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Verma M, Sarfraz A, Hasan I, Vasudev PG, Khan F. Structure-Activity Relationship Studies on VEGFR2 Tyrosine Kinase Inhibitors for Identification of Potential Natural Anticancer Compounds. Med Chem 2024; 20:646-661. [PMID: 38299297 DOI: 10.2174/0115734064247526231129080415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND Over-expression of Vascular Endothelial Growth Factor Receptors (VEGFRs) leads to the hyperactivation of oncogenes. For inhibition of this hyperactivation, the USA Food Drug Administration (FDA) has approved many drugs that show adverse effects, such as hypertension, hypothyroidism, etc. There is a need to discover potent natural compounds that show minimal side effects. In the present study, we have taken structurally diverse known VEGFR2 inhibitors to develop a Quantitative Structure-Activity Relationship (QSAR) model and used this model to predict the inhibitory activity of natural compounds for VEGFR2. METHODS The QSAR model was developed through the forward stepwise Multiple Linear Regression (MLR) method. A developed QSAR model was used to predict the inhibitory activity of natural compounds. Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) assessment and molecular docking studies were performed. The binding stability of the natural compounds with VEGFR2 was elucidated through Molecular Dynamics (MD) simulation. RESULTS The developed QSAR model against VEGFR2 showed the regression coefficient of the training dataset (r2) as 0.81 and the external regression coefficient of the test dataset (r2 test) 0.71. Descriptors, viz., electro-topological state of potential hydrogen bonds (maxHBint2, nHBint6), atom types (minssNH), maximum topological distance matrix (SpMAD_Dt), and 2D autocorrelation (ATSC7v), have been identified. Using this model, 14 natural compounds have been selected that have shown inhibitory activity for VEGFR2, of which six natural compounds have been found to possess a strong binding affinity with VEGFR2. In MD simulation, four complexes have shown binding stability up to 50ns. CONCLUSION The developed QSAR model has identified 5 conserved activity-inducing physiochemical properties, which have been found to be correlated with the anticancer activity of the nonidentical ligand molecules bound with the VEGFR2 kinase. Lavendustin_A, 3'-O-acetylhamaudol, and arctigenin have been obtained as possible lead natural compounds against the VEGFR2 kinase.
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Affiliation(s)
- Meenakshi Verma
- Plant Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.- CIMAP, Kukrail Picnic Spot Road, Lucknow 226015 (Uttar Pradesh), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Aqib Sarfraz
- Technology Dissemination & Computational Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.- CIMAP, Kukrail Picnic Spot Road, Lucknow, 226015 Uttar Pradesh, India
| | - Inamul Hasan
- Technology Dissemination & Computational Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.- CIMAP, Kukrail Picnic Spot Road, Lucknow, 226015 Uttar Pradesh, India
| | - Prema Gauri Vasudev
- Plant Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.- CIMAP, Kukrail Picnic Spot Road, Lucknow 226015 (Uttar Pradesh), India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Feroz Khan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
- Technology Dissemination & Computational Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.- CIMAP, Kukrail Picnic Spot Road, Lucknow, 226015 Uttar Pradesh, India
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Ezelarab HAA, Ali TFS, Abbas SH, Hassan HA, Beshr EAM. Indole-based FLT3 inhibitors and related scaffolds as potential therapeutic agents for acute myeloid leukemia. BMC Chem 2023; 17:73. [PMID: 37438819 DOI: 10.1186/s13065-023-00981-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
Fms-like tyrosine kinase 3 (FLT3) mutation mechanisms are among the most common genetic abnormalities detected in about 30% of acute myeloid leukemia (AML) patients. These mutations are accompanied by poor clinical response, although all these progressions in identifying and interpreting biological AML bio-targets. Several small structured FLT3 inhibitors have been ameliorated to struggle against AML. Despite all these developments regarding these inhibitors, the Overall survival rate is about five years or more in less than one-third of diagnosed AML patients. Midostaurin was the first FDA-approved FLT3 inhibitor in 2017 in the United States and Europe for AML remedy. Next, Gilteritinib was an FDA-approved FLT3 inhibitor in 2018 and in the next year, Quizartinib was approved an as FLT3 inhibitor in Japan. Interestingly, indole-based motifs had risen as advantaged scaffolds with unusual multiple kinase inhibitory activity. This review summarises indole-based FLT3 inhibitors and related scaffolds, including FDA-approved drugs, clinical candidates, and other bioactive compounds. Furthermore, their chemotypes, mechanism of action, and interaction mode over both wild and mutated FLT3 target proteins had been judgmentally discussed. Therefore, this review could offer inspiring future perspectives into the finding of new FLT3-related AML therapies.
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Affiliation(s)
- Hend A A Ezelarab
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Taha F S Ali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Samar H Abbas
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
| | - Heba A Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Eman A M Beshr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
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Patil P, N NB, Satyanarayan ND, Pore S, Zond R, Hangirgekar AGS, Sankpal S. Design, synthesis, docking studies and anticancer evaluation of spiro[indoline-3,4′-pyrano[2,3-c]pyrazole] derivatives on MIN-6 cancer cell line. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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ZHANG BY, ZHENG YF, ZHAO J, KANG D, WANG Z, XU LJ, LIU AL, DU GH. Identification of multi-target anti-cancer agents from TCM formula by in silico prediction and in vitro validation. Chin J Nat Med 2022; 20:332-351. [DOI: 10.1016/s1875-5364(22)60180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/03/2022]
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5
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Wang T, Zhang Q, Wang N, Liu Z, Zhang B, Zhao Y. Research Progresses of Targeted Therapy and Immunotherapy for Hepatocellular Carcinoma. Curr Med Chem 2021; 28:3107-3146. [PMID: 33050856 DOI: 10.2174/0929867327666201013162144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide, with nearly one million new cases and deaths every year. Owing to the complex pathogenesis, hidden early symptoms, rapidly developing processes, and poor prognosis, the morbidity and mortality of HCC are increasing yearly. With the progress being made in modern medicine, the treatment of HCC is no longer limited to traditional methods. Targeted therapy and immunotherapy have emerged to treat advanced and metastatic HCC in recent years. Since Sorafenib is the first molecular targeting drug against angiogenesis, targeted drugs for HCC are continually emerging. Moreover, immunotherapy plays a vital role in clinical trials. In particular, the application of immune checkpoint inhibitors, which have received increasing attention in the field of cancer treatment, is a possible research path. Interestingly, these two therapies generally complement each other at some stages of HCC, bringing new hope for patients with advanced HCC. In this paper, we discuss the research progress of targeted therapy and immunotherapy for HCC in recent years, which will provide a reference for the further development of drugs for HCC.
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Affiliation(s)
- Tao Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Qiting Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ning Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ziqi Liu
- Department of Pharmacy, the PLA Rocket Force Characteristic Medical Center, Beijing 100088, China
| | - Bin Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
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Chen X, Liu H, Xie W, Yang Y, Wang Y, Fan Y, Hua Y, Zhu L, Zhao J, Lu T, Chen Y, Zhang Y. Investigation of Crystal Structures in Structure-Based Virtual Screening for Protein Kinase Inhibitors. J Chem Inf Model 2019; 59:5244-5262. [PMID: 31689093 DOI: 10.1021/acs.jcim.9b00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases are important drug targets in several therapeutic areas ,and structure-based virtual screening (SBVS) is an important strategy in discovering lead compounds for kinase targets. However, there are multiple crystal structures available for each target, and determining which one is the most favorable is a key step in molecular docking for SBVS due to the ligand induce-fit effect. This work aimed to find the most desirable crystal structures for molecular docking by a comprehensive analysis of the protein kinase database which covers 190 different kinases from all eight main kinase families. Through an integrated self-docking and cross-docking evaluation, 86 targets were eventually evaluated on a total of 2608 crystal structures. Results showed that molecular docking has great capability in reproducing conformation of crystallized ligands and for each target, the most favorable crystal structure was selected, and the AGC family outperformed the other family targets based on RMSD comparison. In addition, RMSD values, GlideScore, and corresponding bioactivity data were compared and demonstrated certain relationships. This work provides great convenience for researchers to directly select the optimal crystal structure in SBVS-based kinase drug design and further validates the effectiveness of molecular docking in drug discovery.
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Affiliation(s)
- Xingye Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Wuchen Xie
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yan Yang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuchen Wang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuanrong Fan
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Lu Zhu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Junnan Zhao
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
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7
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Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient. J Mol Model 2019; 25:98. [PMID: 30904971 DOI: 10.1007/s00894-019-3979-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) is one of the regulatory elements of angiogenesis that is expressed highly in various diseases and is also essential for solid tumor growth. The present study was aimed at identifying potent inhibitors of VEGFR-2 by considering herbal secondary metabolites; as natural molecules are less toxic than synthetic derivatives. A structure-based virtual screening protocol consisting of molecular docking, MM-GBSA and ADME/T analysis was initially used to screen a library of in vivo metabolites of the herbal ingredient. Using a fixed cutoff value, four potent virtual hits were identified from molecular docking, ADME/T and binding affinity calculations, which were considered further for molecular dynamics (MD) simulation to broadly describe the binding mechanisms to VEGFR-2. The results suggested that these molecules have high affinity for the catalytic region of VEGFR-2, and form strong hydrophobic and polar interactions with the amino acids involved in the binding site of ATP and linker regions of the catalytic site. Subsequently, the stability of the docked complexes and binding mechanisms were evaluated by MD simulations, and the energy of binding was calculated through MM-PBSA analysis. The results uncovered two virtual hits, designated ZINC14762520 and ZINC36470466, as VEGFR-2 inhibitors, and suggested that they bind to kinase domain in an ATP-competitive manner. These virtual hits will offer a suitable starting point for the further design of their various analogs, allowing a rational search for more effective inhibitors in the future. Graphical abstract.
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8
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Mohl G, Liddle N, Nygaard J, Dorius A, Lyons N, Hodek J, Weber J, Michaelis DJ, Busath DD. Novel influenza inhibitors designed to target PB1 interactions with host importin RanBP5. Antiviral Res 2019; 164:81-90. [PMID: 30742842 DOI: 10.1016/j.antiviral.2019.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/30/2019] [Accepted: 02/03/2019] [Indexed: 11/19/2022]
Abstract
In search of novel targets for influenza inhibitors, a site on PB1 was selected for its high conservation and probable interaction with a host protein, RanBP5, that is key to nuclear import of PB1, where it complexes with PB2, PA, and NP to transcribe viral RNA. Docking with libraries of drug-like compounds led to a selection of five candidates that bound tightly and with a pose likely to inhibit protein binding. These were purchased and tested in vitro, found to be active, and then one was synthetically expanded to explore the structure-activity relationship. The top candidates had a carboxylic acid converted to an ester and electron-withdrawing substituents added to a phenyl group in the original structure. Resistance was slow to develop, but cytotoxicity was moderately high. Nuclear localization of PB1 and in vitro polymerase activity were both strongly inhibited.
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Affiliation(s)
- Gregory Mohl
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Nathan Liddle
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Joseph Nygaard
- Department of Chemistry and Biochemistry, Brigham Young University, USA
| | - Alexander Dorius
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Nathan Lyons
- Department of Chemistry and Biochemistry, Brigham Young University, USA
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague, Czech Republic
| | - David J Michaelis
- Department of Chemistry and Biochemistry, Brigham Young University, USA.
| | - David D Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
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9
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Che J, Wang Z, Sheng H, Huang F, Dong X, Hu Y, Xie X, Hu Y. Ligand-based pharmacophore model for the discovery of novel CXCR2 antagonists as anti-cancer metastatic agents. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180176. [PMID: 30109074 PMCID: PMC6083693 DOI: 10.1098/rsos.180176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/25/2018] [Indexed: 05/05/2023]
Abstract
Metastatic cancer is considered a fatal progression of cancer worldwide. It has been shown that a key player in this scenario is the CXC chemokine receptor 2 (CXCR2). To identify novel CXCR2 antagonists, a pharmacophore model was built with the HipHop program by screening a database containing compounds which were designed based on the known structure-activity relationship (SAR) of the diarylurea series CXCR2 antagonists. Compound 1a bearing the novel skeleton was selected from database screening and subjected to the in vitro biological test which showed a moderate CXCR2 antagonist potential. With further modification and exploration of SAR, compound 1e demonstrated improved CXCR2 antagonist activity with an IC50 value of 14.8 µM. Furthermore, wound healing assay using the NCI-H1299 cell line indicated that 1e showed an excellent anti-cancer metastatic effect (72% inhibition in cell migration at 50 µg ml-1).
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Affiliation(s)
- Jinxin Che
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhilong Wang
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
| | - Haichao Sheng
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Feng Huang
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaowu Dong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Youhong Hu
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
| | - Xin Xie
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
- Chinese Academy of Sciences, CAS Key Laboratory of Receptor Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
- Authors for correspondence: Xin Xie e-mail:
| | - Yongzhou Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Authors for correspondence: Yongzhou Hu e-mail:
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10
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Kang D, Pang X, Lian W, Xu L, Wang J, Jia H, Zhang B, Liu AL, Du GH. Discovery of VEGFR2 inhibitors by integrating naïve Bayesian classification, molecular docking and drug screening approaches. RSC Adv 2018; 8:5286-5297. [PMID: 35542432 PMCID: PMC9078101 DOI: 10.1039/c7ra12259d] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023] Open
Abstract
The high morbidity and mortality of cancer make it one of the leading causes of global death, thus it is an urgent need to develop effective drugs for cancer therapy.
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Affiliation(s)
- De Kang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Xiaocong Pang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Wenwen Lian
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Lvjie Xu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Jinhua Wang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Hao Jia
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Baoyue Zhang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Ai-Lin Liu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Guan-Hua Du
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
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Wang GM, Wang X, Zhu JM, Guo BB, Yang Z, Xu ZJ, Li B, Wang HY, Meng LH, Zhu WL, Ding J. Docking-based structural splicing and reassembly strategy to develop novel deazapurine derivatives as potent B-Raf V600E inhibitors. Acta Pharmacol Sin 2017; 38:1059-1068. [PMID: 28414204 DOI: 10.1038/aps.2016.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022] Open
Abstract
The mutation of B-RafV600E is widespread in a variety of human cancers. Its inhibitors vemurafenib and dabrafenib have been launched as drugs for treating unresectable melanoma, demonstrating that B-RafV600E is an ideal drug target. This study focused on developing novel B-RafV600E inhibitors as drug leads against various cancers with B-RafV600E mutation. Using molecular modeling approaches, 200 blockbuster drugs were spliced to generate 283 fragments followed by molecular docking to identify potent fragments. Molecular structures of potential inhibitors of B-RafV600E were then obtained by fragment reassembly followed by docking to predict the bioactivity of the reassembled molecules. The structures with high predicted bioactivity were synthesized, followed by in vitro study to identify potent B-RafV600E inhibitors. A highly potent fragment binding to the hinge area of B-RafV600E was identified via a docking-based structural splicing approach. Using the fragment, 14 novel structures were designed by structural reassembly, two of which were predicted to be as strong as marketed B-RafV600E inhibitors. Biological evaluation revealed that compound 1m is a potent B-RafV600E inhibitor with an IC50 value of 0.05 μmol/L, which was lower than that of vemurafenib (0.13 μmol/L). Moreover, the selectivity of 1m against B-RafWT was enhanced compared with vemurafenib. In addition, 1m exhibits desirable solubility, bioavailability and metabolic stability in in vitro assays. Thus, a highly potent and selective B-RafV600E inhibitor was designed via a docking-based structural splicing and reassembly strategy and was validated by medicinal synthesis and biological evaluation.
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12
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Balaji GA, Nagendra HG, Balaji VN, Rao SN. Experimental conformational energy maps of proteins and peptides. Proteins 2017; 85:979-1001. [PMID: 28168743 DOI: 10.1002/prot.25266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 01/26/2023]
Abstract
We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol-1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Govardhan A Balaji
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - H G Nagendra
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - Vitukudi N Balaji
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - Shashidhar N Rao
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08552
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Bittencourt IDA, Serpeloni M, Hiraiwa PM, de Arruda Campos Brasil de Souza T, Ávila AR. Dissecting biochemical peculiarities of the ATPase activity of TcSub2, a component of the mRNA export pathway in Trypanosoma cruzi. Int J Biol Macromol 2017; 98:793-801. [PMID: 28212935 DOI: 10.1016/j.ijbiomac.2017.02.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/16/2022]
Abstract
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional. However, the Vmax of TcSub2 was much higher than the Vmax described for the human protein UAP56, which suggests that the TcSub2 enzyme hydrolyzes ATP faster than its human homolog. Furthermore, we demonstrate that RNA association is less important to the activity of TcSub2 compared to UAP56. Our results show differences in activity of this protein, even though the structure of TcSub2 is very similar to UAP56. Functional complementation assays indicate that these differences may be common to other trypanosomatids. Distinct features of RNA influence and ATPase efficiency between UAP56 and TcSub2 may reflect distinct structures for functional sites of TcSub2. For this reason, ligand-based or structure-based methodologies can be applied to investigate the potential of TcSub2 as a target for new drugs.
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Abstract
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Affiliation(s)
- Ashwani Kumar
- Guru Jambheshwar University of Science and Technology, India
| | - Ruchika Goyal
- Guru Jambheshwar University of Science and Technology, India
| | - Sandeep Jain
- Guru Jambheshwar University of Science and Technology, India
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15
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García-Vilas JA, Pino-Ángeles A, Martínez-Poveda B, Quesada AR, Medina MÁ. The noni anthraquinone damnacanthal is a multi-kinase inhibitor with potent anti-angiogenic effects. Cancer Lett 2016; 385:1-11. [PMID: 27816491 DOI: 10.1016/j.canlet.2016.10.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 12/29/2022]
Abstract
The natural bioactive compound damnacanthal inhibits several tyrosine kinases. Herein, we show that -in fact- damancanthal is a multi kinase inhibitor. A docking and molecular dynamics simulation approach allows getting further insight on the inhibitory effect of damnacanthal on three different kinases: vascular endothelial growth factor receptor-2, c-Met and focal adhesion kinase. Several of the kinases targeted and inhibited by damnacanthal are involved in angiogenesis. Ex vivo and in vivo experiments clearly demonstrate that, indeed, damnacanthal is a very potent inhibitor of angiogenesis. A number of in vitro assays contribute to determine the specific effects of damnacanthal on each of the steps of the angiogenic process, including inhibition of tubulogenesis, endothelial cell proliferation, survival, migration and production of extracellular matrix remodeling enzyme. Taken altogether, these results suggest that damancanthal could have potential interest for the treatment of cancer and other angiogenesis-dependent diseases.
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Affiliation(s)
- Javier A García-Vilas
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain; IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain
| | | | - Beatriz Martínez-Poveda
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain; IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain
| | - Ana R Quesada
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain; IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain; CIBER de Enfermedades Raras (CIBERER), E-29071 Málaga, Spain
| | - Miguel Ángel Medina
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain; IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain; CIBER de Enfermedades Raras (CIBERER), E-29071 Málaga, Spain.
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16
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Caldwell GW. In silico tools used for compound selection during target-based drug discovery and development. Expert Opin Drug Discov 2015; 10:901-23. [DOI: 10.1517/17460441.2015.1043885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gary W Caldwell
- Janssen Research & Development LLC, Discovery Sciences, Spring House, PA, USA
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