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Ren Z, Lv M, Liu H, Wen H, Zhang Y, Xu H. Optimization of Osthole as a Pesticide Candidate: Synthesis, Crystal Structures, and Agrochemical Properties of Acrylate Derivatives of Isopropenyl 2,3-Dihydrobenzofurans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18301-18311. [PMID: 37966481 DOI: 10.1021/acs.jafc.3c02213] [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: 11/16/2023]
Abstract
For high-value-added application of osthole derivatives as a pesticide candidate in crop protection, by the use of osthole as a lead compound, a series of novel acrylate derivatives of isopropenyl 2,3-dihydrobenzofurans were prepared by the successive bromination, rearrangement, and esterization reactions. Three-dimensional structures of four compounds were determined by single-crystal X-ray diffraction. The possible mechanism for construction of this new isopropenyl 2,3-dihydrobenzofuran skeleton from the osthole was presented. Against Plutella xylostella Linnaeus, compound 32 (R = PhCH2CH2) displayed 3.5-fold potent insecticidal activity of osthole. Against Tetranychus cinnabarinus Boisduval, compound 40 (LC50: 0.165 mg/mL; R = (CH2)13CH3) showed 8.3-fold pronounced acaricidal activity of osthole (LC50: 1.367 mg/mL); notably, its control effect can be comparable to that of the commercial acaricide spirodiclofen. Additionally, the scanning electron microscopy imaging method demonstrated that compound 40 can destroy the stratum corneum of T. cinnabarinus. Compound 40 can be further explored as a lead acaricidal agent.
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Affiliation(s)
- Zili Ren
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Min Lv
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Huqi Liu
- College of Life Science, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Houpeng Wen
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuling Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Xu
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Cole AG, Kultgen SG, Mani N, Quintero JG, Yi Fan K, Ardzinski A, Stever K, Dorsey BD, Phelps JR, Lee ACH, Thi EP, Chiu T, Tang S, Horanyi PS, Mayclin SJ, Harasym TO, Sofia MJ. Design, synthesis, and structure-activity relationship of a bicyclic HBV capsid assembly modulator chemotype leading to the identification of clinical candidate AB-506. Bioorg Med Chem Lett 2023; 94:129456. [PMID: 37633618 DOI: 10.1016/j.bmcl.2023.129456] [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: 07/06/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Disruption of the HBV capsid assembly process through small-molecule interaction with HBV core protein is a validated target for the suppression of hepatitis B viral replication and the development of new antivirals. Through combination of key structural features associated with two distinct series of capsid assembly modulators, a novel aminochroman-based chemotype was identified. Optimization of anti-HBV potency through generation of SAR in addition to further core modifications provided a series of related functionalized aminoindanes. Key compounds demonstrated excellent cellular potency in addition to favorable ADME and pharmacokinetic profiles and were shown to be highly efficacious in a mouse model of HBV replication. Aminoindane derivative AB-506 was subsequently advanced into clinical development.
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Affiliation(s)
- Andrew G Cole
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA.
| | - Steven G Kultgen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Nagraj Mani
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Jorge G Quintero
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Kristi Yi Fan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Andrzej Ardzinski
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Kim Stever
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Bruce D Dorsey
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Janet R Phelps
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Amy C H Lee
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Emily P Thi
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Tim Chiu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Sunny Tang
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Peter S Horanyi
- UCB Pharma, 87 Cambridge Park Drive, Cambridge, MA 02140, USA
| | | | - Troy O Harasym
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Michael J Sofia
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
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3
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Wang K, Wu Y, Lai L, Wang X, Sun S. How ligands regulate the binding of PARP1 with DNA: Deciphering the mechanism at the molecular level. PLoS One 2023; 18:e0290176. [PMID: 37582112 PMCID: PMC10426920 DOI: 10.1371/journal.pone.0290176] [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: 02/21/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
The catalytic (CAT) domain is a key region of poly (ADP-ribose) polymerase 1 (PARP1), which has crucial interactions with inhibitors, DNA, and other domains of PARP1. To facilitate the development of potential inhibitors of PARP1, it is of great significance to clarify the differences in structural dynamics and key residues between CAT/inhibitors and DNA/PARP1/inhibitors through structure-based computational design. In this paper, conformational changes in PAPR1 and differences in key residue interactions induced by inhibitors were revealed at the molecular level by comparative molecular dynamics (MD) simulations and energy decomposition. On one hand, PARP1 inhibitors indirectly change some residues of the CAT domain which interact with DNA and other domains. Furthermore, the interaction between ligands and catalytic binding sites can be transferred to the DNA recognition domain of PARP1 by a strong negative correlation movement among multi-domains of PARP1. On the other hand, it is not reliable to use the binding energy of CAT/ligand as a measure of ligand activity, because it may in some cases differs greatly from the that of PARP1/DNA/ligand. For PARP1/DNA/ligand, the stronger the binding stability between the ligand and PARP1, the stronger the binding stability between PARP1 and DNA. The findings of this work can guide further novel inhibitor design and the structural modification of PARP1 through structure-based computational design.
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Affiliation(s)
- Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P. R. China
| | - Yizhou Wu
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P. R. China
| | - Lizhu Lai
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P. R. China
| | - Xin Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P. R. China
| | - Shuya Sun
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, P. R. China
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4
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Rana M, Thakur A, Kaur C, Pan CH, Lee SB, Liou JP, Nepali K. Prudent tactics to sail the boat of PARP inhibitors as therapeutics for diverse malignancies. Expert Opin Drug Discov 2023; 18:1169-1193. [PMID: 37525475 DOI: 10.1080/17460441.2023.2241818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
INTRODUCTION PARP inhibitors block the DNA-repairing mechanism of PARP and represent a promising class of anti-cancer therapy. The last decade has witnessed FDA approvals of several PARP inhibitors, with some undergoing advanced-stage clinical investigation. Medicinal chemists have invested much effort to expand the structure pool of PARP inhibitors. Issues associated with the use of PARP inhibitors that make their standing disconcerting in the pharmaceutical sector have been addressed via the design of new structural assemblages. AREA COVERED In this review, the authors present a detailed account of the medicinal chemistry campaigns conducted in the recent past for the construction of PARP1/PARP2 inhibitors, PARP1 biased inhibitors, and PARP targeting bifunctional inhibitors as well as PARP targeting degraders (PROTACs). Limitations associated with FDA-approved PARP inhibitors and strategies to outwit the limitations are also discussed. EXPERT OPINION The PARP inhibitory field has been rejuvenated with numerous tractable entries in the last decade. With numerous magic bullets in hand coupled with unfolded tactics to outwit the notoriety of cancer cells developing resistance toward PARP inhibitors, the dominance of PARP inhibitors as a sagacious option of targeted therapy is highly likely to be witnessed soon.
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Affiliation(s)
- Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Charanjit Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
| | - Sung-Bau Lee
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
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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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Akber Aisa H, Niu C, Wu H, Maimaitijiang A, Tang D, Xie B. Synthesis and Antitumor Activity of Heterocylic Aurone and Its Analogue Indanone Derivatives. HETEROCYCLES 2023. [DOI: 10.3987/com-22-14764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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7
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Lazinski LM, Royal G, Robin M, Maresca M, Haudecoeur R. Bioactive Aurones, Indanones, and Other Hemiindigoid Scaffolds: Medicinal Chemistry and Photopharmacology Perspectives. J Med Chem 2022; 65:12594-12625. [PMID: 36126323 DOI: 10.1021/acs.jmedchem.2c01150] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hemiindigoids comprise a range of natural and synthetic scaffolds that share the same aromatic hydrocarbon backbone as well as promising biological and optical properties. The encouraging therapeutic potential of these scaffolds has been unraveled by many studies over the past years and uncovered representants with inspiring pharmacophoric features such as the acetylcholinesterase inhibitor donezepil and the tubulin polymerization inhibitor indanocine. In this review, we summarize the last advances in the medicinal potential of hemiindigoids, with a special attention to molecular design, structure-activity relationship, ligand-target interactions, and mechanistic explanations covering their effects. As their strong fluorogenic potential and photoswitch behavior recently started to be highlighted and explored in biology, giving rise to the development of novel fluorescent probes and photopharmacological agents, we also discuss these properties in a medicinal chemistry perspective.
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Affiliation(s)
- Leticia M Lazinski
- Université Grenoble Alpes, CNRS 5063, DPM, 38000 Grenoble, France.,Université Grenoble Alpes, CNRS 5250, DCM, 38000 Grenoble, France
| | - Guy Royal
- Université Grenoble Alpes, CNRS 5250, DCM, 38000 Grenoble, France
| | - Maxime Robin
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
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8
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Sun S, Wang X, Lin R, Wang K. Deciphering the functional mechanism of zinc ions of PARP1 binding with single strand breaks and double strand breaks. RSC Adv 2022; 12:19029-19039. [PMID: 35865614 PMCID: PMC9240923 DOI: 10.1039/d2ra02683j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022] Open
Abstract
Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for the treatment of cancer-related diseases, and plays an important role in biological processes such as DNA repair, regulating a variety of metabolic and signal transduction processes. Understanding the dynamic binding mechanisms between each domain of PARP1 and DNA is of great significance to deepen the understanding on the function of PARP1 and to facilitate the design of inhibitors. Herein, strategies such as classical molecular dynamics simulation, conformational analysis, binding free energy calculation and energy decomposition were used to shed light on the binding mechanisms of different DNA binding domains (DBDs, including ZnF1, ZnF2 and ZnF3) in PARP1 with DNA and on the influences of zinc ions on the binding process. On one hand, during binding with DNA, ZnF2 tends to expand its space to identify the DNA damage sites and ZnF1/ZnF2 recognizes the interfaces on both sides of DNA damage rather than one side during the process of DNA repair. More importantly, the stable secondary structure of L2 of ZnF2 (PRO146 to MET153) is the key conformational change for ZnF1 and ZnF2 to recognize DNA damage. Meanwhile, ZnF3 has little effect on the binding mechanisms of PARP1. On the other hand, for the structural differences of DBD domains, zinc ions in ZnF1 and ZnF2 (Zn1 and Zn2) have an impact not only on the conformational changes of PARP1, but also on the conformational changes brought by the interaction of double strand breaks (DSB) and single strand breaks (SSB). And meanwhile, Zn3 also has little effect on ZnF3 for the system of ZnF3/DSB. The findings presented in this work deepen the understanding on the functional mechanism of PARP1 and provide a theoretical basis for further study on the interaction between different inhibitors and DBD domains to design more potential inhibitors. Poly(ADP-ribose)polymerase 1 (PARP1) is a key target for treatment of cancer-related diseases. Detailed structural changes DBD in PARP1 during the binding process with DNA were investigated and the dynamic conformational differences of DBD caused by zinc ions were revealed.![]()
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Affiliation(s)
- Shuya Sun
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine No. 232, Waihuan East Road Guangzhou 510006 China
| | - Xin Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering Guangzhou 510000 P. R. China
| | - Rongfeng Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine No. 232, Waihuan East Road Guangzhou 510006 China
| | - Kai Wang
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering Guangzhou 510000 P. R. China .,Abinitio Technology Company, Ltd Guangzhou 510640 P. R. China
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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Shankaraiah N, Tokala R, Bora D. Contribution of Knoevenagel Condensation Products towards Development of Anticancer Agents: An Updated Review. ChemMedChem 2022; 17:e202100736. [PMID: 35226798 DOI: 10.1002/cmdc.202100736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/23/2022] [Indexed: 11/10/2022]
Abstract
Knoevenagel condensation is an entrenched, prevailing, prominent arsenal following greener principles in the generation of α, β-unsaturated ketones/carboxylic acids by involving carbonyl functionalities and active methylenes. This reaction has proved to be a major driving force in many multicomponent reactions indicating the prolific utility towards the development of biologically fascinating molecules. This eminent reaction was acclimatised on different pharmacophoric aldehydes (benzimidazole, β-carboline, phenanthrene, indole, imidazothiadiazole, pyrazole etc.) and active methylenes (oxindole, barbituric acid, Meldrum's acid, thiazolidinedione etc.) to generate the library of chemical compounds. Their potential was also explicit to understand the significance of functionalities involved, which thereby evoke further developments in drug discovery. Furthermore, most of these reaction products exhibited remarkable anticancer activity in nanomolar to micromolar ranges by targeting different cancer targets like DNA, microtubules, Topo-I/II, and kinases (PIM, PARP, NMP, p300/CBP) etc. This review underscores the efficiency of the Knoevenagel condensation explored in the past six-year to generate molecules of pharmacological interest, predominantly towards cancer. The present review also provides the aspects of structure-activity relationships, mode of action and docking study with possible interaction with the target protein.
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Affiliation(s)
- Nagula Shankaraiah
- National Institute of Pharmaceutical Education and Research NIPER, Department of Medicinal Chemistry, Balanagar, 500037, Hyderabad, INDIA
| | - Ramya Tokala
- NIPER Hyderabad: National Institute of Pharmaceutical Education and Research Hyderabad, Medicinal Chemistry, INDIA
| | - Darshana Bora
- NIPER Hyderabad: National Institute of Pharmaceutical Education and Research Hyderabad, Medicinal Chemistry, INDIA
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11
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Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst) 2021; 103:103125. [PMID: 33940558 PMCID: PMC8206044 DOI: 10.1016/j.dnarep.2021.103125] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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12
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Gao D, Jin N, Fu Y, Zhu Y, Wang Y, Wang T, Chen Y, Zhang M, Xiao Q, Huang M, Li Y. Rational drug design of benzothiazole-based derivatives as potent signal transducer and activator of transcription 3 (STAT3) signaling pathway inhibitors. Eur J Med Chem 2021; 216:113333. [PMID: 33689932 DOI: 10.1016/j.ejmech.2021.113333] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022]
Abstract
The cumulative evidence supports STAT3, a transcriptional mediator of oncogenic signaling, as a therapeutic target in cancer. The development of STAT3 inhibitors remain an active area of research as no inhibitors have yet to be approved for cancer treatment. In a continuing effort to develop more potent STAT3 inhibitors based on our previously identified hit compound 16w, a series of benzothiazole derivatives with unique binding mode in SH2 domain of STAT3 were designed, synthesized and biologically evaluated. Of note, compound B19 demonstrated excellent activity against IL-6/STAT3 signaling pathway with the IC50 value as low as 0.067 μM as determined by a luciferase reporter assay. Moreover, multiple compounds displayed potent antiproliferative activity against MDA-MB-468 and JAK2 mutant HEL cell lines. Further biochemical study using Western blot assay indicated that B19 blocked the phosphorylation of STAT3 at Tyr 705 and Ser 727 and thus suppressed STAT3-mediated gene expression of c-MYC and MCL-1. Simultaneously, it induced cancer cell G2/M phase arrest and apoptosis both in MDA-MB-468 and HEL cell lines. Finally, molecular docking study along with surface plasmon resonance (SPR) and fluorescence polarization (FP) assays disclosed the binding mode of B19 in STAT3 SH2 domain. Taken together, our finding suggests that B19 is a promising therapeutic STAT3 inhibitor for cancer treatment.
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Affiliation(s)
- Dingding Gao
- School of Pharmacy, Fudan University, Shanghai, 201203, China; Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Nan Jin
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yixian Fu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yueyue Zhu
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yujie Wang
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ting Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yuehong Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mingming Zhang
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiang Xiao
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Min Huang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxia Li
- School of Pharmacy, Fudan University, Shanghai, 201203, China.
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Massively parallel assessment of human variants with base editor screens. Cell 2021; 184:1064-1080.e20. [PMID: 33606977 DOI: 10.1016/j.cell.2021.01.012] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022]
Abstract
Understanding the functional consequences of single-nucleotide variants is critical to uncovering the genetic underpinnings of diseases, but technologies to characterize variants are limiting. Here, we leverage CRISPR-Cas9 cytosine base editors in pooled screens to scalably assay variants at endogenous loci in mammalian cells. We benchmark the performance of base editors in positive and negative selection screens, identifying known loss-of-function mutations in BRCA1 and BRCA2 with high precision. To demonstrate the utility of base editor screens to probe small molecule-protein interactions, we screen against BH3 mimetics and PARP inhibitors, identifying point mutations that confer drug sensitivity or resistance. We also create a library of single guide RNAs (sgRNAs) predicted to generate 52,034 ClinVar variants in 3,584 genes and conduct screens in the presence of cellular stressors, identifying loss-of-function variants in numerous DNA damage repair genes. We anticipate that this screening approach will be broadly useful to readily and scalably functionalize genetic variants.
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14
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Jeon W, Kim D. Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors. Sci Rep 2020; 10:22104. [PMID: 33328504 PMCID: PMC7744578 DOI: 10.1038/s41598-020-78537-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022] Open
Abstract
We developed a computational method named Molecule Optimization by Reinforcement Learning and Docking (MORLD) that automatically generates and optimizes lead compounds by combining reinforcement learning and docking to develop predicted novel inhibitors. This model requires only a target protein structure and directly modifies ligand structures to obtain higher predicted binding affinity for the target protein without any other training data. Using MORLD, we were able to generate potential novel inhibitors against discoidin domain receptor 1 kinase (DDR1) in less than 2 days on a moderate computer. We also demonstrated MORLD's ability to generate predicted novel agonists for the D4 dopamine receptor (D4DR) from scratch without virtual screening on an ultra large compound library. The free web server is available at http://morld.kaist.ac.kr .
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Affiliation(s)
- Woosung Jeon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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15
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Zhou Z, Huang F, Shrivastava I, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y. New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy. EMBO Mol Med 2020; 12:e12391. [PMID: 33231937 PMCID: PMC7721363 DOI: 10.15252/emmm.202012391] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 01/17/2023] Open
Abstract
KLF4 plays a critical role in determining cell fate responding to various stresses or oncogenic signaling. Here, we demonstrated that KLF4 is tightly regulated by poly(ADP‐ribosyl)ation (PARylation). We revealed the subcellular compartmentation for KLF4 is orchestrated by PARP1‐mediated PARylation. We identified that PARylation of KLF4 is critical to govern KLF4 transcriptional activity through recruiting KLF4 from soluble nucleus to the chromatin. We mapped molecular motifs on KLF4 and PARP1 that facilitate their interaction and unveiled the pivotal role of the PBZ domain YYR motif (Y430, Y451 and R452) on KLF4 in enabling PARP1‐mediated PARylation of KLF4. Disruption of KLF4 PARylation results in failure in DNA damage response. Depletion of KLF4 by RNA interference or interference with PARP1 function by KLF4YYR/AAA (a PARylation‐deficient mutant) significantly sensitizes breast cancer cells to PARP inhibitors. We further demonstrated the role of KLF4 in modulating homologous recombination through regulating BRCA1 transcription. Our work points to the synergism between KLF4 and PARP1 in tumorigenesis and cancer therapy, which provides a potential new therapeutic strategy for killing BRCA1‐proficient triple‐negative breast cancer cells.
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Affiliation(s)
- Zhuan Zhou
- Department of Obstetrics and Gynecology, Department of Pharmacology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Furong Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Indira Shrivastava
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rui Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aiping Luo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Michael Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Massimo Cristofanilli
- Lynn Sage Breast Cancer Program, Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yong Wan
- Department of Obstetrics and Gynecology, Department of Pharmacology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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16
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Eldin A Osman E, Hanafy NS, George RF, El-Moghazy SM. Design and synthesis of some barbituric and 1,3-dimethylbarbituric acid derivatives: A non-classical scaffold for potential PARP1 inhibitors. Bioorg Chem 2020; 104:104198. [PMID: 32920355 DOI: 10.1016/j.bioorg.2020.104198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/26/2020] [Accepted: 08/17/2020] [Indexed: 01/02/2023]
Abstract
Six series based on barbituric acid 5a-e, 10a-d; thiobarbituric acid 6a-e, 11a-d and 1,3-dimethylbarbituric acid 7a-e, 12a-d were prepared and screened for their in vitro PARP1 inhibition. They revealed promising inhibition at nanomolar level especially compounds 5c, 7b, 7d and 7e (IC50 = 30.51, 41.60, 41.53 and 36.33 nM) with higher potency than olaparib (IC50 = 43.59 nM). Moreover, compounds 5b, 5d, 7a, 12a and 12c exhibited good comparable activity (IC50 = 65.93, 58.90, 66.57, 45.40 and 50.62 nM, respectively). Furthermore, the most active compounds 5c, 7b, 7d, 7e, 12a and 12c against PARP1 in vitro were evaluated in the BRCA1 mutated triple negative breast cancer cell line MDA-MB-436 where 5c and 12c showed higher potency compared to olaparib and result in cell cycle arrest at G2/M phase. 5c and 12c showed apoptotic effects in MDA-MB-436 and potentiated the cytotoxicity of temozolomide in A549 human lung epithelial cancer cell line. Compounds 5c and 12c represent interesting starting points towards PARP1 inhibitors.
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Affiliation(s)
- Essam Eldin A Osman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Noura S Hanafy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo 11777, Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Samir M El-Moghazy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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17
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Design, synthesis, antitrypanosomal activity, DNA/RNA binding and in vitro ADME profiling of novel imidazoline-substituted 2-arylbenzimidazoles. Eur J Med Chem 2020; 207:112802. [PMID: 32927230 DOI: 10.1016/j.ejmech.2020.112802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 01/10/2023]
Abstract
Novel imidazoline benzimidazole derivatives containing diversely substituted phenoxy moieties were synthesized with the aim of evaluating their antitrypanosomal activity, DNA/RNA binding affinity and in vitro ADME properties. The presence of the diethylaminoethyl subunit in 18a-18c led to enhanced antitrypanosomal potency, particularly for 18a and 18c, which contain unsubstituted and methoxy-substituted phenoxy moieties. They were found to be > 2-fold more potent against African trypanosomes than nifurtimox. Fluorescence and CD spectroscopy, thermal denaturation assays and computational analysis indicated a preference of 18a-18c toward AT-rich DNA and their minor groove binding mode. Replacement of the amidine group with less basic and ionisable nitrogen-containing moieties failed to improve membrane permeability of the investigated compounds. Due to structural diversification, the compounds displayed a range of physico-chemical features resulting in variable in vitro ADME properties, leaving space for further optimization of the biological profiles.
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18
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Shao X, Pak S, Velagapudi UK, Gobbooru S, Kommaraju SS, Low WK, Subramaniam G, Pathak SK, Talele TT. Synthesis of 2,3-dihydrobenzo[b][1,4]dioxine-5-carboxamide and 3-oxo-3,4-dihydrobenzo[b][1,4]oxazine-8-carboxamide derivatives as PARP1 inhibitors. Bioorg Chem 2020; 102:104075. [PMID: 32777641 DOI: 10.1016/j.bioorg.2020.104075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/27/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1), a widely explored anticancer drug target, plays an important role in single-strand DNA break repair processes. High-throughput virtual screening (HTVS) of a Maybridge small molecule library using the PARP1-benzimidazole-4-carboxamide co-crystal structure and pharmacophore model led to the identification of eleven compounds. These compounds were evaluated using recombinant PARP1 enzyme assay that resulted in the acquisition of three PARP1 inhibitors: 3 (IC50 = 12 μM), 4 (IC50 = 5.8 μM), and 10 (IC50 = 0.88 μM). Compound 4 (2,3-dihydro-1,4-benzodioxine-5-carboxamide) was selected as a lead and was subjected to further chemical modifications, involving analogue synthesis and scaffold hopping. These efforts led to the identification of (Z)-2-(4-hydroxybenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-carboxamide (49, IC50 = 0.082 μM) as the most potent inhibitor of PARP1 from the series.
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Affiliation(s)
- Xuwei Shao
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Steven Pak
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Uday Kiran Velagapudi
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Shruthi Gobbooru
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Sai Shilpa Kommaraju
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Woon-Kai Low
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Gopal Subramaniam
- Chemistry and Biochemistry Department, Queens College of the City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA
| | - Sanjai Kumar Pathak
- Chemistry and Biochemistry Department, Queens College of the City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA; Chemistry Doctoral Program, Biochemistry Doctoral Program, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA.
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19
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Spiegel JO, Durrant JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 2020; 12:25. [PMID: 33431021 PMCID: PMC7165399 DOI: 10.1186/s13321-020-00429-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. It is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands. By leveraging recent computational and cheminformatics advancements, AutoGrow4 is faster, more stable, and more modular than previous versions. It implements new docking-program compatibility, chemical filters, multithreading options, and selection methods to support a wide range of user needs. To illustrate both de novo design and lead optimization, we here apply AutoGrow4 to the catalytic domain of poly(ADP-ribose) polymerase 1 (PARP-1), a well characterized DNA-damage-recognition protein. AutoGrow4 produces drug-like compounds with better predicted binding affinities than FDA-approved PARP-1 inhibitors (positive controls). The predicted binding modes of the AutoGrow4 compounds mimic those of the known inhibitors, even when AutoGrow4 is seeded with random small molecules. AutoGrow4 is available under the terms of the Apache License, Version 2.0. A copy can be downloaded free of charge from http://durrantlab.com/autogrow4.
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Affiliation(s)
- Jacob O. Spiegel
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260 USA
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260 USA
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20
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Abstract
We propose a new model for prochirality that satisfies all known examples: the prochiral plane. This plane contains the prochiral carbon and defines two separate faces for chemical modification. We extend this to enzyme catalysis, replacing the "three point attachment" hypothesis and its variants. Once a prochiral substrate is fixed on an enzyme surface, the asymmetry of the enzyme provides reactants exclusively on one side of the prochiral plane, producing an enantiomerically pure chiral product. The aconitase reaction is detailed as an example, using molecular modeling and its known enzymatic mechanism. We show that the prochiral substrate for this enzyme is not citrate, but rather cis-aconitate. The number of interaction points of cis-aconitate is not relevant to prochirality, but rather to substrate specificity. A second detailed example is the enzyme fumarase; here the substrate fumarate has only two binding sites, but is nonetheless fixed onto the enzyme and has a defined prochiral plane. We also provide a literature survey of more prochiral substrates, all of which have sp2 hybridized carbon and contain a prochiral plane. An example of a prochiral unnatural substrate for sphingosine kinase 2, fingolimod, has an sp3 hybridized prochiral carbon and also contains a prochiral plane. Finally, we provide an intuitive example of a prochiral physical object, a coffee cup, interacting with one hand and lip.
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Affiliation(s)
- Raymond S Ochs
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
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21
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Shao X, AbdelKhalek A, Abutaleb NS, Velagapudi UK, Yoganathan S, Seleem MN, Talele TT. Chemical Space Exploration around Thieno[3,2- d]pyrimidin-4(3 H)-one Scaffold Led to a Novel Class of Highly Active Clostridium difficile Inhibitors. J Med Chem 2019; 62:9772-9791. [PMID: 31584822 DOI: 10.1021/acs.jmedchem.9b01198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Clostridium difficile infection (CDI) is the leading cause of healthcare-associated infection in the United States. Therefore, development of novel treatments for CDI is a high priority. Toward this goal, we began in vitro screening of a structurally diverse in-house library of 67 compounds against two pathogenic C. difficile strains (ATCC BAA 1870 and ATCC 43255), which yielded a hit compound, 2-methyl-8-nitroquinazolin-4(3H)-one (2) with moderate potency (MIC = 312/156 μM). Optimization of 2 gave lead compound 6a (2-methyl-7-nitrothieno[3,2-d]pyrimidin-4(3H)-one) with improved potency (MIC = 19/38 μM), selectivity over normal gut microflora, CC50s > 606 μM against mammalian cell lines, and acceptable stability in simulated gastric and intestinal fluid. Further optimization of 6a at C2-, N3-, C4-, and C7-positions resulted in a library of >50 compounds with MICs ranging from 3 to 800 μM against clinical isolates of C. difficile. Compound 8f (MIC = 3/6 μM) was identified as a promising lead for further optimization.
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Affiliation(s)
- Xuwei Shao
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , St. John's University , Queens , New York 11439-0001 , United States
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology , Purdue University College of Veterinary Medicine , West Lafayette , Indiana 47907-2027 , United States
| | - Nader S Abutaleb
- Department of Comparative Pathobiology , Purdue University College of Veterinary Medicine , West Lafayette , Indiana 47907-2027 , United States
| | - Uday Kiran Velagapudi
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , St. John's University , Queens , New York 11439-0001 , United States
| | - Sabesan Yoganathan
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , St. John's University , Queens , New York 11439-0001 , United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology , Purdue University College of Veterinary Medicine , West Lafayette , Indiana 47907-2027 , United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease , West Lafayette , Indiana 47907-2027 , United States
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , St. John's University , Queens , New York 11439-0001 , United States
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22
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Karataş S, Çapan İ, Servi S. Synthesis of Indole and Benzimidazole Substituted Novel 16-Arylidene Steroid Derivatives. LETT ORG CHEM 2019. [DOI: 10.2174/1570178616666190305130217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Novel aza-heterocyclic substituted dehydroepiandrosterone derivatives were synthesized
through a three-step reaction sequence. Some new O-alkylated 4-hydroxybenzaldehydes were synthesized
from the reaction of substituted benzaldehydes with dihalogen compounds which have different
chain lengths. 16-Arylidene steroids were synthesized from the base-catalyzed aldol condensation of
O-alkylated 4-hydroxybenzaldehydes and dehydroepiandrosterone. New indolyl and benzimidazolyl
substituted steroid derivatives as hybrid molecules were obtained from the reaction of 16-arylidene
steroids with indole or benzimidazole.
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Affiliation(s)
- Semra Karataş
- Department of Chemistry, Faculty of Science, Firat University, Elazıg, Turkey
| | - İrfan Çapan
- Department of Polymer Technology, Technical Sciences Vocational College, Gazi University, Ankara, Turkey
| | - Süleyman Servi
- Department of Chemistry, Faculty of Science, Firat University, Elazıg, Turkey
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23
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Kumar C, P T V L, Arunachalam A. A mechanistic approach to understand the allosteric reverse signaling by selective and trapping poly(ADP-ribose) polymerase 1 (PARP-1) inhibitors. J Biomol Struct Dyn 2019; 38:2482-2492. [PMID: 31204582 DOI: 10.1080/07391102.2019.1633406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Chandan Kumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, India
| | - Lakshmi P T V
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, India
| | - Annamalai Arunachalam
- Postgraduate and Research Department of Botany, Arignar Anna Government Arts College, Villupuram, Tamil Nadu, India
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24
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Velagapudi UK, Langelier MF, Delgado-Martin C, Diolaiti ME, Bakker S, Ashworth A, Patel BA, Shao X, Pascal JM, Talele TT. Design and Synthesis of Poly(ADP-ribose) Polymerase Inhibitors: Impact of Adenosine Pocket-Binding Motif Appendage to the 3-Oxo-2,3-dihydrobenzofuran-7-carboxamide on Potency and Selectivity. J Med Chem 2019; 62:5330-5357. [PMID: 31042381 PMCID: PMC7378964 DOI: 10.1021/acs.jmedchem.8b01709] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Poly(adenosine 5'-diphosphate-ribose) polymerase (PARP) inhibitors are a class of anticancer drugs that block the catalytic activity of PARP proteins. Optimization of our lead compound 1 (( Z)-2-benzylidene-3-oxo-2,3-dihydrobenzofuran-7-carboxamide; PARP-1 IC50 = 434 nM) led to a tetrazolyl analogue (51, IC50 = 35 nM) with improved inhibition. Isosteric replacement of the tetrazole ring with a carboxyl group (60, IC50 = 68 nM) gave a promising new lead, which was subsequently optimized to obtain analogues with potent PARP-1 IC50 values (4-197 nM). PARP enzyme profiling revealed that the majority of compounds are selective toward PARP-2 with IC50 values comparable to clinical inhibitors. X-ray crystal structures of the key inhibitors bound to PARP-1 illustrated the mode of interaction with analogue appendages extending toward the PARP-1 adenosine-binding pocket. Compound 81, an isoform-selective PARP-1/-2 (IC50 = 30 nM/2 nM) inhibitor, demonstrated selective cytotoxic effect toward breast cancer gene 1 ( BRCA1)-deficient cells compared to isogenic BRCA1-proficient cells.
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Affiliation(s)
- Uday Kiran Velagapudi
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, United States
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal H3T 1J4 Canada
| | - Cristina Delgado-Martin
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States
| | - Morgan E. Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States
| | - Sietske Bakker
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, California 94158, United States
| | - Bhargav A. Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, United States
| | - Xuwei Shao
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, United States
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal H3T 1J4 Canada
| | - Tanaji T. Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, United States
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25
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26
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Murai J, Pommier Y. PARP Trapping Beyond Homologous Recombination and Platinum Sensitivity in Cancers. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2019. [DOI: 10.1146/annurev-cancerbio-030518-055914] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPis) have recently been approved for the treatment of ovarian and breast cancers with BRCA mutations, as well as for maintenance therapies regardless of BRCA mutation for ovarian and primary peritoneal cancers that previously responded to platinum-based chemotherapy. The rationale of these indications is derived from the facts that cancer cells with BRCA mutations are defective in homologous recombination (HR), which confers synthetic lethality with PARPis, and that some of the sensitivity-determining factors for PARPis are shared with platinums. Although BRCA1 and BRCA2 are central for HR, more players within and beyond HR are emerging as response determinants to PARPis. Furthermore, there are similarities as well as differences in the DNA lesions and repair pathways induced by PARPis, platinums, and camptothecin topoisomerase 1 (TOP1) inhibitors. Here we review the sensitivity-determining factors for PARPis and the rationale for using PARPis as single agents and in combination therapy for cancers.
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Affiliation(s)
- Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;,
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;,
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27
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Early Treatment with Poly(ADP-Ribose) Polymerase-1 Inhibitor (JPI-289) Reduces Infarct Volume and Improves Long-Term Behavior in an Animal Model of Ischemic Stroke. Mol Neurobiol 2018; 55:7153-7163. [DOI: 10.1007/s12035-018-0910-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/11/2018] [Indexed: 12/22/2022]
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28
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Design, synthesis and biological evaluation of 4-amidobenzimidazole acridine derivatives as dual PARP and Topo inhibitors for cancer therapy. Eur J Med Chem 2017; 138:1135-1146. [DOI: 10.1016/j.ejmech.2017.07.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/20/2017] [Accepted: 07/22/2017] [Indexed: 11/18/2022]
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29
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Yuan Z, Chen S, Sun Q, Wang N, Li D, Miao S, Gao C, Chen Y, Tan C, Jiang Y. Olaparib hydroxamic acid derivatives as dual PARP and HDAC inhibitors for cancer therapy. Bioorg Med Chem 2017; 25:4100-4109. [DOI: 10.1016/j.bmc.2017.05.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/17/2017] [Accepted: 05/29/2017] [Indexed: 01/01/2023]
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30
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Zinin AI, Stepanova EV, Jost U, Kondakov NN, Shpirt AM, Chizhov AO, Torgov VI, Kononov LO. An efficient multigram-scale synthesis of 4-(ω-chloroalkoxy)phenols. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1732-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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A comprehensive look of poly(ADP-ribose) polymerase inhibition strategies and future directions for cancer therapy. Future Med Chem 2016; 9:37-60. [PMID: 27995810 DOI: 10.4155/fmc-2016-0113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The finding of promising drugs represents a huge challenge in cancer therapeutics, therefore it is important to seek out novel approaches and elucidate essential cellular processes in order to identify potential drug targets. Studies on DNA repair pathway suggested that an enzyme, PARP, which plays a significant role in DNA repair responses, could be targeted in cancer therapy. Hence, the efficacy of PARP inhibitors in cancer therapy has been investigated and has progressed from the laboratory to clinics, with olaparib having already been approved by the US FDA for ovarian cancer treatment. Here, we have discussed the development of PARP inhibitors, strategies to improve their selectivity and efficacy, including innovative combinational and synthetic lethality approaches to identify effective PARP inhibitors in cancer treatment.
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Fu L, Wang S, Wang X, Wang P, Zheng Y, Yao D, Guo M, Zhang L, Ouyang L. Crystal structure-based discovery of a novel synthesized PARP1 inhibitor (OL-1) with apoptosis-inducing mechanisms in triple-negative breast cancer. Sci Rep 2016; 6:3. [PMID: 28442756 PMCID: PMC5431371 DOI: 10.1038/s41598-016-0007-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/24/2016] [Indexed: 02/05/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a highly conserved enzyme focused on the self-repair of cellular DNA damage. Until now, numbers of PARP inhibitors have been reported and used for breast cancer therapy in recent years, especially in TNBC. However, developing a new type PARP inhibitor with distinctive skeleton is alternatively promising strategy for TNBC therapy. In this study, based on co-crystallization studies and pharmacophore-docking-based virtual screening, we discovered a series of dihydrodibenzo[b,e]-oxepin compounds as PARP1 inhibitors. Lead optimization result in the identification of compound OL-1 (2-(11-(3-(dimethylamino)propylidene)-6,11- dihydrodibenzo[b,e]oxepin )-2-yl)acetohydrazide), which has a novel chemical scaffold and unique binding interaction with PARP1 protein. OL-1 demonstrated excellent potency (inhibiting PARP1 enzyme activity with IC50 = 0.079 μM), as well as inhibiting PARP-modulated PARylation and cell proliferation in MDA-MB-436 cells (BRAC1 mutation). In addition, OL-1 also inhibited cell migration that closely related to cancer metastasis and displayed remarkable anti-tumor efficacy in MDA-MB-436 xenograft model without apparent toxicities. These findings highlight a new small-molecule PAPR1 inhibitor (OL-1) that has the potential to impact future TNBC therapy.
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Affiliation(s)
- Leilei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Shuya Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.,Northwestern University, Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, Illinois, 60611, USA
| | - Xuan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Peiqi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yaxin Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Dahong Yao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Mingrui Guo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Lan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
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Yuan Z, Chen J, Li W, Li D, Chen C, Gao C, Jiang Y. PARP inhibitors as antitumor agents: a patent update (2013-2015). Expert Opin Ther Pat 2016; 27:363-382. [PMID: 27841036 DOI: 10.1080/13543776.2017.1259413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION PARP inhibitors have been extensively explored as antitumor agents and have shown potent efficacy both in vitro and in vivo. They can be used in monotherapy under the synthetic lethality concept or in combination with radiotherapy or chemotherapy, inducing a synergistic effect. Areas covered: This review covers relevant efforts in the development of PARP inhibitors with a particular focus on recently patented PARP inhibitors, combination therapy involving PARP inhibitors, tumor responsiveness to PARP inhibitors as detailed in reports made from 2013 - 2015, and PARP drugs in clinical trials and other novel inhibitors that emerged in 2013 - 2015. Expert opinion: Clinical studies and applications of PARP inhibitors as antitumor agents have gained considerable recognition in the last few years. In addition to FDA-approved olaparib, an increasing number of new inhibitors have been designed and synthesized, some of which are under preclinical or clinical evaluation. Novel inhibitors are still required, especially new scaffold compounds or drugs with improved properties, such as higher selectivity, higher potency and lower toxicity. The development of combination therapies involving PARP inhibitors and the exploration of biomarkers to predict outcomes with PARP inhibitors would expand the applications of these inhibitors, allowing more patients to benefit from this promising class of drugs in the future.
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Affiliation(s)
- Zigao Yuan
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Jiwei Chen
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Wenlu Li
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Dan Li
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Changjun Chen
- a Department of Chemistry , Tsinghua University , Beijing , P. R. China.,b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Chunmei Gao
- b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,c National & Local United Engineering Lab for Personalized anti-tumor drugs, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China
| | - Yuyang Jiang
- b The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,c National & Local United Engineering Lab for Personalized anti-tumor drugs, the Graduate School at Shenzhen , Tsinghua University , Shenzhen , P. R. China.,d School of Medicine , Tsinghua University , Beijing , P. R. China
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Wang YQ, Wang PY, Wang YT, Yang GF, Zhang A, Miao ZH. An Update on Poly(ADP-ribose)polymerase-1 (PARP-1) Inhibitors: Opportunities and Challenges in Cancer Therapy. J Med Chem 2016; 59:9575-9598. [PMID: 27416328 DOI: 10.1021/acs.jmedchem.6b00055] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly(ADP-ribose)polymerase-1 (PARP-1) is a critical DNA repair enzyme in the base excision repair pathway. Inhibitors of this enzyme comprise a new type of anticancer drug that selectively kills cancer cells by targeting homologous recombination repair defects. Since 2010, important advances have been achieved in PARP-1 inhibitors. Specifically, the approval of olaparib in 2014 for the treatment of ovarian cancer with BRCA mutations validated PARP-1 as an anticancer target and established its clinical importance in cancer therapy. Here, we provide an update on PARP-1 inhibitors, focusing on breakthroughs in their clinical applications and investigations into relevant mechanisms of action, biomarkers, and drug resistance. We also provide an update on the design strategies and the structural types of PARP-1 inhibitors. Opportunities and challenges in PARP-1 inhibitors for cancer therapy will be discussed based on the above advances.
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Affiliation(s)
- Ying-Qing Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Ping-Yuan Wang
- CAS Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal Chemistry Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Lu, Building 3, Room 426, Pudong, Shanghai 201203, China.,Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, China
| | - Yu-Ting Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, China
| | - Ao Zhang
- CAS Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal Chemistry Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Lu, Building 3, Room 426, Pudong, Shanghai 201203, China
| | - Ze-Hong Miao
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
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Drenichev MS, Mikhailov SN. Poly(ADP-ribose): From chemical synthesis to drug design. Bioorg Med Chem Lett 2016; 26:3395-403. [PMID: 27318540 DOI: 10.1016/j.bmcl.2016.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/17/2022]
Abstract
Poly(ADP-ribose) (PAR) is an important biopolymer, which is involved in various life processes such as DNA repair and replication, modulation of chromatin structure, transcription, cell differentiation, and in pathogenesis of various diseases such as cancer, diabetes, ischemia and inflammations. PAR is the most electronegative biopolymer and this property is essential for its binding with a wide range of proteins. Understanding of PAR functions in cell on molecular level requires chemical synthesis of regular PAR oligomers. Recently developed methodologies for chemical synthesis of PAR oligomers, will facilitate the study of various cellular processes, involving PAR.
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Affiliation(s)
- Mikhail S Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation.
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Di Micco S, Spatafora C, Cardullo N, Riccio R, Fischer K, Pergola C, Koeberle A, Werz O, Chalal M, Vervandier-Fasseur D, Tringali C, Bifulco G. 2,3-Dihydrobenzofuran privileged structures as new bioinspired lead compounds for the design of mPGES-1 inhibitors. Bioorg Med Chem 2016; 24:820-6. [DOI: 10.1016/j.bmc.2016.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 12/03/2015] [Accepted: 01/03/2016] [Indexed: 12/22/2022]
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37
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Staegemann MH, Gräfe S, Haag R, Wiehe A. A toolset of functionalized porphyrins with different linker strategies for application in bioconjugation. Org Biomol Chem 2016; 14:9114-9132. [DOI: 10.1039/c6ob01551d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Polar, functionalized A3B-porphyrins are conjugated to hyperbranched polyglycerol (hPG) as an example of a biocompatible carrier system for photodynamic therapy.
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Affiliation(s)
- M. H. Staegemann
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Biolitec research GmbH
| | - S. Gräfe
- Biolitec research GmbH
- 07745 Jena
- Germany
| | - R. Haag
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
| | - A. Wiehe
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
- Biolitec research GmbH
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38
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Xie Z, Chen Y, Xu P, Zhou Y, Zhao Q, Jiao H, Li Z. Design, synthesis and bioevaluation of 1H-indole-4-carboxamide derivatives as potent poly(ADP-ribose) polymerase-1 inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra12591c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
LX15 is more potent than AG014699 in PARP-1 inhibitory activity and BRCA-1 deficient cell inhibitory activity. It is more effective than AG014699 in potentiating the antitumor activity of TMZin vitro and in vivo.
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Affiliation(s)
- Zhouling Xie
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - Yu Chen
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - Pengfei Xu
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - Youli Zhou
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - Qian Zhao
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - He Jiao
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization
- China Pharmaceutical University
- Nanjing 21009
- China
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39
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Drenichev MS, Mikhailov SN. Poly(ADP-ribose)--a unique natural polymer structural features, biological role and approaches to the chemical synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:258-76. [PMID: 25774719 DOI: 10.1080/15257770.2014.984073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR. One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism. The structure of PAR was established by enzymatic hydrolysis and further analysis of the products, but total chemical synthesis of PAR hasn't been described yet. Several approaches have been developed on the way to chemical synthesis of this unique biopolymer.
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Affiliation(s)
- Mikhail S Drenichev
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russian Federation
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40
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Shen Y, Aoyagi-Scharber M, Wang B. Trapping Poly(ADP-Ribose) Polymerase. J Pharmacol Exp Ther 2015; 353:446-57. [DOI: 10.1124/jpet.114.222448] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/09/2015] [Indexed: 12/16/2022] Open
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41
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Yao H, Ji M, Zhu Z, Zhou J, Cao R, Chen X, Xu B. Discovery of 1-substituted benzyl-quinazoline-2,4(1H,3H)-dione derivatives as novel poly(ADP-ribose)polymerase-1 inhibitors. Bioorg Med Chem 2015; 23:681-93. [PMID: 25614115 DOI: 10.1016/j.bmc.2014.12.071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/31/2014] [Accepted: 12/31/2014] [Indexed: 11/26/2022]
Abstract
Poly(ADP-ribose)polymerase-1 (PARP-1) has emerged as a promising anticancer drug target due to its key role in the DNA repair process. In this work, a novel series of 1-benzyl-quinazoline-2,4(1H,3H)-dione derivatives were designed and synthesized as human PARP-1 inhibitors, structure-activity relationships were conducted and led to a number of potent PARP-1 inhibitors having IC50 values of single or double digit nanomolar level. Compound 7j was a potent PARP-1 and PARP-2 inhibitor and it could selectively kill the breast cancer cells MX-1 and MDA-MB-468 with mutated BRCA1/2 and PTEN, respectively, in comparison with homologous recombination proficient cell types such as breast cancer cells MDA-MB-231. In addition, compound 7j displayed the strongest potentiation effect on temozolomide in MX-1 cells (PF50=3.77) in this series of PARP-1 inhibitors.
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Affiliation(s)
- Haiping Yao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ming Ji
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhixiang Zhu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jie Zhou
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ran Cao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Bailing Xu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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