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Lu T, Li T, Wu MK, Zheng CC, He XM, Zhu HL, Li L, Man RJ. Molecular simulations required to target novel and potent inhibitors of cancer invasion. Expert Opin Drug Discov 2023; 18:1367-1377. [PMID: 37676052 DOI: 10.1080/17460441.2023.2254695] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
INTRODUCTION Computer-aided drug design (CADD) is a computational approach used to discover, develop, and analyze drugs and active molecules with similar biochemical properties. Molecular simulation technology has significantly accelerated drug research and reduced manufacturing costs. It is an optimized drug discovery method that greatly improves the efficiency of novel drug development processes. AREASCOVERED This review discusses the development of molecular simulations of effective cancer inhibitors and traces the main outcomes of in silico studies by introducing representative categories of six important anticancer targets. The authors provide views on this topic from the perspective of both medicinal chemistry and artificial intelligence, indicating the major challenges and predicting trends. EXPERT OPINION The goal of introducing CADD into cancer treatment is to realize a highly efficient, accurate, and desired approach with a high success rate for identifying potent drug candidates. However, the major challenge is the lack of a sophisticated data-filtering mechanism to verify bottom data from mixed-quality references. Consequently, despite the continuous development of algorithms, computer power, and interface optimization, specific data filtering mechanisms will become an urgent and crucial issue in the future.
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Affiliation(s)
| | - Tong Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Meng-Ke Wu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Chi-Chong Zheng
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
| | - Xue-Mei He
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Hai-Liang Zhu
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Li Li
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Ruo-Jun Man
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, China
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Tharamelveliyil Rajendran A, Dheeraj Rajesh G, Kumar P, Shivam Raju Dwivedi P, Shashidhara Shastry C, Narayanan Vadakkepushpakath A. Selection of potential natural compounds for poly-ADP-ribose polymerase (PARP) inhibition in glioblastoma therapy by in silico screening methods. Saudi J Biol Sci 2023; 30:103698. [PMID: 37485452 PMCID: PMC10362462 DOI: 10.1016/j.sjbs.2023.103698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Glioblastoma (GBM), the most prevalent brain tumor, is one of the least treatable malignancies due to its propensity for intracranial spread, high proliferative potential, and innate resistance to radiation and chemotherapy. Current GBM therapy is limited due to unfavorable, non-specific therapeutic effects in healthy cells and the difficulty of small molecules to penetrate the blood brain barrier (BBB) and reach the tumor microenvironment. Adding PARP-1 inhibitors inhibit DNA repair enzymes thereby increasing the cytotoxicity of anticancer agents. Hence, we aimed to discover potential naturally occurring PARP-1 inhibitors that can be utilized in the treatment of glioma by using multiple in silico tools like molecular docking, absorption, distribution, metabolism, and excretion (ADME) profile, pharmacophore modeling, and molecular dynamic (MD) simulations. Among 43 phytocompounds we screened, two of them (Ellagic acid and Naringin) were discovered to be bound to the catalytic site of PARP-1 with an affinity more remarkable than commercially available PARP-1 inhibitors (Talazoparib, Niraparib, and Rucaparib) except Olaparib. The molecular interactions were analyzed, and data shows that bound entity attained a conserved domain via hydrogen bond interactions, polar interactions, and π-π stacking. Pharmacophore modeling studies showed electronic and steric features of ligands responsible for supramolecular interaction with PARP-1. ADME properties were studied, to assess drug-likeness, hydrophilic nature, hydrophobicity, brain permeability, and oral bioavailability of the natural PARP-1 inhibitors. The simulation study demonstrated the development of a stable complex between Naringin, Ellagic acid, and PARP-1 protein. Moreover, cell culture studies and animal investigations are essential to determine pharmacokinetics and pharmacodynamics.
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Affiliation(s)
- Arunraj Tharamelveliyil Rajendran
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangalore-575018, Karnataka, India
| | - Gupta Dheeraj Rajesh
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutical chemistry, Mangalore-575018, Karnataka, India
| | - Pankaj Kumar
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutical chemistry, Mangalore-575018, Karnataka, India
| | - Prarambh Shivam Raju Dwivedi
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmacology, Mangalore-575018, Karnataka, India
| | - Chakrakodi Shashidhara Shastry
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmacology, Mangalore-575018, Karnataka, India
| | - Anoop Narayanan Vadakkepushpakath
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangalore-575018, Karnataka, India
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Lerksuthirat T, Chitphuk S, Stitchantrakul W, Dejsuphong D, Malik AA, Nantasenamat C. PARP1pred: a web server for screening the bioactivity of inhibitors against DNA repair enzyme PARP-1. EXCLI JOURNAL 2023; 22:84-107. [PMID: 36814851 PMCID: PMC9939779 DOI: 10.17179/excli2022-5602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/23/2022] [Indexed: 02/24/2023]
Abstract
Cancer is the leading cause of death worldwide, resulting in the mortality of more than 10 million people in 2020, according to Global Cancer Statistics 2020. A potential cancer therapy involves targeting the DNA repair process by inhibiting PARP-1. In this study, classification models were constructed using a non-redundant set of 2018 PARP-1 inhibitors. Briefly, compounds were described by 12 fingerprint types and built using the random forest algorithm concomitant with various sampling approaches. Results indicated that PubChem with an oversampling approach yielded the best performance, with a Matthews correlation coefficient > 0.7 while also affording interpretable molecular features. Moreover, feature importance, as determined from the Gini index, revealed that the aromatic/cyclic/heterocyclic moiety, nitrogen-containing fingerprints, and the ether/aldehyde/alcohol moiety were important for PARP-1 inhibition. Finally, our predictive model was deployed as a web application called PARP1pred and is publicly available at https://parp1pred.streamlitapp.com, allowing users to predict the biological activity of query compounds using their SMILES notation as the input. It is anticipated that the model described herein will aid in the discovery of effective PARP-1 inhibitors.
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Affiliation(s)
- Tassanee Lerksuthirat
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand,*To whom correspondence should be addressed: Tassanee Lerksuthirat, Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand, E-mail:
| | - Sermsiri Chitphuk
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Wasana Stitchantrakul
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Donniphat Dejsuphong
- Program in Translational Medicine, Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
| | - Aijaz Ahmad Malik
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Cao Y, Yang R, Wang W, Jiang S, Yang C, Liu N, Dai H, Lee I, Meng X, Yuan Z. Probing the Formation, Structure and Free Energy Relationships of M Protein Dimers of SARS-CoV-2. Comput Struct Biotechnol J 2022; 20:573-582. [PMID: 35047128 PMCID: PMC8756865 DOI: 10.1016/j.csbj.2022.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The M protein of the novel coronavirus 2019 (SARS-CoV-2) is the major structural component of the viral envelope and is also the minimum requirement for virus particle budding. M proteins generally exist as dimers. In virus assembly, they are the main driving force for envelope formation through lateral interactions and interactions with other viral structural proteins that play a central role. We built 100 candidate models and finally analyzed the six most convincing structural features of the SARS-CoV-2 M protein dimer based on long-timescale molecular dynamics (MD) simulations, multiple free energy analyses (potential mean force (PMF) and molecular mechanics Poisson-Boltzmann surface area (MMPBSA)) and principal component analysis (PCA) to obtain the most reasonable structure. The dimer stability was found to depend on the Leu-Ile zipper motif and aromatic amino acids in the transmembrane domain (TMD). Furthermore, the C-terminal domain (CTD) effects were relatively small. These results highlight a model in which there is sufficient binding affinity between the TMDs of M proteins to form dimers through the residues at the interface of the three transmembrane helices (TMHs). This study aims to help find more effective inhibitors of SARS-CoV-2 M dimers and to develop vaccines based on structural information.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- National Supercomputer Center in Tianjin, 300457 PR China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital. 300031, PR China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Shengpeng Jiang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Chengwen Yang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Ningbo Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Hongji Dai
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- College of Physics, Nankai University, Tianjin 300071, PR China
| | - Imshik Lee
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, PR China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, 300457 PR China
- Corresponding authors.
| | - Zhiyong Yuan
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- Corresponding authors.
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Zhao Y, Wang XG, Ma ZY, Xiong GL, Yang ZJ, Cheng Y, Lu AP, Huang ZJ, Cao DS. Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors. Brief Bioinform 2021; 22:6262239. [PMID: 33940596 DOI: 10.1093/bib/bbab135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
The poly (ADP-ribose) polymerase-1 (PARP1) has been regarded as a vital target in recent years and PARP1 inhibitors can be used for ovarian and breast cancer therapies. However, it has been realized that most of PARP1 inhibitors have disadvantages of low solubility and permeability. Therefore, by discovering more molecules with novel frameworks, it would have greater opportunities to apply it into broader clinical fields and have a more profound significance. In the present study, multiple virtual screening (VS) methods had been employed to evaluate the screening efficiency of ligand-based, structure-based and data fusion methods on PARP1 target. The VS methods include 2D similarity screening, structure-activity relationship (SAR) models, docking and complex-based pharmacophore screening. Moreover, the sum rank, sum score and reciprocal rank were also adopted for data fusion methods. The evaluation results show that the similarity searching based on Torsion fingerprint, six SAR models, Glide docking and pharmacophore screening using Phase have excellent screening performance. The best data fusion method is the reciprocal rank, but the sum score also performs well in framework enrichment. In general, the ligand-based VS methods show better performance on PARP1 inhibitor screening. These findings confirmed that adding ligand-based methods to the early screening stage will greatly improve the screening efficiency, and be able to enrich more highly active PARP1 inhibitors with diverse structures.
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Affiliation(s)
- Yue Zhao
- Xiangya School of Pharmaceutical Sciences, Central South University, P. R. China
| | | | - Zhong-Ye Ma
- Xiangya School of Pharmaceutical Sciences, Central South University, P. R. China
| | - Guo-Li Xiong
- Xiangya School of Pharmaceutical Sciences, Central South University, P. R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, P. R. China
| | - Yan Cheng
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Zhi-Jun Huang
- Center for Clinical Pharmacology, The Third Xiangya Hospital of Central South University, Hunan, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, China
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Gupta PSS, Bhat HR, Biswal S, Rana MK. Computer-aided discovery of bis-indole derivatives as multi-target drugs against cancer and bacterial infections: DFT, docking, virtual screening, and molecular dynamics studies. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhang Q, Sang F, Qian J, Lyu S, Wang W, Wang Y, Li Q, Du L. Identification of novel potential PI3Kα inhibitors for cancer therapy. J Biomol Struct Dyn 2020; 39:3721-3732. [DOI: 10.1080/07391102.2020.1771421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Qingyan Zhang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Feng Sang
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jieyu Qian
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - ShaoLi Lyu
- Department of Ecology and Resource Engineering, Hetao College, Bayannur, Inner Mongolia, PR of China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ying Wang
- The Department of Anesthesiology, the First Affiliated of Henan University, Kaifeng, China
| | - Qiang Li
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - LinFang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Guan S, Zhu K, Dong Y, Li H, Yang S, Wang S, Shan Y. Exploration of Binding Mechanism of a Potential Streptococcus pneumoniae Neuraminidase Inhibitor from Herbaceous Plants by Molecular Simulation. Int J Mol Sci 2020; 21:ijms21031003. [PMID: 32028720 PMCID: PMC7038148 DOI: 10.3390/ijms21031003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 01/11/2023] Open
Abstract
Streptococcus pneumoniae can cause diseases such as pneumonia. Broad-spectrum antibiotic therapy for Streptococcus pneumoniae is increasingly limited due to the emergence of drug-resistant strains. The development of novel drugs is still currently of focus. Abundant polyphenols have been demonstrated to have antivirus and antibacterial ability. Chlorogenic acid is one of the representatives that has been proven to have the potential to inhibit both the influenza virus and Streptococcus pneumoniae. However, for such a potential neuraminidase inhibitor, the interaction mechanism studies between chlorogenic acid and Streptococcus pneumoniae neuraminidase are rare. In the current study, the binding mechanism of chlorogenic acid and Streptococcus pneumoniae neuraminidase were investigated by molecular simulation. The results indicated that chlorogenic acid might establish the interaction with Streptococcus pneumoniae neuraminidase via hydrogen bonds, salt bridge, and cation-π. The vital residues involved Arg347, Ile348, Lys440, Asp372, Asp417, and Glu768. The side chain of Arg347 might form a cap-like structure to lock the chlorogenic acid to the active site. The results from binding energy calculation indicated that chlorogenic acid had strong binding potential with neuraminidase. The results predicted a detailed binding mechanism of a potential Streptococcus pneumoniae neuraminidase inhibitor, which will be provide a theoretical basis for the mechanism of new inhibitors.
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Affiliation(s)
- Shanshan Guan
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
| | - Ketong Zhu
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Yanjiao Dong
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Shuang Yang
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, Jilin, China;
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
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Poly(ADP-Ribose) Polymerases in Host-Pathogen Interactions, Inflammation, and Immunity. Microbiol Mol Biol Rev 2018; 83:83/1/e00038-18. [PMID: 30567936 DOI: 10.1128/mmbr.00038-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The literature review presented here details recent research involving members of the poly(ADP-ribose) polymerase (PARP) family of proteins. Among the 17 recognized members of the family, the human enzyme PARP1 is the most extensively studied, resulting in a number of known biological and metabolic roles. This review is focused on the roles played by PARP enzymes in host-pathogen interactions and in diseases with an associated inflammatory response. In mammalian cells, several PARPs have specific roles in the antiviral response; this is perhaps best illustrated by PARP13, also termed the zinc finger antiviral protein (ZAP). Plant stress responses and immunity are also regulated by poly(ADP-ribosyl)ation. PARPs promote inflammatory responses by stimulating proinflammatory signal transduction pathways that lead to the expression of cytokines and cell adhesion molecules. Hence, PARP inhibitors show promise in the treatment of inflammatory disorders and conditions with an inflammatory component, such as diabetes, arthritis, and stroke. These functions are correlated with the biophysical characteristics of PARP family enzymes. This work is important in providing a comprehensive understanding of the molecular basis of pathogenesis and host responses, as well as in the identification of inhibitors. This is important because the identification of inhibitors has been shown to be effective in arresting the progression of disease.
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Guan S, Xu Y, Qiao Y, Kuai Z, Qian M, Jiang X, Wang S, Zhang H, Kong W, Shan Y. A novel small molecule displays two different binding modes during inhibiting H1N1 influenza A virus neuraminidases. J Struct Biol 2018; 202:142-149. [DOI: 10.1016/j.jsb.2017.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/08/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023]
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Li J, Yang Q, Zhang Y, Huang K, Sun R, Zhao Q. Compound F779-0434 causes synthetic lethality in BRCA2-deficient cancer cells by disrupting RAD52–ssDNA association. RSC Adv 2018; 8:18859-18869. [PMID: 35539677 PMCID: PMC9080615 DOI: 10.1039/c8ra01919c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/04/2018] [Indexed: 11/21/2022] Open
Abstract
A novel compound named F779-0434 caused synthetic lethality in BRCA2-deficient cancer cells by disrupting RAD52–ssDNA associations.
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Affiliation(s)
- Jian Li
- School of Medicine
- Chengdu University
- Chengdu 610106
- China
- Sichuan Industrial Institute of Antibiotics
| | - Qianye Yang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Yang Zhang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Kejia Huang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Rong Sun
- College of Life Sciences and Key Laboratory for Bio-Resources of Ministry of Education
- Sichuan University
- Chengdu 610064
- China
| | - Qi Zhao
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
- College of Pharmacy and Biological Engineering
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12
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Wang L, Liang C, Li F, Guan D, Wu X, Fu X, Lu A, Zhang G. PARP1 in Carcinomas and PARP1 Inhibitors as Antineoplastic Drugs. Int J Mol Sci 2017; 18:E2111. [PMID: 28991194 PMCID: PMC5666793 DOI: 10.3390/ijms18102111] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 09/30/2017] [Accepted: 10/02/2017] [Indexed: 01/06/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1), the best-studied isoform of the nuclear enzyme PARP family, plays a pivotal role in cellular biological processes, such as DNA repair, gene transcription, and so on. PARP1 has been found to be overexpressed in various carcinomas. These all indicate the clinical potential of PARP1 as a therapeutic target of human malignancies. Additionally, multiple preclinical research studies and clinical trials demonstrate that inhibition of PARP1 can repress tumor growth and metastasis. Up until now, PARP1 inhibitors are clinically used not only for monotherapy to suppress various tumors, but also for adjuvant therapy, to maintain or enhance therapeutic effects of mature antineoplastic drugs, as well as protect patients from chemotherapy and surgery-induced injury. To supply a framework for understanding recent research progress of PARP1 in carcinomas, we review the structure, expression, functions, and mechanisms of PARP1, and summarize the clinically mature PARP1-related anticancer agents, to provide some ideas for the development of other promising PARP1 inhibitors in antineoplastic therapy.
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Affiliation(s)
- Luyao Wang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Chao Liang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Fangfei Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Daogang Guan
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Xiaoqiu Wu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Xuekun Fu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
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L1198F Mutation Resensitizes Crizotinib to ALK by Altering the Conformation of Inhibitor and ATP Binding Sites. Int J Mol Sci 2017; 18:ijms18030482. [PMID: 28245558 PMCID: PMC5372498 DOI: 10.3390/ijms18030482] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/01/2017] [Accepted: 02/18/2017] [Indexed: 11/26/2022] Open
Abstract
The efficacy of anaplastic lymphoma kinase (ALK) positive non-small-cell lung cancer (NSCLC) treatment with small molecule inhibitors is greatly challenged by acquired resistance. A recent study reported the newest generation inhibitor resistant mutation L1198F led to the resensitization to crizotinib, which is the first Food and Drug Administration (FDA) approved drug for the treatment of ALK-positive NSCLC. It is of great importance to understand how this extremely rare event occurred for the purpose of overcoming the acquired resistance of such inhibitors. In this study, we exploited molecular dynamics (MD) simulation to dissect the molecular mechanisms. Our MD results revealed that L1198F mutation of ALK resulted in the conformational change at the inhibitor site and altered the binding affinity of ALK to crizotinib and lorlatinib. L1198F mutation also affected the autoactivation of ALK as supported by the identification of His1124 and Tyr1278 as critical amino acids involved in ATP binding and phosphorylation. Our findings are valuable for designing more specific and potent inhibitors for the treatment of ALK-positive NSCLC and other types of cancer.
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Discovery of a Potential HER2 Inhibitor from Natural Products for the Treatment of HER2-Positive Breast Cancer. Int J Mol Sci 2016; 17:ijms17071055. [PMID: 27376283 PMCID: PMC4964431 DOI: 10.3390/ijms17071055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 02/05/2023] Open
Abstract
Breast cancer is one of the most lethal types of cancer in women worldwide due to the late stage detection and resistance to traditional chemotherapy. The human epidermal growth factor receptor 2 (HER2) is considered as a validated target in breast cancer therapy. Even though a substantial effort has been made to develop HER2 inhibitors, only lapatinib has been approved by the U.S. Food and Drug Administration (FDA). Side effects were observed in a majority of the patients within one year of treatment initiation. Here, we took advantage of bioinformatics tools to identify novel effective HER2 inhibitors. The structure-based virtual screening combined with ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction was explored. In total, 11,247 natural compounds were screened. The top hits were evaluated by an in vitro HER2 kinase inhibition assay. The cell proliferation inhibition effect of identified inhibitors was evaluated in HER2-overexpressing SKBR3 and BT474 cell lines. We found that ZINC15122021 showed favorable ADMET properties and attained high binding affinity against HER2. Moreover, ZINC15122021 showed high kinase inhibition activity against HER2 and presented outstanding cell proliferation inhibition activity against both SKBR3 and BT474 cell lines. Results reveal that ZINC15122021 can be a potential HER2 inhibitor.
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