commonly occurs in about 8% of all human malignancies and about 50% of all melanomas. In this study, we employed virtual screening and chemical synthesis to identify a series of N-(thiophen-2-yl) benzamide derivatives as potent BRAF(V600E) inhibitors. Structure-activity relationship studies of these derivatives revealed that compounds b40 and b47 are the two most potent BRAF(V600E) inhibitors in this series.
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Affiliation(s)
- Yunfeng Xie
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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Chai X, Yu S, Wang X, Wang N, Zhu Z, Zhang D, Wu Q, Cao Y, Sun Q. Synthesis and antifungal activity of novel 7-O-substituted pyridyl-4-methyl coumarin derivatives. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0470-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Kwak SH, Lee GH, Gong YD. Synthesis of N-Substituted-2-Aminothiazolo[4,5-b]pyrazines by Tandem Reaction of o-Aminohalopyrazines with Isothiocyanates. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.12.4271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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