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Khedkar NR, Sindkhedkar M, Joseph A. Computational design, synthesis, and assessment of 3-(4-(4-(1,3,4-oxadiazol-2-yl)-1 H-imidazol-2-yl)phenyl)-1,2,4-oxadiazole derivatives as effective epidermal growth factor receptor inhibitors: a prospective strategy for anticancer therapy. RSC Med Chem 2024; 15:1626-1639. [PMID: 38784476 PMCID: PMC11110788 DOI: 10.1039/d4md00055b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/25/2024] [Indexed: 05/25/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) enzyme plays a critical role in governing the cell cycle, positioning it as a promising target for the development of anticancer drugs. In this study, we endeavored to design and synthesize innovative EGFR inhibitors with potential applications in anticancer therapy. A novel series of compounds, namely 3-(4-(4-(1,3,4-oxadiazol-2-yl)-1H-imidazol-2-yl)phenyl)-1,2,4-oxadiazoles (30a-j), were meticulously designed using FBDD efforts and synthesized. The synthesized compounds underwent thorough characterization using 1HNMR, 13CNMR, HRMS, and mass spectrum analyses. The in vitro anticancer activities of the newly developed compounds (30a-j) were evaluated against four human cancer cell lines such as prostate cancer (PC3 & DU-145), lung cancer (A549), and liver cancer (HEPG2) using the MTT method. The results, expressed as IC50 values, demonstrated significant anticancer activity for several compounds, with five compounds (30a, 30b, 30c, 30i, and 30j) exhibiting superior potency compared to the established anticancer drug etoposide. Notably, compound 30a emerged as the most promising compound, displaying potent cytotoxicity. We also conducted a screening of the compounds on the normal Vero cell line, revealing a pronounced selectivity of the compounds against cancer cell lines, with no observable impact on the normal cell lines. Moreover, the synthesized compounds were investigated for their impact on enzyme EGFR activity. The findings revealed a robust inhibitory effect against the EGFR wild-type enzyme and a 10-fold inferior potency against the mutant form of EGFR. This observation underscores the potential of the new derivatives as effective EGFRWT inhibitors with substantial anticancer efficacy. Further studies, including cell cycle analysis and apoptosis assays in HEPG2 cell lines, revealed cell cycle arrest at G1/G0 and G2 phases. We also evaluated the potential influence of compound 30a on the EGFR pathway using western blot analysis, revealing a significant inhibition of EGFR autophosphorylation in HEPG2 cells. In conclusion, our findings highlight the promise of these novel compounds as potent EGFR inhibitors, encouraging further investigation and development for the creation of novel and effective anticancer therapeutics.
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Affiliation(s)
| | - Milind Sindkhedkar
- Novel Drug Discovery & Development, Lupin Research Park, Lupin Ltd. Pune-412115 India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal, Academy of Higher Education Manipal Karnataka-576104 India
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2
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Milesi P, Baldelli Bombelli F, Lanfrancone L, Gomila RM, Frontera A, Metrangolo P, Terraneo G. Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes. Chem Asian J 2024; 19:e202301033. [PMID: 38501888 DOI: 10.1002/asia.202301033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.
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Affiliation(s)
- Pietro Milesi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Luisa Lanfrancone
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
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3
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Elsaman T, Ahmad I, Eltayib EM, Suliman Mohamed M, Yusuf O, Saeed M, Patel H, Mohamed MA. Flavonostilbenes natural hybrids from Rhamnoneuron balansae as potential antitumors targeting ALDH1A1: molecular docking, ADMET, MM-GBSA calculations and molecular dynamics studies. J Biomol Struct Dyn 2024; 42:3249-3266. [PMID: 37261483 DOI: 10.1080/07391102.2023.2218936] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]
Abstract
Several studies have linked Cancer stem cells (CSCs) to cancer resistance development to chemotherapy and radiotherapy. ALDH1A1 is a key enzyme that regulates the gene expression of CSCs and creates an immunosuppressive tumor microenvironment. It was reported that quercetin and resveratrol were among the inhibitors of ALDH1A1. In early 2022, it was reported that new 11 flavonostilbenes (rhamnoneuronal D-N) were isolated from Rhamnoneuron balansae as potential antiaging natural products. Rhamnoneuronal H (5) could be envisioned as a natural hybrid of quercetin and resveratrol. It was therefore hypothesized that 5 and its analogous isolates rhamnoneuronal D-G (1-4) and rhamnoneuronal I-N (6-11) would have potential ALDH1A1 inhibitory activity. To this end, all isolates were subjected to molecular docking, MM-GBSA, ADMET, and molecular dynamics simulations studies to assess their potential as new leads for cancer treatment targeting ALDH1A1. In silico findings revealed that natural hybrid 5 has a similar binding affinity, judged by MM-GBSA, to the ALDH1A1 active site when compared to the co-crystalized ligand (-64.71 kcal/mole and -64.12 kcal/mole, respectively). Despite having lesser affinity than that of the co-crystalized ligand, the rest of the flavonostilbenes, except 2-4, displayed better binding affinities (-37.55 kcal/mole to -58.6 kcal/mole) in comparison to either resveratrol (-34.44 kcal/mole) or quercetin (-36.48 kcal/mole). Molecular dynamic simulations showed that the natural hybrids 1, 5-11 are of satisfactory stability up to 100 ns. ADMET outcomes indicate that these hybrids displayed acceptable properties and hence could represent an ideal starting point for the development of potent ALDH1A1 inhibitors for cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, Saudi Arabia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Eyman Mohamed Eltayib
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Al Jouf, Saudi Arabia
| | - Malik Suliman Mohamed
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Al Jouf, Saudi Arabia
| | - Osman Yusuf
- Department of Pharmaceutics, Faculty of Pharmacy, Al-Neelain University, Khartoum, Sudan
| | | | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, Saudi Arabia
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Solozabal N, Tapia L, Solà J, Pérez Y, Alfonso I. Molecular Recognition of Tyrosine-Containing Polypeptides with Pseudopeptidic Cages Unraveled by Fluorescence and NMR Spectroscopies. Bioconjug Chem 2023; 34:2345-2357. [PMID: 38078839 PMCID: PMC10859922 DOI: 10.1021/acs.bioconjchem.3c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
The molecular recognition of Tyr-containing peptide copolymers with pseudopeptidic cages has been studied using a combination of fluorescence and NMR spectroscopies. Fluorescence titrations rendered a reasonable estimation of the affinities, despite the presence of dynamic quenching masking the unambiguous detection of the supramolecular complexes. Regarding NMR, the effect of polypeptide (PP) binding on relaxation and diffusion parameters of the cages is much more reliable than the corresponding chemical shift perturbations. To that, purification of the commercial PPs is mandatory to obtain biopolymers with lower polydispersity. Thus, the relaxation/diffusion-filtered 1H spectra of the cages in the absence vs presence of the PPs represent a suitable setup for the fast detection of the noncovalent interactions. Additional key intermolecular NOE cross-peaks supported by molecular models allow the proposal of a structure of the supramolecular species, stabilized by the Tyr encapsulation within the cage cavity and additional attractive polar interactions between the side chains of cage and PP, thus defining a binding epitope with a potential for implementing sequence selectivity. Accordingly, the cages bearing positive/negative residues prefer to bind the peptides having complementary negative/positive side chains close to the target Tyr, suggesting an electrostatic contribution to the interaction. Overall, our results show that both techniques represent a powerful and complementary combination for studying cage-to-PP molecular recognition processes.
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Affiliation(s)
- Naiara Solozabal
- NMR
Facility, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
| | - Lucía Tapia
- Department
of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
| | - Jordi Solà
- Department
of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
| | - Yolanda Pérez
- NMR
Facility, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
| | - Ignacio Alfonso
- Department
of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
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5
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Magwaza NM, More GK, Gildenhuys S, Mphahlele MJ. In Vitro α-Glucosidase and α-Amylase Inhibition, Cytotoxicity and Free Radical Scavenging Profiling of the 6-Halogeno and Mixed 6,8-Dihalogenated 2-Aryl-4-methyl-1,2-dihydroquinazoline 3-Oxides. Antioxidants (Basel) 2023; 12:1971. [PMID: 38001824 PMCID: PMC10669220 DOI: 10.3390/antiox12111971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Series of the 6-bromo/iodo substituted 2-aryl-4-methyl-1,2-dihydroquinazoline-3-oxides and their mixed 6,8-dihalogenated (Br/I and I/Br) derivatives were evaluated for inhibitory properties against α-glucosidase and/or α-amylase activities and for cytotoxicity against breast (MCF-7) and lung (A549) cancer cell lines. The 6-bromo-2-phenyl substituted 3a and its corresponding 6-bromo-8-iodo-2-phenyl-substituted derivative 3i exhibited dual activity against α-glucosidase (IC50 = 1.08 ± 0.02 μM and 1.01 ± 0.05 μM, respectively) and α-amylase (IC50 = 5.33 ± 0.01 μM and 1.18 ± 0.06 μM, respectively) compared to acarbose (IC50 = 4.40 ± 0.05 μM and 2.92 ± 0.02 μM, respectively). The 6-iodo-2-(4-fluorophenyl)-substituted derivative 3f, on the other hand, exhibited strong activity against α-amylase and significant inhibitory effect against α-glucosidase with IC50 values of 0.64 ± 0.01 μM and 9.27 ± 0.02 μM, respectively. Compounds 3c, 3l and 3p exhibited the highest activity against α-glucosidase with IC50 values of 1.04 ± 0.03, 0.92 ± 0.01 and 0.78 ± 0.05 μM, respectively. Moderate cytotoxicity against the MCF-7 and A549 cell lines was observed for these compounds compared to the anticancer drugs doxorubicin (IC50 = 0.25 ± 0.05 μM and 0.36 ± 0.07 μM, respectively) and gefitinib (IC50 = 0.19 ± 0.04 μM and 0.25 ± 0.03 μM, respectively), and their IC50 values are in the range of 10.38 ± 0.08-25.48 ± 0.08 μM and 11.39 ± 0.12-20.00 ± 0.05 μM, respectively. The test compounds generally exhibited moderate to strong antioxidant capabilities, as demonstrated via robust free radical scavenging activity assays, viz., DPPH and NO. The potential of selected derivatives to inhibit superoxide dismutase (SOD) was also investigated via enzymatic assay in vitro. Molecular docking revealed the N-O moiety as essential to facilitate electrostatic interactions of the test compounds with the protein residues in the active site of α-glucosidase and α-amylase. The presence of bromine and/or iodine atoms resulted in increased hydrophobic (alkyl and/or π-alkyl) interactions and therefore increased inhibitory effect against both enzymes.
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Affiliation(s)
- Nontokozo M. Magwaza
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa;
| | - Garland K. More
- College of Agriculture and Environmental Sciences Laboratories, University of South Africa, Private Bag X06, Florida 1710, South Africa;
| | - Samantha Gildenhuys
- Department of Life & Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X06, Florida 1710, South Africa;
| | - Malose J. Mphahlele
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa;
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6
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Zhu W, Liu X, Li Q, Gao F, Liu T, Chen X, Zhang M, Aliper A, Ren F, Ding X, Zhavoronkov A. Discovery of novel and selective SIK2 inhibitors by the application of AlphaFold structures and generative models. Bioorg Med Chem 2023; 91:117414. [PMID: 37467565 DOI: 10.1016/j.bmc.2023.117414] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Salt-inducible kinase 2 (SIK2) has been recognized as a potential target for anti-inflammation and anti-cancer therapy. In this paper, based on the binding pose of the reported compound (GLPG-3970, 3) with AlphaFold protein structure, a series of hinge cores were generated via AI-generative models (Chemistry42). After the molecular docking, synthesis, and biological evaluation, a hit molecule (7f) targeting SIK2 was obtained with a novel scaffold. Further SAR exploration led to the discovery of compound 8g with superior potency against SIK2 compared with the reported inhibitors. Furthermore, 8g also demonstrated excellent selectivity over other AMPK kinases, favorable in vitro ADMET profiles and decent cellular activities. This work provides an alternative approach to the discovery of novel and selective kinase inhibitors.
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Affiliation(s)
- Wei Zhu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xiaosong Liu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Qi Li
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Feng Gao
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Tingting Liu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xiaojing Chen
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, UAE
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China.
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, UAE.
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Sun HH, Wang ZZ, Gao YY, Hao GF, Yang GF. Protein Kinases as Potential Targets Contribute to the Development of Agrochemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:52-64. [PMID: 36592042 DOI: 10.1021/acs.jafc.2c06222] [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: 06/17/2023]
Abstract
Using agrochemicals against pest insects, fungi, and weeds plays a major part in maintaining and improving crop yields, which helps to solve the issue of food security. Due to the limited targets and resistance of agrochemicals, protein kinases are regarded as attractive potential targets to develop new agrochemicals. Recently, a lot of investigations have shown the extension of agrochemicals by targeting protein kinases, implying an increasing concern for this kind of method. However, few people have summarized and discussed the targetability of protein kinases contributing to the development of agrochemicals. In this work, we introduce the research on protein kinases as potential targets used in crop protection and discuss the prospects of protein kinases in the field of agrochemical development. This study may not only provide guidance for the contribution of protein kinases to the development of agrochemicals but also help nonprofessionals such as students learn and understand the role of protein kinases quickly.
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Affiliation(s)
- Hao-Han Sun
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Zhi-Zheng Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yang-Yang Gao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, People's Republic of China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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8
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Zhu Y, Hu X. Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27207124. [PMID: 36296718 PMCID: PMC9611543 DOI: 10.3390/molecules27207124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Protein kinases are key enzymes that catalyze the covalent phosphorylation of substrates via the transfer of the γ-phosphate of ATP, playing a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. Due to their pivotal cellular role, the aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Decades of intense development of protein kinase inhibitors (PKIs) resulted in 71 FDA-approved PKI drugs that target dozens of protein kinases for the treatment of various diseases. How do FDA-approved protein kinase inhibitor PKI drugs compete with ATP in their own binding pocket? This is the central question we attempt to address in this work. Based on modes of non-bonded interactions and their calculated interaction strengths by means of the advanced double hybrid DFT method B2PLYP, the molecular recognition of PKI drugs in the ATP-binding pockets was systematically analyzed. It was found that (1) all the FDA-approved PKI drugs studied here form one or more hydrogen bond(s) with the backbone amide N, O atoms in the hinge region of the ATP binding site, mimicking the adenine base; (2) all the FDA-approved PKI drugs feature two or more aromatic rings. The latter reach far and deep into the hydrophobic regions I and II, forming multiple CH-π interactions with aliphatic residues L(3), V(11), A(15), V(36), G(51), L(77) and π-π stacking interactions with aromatic residues F(47) and F(82), but ATP itself does not utilize these regions extensively; (3) all FDA-approved PKI drugs studied here have one thing in common, i.e., they frequently formed non-bonded interactions with a total of 12 residues L(3),V(11), A(15), K(17), E(24),V(36),T(45), F(47), G(51), L(77), D(81) and F(82) in the ATP binding. Many of those 12 commonly involved residues are highly conserved residues with important structural and catalytic functional roles. K(17) and E(24) are the two highly conserved residues crucial for the catalytic function of kinases. D(81) and F(82) belong to the DFG motif; T(45) was dubbed the gate keeper residue. F(47) is located on the hinge region and G(51) sits on the linker that connects the hinge to the αD-helix. It is this targeting of highly conserved residues in protein kinases that led to promiscuous PKI drugs that lack selectivity. Although the formation of hydrogen bond(s) with the backbone of the hinge gives PKI drugs the added binding affinity and the much-needed directionality, selectivity is sacrificed. That is why so many FDA-approved PKI drugs are known to have multiple targets. Moreover, off-target-mediated toxicity caused by a lack of selectivity was one of the major challenges facing the PKI drug discovery community. This work suggests a road map for future PKI drug design, i.e., targeting non-conserved residues in the ATP binding pocket to gain better selectivity so as to avoid off-target-mediated toxicity.
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Affiliation(s)
| | - Xiche Hu
- Correspondence: ; Tel.: +1-4195301513
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9
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Scarpi-Luttenauer M, Galentino K, Orvain C, Cecchini M, Gaiddon C, Mobian P. TiO4N2 complexes formed with 1,10-phenanthroline ligands containing a donor-acceptor hydrogen bond site: synthesis, cytotoxicity and docking experiments. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Weng YY, Sun X, Wang LX, Liao YY, Wang CJ. Density functional methods study on the structures and spectral characteristics for pharmacophoric conformers, metabolites, and combined fragments of Erlotinib. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Sepay N, Mondal R, Al-Muhanna MK, Saha D. Identification of natural flavonoids as novel EGFR inhibitors using DFT, molecular docking, and molecular dynamics. NEW J CHEM 2022. [DOI: 10.1039/d2nj00389a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum mechanical descriptors from DFT, molecular docking, molecular dynamics, and NCIplot methodology have been utilized to find a potential anti-EGFR flavonoid.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Kolkata, 700017, India
| | - Rina Mondal
- Department of Chemistry, Uluberia College, Howrah, West Bengal, 711 315, India
| | - Muhanna K. Al-Muhanna
- Material Science Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Debajyoti Saha
- Department of Chemistry, Krishnagar Govt College, Krishnagar, West Bengal, 74110, India
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12
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Ma Z, Qiu S, Chen HC, Zhang D, Lu YL, Chen XL. Maleimide structure: a promising scaffold for the development of antimicrobial agents. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:1-14. [PMID: 33511872 DOI: 10.1080/10286020.2021.1877675] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Natural compounds bearing maleimide rings are a series of secondary metabolites derived from fungi/marine microorganisms, which are characterized by a general structure -CO-N(R)-CO-, and the R group is normally substituted with alkyl or aryl groups. Maleimide compounds show various biological activities such as antibacterial, antifungal, and anticancer activity. In this review, the broad-spectrum antimicrobial activities of 15 maleimide compounds from natural sources and 32 artificially synthesized maleimides were summarized, especially against Candida albicans, Sclerotinia sclerotiorum, and Staphylococcus aureus. It highlights that maleimide scaffold has tremendous potential to be utilized in the development of novel antimicrobial agents.
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Affiliation(s)
- Zhi Ma
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shuo Qiu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Han-Chi Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dong Zhang
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yue-Le Lu
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiao-Long Chen
- Institute of Fermentation Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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13
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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14
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Li M, Xue N, Liu X, Wang Q, Yan H, Liu Y, Wang L, Shi X, Cao D, Zhang K, Zhang Y. Discovery of Potent EGFR Inhibitors With 6-Arylureido-4-anilinoquinazoline Derivatives. Front Pharmacol 2021; 12:647591. [PMID: 34122069 PMCID: PMC8187944 DOI: 10.3389/fphar.2021.647591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/06/2021] [Indexed: 12/22/2022] Open
Abstract
According to the classical pharmacophore fusion strategy, a series of 6-arylureido-4-anilinoquinazoline derivatives ( Compounds 7a - t ) were designed, synthesized, and biologically evaluated by the standard CCK-8 method and enzyme inhibition assay. Among the title compounds, Compounds 7a , 7c , 7d , 7f , 7i , 7o , 7p , and 7q exhibited promising anti-proliferative bioactivities, especially Compound 7i , which had excellent antitumor activity against the A549, HT-29, and MCF-7 cell lines (IC50 = 2.25, 1.72, and 2.81 μM, respectively) compared with gefitinib, erlotinib, and sorafenib. In addition, the enzyme activity inhibition assay indicated that the synthesized compounds had sub-micromolar inhibitory levels (IC50, 11.66-867.1 nM), which was consistent with the results of the tumor cell line growth inhibition tests. By comparing the binding mechanisms of Compound 7i (17.32 nM), gefitinib (25.42 nM), and erlotinib (33.25 nM) to the EGFR, it was found that Compound 7i could extend into the effective region with a similar action conformation to that of gefitinib and interact with residues L85, D86, and R127, increasing the binding affinity of Compound 7i to the EGFR. Based on the molecular hybridization strategy, 14 compounds with EGFR inhibitory activity were designed and synthesized, and the action mechanism was explored through computational approaches, providing valuable clues for the research of antitumor agents based on EGFR inhibitors.
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Affiliation(s)
- Meng Li
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Na Xue
- Department of Pharmaceutical Engineering, Hebei Chemical and Pharmaceutical College, Shijiazhuang, China
| | - Xingang Liu
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Qiaoyun Wang
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Hongyi Yan
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Yifan Liu
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Lei Wang
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Xiaowei Shi
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Deying Cao
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Kai Zhang
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
| | - Yang Zhang
- Department of Medicinal Chemistry, Hebei Medical University, Shijiazhuang, China
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15
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Zhu Y, Alqahtani S, Hu X. Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors. Molecules 2021; 26:1776. [PMID: 33810025 PMCID: PMC8005117 DOI: 10.3390/molecules26061776] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022] Open
Abstract
Protein kinases are key enzymes in many signal transduction pathways, and play a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. However, aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Over the past three decades, thousands of protein kinase inhibitors (PKIs) with varying molecular frames have been developed. Large-scale data mining of the Protein Data Bank resulted in a database of 2139 non-redundant high-resolution X-ray crystal structures of PKIs bound to protein kinases. This provided us with a unique opportunity to study molecular determinants for the molecular recognition of PKIs. A chemoinformatic analysis of 2139 PKIs resulted in findings that PKIs are "flat" molecules with high aromatic ring counts and low fractions of sp3 carbon. All but one PKI possessed one or more aromatic rings. More importantly, it was found that the average weighted hydrogen bond count is inversely proportional to the number of aromatic rings. Based on this linear relationship, we put forward the exchange rule of hydrogen bonding interactions and non-bonded π-interactions. Specifically, a loss of binding affinity caused by a decrease in hydrogen bonding interactions is compensated by a gain in binding affinity acquired by an increase in aromatic ring-originated non-bonded interactions (i.e., π-π stacking interactions, CH-π interactions, cation-π interactions, etc.), and vice versa. The very existence of this inverse relationship strongly suggests that both hydrogen bonding and aromatic ring-originated non-bonded interactions are responsible for the molecular recognition of PKIs. As an illustration, two representative PKI-kinase complexes were employed to examine the relative importance of different modes of non-bonded interactions for the molecular recognition of PKIs. For this purpose, two FDA-approved PKI drugs, ibrutinib and lenvatinib, were chosen. The binding pockets of both PKIs were thoroughly examined to identify all non-bonded intermolecular interactions. Subsequently, the strengths of interaction energies between ibrutinib and its interacting residues in tyrosine kinase BTK were quantified by means of the double hybrid DFT method B2PLYP. The resulting energetics for the binding of ibrutinib in tyrosine kinase BTK showed that CH-π interactions and π-π stacking interactions between aromatic rings of the drug and hydrophobic residues in its binding pocket dominate the binding interactions. Thus, this work establishes that, in addition to hydrogen bonding, aromatic rings function as important molecular determinants for the molecular recognition of PKIs. In conclusion, our findings support the following pharmacophore model for ATP-competitive kinase inhibitors: a small molecule features a scaffold of one or more aromatic rings which is linked with one or more hydrophilic functional groups. The former has the structural role of acting as a scaffold and the functional role of participating in aromatic ring-originated non-bonded interactions with multiple hydrophobic regions in the ATP binding pocket of kinases. The latter ensure water solubility and form hydrogen bonds with the hinge region and other hydrophilic residues of the ATP binding pocket.
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Affiliation(s)
- Yan Zhu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
| | - Saad Alqahtani
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
- Department of Chemistry, King Saud University, Riyadh 12372, Saudi Arabia
| | - Xiche Hu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
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16
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Chen P, Luo K, Yu X, Yuan X, Liu X, Lin J, Jin Y. Cu-Catalyzed Direct Amination of Cyclic Amides via C-OH Bond Activation Using DMF. Org Lett 2020; 22:6547-6551. [PMID: 32806150 DOI: 10.1021/acs.orglett.0c02320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we describe a Cu-catalyzed approach to directly accessing aromatic heterocyclic amines from cyclic amides. The most-reported methods for cyclic amide conversions to aromatic heterocyclic amines use an activating group, such as a halogen atom or a trifluoromethane sulfonyl group. However, subsequent elimination of activating groups during the amination process results in significant waste. This copper-catalyzed direct amination of cyclic amides in DMF forms aromatic heterocyclic amines with environmental friendliness and readily available reagents. A plausible radical mechanism has been proposed for the reaction. Meanwhile, the coordinating effect of the N1 atom is key to the success of this reaction, which provides assistance to the copper ions for the activation and amination of C-O bonds.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Kaixiu Luo
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Xianglin Yu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Xu Yuan
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Xiaoyu Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Jun Lin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P.R. China
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17
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Qin Q, Wu T, Yin W, Sun Y, Zhang X, Wang R, Guo J, Zhao D, Cheng M. Discovery of 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4: Biological evaluation and docking studies. Arch Pharm (Weinheim) 2020; 353:e2000097. [PMID: 32627873 DOI: 10.1002/ardp.202000097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/05/2023]
Abstract
In this study, novel 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4 (PAK4) were discovered and evaluated for their biological activity against PAK4. Among the derivatives studied, promising compounds A2, B6, and B8 displayed the highest inhibitory activities against PAK4 (IC50 = 18.4, 5.9, and 20.4 nM, respectively). From the cellular assay, compound B6 exhibited the highest potency with an IC50 value of 2.533 μM against A549 cells. Some compounds were selected for computational ADME (absorption, distribution, metabolism, and elimination) properties and molecular docking studies against PAK4. The detailed structure-activity relationship based on the biochemical activities and molecular docking studies were explored. According to the docking studies, compound B6 had the lowest docking score (docking energy: -7.593 kcal/mol). The molecular docking simulation indicated the binding mode between compound B6 and PAK4. All these results suggest compound B6 as a useful candidate for the development of a PAK4 inhibitor.
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Affiliation(s)
- Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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18
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Jarapula R, Badavath VN, Rekulapally S, Manda S. Computational Studies of bis-2-Oxoindoline Succinohydrazides and their In Vitro Cytotoxicity. Curr Comput Aided Drug Des 2020; 16:270-280. [DOI: 10.2174/1573409915666190117122139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/24/2018] [Accepted: 01/03/2019] [Indexed: 11/22/2022]
Abstract
Background:
The discovery of clinically relevant EGFR inhibitors for cancer therapy has proven
to be a challenging task. To identify novel and potent EGFR inhibitors, the quantitative structure-activity
relationship (QSAR) and molecular docking approach became a very useful and largely widespread technique
for drug design.
Methods:
We performed the in vitro cytotoxic activity on HEPG-2 cell line and earlier on MCF-7 and A
549 by using MTT assay method. The development of 3D QSAR model of N1,N4-bis(2-oxoindolin-3-
ylidene) succinohydrazides using the stepwise-backward variable methods to generate Multiple Linear Regression
method elucidates the structural properties required for EGFR inhibitory activity and also perform
the Molecular Docking studies on EGFR (PDB ID:1M17). Further, we analysed for Lipinski’s rule of five
to evaluate the drug-likeness and established in silico ADMET properties.
Results:
The resulting cytotoxicity (IC50) values ranged from 9.34 to 100 μM and compared with cisplatin
as a standard. Among the series of compounds, 6j showed good cytotoxic activity on HEPG-2 cell line with
9.34 μM, IC50 value. Most of the evaluated compounds showed good antitumor activity on HEPG-2 than
MCF-7and A549. The developed 3D QSAR Multiple Linear Regression models are statistically significant
with non-cross-validated correlation coefficient r2 = 0.9977, cross-validated correlation coefficient q2 =
0.902 and predicted_r2 = 0.9205. Molecular docking studies on EGFR (PDB ID: 1M17) results, compounds
6d, 6j and 6l showed good dock/PLP scores i.e. -81.28, -73.98 and -75.37, respectively, by interacting with
Leu-694, Val-702 and Gly-772 amino acids via hydrophobic and hydrogen bonds with Asn818 and Met-
769. Further, we analysed drug-likeness and established in silico ADMET properties.
Conclusion:
The results of 3D QSAR studies suggest that the electrostatic and steric descriptors influence
the cytotoxic activity of succinohydrazides. From the molecular docking studies, it is evident that
hydrophobic, hydrogen and Van Der Waal’s interactions determine binding affinities. In addition to this, druglikeness
and ADMET properties were analysed. It is evident that there is a correlation between the QSAR and
docking results. Compound 6j was found to be too lipophilic due to its dihalo substitution on isatin nucleus,
and can act as a lead molecule for further and useful future development of new EGFR Inhibitors.
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Affiliation(s)
- Ravi Jarapula
- Department of Pharmaceutical Chemistry, University College of Pharmaceutical Sciences, Kakatiya University, Warangal-506009, Telangana, India
| | - Vishnu N. Badavath
- Department of Chemistry, Indian Institute of Technology, (IIT-BHU), Varanasi- 221005, Uttar Pradesh, India
| | - Shriram Rekulapally
- Department of Pharmaceutical Chemistry, University College of Pharmaceutical Sciences, Kakatiya University, Warangal-506009, Telangana, India
| | - Sarangapani Manda
- Department of Pharmaceutical Chemistry, University College of Pharmaceutical Sciences, Kakatiya University, Warangal-506009, Telangana, India
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19
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Yuan X, Bu H, Zhou J, Yang CY, Zhang H. Recent Advances of SHP2 Inhibitors in Cancer Therapy: Current Development and Clinical Application. J Med Chem 2020; 63:11368-11396. [DOI: 10.1021/acs.jmedchem.0c00249] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinrui Yuan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Hong Bu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
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20
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Allam HA, Aly EE, Farouk AK, El Kerdawy AM, Rashwan E, Abbass SE. Design and Synthesis of some new 2,4,6-trisubstituted quinazoline EGFR inhibitors as targeted anticancer agents. Bioorg Chem 2020; 98:103726. [DOI: 10.1016/j.bioorg.2020.103726] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/20/2020] [Accepted: 03/04/2020] [Indexed: 12/30/2022]
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21
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Monier M, Abdel-Latif D, El-Mekabaty A, Mert BD, Elattar KM. Advances in the Chemistry of 6-6 Bicyclic Systems: Chemistry of Pyrido[3,4- d]pyrimidines. Curr Org Synth 2019; 16:812-854. [DOI: 10.2174/1570179416666190704113647] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/27/2019] [Accepted: 05/17/2019] [Indexed: 12/23/2022]
Abstract
The aim of this work is to discuss the chemistry of pyrido[3,4-d]pyrimidines as one of the most
important heterocyclic compounds with remarkable synthetic, biological and medical applications. In this
overview, the chemistry of heterocyclic compounds incorporated the pyrido[3,4-d]pyrimidine scaffold as
demonstrated by chemical reactions and different preparation processes. The anticipated compounds were
synthesized from pyridine or pyrimidine compounds and a description of the reactivity of substituents attached
to ring carbon and nitrogen atoms is discussed. On the other hand, the synthesis and reactions of fused
heterocycles incorporated pyrido[3,4-d]pyrimidine scaffold is described. The diamine analogs included
pyrido[3,4-d]pyrimidine core were reported as tyrosine kinase inhibitors. The chemical reactions of certain
unexpected and chemically substantial compounds have been discussed.
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Affiliation(s)
- Mohamed Monier
- Chemistry Department, Faculty of Science, Mansoura University, El-Gomhoria Street, Mansoura 35516, Egypt
| | - Doaa Abdel-Latif
- Chemistry Department, Faculty of Science, Mansoura University, El-Gomhoria Street, Mansoura 35516, Egypt
| | - Ahmed El-Mekabaty
- Chemistry Department, Faculty of Science, Mansoura University, El-Gomhoria Street, Mansoura 35516, Egypt
| | - Başak D. Mert
- Department of Energy Systems Engineering, Adana Alparslan Turkes Science and Technology University, Adana 01250, Turkey
| | - Khaled M. Elattar
- Chemistry Department, Faculty of Science, Mansoura University, El-Gomhoria Street, Mansoura 35516, Egypt
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22
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Sayed AR, Gomha SM, Abdelrazek FM, Farghaly MS, Hassan SA, Metz P. Design, efficient synthesis and molecular docking of some novel thiazolyl-pyrazole derivatives as anticancer agents. BMC Chem 2019; 13:116. [PMID: 31572983 PMCID: PMC6760062 DOI: 10.1186/s13065-019-0632-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/10/2019] [Indexed: 11/29/2022] Open
Abstract
Pyrazoles, thiazoles and fused thiazoles have been reported to possess many biological activities. 3-Methyl-5-oxo-4-(2-arylhydrazono)-4,5-dihydro-1H-pyrazole-1-carbothioamides 3a,b (obtained from the reaction of ethyl 3-oxo-2-(2-arylhydrazono)butanoates 1a,b with thiosemicarbazide) could be transformed into a variety of thiazolyl-pyrazole derivatives 6a–h, 10a–c, 15a–c, 17, 19 and 21 via their reaction with a diversity hydrazonoyl chlorides as well as bromoacetyl derivatives. Moreover, the computational studies were carried out for all new compounds. The results indicated that five compounds showed promising binding affinities (10a: − 3.4 kcal/mol, 6d: − 3.0 kcal/mol, 15a: − 2.2 kcal/mol, 3a: − 1.6 kcal/mol, and 21: − 1.3 kcal/mol) against the active site of the epidermal growth factor receptor kinase (EGFR). The cytotoxicity of the potent products 3a, 6d, 10a, 15a, and 21 was examined against human liver carcinoma cell line (HepG-2) and revealed activities close to Doxorubicin standard drug. There was an understanding between the benefits of restricting affinities and the data obtained from the practical anticancer screening of the tested compounds.![]()
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Affiliation(s)
- Abdelwahed R Sayed
- 1Department of Chemistry, Faculty of Science, King Faisal University, Hofuf, Saudi Arabia.,3Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Sobhi M Gomha
- 2Chemistry Department, Faculty of Science, Cairo University, Giza, 12613 Egypt.,Department of Chemistry, Faculty of Science, Islamic University in Almadinah Almonawara, Almadinah Almonawara, 42351 Saudi Arabia
| | - Fathy M Abdelrazek
- 2Chemistry Department, Faculty of Science, Cairo University, Giza, 12613 Egypt.,Science and Technology Center of Excellence, Ministry of Military Production, Cairo, Egypt
| | - Mohamed S Farghaly
- 2Chemistry Department, Faculty of Science, Cairo University, Giza, 12613 Egypt.,Science and Technology Center of Excellence, Ministry of Military Production, Cairo, Egypt
| | - Shaimaa A Hassan
- 2Chemistry Department, Faculty of Science, Cairo University, Giza, 12613 Egypt
| | - Peter Metz
- 6Fakultat Chemie und Lebensmittelchemie, TU-Dresden, 01069 Dresden, Germany
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23
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El-Gazzar MG, El-Hazek RM, Zaher NH, El-Ghazaly MA. Design and synthesis of novel pyridazinoquinazoline derivatives as potent VEGFR-2 inhibitors: In vitro and in vivo study. Bioorg Chem 2019; 92:103251. [PMID: 31525526 DOI: 10.1016/j.bioorg.2019.103251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023]
Abstract
Worldwide, Hepatocellular Carcinoma (HCC) endures to be a prominent cause of cancer death. Treatment of HCC follows multiple therapies which are not entirely applicable for treatment of all patients. HCC usually arises contextual to chronic liver diseases and is often discovered at later stages which makes treatment options more complex. The present study aimed at design, synthesis & evaluation of new pyridazinoquinazoline derivatives as potential nontoxic anti-hepatocellular carcinoma (HCC) agents, through inhibition of Vascular endothelial growth factor -2 (VEGFR-2). Novel Pyridazino[3, 4, 5-de]quinazoline derivatives (2-6) were designed & synthesized. Their structures were confirmed via spectral and microanalytical data. They were tested for their in vitro VEGFR-2 inhibition & anticancer activity against human liver cancer cell line (HEPG-2). Molecular docking was investigated into VEGFR-2 site. In vivo studies of VEGRF-2 inhibition and the anti-apoptotic effect of the new compounds were determined in liver of irradiated rats. Toxicity of synthesized compounds was also assessed. The results showed that compounds 3-6 have significant antitumor activity and proved to be non-toxic. The ethoxy aniline derivative 6, exhibited the highest activity both in vitro and in vivo compared to the reference drug used, sorafenib. Compound 6 could be considered a promising nontoxic anti HCC agent and this could be partially attributed to its VEGFR-2 inhibition. Future preclinical investigation would be carried out to confirm the specific and exact mechanism of action of these derivatives especially compound 6 as an effective pharmaceutical agent after full toxicological and pharmacological assessment.
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Affiliation(s)
- Marwa G El-Gazzar
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), PO Box 29, Nasr City, Cairo 11765, Egypt
| | - Rania M El-Hazek
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), PO Box 29, Nasr City, Cairo 11765, Egypt
| | - Nashwa H Zaher
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), PO Box 29, Nasr City, Cairo 11765, Egypt.
| | - Mona A El-Ghazaly
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), PO Box 29, Nasr City, Cairo 11765, Egypt
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24
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Gouhar RS, Haneen DSA, El‐Hallouty SM. Synthesis and Anticancer Evaluation of Some Novel Quinazolin‐4(3
H
)‐one Derivatives. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3559] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rasha S. Gouhar
- Therapeutical Chemistry DepartmentNational Research Centre, Dokki P. O 12622, Giza Egypt
| | - David S. A. Haneen
- Chemistry Department, Faculty of ScienceAin Shams University, Abbassia P. O 11566, Cairo Egypt
| | - Salwa M. El‐Hallouty
- Drug Bioassay‐Cell Culture Laboratory, Department of PharmacognosyNational Research Centre, Dokki P. O 12622, Giza Egypt
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Heffron TP. Challenges of developing small-molecule kinase inhibitors for brain tumors and the need for emphasis on free drug levels. Neuro Oncol 2019; 20:307-312. [PMID: 29016919 DOI: 10.1093/neuonc/nox179] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Despite biological rationale and significant clinical study, the pursuit of small-molecule kinase inhibitors for the treatment of brain cancers has had very limited success. This Advance-in-Brief discusses the need for drugs to achieve free brain penetration to engage their targets where CNS tumors reside. This need to achieve free, as opposed to total, drug concentrations in the brain may be a contributing factor to why so many small-molecule kinase inhibitors have not realized success in the neuro-oncology setting. For kinase targets of interest for brain cancer, either the vast majority of small-molecule inhibitors have data suggesting that free brain penetration would be limited or there are inadequate data to suggest that free brain penetration could be expected. Therefore, kinase targets of interest in the treatment of brain cancers may be inadequately assessed due to a lack of freely brain-penetrant inhibitors available for clinical study. Encouraging recent drug discovery efforts that focused on achieving free brain penetration for cancers in the CNS are highlighted. Still, further efforts are needed to enable thorough clinical evaluation of biological hypotheses.
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Awad MK, Abdel-Aal MF, Atlam FM, Hekal HA. Molecular docking, molecular modeling, vibrational and biological studies of some new heterocyclic α-aminophosphonates. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 206:78-88. [PMID: 30081271 DOI: 10.1016/j.saa.2018.07.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
A new diphenyl (aryl) (Ǹ-quinazolin-4-yl-hydrazino) methylphosphonates 3a-3d was synthesized via anhydrous zinc chloride catalyzed Kabachnic-Fields reaction. The structure of the synthesized compounds was confirmed by elemental analysis, FT-IR, 1H NMR, 13C NMR, 31P NMR and MS spectral data. The synthesized compounds showed significant antimicrobial and also remarkable cytotoxicity anticancer activities against breast carcinoma cell line (MCF7). The quantum chemical calculations were performed using density functional theory (DFT) to study the effect of the changes of molecular and electronic structures on the biological activity of the investigated compounds. Also, NBO and theoretical FT-IR were calculated. The experimental results were validated by molecular docking simulation of compound 3b in the active pocket of the enzyme. The important binding interactions with the key residues in the active site were revealed. A good correlation was found between the quantum chemical parameters and experimental data.
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Affiliation(s)
- Mohamed K Awad
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Mahmoud F Abdel-Aal
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Faten M Atlam
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Hend A Hekal
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
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Kumar P, Mazlee MTF, Abdul Wahab MK, Belwal CK, Kumar R, Sajid S. Improved protocol for synthesis of N-(3-chloro-4-fluorophenyl)-7-methoxy-6-(3-morpholin-4-ylpropoxy) quinazolin-4-amine (gefitinib). CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-018-0564-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Go T, Morimatsu A, Wasada H, Tanabe G, Muraoka O, Sawada Y, Yoshimatsu M. Unprecedented nucleophile-promoted 1,7-S or Se shift reactions under Pummerer reaction conditions of 4-alkenyl-3-sulfinylmethylpyrroles. Beilstein J Org Chem 2018; 14:2722-2729. [PMID: 30498522 PMCID: PMC6244179 DOI: 10.3762/bjoc.14.250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/03/2018] [Indexed: 01/28/2023] Open
Abstract
A unique 1,7-S- and Se-shift reaction under Pummerer reaction conditions of 4-alkenyl-3-sulfinyl- and seleninylpyrroles was described. The usual Pummerer reaction of 4-(alkenylaminomethyl)-3-phenylsulfinylpyrroles and a successive reaction with tetrabutylammonium hydroxide (TBAH) yielded either pyrrolo[3,2-c]azepines or N-pyrrol-3-ylmethyl-N-(4-hydroxy-3-sulfanylpropyl)-p-toluenesulfonamides (diols). Seleno-Pummerer reactions of 3-selanylmethylpyrroles also proceeded via in situ generation of selenoxides, followed by a treatment with TBAH.
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Affiliation(s)
- Takashi Go
- Department of Chemistry, Faculty of Education, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Akane Morimatsu
- Department of Chemistry, Faculty of Education, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Hiroaki Wasada
- Department of Chemistry, Faculty of Regional Study, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Genzoh Tanabe
- School of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Osamu Muraoka
- School of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Yoshiharu Sawada
- Life Science Research Center, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Mitsuhiro Yoshimatsu
- Department of Chemistry, Faculty of Education, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
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Mphahlele MJ, Maluleka MM, Aro A, McGaw LJ, Choong YS. Benzofuran-appended 4-aminoquinazoline hybrids as epidermal growth factor receptor tyrosine kinase inhibitors: synthesis, biological evaluation and molecular docking studies. J Enzyme Inhib Med Chem 2018; 33:1516-1528. [PMID: 30274538 PMCID: PMC6171423 DOI: 10.1080/14756366.2018.1510919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A series of 2-arylbenzo[b]furan–appended 4-aminoquinazoline hybrids were prepared and evaluated for cytotoxicity in vitro against the human lung cancer (A549), colorectal adenocarcinoma (Caco-2), hepatocellular carcinoma (C3A) and cervical cancer (HeLa) cell lines. Compounds 10d and 10j exhibited significant cytotoxicity against the C3A and Caco-2 cell lines and induced apoptosis in these cell lines. Likewise, compounds 10d and 10e exhibited significant inhibitory activity towards epidermal growth factor receptor-tyrosine kinase phosphorylation (IC50 values of 29.3 nM and 31.1 nM, respectively) against Gefitinib (IC50 = 33.1 nM). Molecular docking of compounds 10 into EGFR-TK active site suggests that they bind to the region of EGFR like Gefitinib does.
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Affiliation(s)
- Malose J Mphahlele
- a Department of Chemistry, College of Science, Engineering and Technology , University of South Africa , Florida , South Africa
| | - Marole M Maluleka
- a Department of Chemistry, College of Science, Engineering and Technology , University of South Africa , Florida , South Africa
| | - Abimbola Aro
- b Phytomedicine Programme , Department of Paraclinical Sciences , University of Pretoria , Onderstepoort , South Africa
| | - Lyndy J McGaw
- b Phytomedicine Programme , Department of Paraclinical Sciences , University of Pretoria , Onderstepoort , South Africa
| | - Yee Siew Choong
- c Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , Minden , Malaysia
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Synthesis, Biological Evaluation and Molecular Docking of Novel Indole-Aminoquinazoline Hybrids for Anticancer Properties. Int J Mol Sci 2018; 19:ijms19082232. [PMID: 30065164 PMCID: PMC6121530 DOI: 10.3390/ijms19082232] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
A series of indole-aminoquinazolines was prepared via amination of the 2-aryl-4-chloroquinazolines with the 7-amino-2-aryl-5-bromoindoles. It was then evaluated for cytotoxicity in vitro against human lung cancer (A549), epithelial colorectal adenocarcinoma (Caco-2), hepatocellular carcinoma (C3A), breast adenocarcinoma (MCF-7), and cervical cancer (HeLa) cells. A combination on the quinazoline and indole moieties of a 2-phenyl and 2-(4-fluorophenyl) rings in compound 4b; 2-(4-fluorophenyl) and 3-chlorophenyl rings in compound 4f; or the two 2-(4-fluorophenyl) rings in compound 4g, resulted in significant and moderate activity against the Caco-2 and C3A cell lines. The indole-aminoquinazoline hybrids compounds 4f and 4g induced apoptosis in Caco-2 and C3A cells, and were also found to exhibit moderate (IC50 = 52.5 nM) and significant (IC50 = 40.7 nM) inhibitory activity towards epidermal growth factor receptor (EGFR) against gefitinib (IC50 = 38.9 nM). Molecular docking suggests that 4a–h could bind to the ATP region of EGFR like erlotinib.
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31
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Elgemeie GH, Fathy NM, Farag AB, Alkhursani SA. Design, synthesis, molecular docking and anti-hepatocellular carcinoma evaluation of novel acyclic pyridine thioglycosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:186-198. [PMID: 29608403 DOI: 10.1080/15257770.2018.1450508] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A novel series of acyclic pyridine thioglycosides has been synthesized. Evaluation of the anti proliferative activity of these compounds against HEPG-2 cell lines (liver carcinoma cell lines) shows that most of the compounds have high anti-tumor activities especially 6b, 6c, 7b and 7c. Furthermore, in the modeling study, these compounds showed that they have high binding affinity with thymidylate synthase dihydrofolate reductase (TS-DHFR).
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Affiliation(s)
- Galal H Elgemeie
- a Chemistry Department, Faculty of Science , Helwan University , Helwan , Cairo , Egypt
| | - Nahed M Fathy
- b Photochemistry Department , National Research Centre , Dokki , Cairo , Egypt
| | - Ayman B Farag
- c Pharmaceutical Chemistry Department, Faculty of Pharmacy , Ahram Canadian University , Giza , Egypt
| | - Sheikha A Alkhursani
- d Chemistry Department , Girls College of Science , Dammam , Kingdom of Saudi Arabia
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32
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Lin FY, Esposito EX, Tseng YJ. LeadOp+R: Structure-Based Lead Optimization With Synthetic Accessibility. Front Pharmacol 2018; 9:96. [PMID: 29556192 PMCID: PMC5845126 DOI: 10.3389/fphar.2018.00096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
We previously described a structure-based fragment hopping for lead optimization using a pre-docked fragment database, “LeadOp,” that conceptually replaced “bad” fragments of a ligand with “good” fragments while leaving the core of the ligand intact thus improving the compound's activity. LeadOp was proven to optimize the query molecules and systematically developed improved analogs for each of our example systems. However, even with the fragment-based design from common building blocks, it is still a challenge for synthesis. In this work, “LeadOp+R” was developed based on 198 classical chemical reactions to consider the synthetic accessibility while optimizing leads. LeadOp+R first allows user to identify a preserved space defined by the volume occupied by a fragment of the query molecule to be preserved. Then LeadOp+R searches for building blocks with the same preserved space as initial reactants and grows molecules toward the preferred receptor-ligand interactions according to reaction rules from reaction database in LeadOp+R. Multiple conformers of each intermediate product were considered and evaluated at each step. The conformer with the best group efficiency score would be selected as the initial conformer of the next building block until the program finished optimization for all selected receptor-ligand interactions. The LeadOp+R method was tested with two biomolecular systems: Tie-2 kinase and human 5-lipoxygenase. The LeadOp+R methodology was able to optimize the query molecules and systematically developed improved analogs for each of our example systems. The suggested synthetic routes for compounds proposed by LeadOp+R were the same as the published synthetic routes devised by the synthetic/organic chemists.
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Affiliation(s)
- Fang-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Yufeng J Tseng
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.,Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
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33
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Iqbal S, Anantha Krishnan D, Gunasekaran K. Identification of potential PKC inhibitors through pharmacophore designing, 3D-QSAR and molecular dynamics simulations targeting Alzheimer’s disease. J Biomol Struct Dyn 2017; 36:4029-4044. [DOI: 10.1080/07391102.2017.1406824] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Saleem Iqbal
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Dhanabalan Anantha Krishnan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Krishnasamy Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
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Mphahlele MJ, Paumo HK, Choong YS. Synthesis and In Vitro Cytotoxicity of the 4-(Halogenoanilino)-6-bromoquinazolines and Their 6-(4-Fluorophenyl) Substituted Derivatives as Potential Inhibitors of Epidermal Growth Factor Receptor Tyrosine Kinase. Pharmaceuticals (Basel) 2017; 10:ph10040087. [PMID: 29156606 PMCID: PMC5748644 DOI: 10.3390/ph10040087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 12/18/2022] Open
Abstract
Series of the 2-unsubstituted and 2-(4-chlorophenyl)–substituted 4-anilino-6-bromoquinazolines and their 6-(4-fluorophenyl)–substituted derivatives were evaluated for in vitro cytotoxicity against MCF-7 and HeLa cells. The 2-unsubstituted 4-anilino-6-bromoquinazolines lacked activity, whereas most of their 2-(4-chlorophenyl) substituted derivatives were found to exhibit significant cytotoxicity and selectivity against HeLa cells. Replacement of bromine with 4-fluorophenyl group for the 2-unsubstituted 4-anilinoquinazolines resulted in superior activity against HeLa cells compared to Gefitinib. The presence of a 4-fluorophenyl group in the 2-(4-chlorophenyl) substituted derivatives led to increased cytotoxicity against HeLa cells, except for the 3-chloroanilino derivative. The most active compounds, namely, 3g, 3l, and 4l, were found to exhibit a moderate to significant inhibitory effect against epidermal growth factor receptor tyrosine kinase (EGFR-TK). The EGFR molecular docking model suggested that these compounds are nicely bound to the region of EGFR.
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Affiliation(s)
- Malose Jack Mphahlele
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Hugues K Paumo
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia.
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35
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Rani L, Mallajosyula SS. Phosphorylation versus O-GlcNAcylation: Computational Insights into the Differential Influences of the Two Competitive Post-Translational Modifications. J Phys Chem B 2017; 121:10618-10638. [DOI: 10.1021/acs.jpcb.7b08790] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India - 382355
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India - 382355
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36
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Lee H, Landgraf R, Wilson JN. Synthesis and photophysical properties of a fluorescent cyanoquinoline probe for profiling ERBB2 kinase inhibitor response. Bioorg Med Chem 2017; 25:6016-6023. [PMID: 28974323 DOI: 10.1016/j.bmc.2017.09.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 02/06/2023]
Abstract
A fluorescent probe targeting the ERBB2 receptor tyrosine was designed, synthesized and evaluated as reporter of ERBB2 dynamics in overexpressing BT474, i.e. Her2(+), cells. Two cyanoquinazoline (CQ) probes modeled after type-I (CQ1) or active state and type-II (CQ2) or inactive state inhibitors were designed and synthesized with extended π systems that impart binding-induced, turn-on fluorescence. Solution spectroscopy revealed that CQ1 exhibited attractive photophysical properties and displayed turn-on emission in the presence of purified, soluble ERBB2 kinase domain, while CQ2 was found to be non-emissive, likely due to quenching via a photoinduced electron transfer mechanism. Live cell imaging with CQ1 revealed that this probe targeted an intracellular population of ERBB2, which increased following treatment with type-I inhibitors, gefinitib and canertinib, but showed no response to type-II inhibitors. CQ1 thus provides a novel means of imaging the dynamic response of ERBB2(+) cells to kinase inhibitors.
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Affiliation(s)
- Heajin Lee
- Department of Chemistry, University of Miami, Coral Gables, FL 33124, United States
| | - Ralf Landgraf
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL 33101, United States; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33101, United States
| | - James N Wilson
- Department of Chemistry, University of Miami, Coral Gables, FL 33124, United States; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33101, United States.
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37
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Saptal VB, Bhanage BM. Bifunctional Ionic Liquids Derived from Biorenewable Sources as Sustainable Catalysts for Fixation of Carbon Dioxide. CHEMSUSCHEM 2017; 10:1145-1151. [PMID: 27763737 DOI: 10.1002/cssc.201601228] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Indexed: 06/06/2023]
Abstract
A series of highly efficient, bifunctional ionic liquids containing a quaternary alkyl ammonium cation and an amine anion were prepared from choline and amino acids, respectively. Nine ILs were synthesized, characterized, and applied as organocatalysts for the chemical fixation of carbon dioxide to form cyclic carbonates and quinazoline-2,4(1 H,3 H)-diones. A binary mixture of an IL and a co-catalysts generates deep eutectic solvents (DESs) and accelerates the rate of the cycloaddition reaction at atmospheric pressure and low temperature (70 °C). The presence of the hydroxyl functional group of choline and the free amine group of the amino acids in the ILs has a synergistic effect on the activation of the epoxide and carbon dioxide towards the cycloaddition reactions. These ILs are biodegradable and are synthesized from easily available biorenewable sources. Additionally, this catalytic method demonstrates ultimate environmental benignity because of the mild metal- and solvent-free conditions as well as the recyclability of the catalyst and co-catalyst.
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Affiliation(s)
- Vitthal B Saptal
- Department of Chemistry, Institute of Chemical Technology, Matunga, Mumbai-, 400 019, India
| | - Bhalchandra M Bhanage
- Department of Chemistry, Institute of Chemical Technology, Matunga, Mumbai-, 400 019, India
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Boobalan R, Liu KK, Chao JI, Chen C. Synthesis and biological assay of erlotinib analogues and BSA-conjugated erlotinib analogue. Bioorg Med Chem Lett 2017; 27:1784-1788. [PMID: 28268137 DOI: 10.1016/j.bmcl.2017.02.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/28/2022]
Abstract
A series of erlotinib analogues that have structural modification at 6,7-alkoxyl positions is efficiently synthesized. The in vitro anti-tumor activity of synthesized compounds is studied in two non-small cell lung cancer (NSCLC) cell lines (A549 and H1975). Among the synthesized compounds, the iodo compound 6 (ETN-6) exhibits higher anti-cancer activity compared to erlotinib. An efficient method is developed for the conjugation of erlotinib analogue-4, alcohol compound, with protein, bovine serum albumin (BSA), via succinic acid linker. The in vitro anti-tumor activity of the protein attached erlotinib analogue, 8 (ETN-4-Suc-BSA), showed stronger inhibitory activity in both A549 and H1975 NSCLC cell lines.
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Affiliation(s)
- Ramalingam Boobalan
- Department of Chemistry, National Dong Hwa University, Soufeng, Hualien 974, Taiwan; Department of Nursing, Tzu Chi University of Science and Technology, Hualien 970, Taiwan
| | - Kuang-Kai Liu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jui-I Chao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan.
| | - Chinpiao Chen
- Department of Chemistry, National Dong Hwa University, Soufeng, Hualien 974, Taiwan; Department of Nursing, Tzu Chi University of Science and Technology, Hualien 970, Taiwan.
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Novel Selective and Potent EGFR Inhibitor that Overcomes T790M-Mediated Resistance in Non-Small Cell Lung Cancer. Molecules 2016; 21:molecules21111462. [PMID: 27827863 PMCID: PMC6274483 DOI: 10.3390/molecules21111462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/26/2016] [Accepted: 10/29/2016] [Indexed: 12/31/2022] Open
Abstract
Treating patients suffering from EGFR mutant non-small cell lung cancer (NSCLC) with first-generation EGFR tyrosine kinase inhibitors (EGFR TKI) provides excellent response rates. However, approximately 60% of all patients ultimately develop drug resistance due to a second T790M EGFR TKI mutation. In this study, we report the novel molecule N-(3-((5-chloro-2-(4-((1-morpholino)methyl)phenylamino)-4-pyrimidinyl)amino)phenyl)acrylamide (DY3002) to preferentially inhibit the EGFR T790M mutant (EGFRT790M) (IC50 = 0.71 nM) over wild-type EGFR (IC50 = 448.7 nM) in kinase assays. Compared to rociletinib (SI = 21.4) and osimertinib (SI = 40.9), it significantly increased selectivity (SI = 632.0) against EGFRT790M over wild-type EGFR. Furthermore, in cell-based tests, DY3002, with an IC50 value of 0.037 μM, exhibited enhanced inhibitory potency against H1975 cells. Moreover, AO/EB and DAPI staining assays as well as flow cytometer analyses indicated that DY3002 possesses superior biological properties compared to alternatives. In addition, a rat oral glucose tolerance test revealed that treatment with high drug doses (50 mg/kg) of DY3002 did not result in hyperglycemia, suggesting a reduction of side effects in NSCLC patients will be achievable relative to established EGFR inhibitors. In summary, our findings indicate DY3002 as a promising preclinical candidate for effective treatment of patients with EGFRT790M-mutated NSCLC.
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Song Z, Jin Y, Ge Y, Wang C, Zhang J, Tang Z, Peng J, Liu K, Li Y, Ma X. Synthesis and biological evaluation of azole-diphenylpyrimidine derivatives (AzDPPYs) as potent T790M mutant form of epidermal growth factor receptor inhibitors. Bioorg Med Chem 2016; 24:5505-5512. [DOI: 10.1016/j.bmc.2016.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
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Synthesis and In Vitro Cytotoxic Properties of Polycarbo-Substituted 4-(Arylamino)quinazolines. Molecules 2016; 21:molecules21101366. [PMID: 27754446 PMCID: PMC6274161 DOI: 10.3390/molecules21101366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022] Open
Abstract
Herein, we describe the synthesis of novel unsymmetrical polycarbo-substituted 4-anilinoquinazolines derived from the 2-aryl-6-bromo-8-iodoquinazolines via one-pot three-step reaction sequences involving initial amination and subsequent double cross-coupling (bis-Suzuki, Sonogashira/Stille or Sonogashira/Suzuki-Miyaura) reactions with different cross coupling partners for the two carbon–carbon bond formation steps. The 4-anilinoquinazolines were evaluated for potential cytotoxicity against three cancer cell lines, namely, human breast adenocarcinoma (MCF-7) cells, human cervical cancer (HeLa) and human lung cancer (A549) cells. The most active compounds, 2b, 2c, 3c, 4a, 4c and 5a, were found to be more selective against the MCF-7 and HeLa cell lines than the human lung carcinoma (A549) cells. We selected compounds 2c, 3c and 7a as representatives for further evaluation for potential to induce apoptosis and/or necrotic properties in the three cancer cell lines. Compound 2c induced apoptosis of MCF-7 cells through cell membrane alteration. Treatment of Hela and A549 cell lines with compounds 3c and 7a, respectively, led to caspase-3 activation in both cell lines. Compound 3c, on the other hand, caused more necrosis than apoptosis induction in the membrane alteration assay.
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42
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Affiliation(s)
- Timothy P. Heffron
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Lead Discovery of Type II BRAF V600E Inhibitors Targeting the Structurally Validated DFG-Out Conformation Based upon Selected Fragments. Molecules 2016; 21:molecules21070879. [PMID: 27438814 PMCID: PMC6272942 DOI: 10.3390/molecules21070879] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/13/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022] Open
Abstract
The success of the first approved kinase inhibitor imatinib has spurred great interest in the development of type II inhibitors targeting the inactive DFG-out conformation, wherein the Phe of the DFG motif at the start of the activation loop points into the ATP binding site. Nevertheless, kinase inhibitors launched so far are heavily biased toward type I inhibitors targeting the active DFG-in conformation, wherein the Phe of the DFG motif flips by approximately 180° relative to the inactive conformation, resulting in Phe and Asp swapping their positions. Data recently obtained with structurally validated type II inhibitors supported the conclusion that type II inhibitors are more selective than type I inhibitors. In our type II BRAF V600E inhibitor lead discovery effort, we identified phenylaminopyrimidine (PAP) and unsymmetrically disubstituted urea as two fragments that are frequently presented in FDA-approved protein kinase inhibitors. We therefore defined PAP and unsymmetrically disubstituted urea as privileged fragments for kinase drug discovery. A pharmacophore for type II inhibitors, 4-phenylaminopyrimidine urea (4-PAPU), was assembled based upon these privileged fragments. Lead compound SI-046 with BRAF V600E inhibitory activity comparable to the template compound sorafenib was in turn obtained through preliminary structure-activity relationship (SAR) study. Molecular docking suggested that SI-046 is a bona fide type II kinase inhibitor binding to the structurally validated "classical DFG-out" conformation of BRAF V600E. Our privileged fragments-based approach was shown to efficiently deliver a bona fide type II kinase inhibitor lead. In essence, the theme of this article is to showcase the strategy and rationale of our approach.
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Yu H, Li Y, Ge Y, Song Z, Wang C, Huang S, Jin Y, Han X, Zhen Y, Liu K, Zhou Y, Ma X. Novel 4-anilinoquinazoline derivatives featuring an 1-adamantyl moiety as potent EGFR inhibitors with enhanced activity against NSCLC cell lines. Eur J Med Chem 2016; 110:195-203. [DOI: 10.1016/j.ejmech.2016.01.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022]
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Faggi E, Pérez Y, Luis SV, Alfonso I. Supramolecular protection from the enzymatic tyrosine phosphorylation in a polypeptide. Chem Commun (Camb) 2016; 52:8142-5. [DOI: 10.1039/c6cc03875a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two pseudopeptidic cages bind the EYE peptide motif of poly(EY) in buffered water, as shown by NMR and fluorescence spectroscopy. This supramolecular interaction protects the Tyr residues from the enzymatic phosphorylation by PTK.
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Affiliation(s)
- Enrico Faggi
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
| | | | - Santiago V. Luis
- Department of Inorganic and Organic Chemistry
- ESTCE Universitat Jaume I
- Castellón
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
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Wang C, Sun Y, Zhu X, Wu B, Wang Q, Zhen Y, Shu X, Liu K, Zhou Y, Ma X. Novel Quinazoline Derivatives Bearing Various 4-Aniline Moieties as Potent EGFR Inhibitors with Enhanced Activity Against NSCLC Cell Lines. Chem Biol Drug Des 2015; 87:635-43. [PMID: 26613384 DOI: 10.1111/cbdd.12692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 11/12/2015] [Indexed: 12/25/2022]
Abstract
A class of novel quinazoline derivatives bearing various C-4 aniline moieties was synthesized and biologically evaluated as potent epidermal growth factor receptor (EGFR) inhibitors for intervention of non-small-cell lung cancer (NSCLC). Most of these inhibitors are comparable to gefitinib in inhibiting these cancer cell lines, and several of them even displayed superior inhibitory activity. In particular, analogue 5b with an IC50 of 0.10 μm against the EGFR wild-type A431 cells and 5c with an IC50 of 0.001 μm against the gefitinib-sensitive HCC827 cells (EGFR del E746-A750) was identified as highly active EGFR inhibitors. It was also significant that the discovered analogue 2f, not only has high potency against the gefitinib-sensitive cells (IC50 = 0.031 μm), but also possesses remarkably improved activity against the gefitinib-resistant cells. In addition, the enzymatic assays and the Western blot analysis for evaluating the effects of the typical inhibitors indicated that these molecules strongly interfere with the EGFR target.
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Affiliation(s)
- Changyan Wang
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Yajun Sun
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Xingqi Zhu
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Bin Wu
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Qiao Wang
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Yuhong Zhen
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Xiaohong Shu
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Youwen Zhou
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, V5Z 4E8, Canada
| | - Xiaodong Ma
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
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Saptal VB, Bhanage BM. Bifunctional Ionic Liquids for the Multitask Fixation of Carbon Dioxide into Valuable Chemicals. ChemCatChem 2015. [DOI: 10.1002/cctc.201501044] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Vitthal B. Saptal
- Institute of Chemical Technology; Nathalal parekh Marg, Matunga East Mumbai, Maharashtra 400019 India
| | - Bhalchandra M. Bhanage
- Institute of Chemical Technology; Nathalal parekh Marg, Matunga East Mumbai, Maharashtra 400019 India
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Grewal BK, Krishnan RV, Sobhia ME. Structural basis of conformational variance in phosphorylated and non-phosphorylated states of PKCβII. Proteins 2015; 82:1332-47. [PMID: 25050443 DOI: 10.1002/prot.24500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
PKCβII activation is achieved by primary phosphorylation at three phosphorylation sites, followed by the addition of secondary messengers for full activation. Phosphorylation is essential for enzyme maturation, and the associated conformational changes are known to modulate the enzyme activation. To probe into the structural basis of conformational changes on phosphorylation of PKCβII, a comprehensive study of the changes in its complexes with ATP and ruboxistaurin was performed. ATP is a phosphorylating agent in its phosphorylation reaction, and ruboxistaurin is its specific inhibitor. This study provides insight into the differences in the important structural features in phosphorylated and non-phosphorylated states of PKCβII. Less conformational changes when PKCβII is bound to inhibitor in comparison to when it is bound to its phosphorylating agent in both states were observed. The interactions of ruboxistaurin significant in restricting PKCβII to attain the conformational state competent for full activation are reported.
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Paluch P, Pawlak T, Oszajca M, Lasocha W, Potrzebowski MJ. Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 65:2-11. [PMID: 25240460 DOI: 10.1016/j.ssnmr.2014.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/29/2014] [Indexed: 05/25/2023]
Abstract
We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924.
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Affiliation(s)
- Piotr Paluch
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | - Tomasz Pawlak
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | - Marcin Oszajca
- Jerzy Haber Institute of Catalysis and Surface Chemistry, PAS, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wieslaw Lasocha
- Jerzy Haber Institute of Catalysis and Surface Chemistry, PAS, Niezapominajek 8, 30-239 Krakow, Poland; Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek J Potrzebowski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland.
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